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Date: 2006/03/04 14:56:57, Link
Author: qetzal
Jay Ray's demo is a nice one.

However, the whole deck of cards analogy is a red herring. The odds of getting a specific hand only mean something if you specify the desired hand in advance. As has been noted, every possible hand is equally unlikely. The only reason a royal flush is remarkable is because we define it as desirable in advance.

The same thing applies to the argument about life. Even if you could positively establish that life on earth was exceedingly unlikely, it doesn't prove anything unless you assume that life is a desired outcome.

But of course, if you assume life is desired in advance, then you're assuming God in advance. (Or at least, some entity capable of creating life.) It's a circular argument, one that proves nothing at all.

Date: 2006/03/06 11:43:34, Link
Author: qetzal
Jay Ray

Don't get me wrong. I like your analogy for its intended purpose. It's a great way to demonstrate how evolution operates in a stepwise fashion, unlike re-shuffling a deck over and over until you get a perfect bridge hand or something.

But your analogy still contains conscious design. You chose the target sequence in advance, and then you went through after every shuffle and chose which cards to tape together. You've shown how the process can be speeded up enormously, but not how it can happen without purposeful intervention.

Let me try expanding on your analogy to make my point. Suppose we think of the randomized deck (after your step 1) as representing the pre-biotic earth, and your final configuration as representing today's earth, with its current diversity of life.

Mr. ID/Creationist will argue that your analogy still shows that intelligent intervention is essential. An undirected process can't work. As "proof" (says Mr. ID/C), try this:

1) Shuffle the deck up nice and good.  
2) Then go through the deck without looking.  
3) Every now and then, select two or more cards in a row, pull them out and put a little flap of masking tape around the short edges.  Again, no looking at the cards before you pick them.
4) Then put them back in the deck, and reshuffle.  
5) Keep doing this until all the cards are taped together.
6) Check to see if the deck is in order. If not, start all over.

How many rounds will it take? Probably the same 8 x 10^67, or whatever it is. See, says Mr. ID/C? This just proves that intelligent intervention is required. Whether you try to get there in one shuffle, or by taping cards together in multiple steps, the probability of getting that exact order of cards is unrealistically small.

The thing is, he's right, but only because you agreed in advance on the desired result.

Similarly, Mr. ID/C is quite sure that the current state of life on earth is also the desired result. And since life is much more complicated than a deck of cards, it must be even less probable that life evolved without intelligent intervention.

This is the viewpoint I'm trying to debunk. I'm trying to point out to Mr. (or Ms.) ID/C that this argument depends on the prior assumption that life is the desired result. This means that they're assuming the pre-existence of some entity that a) desired this result, and b) was capable of making it happen. IOW, they're assuming God (or the equivalent) exists and desires life on earth, in order to prove that God is responsible for life on earth.

If you don't assume God to begin with, you can't assume that life is the desired result. In that case, life is just a result. And of course, there is nothing we can say about the probability of one result from a sample of one.

I hope that clarifies my point, and apologize if I seemed to be disparaging your analogy. It wasn't intended; I just didn't express myself very well.

Date: 2006/03/12 07:57:46, Link
Author: qetzal
Avocationist, I'll try to explain.

You seem to be saying that, yes, the chances of life occurring are indeed one divided by many trillions, but it was just the way the random shuffle happened to fall. Nonetheless, there is something noteworthy about the fact that we have a planet teeming with millions of life forms when the chances of that were vanishingly small. I don't think we need to extrapolate further about having specified it in advance. Now, you can say that each and every shuffle of the deck is also very unlikely. But we can also say that they all do nothing different from one another, nor would a random shuffling of pebbles and shells on the beach. No matter how many times the waves toss them about, and no matter that each one is unlikely if specified in advance, they also do not stand out one from another in any discernable way. But that one shuffle - life, does.


1.  We have no idea of the chances of life occurring. We know of one universe. We know there's life in our tiny, tiny, remote corner of it. That's all we know. We can't even say whether life is likely anywhere else in this universe, much less how unlikely the universe itself is.

2.  Even if we knew that life was a very unlikely outcome, that tells us nothing about God. How do we know that life is a special outcome, and not just one outcome at random? We don't.

Of course, it's special to us. But that's not relevant to this discussion. You're assuming life is special to God. That God created life because that's what he wanted. And you may be right. The existence of life is consistent with that belief, but it isn't evidence for it.

Date: 2006/03/16 19:13:44, Link
Author: qetzal
I will say it again, there is NO process outside the interpretation of empirical evidence in which a person comes to "believe" or have "faith" in an IDer.  If there is, please explain?

Easy. Most people come to believe in an "IDer" because they are raised in religious households and indoctrinated into religious traditions from an early age. Empirical evidence has nothing to do with that.

Remember, let's focus on that first human that looked into the sky and pondered the creator.  What was the process that allowed such insight and speculation?  Physics theory doesn't leave you much wiggle room, does it?

So we agree there are processes for some people to believe without evidence, right? Now the question is, how did the first person come to believe?

Who knows? My guess is, s/he looked at the available evidence and misinterpreted it to mean that "IDers" (gods) existed. That's not the same as claiming there was (or is) actual evidence for an IDer.

Or maybe, s/he realized s/he could get others to do what s/he wanted, if s/he claimed to represent some powerful but invisible IDer.

It doesn't really matter. Just because someone believes something, that doesn't prove there must be evidence to support their belief.

Well, since you have no evidence for "no evidence" then it leaves only one possible answer, doesn't it?

Apparently, the "answer" is for you to dodge the question by spouting nonsense.

The claim is very simple.  There is NO process outside of interpreting empirical evidence for the "belief" in a creator or creators.

This claim is very simple and very wrong, as already explained.

If no empirical evidence exists for an IDer(s) then how, scientifically speaking, did such a belief come into existence?  What's the process that initiated this pondering of an IDer where NO evidence existed for such a pondering?

In case you missed my answer above, there are many possible processes. Self-delusion. Desire to control others. Wrongly interpreting evidence. (Note - I'm not claiming this proves there really is no evidence. I'm just pointing out that evidence isn't required to explain belief.)


I don't believe you to be a serious participator in this thread.  The point is simple.  Judges are defining science.  This begs the question.

Why can't preachers define science?
Why can't teachers define science?
Why can't politicians define science?

Judges do!

Please come up with a good answer for these questions.

Another simple one. Judges are doing this because people are bringing suit in court. You may remember from civics class that judges are expected to make rulings during court cases.

For example, in Dover, parents alleged that the school board was unconstitutionally trying to introduce religion into the classroom. So in that case, the judge was required to decide whether ID was science or religion. Pretty simple, huh?

Now, preachers, teachers, and politicians are all welcome to come up with their own personal definitions of science, too, if they want to. But, they're not allowed to decide court cases. So their definitions don't matter in court. Which is where lawsuits get decided. As in, lawsuits over unconstitutionally teaching religion in public schools.

This stuff isn't that hard; you can get this. And the best part is, once you understand why judges are doing this, you're still allowed to think they're wrong. Try it; you'll be amazed how easy it is!

Read through this forum a little and you will see a pattern emerge.  No one outside evolutionary science seems to understand it even with all the "expert" testimony.

No, that's wrong. Lots of people outside evolutionary science are able to understand it, at least at a basic level. It really isn't too difficult. Many of those people even accept evolution (gasp!;). Others understand it, but reject it, usually for religious or philosophical reasons. (Of course, there are some who are incapable of understanding even the basics, or are so threatened by the whole concept that they refuse to even attempt to understand. Ring any bells?)

Did this "conservative" judge get the crash course of ToE and properly decide this case?  How was he able to understand what so many outside science are still vigorously debating and trying to comprehend?

Well, the judge was able to understand all this because there was a trial, and both sides presented evidence. Judges are trained and experienced in evaluating evidence. This judge was able to see that one side presented a lot of evidence in favor of their arguments, and the other side presented none. So I don't think it was really that hard for him.

I hope I was able to answer some of your questions. I tried to give simple answers that you could understand, since it's clear you've had some trouble following previous answers.

Now perhaps you can answer a question for me. What did you mean when you said:

Remember, he's supposedly a "conservative" judge.

Are you saying real conservative judges aren't smart enough to understand this? Or maybe that real conservative judges would rule in favor of religion regardless of the laws or the evidence?

Date: 2006/03/17 04:21:19, Link
Author: qetzal
Tell me though... How is anything you've said not equally applicable to science?

Because science ultimately requires that conclusions are based on objective evidence. Evidence that others can verify for themselves, if they so choose.

Science also requires that accepted hypotheses and theories must accurately predict new observations. Otherwise, the hypotheses or theories must be modified or discarded. An accepted theory says "under these conditions, expect to see A, not B." That's why theories are useful in understanding our world.

ID doesn't do that. It makes no useful predictions (that I know of). At most, it predicts "such and such biological structure or system is too complicated to have evolved 'naturally' without intelligent intervention." That's an unproveable (and thus useless) prediction. Moreover, for many specific systems and structures, it's been proven wrong.

Afterall, you aren't suggesting that the majority of those that believe "descent with modification" actually go through the rigors of the scientific method to give meaning to their interpretations of the empirical evidence?

Of course I'm not. Most of what any of us "know" is based on what others tell us. That's simple expedience. So what?

I guess you're trying to say "belief" in evolution is no more valid than "belief" in ID, because most people can only base such beliefs on what others tell them. If that's your point, it's bull.

I can't say I agree with your first statement because materialist philosophy seems to suggests it's not possible.

You can't agree that people sometimes believe things without evidence? Seriously? I'm flabbergasted.

The only way I can make sense of that is if you define evidence to mean anything that influences belief. I guess that's what you meant by "no such thing as non-evidence." That's not exactly the standard definition of evidence, though.

The question then becomes how did the first human come to interpret the creator only to be followed by billions of other "believers" if the creator does not exist?  That's a heck of a mass "self-delusion" and a bold claim indeed.

I'm not claiming self-delusion is the explanation. I'm saying it's a possible explanation.

You were the one making a bold claim:
...there is NO process outside the interpretation of empirical evidence in which a person comes to "believe" or have "faith" in an IDer.

I was merely disproving your claim. Self-delusion is ONE process outside the interpretation of empirical evidence in which a person may come to "believe" or have "faith" in an IDer. (Unless one plays Humpty-Dumpty with the definition of evidence.)

ONE possible process is adequate to refute a claim of NO possible process.

I did not claiming that belief in a creator IS based on self-delusion. See, I even said as much in my previous post:

...there are many possible processes. Self-delusion. Desire to control others. Wrongly interpreting evidence. (Note - I'm not claiming this proves there really is no evidence. I'm just pointing out that evidence isn't required to explain belief.)

The point is, you seem to be arguing that if someone believes something, that proves there is evidence to support their belief, because all beliefs are based on evidence. But, as has been repeatedly explained, that is wrong. People are perfectly capable of believing things in the complete absence of evidence, or even in direct contradiction of the evidence.

Therefore, the sole fact that someone believes in "X" (e.g., an "IDer") tells us nothing about whether there is evidence for "X."

So know we have a judge deciding the definition of science, but only those in the public sphere are mandated to accept the definition while the rest of us have the freedom to point out the flaws.

Close. Public schools are mandated to not teach religion. It's based on the 1st Amendment to the Constitution. (Maybe you've heard of it?) If someone thinks a public school is teaching religion, they can sue to make them stop. Then a judge may have to decide who's right. If the school claims they're teaching science, not religion, the judge will have to decide if that's true. In the Dover case, it was clear that ID is NOT science and it IS religiously motivated.

In the meantime, you and everyone else are entirely free to point out all the flaws you like. Just don't try to teach religion in public schools.

It seems odd that scientists fear the infusion of ID and welcome the infusion of the judicial bureaucracy?  It is quite the contradiction.

No, it's quite the misunderstanding. On your part.

I don't fear ID per se, and I doubt scientists in general do either. I fear religious zealots who want to force their religious beliefs into public schools. I happen to believe that separation of church and state is an important, fundamental principle in the US. I despise efforts to undermine that principle by dressing up simple religious apologetics, calling it ID, claiming it's science, and trying to wedge it into public science classes. I welcome the role of the judicial bureaucracy in preventing that.

Outside of public schools, I welcome ID to step up and prove its scientific worth. Make some predictions. Do some experiments. Generate some real data that supports ID and undercuts evolution. In short, if ID proponents are convinced that ID is really science, then do some #### science!


[re:] Are you saying real conservative judges aren't smart enough to understand this? Or maybe that real conservative judges would rule in favor of religion regardless of the laws or the evidence?

Actually, that was your point or else why include the desciptor in the first place?  Was I supposed to be impressed that this was a "conservative" judge?  Why?  They claim President Bush is a "conservative," too.  How do you know that of which you do not know?

No, that wasn't my quote. I took the descriptor from your post. I was quoting you. Why did you include the descriptor in the first place?

Date: 2006/03/19 05:54:19, Link
Author: qetzal

You speak of parts A, B, and C evolving together, so that the subsequent removal of one part would of course cause nonfunction. But all this is speculation until we can understand systems closely enough to know if it is plausible. And to the best of my layman's comprehension ability, the plausibility is seriously called into question by an essay series like Mike Gene's.

I believe we know for a fact that this kind of co-evolution is not only plausible, it really happens. Jeannot gave you one link, and a search phrase to use if you want more info.

Mike Gene's essays only call into question whether the flagellum can be adequately explained by 'undirected' mechansims such as co-evolution. I freely admit I'm not in a position to refute all of his points. This isn't really my area.

But consider: Mike Gene is doing what many ID proponents do. He's selecting one particular system and saying, "This system is way too complex to have evolved without intelligent guidance." In doing so, he in no way refutes non-directed evolution in general. At best, he can only claim that we don't know enough at present to adequately explain how the flagellum might have evolved. But he presumably wants to take that a step further, and claim there is no way in principle that the flagellum could have evolved without intelligent intervention.

That step isn't supported by evidence.

Let's suppose he's right - that currently understood evolutionary mechanisms cannot explain the flagellum. What does that tell us? Only that some other mechanism must have been involved. It doesn't prove that said mechanism must be intelligently guided.

You can hope that it isn't true, but so far as I know, there just isn't any knowledge of how it could occur, it is just assumed to occur.

Again, I think this is mistaken. I think it's well known that it can occur. The question is whether such mechanisms are adequate to explain specific examples like the flagellum.

Of course we cannot calculate the possibility of the flagellum evolving, we can only pick it apart and get a feel for the problems and the odds.

I agree. But even if our feeling is that the odds are too long in light of known mechanisms, that only suggests there are probably additional unknown mechanisms. It does not mean that intelligent guidance is the only reasonable answer.

And here's where the testing thing comes into play. If there's a way to test for intelligent guidance, then we can scientifically ask if it was involved. If there's no way to test for it, we're stuck, scientifically speaking.

I have no problem with people who believe an intelligence was/is involved. I have a problem with people who claim that we can scientifically conclude such is the case, based entirely on negative data.

So I didn't get a clear answer on the chromosome question. Apparently if there are different chromosome numbers, hybridization is possible, as in horse and donkey. But hybrids aren't viable. And I am wondering how the chromosome number change happens in the first place. If there is a fusion of two, it must occur during one meiosis. How does a chromosome know how to fuse itself with another and come out with a beautiful and coherent result?

For an extreme example of chromosome rearrangement in a human, who is still fertile, see Pharyngula's
Life will find a way.

Also, please note that a chromosome does not "know how to fuse itself with another." Sometimes it just happens. And, as Pharyngula's essay shows, the result needn't bee particularly beautiful or coherent.

It's interesting that you would even ask how a chromosome "knows" something. I think that reflects your basic assumption that such things must be purposeful and directed.

That's not the scientific view, however. As best we can tell, things like that just happen. If the result is advantageous for the organism, that organism will probably leave more offspring than others of its species, increasing the frequency of that trait in the next generation. If it's disadvantageous, the opposite is more likely. There's no scientific evidence of purpose.

ID doesn't say God can be scientifically proven. ID says it can be shown that beyond reasonable doubt that some systems could not have brung themselves into existence.

Whether we can ever test for god or not god I don't know, but ID might be indirect evidence. But I don't consider it good indirect evidence, because lesser beings than God might have done the designing.

ID may not claim proof of God, but it does claim the ability to prove intelligent intervention in life. It just doesn't live up to that claim.

Jay Ray:

I think your speculations on bacterial locomotion are incorrect. The Wikipedia entry on Chemotaxis gives details.

Basically, the frequency and duration of straight-line swimming versus tumbling is related to whether the bacterium is moving towards (or away from) an attractive (or repellant) chemical, such as food (or toxin).

It's a simple yet impressive system, and it's not hard to see how such a useful behavior could evolve without any external guidance.

Date: 2006/03/20 12:13:45, Link
Author: qetzal
Quote (shi @ Mar. 20 2006,13:16)
Just realized that S100A14 is not the example I intended.  it actually shows that same pattern as cyto C.  Let me replace it with DNMT1, which shows 83% identity between human and chicken and 80% between the fishes.  There are just too many such genes and it is easy to make a mistake in picking the wrong ones.

I don't agree that this example shows a "factual contradiction" with molecular clock theory. Clock theory can be true without insisting that every single protein lines up as expected.

However, following your reference to Ayala, I found this paper, which does indeed argue against clock theory, saying:

Whichever may be the explanation for the lower variation of evolutionary rates in XDH, our observations for all three genes are inconsistent not only with the molecular clock predicted by the neutrality theory, but also with subsidiary hypotheses, such as i, ii, and iii, that predict that patterns of evolution will be consistent across genes even if variable between lineages for any given gene. We are left with hypotheses that attribute rate variation to the vagaries of natural selection, whether as a consequence of functional shifts that change rates of neutral mutation through time differently for different genes in different organisms (hypothesis iv) or in response to phenotypic evolution and environmental heterogeneities (hypothesis v). These two hypotheses amount to a denial of there being a molecular clock, although there would be an overall correlation between amount of change and time elapsed, expected from any time-dependent process such as evolution.

My question is, how does this any of this relate to falsifying Darwinism? I thought that was the topic of this thread (which you started).

If you're right, and there is no molecular clock, what does that prove?

Date: 2006/03/22 10:40:56, Link
Author: qetzal

Now, you say that if we don't know how something evolved, the only reasonble conclusion is to assume that our present knowledge is insufficient to explain how. But it is more than just a lack of knowledge of how. It is a thing which gives every indication of being utterly outside of the capability of anything we know about nature's processes and quite readily recognizable as just the sort of thing a purposeful intelligence might set out to accomplish.

I disagree with your last sentence. Strongly.

What we currently know about evolution is certainly adequate in principle to explain complex features of life. One can reasonably question whether we have a specific, well-supported evolutionary explanation for any given feature, such as the flagellum. One can reasonably question whether that evolutionary explanation is correct.

But if you're claiming that things like flagella are "utterly outside" our ability to explain by evolution, you're seriously mistaken.

Must? Well, yeah, and one of those other mechanisms might have been purposeful design. But if you say that unintelligent processes must have been involved, then you are saying that your mind is made up and will not take in any contrary information.

I don't say unintelligent processes must have been involved. Only that there are certain unintelligent processes that we know exist. In many cases, they provide more than adequate explanations. In other cases, they have the clear potential to provide adequate explanations, even if we don't have the details yet.

More important, I know of no case where unintelligent processes are clearly inadequate to explain the diversity and complexity of life. Nor have I seen any scientific data to support purposeful design. It's not that I've made up my mind not to take in contrary information. There is no significant contrary information to take in.

Evidence against current evolutionary explanations does not qualify as evidence for intelligent intervention. Claims that evolution is too improbable do not qualify as evidence for intelligent design. Claims that we can recognize the hallmarks of design don't qualify either. Not unless there's an objective, testable way to distinguish designed from not-designed. So far, there isn't.

I agree, but neither is it [intelligent guidance] an unreasonable answer.

Well, since it is unsupported by scientific evidence, it is certainly quite unreasonable as a scientific answer.

At some point if intelligence was indeed involved, we must surely be able to discern the difference between what an intelligence can do versus lack of same.

I applaud this attitude, especially if discern means scientifically demonstrate. My question is, do you think there's any chance the major ID proponents will try to do this? When do you think they'll start developing rigorous design hypotheses, making predictions, testing those predictions, and showing how ID can usefully explain things that evolution can't? So far, I see no evidence that they're doing any of that.

I assure, I am quite willing to accept good scientific evidence in favor of ID. Too bad no one seems to be interested in generating any. They mostly seem preoccupied with bashing evolution. Their few arguments in favor of ID are subjective, philosophical, and unscientific. They make no testable predictions. They don't do science.

When and if there's real science to support ID, I'll be happy to consider it. Until then, it's philosophy on a good day, and plain garbage most of the time.

Date: 2006/03/23 10:02:20, Link
Author: qetzal
Quote (thordaddy @ Mar. 23 2006,02:25)
I should clarify that science can say something about a women who drowns her five children, but it seems it's limited to describing the action and parroting the women's thoughts about the situation.  Where's the real science, I wonder?  In essence, science is saying nothing profound on the situation.  It's a futile exercise that gives the illusion that science is breaking new barriers.

What if science could study the women's thoughts and actions, and thereby learn to predict which women might do that and when? Yep, that would be futile, wouldn't it.

If, as you say, science has thoroughly vetted IDT, what does it say of "faith" in a creator.  What's the conventional scientific wisdom?  Giant delusion?

The conventional scientific wisdom is simply that there is no scientific evidence of a creator. Anyone who chooses to have "faith" in a creator will have to base that "faith" on something other than scientific evidence. (By the way, why are we putting scare quotes on "faith?")

I think the point should be clear.  Science has limitations and can't say anything about IDT.

Yes, it can. It can say that ID"T" is not science. Which helps judges to say that ID"T" doesn't belong in public science classes. (By the way, I put scare quotes around "T" because we're talking about science, and ID is not a theory in any scientific sense.)

You yourself admitted that ID isn't science when you claimed that it isn't constrained by the rules of science.

Really, thordaddy, these are some of the dumbest comments I have yet seen. Do yourself a favor and think before you type.

Date: 2006/03/26 07:38:00, Link
Author: qetzal
I was surprised to learn from Mrs. Barton that:

Natural selection clearly occurs within species as an adaptive mechanism. I.D. theory does not deny or even address this, nor does it address the question of whether natural selection could lead to the development of entirely new species. I.D. theory is concerned with the origin of life only.

Has anyone told Behe? Dembski? The DI?

Date: 2006/03/28 14:57:38, Link
Author: qetzal
Quote (Stephen Elliott @ Mar. 28 2006,20:28)

You seem to be mixing consciousnes with memmmory now.

To make things easier, why do you not state your point clearly?

Because that's beyond his ability. Obviously.

Date: 2006/03/29 14:34:26, Link
Author: qetzal

The amusing thing is, that grandmother's beliefs are at least logically consistent, which is much more than can be said for the average ID advocate.

Date: 2006/03/29 14:48:12, Link
Author: qetzal
See? This is why science isn't respected. All you "scientists" are talking about matching socks, when it's a scientific "fact" that homosocksuality causes AIDS.

And "don't" even get "me" started on premarital socks.

[extra scare quotes, in case you need 'em: """""]

Date: 2006/03/29 14:58:05, Link
Author: qetzal
Also, you can't prove that your parents weren't wearing socks when you were conceived. Why isn't science and public schools debating this with Hanes?

Date: 2006/04/04 13:51:39, Link
Author: qetzal
Quote (hereoisreal @ April 04 2006,13:34)
I went to work one morning and turned to the mechanic next to me and said, "If God wanted to, he could turn the oceans into gas and look for someone with a match."  A couple of hours later I was listening to the radio when the news came on.  The announcer said that a Cuban refugee had boarded an airliner, thrown gasoline on a stewardess and threatened to strike a match.

Wow, man, that's deep!

Hey, have you ever really looked at your hand? I mean, really looked at your hand?

Date: 2006/04/05 05:49:37, Link
Author: qetzal
thordaddy reminds me a lot of someone with brain damage.

It's like a case where someone has normal vision, but due to some brain injury, they can't process any input from one side of their field of vision. They can see it, but the visual information is blocked from their conscious awareness.

thordaddy is like that, but his block is related to conceptual areas. No matter how you phrase it, or how many times, if you're trying to convey something in one of those areas, it will never, ever enter his conscious understanding.

Date: 2006/04/06 08:56:43, Link
Author: qetzal
Quote (avocationist @ April 06 2006,11:44)
It may be that the organism turns on a mutation feature, and in a specific area of the genome, and then suddenly gets the mutation for digesting nylon. For me, that's just too good to be true but we must also account for the organism's ability to direct itself like that in the first place.

There is NO EVIDENCE that organisms "turn on a mutation feature" to "direct" themselves in any particular way (e.g., towards an ability to digest nylon). People have looked for that evidence. They haven't found any. (Various people, including reputable scientists, have sometimes thought they'd found such evidence, but it's never panned out.) The reasonable scientific conclusion is that it doesn't work that way!

I'm referring to the problem that homologous organs often do not arise from the same genes, and that during development, they are often grown from different body segments or in a different order or from a different group of cells. Animal forelimbs develop from different body segments. Homology is difficult because many or most genes control widely divergent body parts.

Perhaps you mean analogous instead of homologous? By definition, homologous structures are those that can be traced to a common ancestor. A human heart and a dog heart are homologous, not because they do the same job, but because they are both derived from the same organ that existed in the last common ancestor of humans and dogs.

I admit I don't know that much developmental genetics. It wouldn't surprise me at all if there are some genes involved in human heart development that are different from some genes involved in dog heart development. However, I think a general claim that truly homologous organs "often do not arise from the same genes" is almost certainly wrong.

No only do homologous structures in closely related species arise from different genes, but nonhomologous structures can arise from the same gene.

I agree with the latter (with the obvious proviso that entire structures do not typically arise from a single gene). I strongly doubt the former, unless you merely mean that there can be some limited discrepancies between the relevant gene sets for the two species.

If you really believe that very different gene sets can give rise to the same homologous organ in closely related species, can you please provide an example? Thanks.

Date: 2006/04/07 03:47:33, Link
Author: qetzal
Quote (thordaddy @ April 06 2006,17:53)
Given these very simple facts, is it wise and prudent, let alone "educational," to teach children of the "normalcy" of homosexuality (normal as compared to what)?

Quote (thordaddy @ April 06 2006,18:17)
I only asked if it was wise and prudent, let alone "educational," to teach about the "normalcy" of homosexuality.

Quote (thordaddy @ April 06 2006,22:33)
Why and/or how are we teaching the "complex set of behaviors" of homosexuality to grade school children?

It has been repeatedly pointed out that public schools do not teach grade school children about homosexuality! Yet you keep asking the question. Why, I wondered?

Suddenly, I realized my misunderstanding. "We" in your questions obviously refers to you and your spouse/significant other/life partner/whatever. You are teaching your grade school children that homosexuality is normal, and you want to know if we can explain why. Right?

Sorry, can't help you. I have no idea why you teach your grade school children that homosexuality is normal, since you clearly don't believe it. Maybe you need some counseling?

Date: 2006/04/07 04:09:49, Link
Author: qetzal
Quote (thordaddy @ April 06 2006,22:53)
Let me propose another question...perhaps this one will get an answer?
What is your definition for life?(Your personal definition)

ME!  And I started at conception.

Well, there we go. Life is defined as thordaddy, who began at conception.

By extension, it must therefore be completely moral and ethical to abort any other fetus at any time. It isn't thordaddy, so it's not life.

Similarly, there's nothing immoral about terminating the existence of babies, kids, or adults, as long as they aren't thordaddy. (I almost said there's nothing immoral about killing, but obviously that term doesn't apply to anything but thordaddy.)

That clears things up enormously. Plus, think of all the cash we can save after we reduce the police force, medical system, armed forces, etc. We only need enough to guard the human rights of thordaddy, right?

In case you miss the point of this sarcasm, thordaddy, (and judging from your posts, it wouldn't surprise me), it's really contemptible for you to bitch and whine that someone else's definition isn't acceptable to you, but refuse to give an honest definition of your own.

Grow up already.

(Also, look up the definitions of the verbs is and become. They don't mean the same thing. Once you figure that out, maybe you'll understand Stephen Elliott's analogy.)

Date: 2006/04/08 04:34:05, Link
Author: qetzal
Quote (Russell @ April 07 2006,19:15)
[A]pparently Thordude has the "most enjoyable time on this website" by avoiding ever answering questions.
Nor ever reading any answers to his.

I see no point in attempting to engage him in honest discussion. He is quite clearly incapable of it. He's either being deliberately obtuse and dishonest, or he has some deficit in mental capacity. Perhaps both.

Date: 2006/05/08 16:02:08, Link
Author: qetzal
Alan Fox:

Did you ever get a satisfactory answer to your questions about genes and DNA strands?

Different genes can definitely be on different strands of a given chromosome. However, to the best of my knowledge, no single gene ever goes from one strand to another. Given the way that genes are transcribed, it's hard to imagine how that would even be possible.

Date: 2006/05/12 10:57:17, Link
Author: qetzal
Quote (afdave @ May 12 2006,11:58)
Does anyone have any good arguments for why this is a good assumption to make?

Suppose you see a man who is missing half of his ring finger. It ends at the first joint, with what looks like an obvious scar.

Do you conclude that he used to have a complete finger, like everyone else, and somehow lost the end? Or do you decide he was probably designed that way on purpose, because having half a finger serves some important function for him?

By the way - I'm another non-believer who has yet to kill or rape someone. Is there a list I should sign, or something?

Date: 2006/05/12 16:39:17, Link
Author: qetzal
Quote (afdave @ May 12 2006,18:40)
Your mistake in logic is that you have ASSUMED that humans and apes at one time in their history actually had a functional GLO gene.

No, dave. It's not an assumption. It's an inference, based on evidence. There's a difference.

By the way, it's rather amusing to see you try to lecture people on mistakes in logic:
IF Common Descent is true, then there is no need for a Creator....There is no afterlife, no heaven, no ####, no judgment for actions in this life, and the best we can do is live in harmony with our fellow man and have a good time until we die.  And when we die, that's the end of the story.

Is this what you consider logic? There couldn't possibly be a God, heaven, he##, and common descent? Why not?
Could it be that the Creator God spoken of in the Bible might in fact be one and the same as the Designer of the Cosmos and Biological Systems...

Yes, it could be. I don't see anyone claiming it's impossible. However, you do understand that mere possibility does not logically support a proposition, right? After all, it could be that the Flying Spaghetti Monster created us with his noodly appendage. What do you think that means, logically?
...for which evidence continues to mount?

Not that I can see, it doesn't. You've promised to provide some, but all I've seen are erroneous attacks on evolutionary theory, references to fine tuning, and incredulity about how life looks designed.

Is that your idea of logic? You keep using that word. I do not think it means what you think it means.

Date: 2006/05/12 16:44:54, Link
Author: qetzal
Quote (normdoering @ May 12 2006,20:19)
What are you talking about?

This? :
Andras Pellionisz claims that so-called junk DNA is actually the "real" blueprints, stored in fractal patterns, that tells genes how to build living tissue. If correct, he stands to make billions of dollars from his patent application, which covers all attempts to count, measure and compare the fractal properties of introns (the more respectable term for junk DNA)

I think that idea sounds a little screwy....

It sure does. Anyone who thinks the word introns is just a "more respectable term for junk DNA" clearly doesn't know what they're talking about.

Date: 2006/05/13 05:10:02, Link
Author: qetzal
Quote (afdave @ May 13 2006,08:59)
Notice carefully what you just did ...

I said this ..."IF Common Descent is true, then there is no need for a Creator"

and you quoted me as saying this ...

"There couldn't possibly be a God, heaven, he##,and common descent?

BIG, BIG difference.  Think about it.

??? YOU'RE the one who said it, not me! YOU claimed that IF CD is true, then there is no need for a Creater, AND then there is no heaven, no ####, no afterlife, etc. I quoted your exact words, only snipping out some intermediate sentences that didn't change your meaning at all. Here, I'll quote the entire passage this time:

Quote (afdave @ May 12 2006,11:58)
The bottom line, of course, is ...

IF Common Descent is true, then there is no need for a Creator.  Humans are free to believe in one, or pretend there is one, or whatever.  None of the 'God talk' really matters much and those who don't care to participate in 'God think' are free to leave 'Him' completely out of their thoughts and discussions.  There is no afterlife, no heaven, no ####, no judgment for actions in this life, and the best we can do is live in harmony with our fellow man and have a good time until we die.  And when we die, that's the end of the story.

That is a clear claim on your part that IF commond descent is true, THEN there is no afterlife, no heaven, and so on. Which is clearly a logical non sequitur. Yet you seem to think it's true "of course."

If that's not what you really mean, then I suggest you retract it. You might also try to express yourself more clearly in the future. And, you might stop chastising others for 'faulty' logic when you clearly are much more deficient in that area yourself.

Date: 2006/05/13 09:25:10, Link
Author: qetzal
Quote (afdave @ May 13 2006,08:59)
Creationists also predicted the limited variation that we see in natural and artificial selection....

This is another example of illogic.

Creationism predicts that we could see radically new species appear every day of the week. Any time God feels like it, he could create a 'dat' (except Sunday, I guess).

Evolution predicts we can only expect to see 'small' speciation events occur in our lifetimes. 'Large' changes should take hundreds of thousands or millions of years.

Date: 2006/05/14 04:47:30, Link
Author: qetzal
Quote (afdave @ May 14 2006,07:08)
It appears that they are saying that humans would be more closely related to guinea pigs (because humans also have broken GLO) than to pro-simians (functional GLO) if we followed evolutionary logic, but this is obviously absurd, because they are not related.  Again, I don't know if I agree with this or not.

I think they are also pointing out that evolutionists agree that guinea pig GLO broke independently from the simian line, so why shouldn't we expect ape GLO to break independently from human GLO?

We should.  At the very least, we cannot dogmatically say that the GLO gene definitely broke in the common ancestor, then was copied to apes and humans.

Do you agree?

It's not simply the fact that GLO is 'broken.' It's the exact nature of the 'breaks.' That's what supports evolution & common descent.

You realize that genes are generally a few thousand base pairs long (or longer), right? And you realize that there are many, many, many different genetic changes that can 'break' (inactivate) any given change?

So, if humans and other great apes all have an inactivated GLO gene, and the cause of the inactivation is virtually identical in all of them, that's evidence for evolution via common descent. Not proof. Evidence.

If you want to cling to the statement that we can't dogmatically say the GLO gene definitely broke in the common ancestor, go right ahead. Of course, the GLO gene is just one piece of evidence, among thousands of others. But even with all that evidence, we can't definitely say evolution and common descent are proven.

What we can say is that evolution not only provides detailed, mechanistic explanations of the available data, is also accurately and reproducibly predicts new observations. Creationism does neither of those things. That's why evolution is science, and creationism is not. That's why evolution should be taught in science class, and creationism should not.

Date: 2006/05/14 06:41:16, Link
Author: qetzal
Quote (afdave @ May 14 2006,06:14)
There are oodles of things that resemble things that people build all through nature:  bat "radar", bird wings, eyes like cameras, ad infinitum ... maybe there is Someone out there who designed this!

I read all you guys' links ... I know what they say ... I always do read your links if they are on topic

You cannot dodge this one ...


The problem with your 'fact' is that's it's untrue. There is no 'overwhelming evidence' that biological 'machines' even look designed. Not unless you're willing to provide an objective definition of looks designed.

What we have is overwhelming evidence that some people think things look designed. And in any case, a subjective judgement that something looks designed is not EVIDENCE that it is.

Which leads back to your earlier point. Yes, maybe there is Someone out there who designed this. I personally don't believe that, but I don't claim it's impossible. But "looks designed" is not really evidence for this Someone. "Looks designed, therefore maybe is designed" is just a hypothesis.

Now what you need to do is make and test some predictions. Let me get you started:

IF Someone designed all this, THEN I predict I should see X. HOWEVER, if I see Y, that would be evidence that Someone did NOT design all this.

Can you supply objective specifics for X and Y? If so, your concept of Someone may be testable. Otherwise, not.

Date: 2006/05/15 05:09:22, Link
Author: qetzal
Quote (afdave @ May 15 2006,08:01)
I agree that it is only a hypothesis and never will be provable.  Put I do make predictions. See my steps above. (and there are more besides this)

I hope there will be more besides this. You only listed one: "This 'ET' probably can communicate to humans."  And your only cited evidence for this prediction is the Bible.

The problem there is that the Bible is more readily explained as a product of purely human activity. We know humans exist. We know they write books. We know different human groups have claimed the existence of different (and often mutually incompatible) Gods throughout history. We know humans sometimes believe things that are objectively false. We know that groups of humans sometimes share common beliefs that are objectively false.

Thus, we can explain the Bible using entirely known phenomenon, without recourse to an undemonstrated God.

Which does NOT, of course, disprove God. Nor does it disprove the Bible as His word. It just means that the Bible is not useful evidence of God communicating with us.

We all know the Bill Gates quote about DNA being software which is far advanced beyond our own software.  I think he should know.

Why? Because he's such an accomplished molecular biologist and geneticist? I submit that the real reason you 'think he should know' is that you've already reached your conclusions (God exists, He made us, etc.), and you accept or reject others' opinions based on whether they agree with those predetermined conclusions.

And that's fine with me. You should just recognize that it's faith, not evidence.

I would turn this around and ask, "What would it take to convince you that the God of the Christian Bible exists and is really as He is described there?"  I'm serious.  What would it take?

Any of the following would certainly make me give it stronger consideration:
*  An objectively verifiable burning bush talks to me and/or to others.
*  A sea gets parted, preferably accompanied by a booming voice.
*  The earth stops rotating for a while, then starts up again, all without killing us.
*  A new species of dats appears suddenly, preferably in a place where there were definitely no previous dats. Molecular analysis shows that half the dats' genes came from dogs, and half from cats.

If the Bible is true, God did all those sorts of things before, so he can presumably do them again, right?

You may say that the Bible shows he already did them, and i should accept that. Unfortunately, we have no corroborating evidence that those things happened. In fact, objective evidence frequently contradicts modern translations of the Bible, e.g. regarding the age of the earth, claims for a global flood, etc.

On the other hand, we do have evidence that people sometimes make up stories like those, or misinterpret 'natural' phenomena as being the work of God.

So, if God exists, and He wants to do some of those things again now, when we're better equipped to observe and record them objectively, I'll reassess my non-belief. Or, maybe you can present actual evidence that is not more readily explained by known phenomena. You haven't done so yet, and I strongly doubt you can, but maybe I'm wrong.

Date: 2006/05/17 11:54:13, Link
Author: qetzal
Quote (afdave @ May 17 2006,08:51)
Creationism does NOT predict everything.  Here are 5 things it does not predict. (but evolution does predict and has been proven wrong)

1) "Upward evolution" ... it predicts "downward"
2) "Seamless fossil record" ... it predicts ubiquitous gaps
3) "Hominid civilizations" (or half-human to make Norm happy on terminology) ... it predicts fully human civilizations and fully ape "civilizations."
4) "Millions of years coal production" ... it predicts rapid coal formation
5) "An infinite universe" ... it predicts a finite universe that had a beginning

How far do you want me to go on?  I could keep going a long time, but you get the idea.  So you are incorrect.  Creationism does not predict everything.

Just in case there are any lurkers out there who think this is persuasive, I'll point out that none of these are predictions of evolution. I will also ask afdave: if we observe any of these things, do you agree that it's evidence against Creationism?

1) Evolution predicts that there is no "up" or "down" in the sense you mean. Even so, bacteria have developed the ability to digest nylon. They didn't have that ability in the past. It's new. We can identify the pre-existing genes that were co-opted to achieve this. Isn't this "upward" evolution by your definition? Does it disprove Creationism?

2) Evolution doesn't predict a seamless fossil record. Given that fossils occur, evolution does make predictions about what those fossils should look like. But evolution does not predict that every creature that ever lived must have left a fossil for us to find. Even so, every time a new fossil is discovered, the size of the gap between its nearest neighbors gets smaller. Your "ubiquitous gaps" are gradually disappearing. Isn't that evidence against Creationism?

3) Evolution doesn't predict that "half-human" civilizations should exist today. Even so, evolution does predict that early hominids should probably have exhibit primitive cultures. Guess what? The evidence shows they did. Does that disprove Creationism?

4) Evolution makes no predictions about coal formation. That aside, if we can prove that coal typically forms over millions of years, does that disprove Creationism?

5) Yet again - not a prediction of evolution. That aside, if astrophysicists find strong evidence that the universe did not have a beginning, or will not have an end, would that disprove Creationism?

Let's simplify. Is there any conceivable objective observation (or combination thereof) that could disprove Creationism? If so, please explain.

And before you ask, yes there are observations that could disprove evolution. You've probably heard the one about rabbit fossils from the pre-Cambrian already. I can list others. But, you first.

P.S. If you want a much better demonstration of why we accept evolution, and why it's so useful, please read incorygible's post on May 16 at 22:42 in this thread. (Minor quibble for incorygible - should you have used "ape" in place of "primate?" Is gulo broken in all primates, or just the apes? That aside, great post!;))

Date: 2006/05/17 14:32:45, Link
Author: qetzal
I didn't read DaVinci Code, and I won't. That's because I read Angels and Demons. After that, I wholeheartedly agree with Faid - utter crap.

Bad writing, worse plot. Totally ludicrous and unbelievable. Horrible characters - worse than in a romance novel. I don't have a single good thing I can say about it.

After that, I'd rather be trapped in a room with Heddle, DaveScot, JAD, Carol Clouser, Blast, afdave, and thordummy than read DaVinci Code. Oh, wait - I have been in that room....

Date: 2006/05/18 03:23:54, Link
Author: qetzal
Quote (sir_toejam @ May 17 2006,22:32)
I will put money on Dave thinking he is "winning" because we insult him so.


Easy bet - I'm in for $20. After all, it's abundantly clear that afdave isn't thinking at all.

You can donate my winnings to Panda's Thumb. ;)

Date: 2006/05/18 03:45:42, Link
Author: qetzal
Quote (ericmurphy @ May 17 2006,22:53)
Just for clarification, Dave:

Remember those three assertions you made? Biblical inerrancy, an age of the earth measured in thousands of years, and the impossibility of evolution? Just so we're clear, am I to understand that you are not planning to support any of them with actual evidence?

I just want to know whether I should continue waiting.

Looks like you have your answer:

Quote (afdave @ May 18 2006,06:14)
Sounds to me like everyone is very interested in hearing about my evidence for the Flood, young age of the earth, etc., so we will move quickly through the CS Lewis morality thing.

Translation: "Since everyone is asking for evidence, it's time for afdave to change the subject again."

Date: 2006/05/19 01:43:13, Link
Author: qetzal
Quote (sir_toejam @ May 18 2006,20:15)
let me try this out:

A handful of raisins can solve any problem.



you might be onto something there...

I am entranced by your knowledge of the real meaning of raisins. If only was a book I could buy.... ;)

Date: 2006/05/25 17:54:19, Link
Author: qetzal
I heard that the FAA took away some pilot's license the other day. When he asked them why, they said:

"Last month, when you flew from Los Angeles to San Francisco, you landed your plane on a freeway, two miles short of the airport! If you don't understand the difference between the airport and a freeway two miles away, you shouldn't be flying"

The pilot's response:

"It's a 400 mile flight! You're taking away my license because I missed the airport by ONE HALF OF ONE LOUSY PERCENTAGE POINT???

Date: 2006/05/28 11:00:29, Link
Author: qetzal
Quote (Arden Chatfield @ May 28 2006,14:31)
I think fundamentalism is not merely poor scholarship and poor science, it is actually the opposite of learning. Everything that is necessary for the acquisition of real knowledge is actively rejected. It's not just ignorance, it goes further than that -- it's actual antiknowledge.

I fully agree. True learning requires reason and questioning. Fundamentalism rejects reason and forbids questioning. Antiknowledge indeed.

Quote (afdave @ May 28 2006,08:42)
I am especially interested in what children are reading because of my involvement with authoring children's materials.

The very thought disgusts me. Better they should learn from chimpanzees.

Date: 2006/05/31 16:12:06, Link
Author: qetzal
Quote (The Ghost of Paley @ May 31 2006,20:02)
At this point, the evos will demand an explicit wave vector.


Now, Darwinists will object that this surface is not regular and thus non-orientable.

Hmm. I realize I have no standing on this thread (by rule), but isn't this supposed to be a cosmological model? Why label critics of this model "evos" and "Darwinists?"

Date: 2006/06/02 10:49:30, Link
Author: qetzal
Quote (skeptic @ May 24 2006,00:14)
[And what would you know about it, Mr. "I accidentally came here looking for info on complexity"?]

I'm a biochemist and a computer programmer and I'm interested in multi-variant systems.  Genetics and genetic algorithms fall into that catagory and that leads to evolution.

I can no longer resist asking: what kind of biochemistry do you do?

I ask because you seem to have very little knowledge of genetics and molecular biology. I realize that these are not the same as biochemistry, but they're closely related fields.

Are you that specialized in biochemistry, that you really don't know genetics & mol biol? Or are you, perhaps, not really a biochemist at all? My money's on the latter, quite frankly. Care to convince me otherwise? Tell me something coherent about your area of expertise, & I'll gladly apologize.

Date: 2006/06/03 11:42:19, Link
Author: qetzal
Quote (Rilke's Granddaughter @ June 03 2006,14:28)
Skeptic, ...[h]ere's a list of some of the factually incorrect (that is blatantly untrue statements you have made).

You forgot one, RG:
I'm a biochemist...

Date: 2006/06/05 14:51:51, Link
Author: qetzal
Quote (normdoering @ June 05 2006,18:18)
Quote (The Ghost of Paley @ June 05 2006,16:54)
But one of the appealing things about religious conservatism is the pressure it puts on its adherents to refine their ethical behavior and thought.

You  mean like George W. Bush endorsing torture and rendition and using signing statements to get  past the McCain amendment? Or do you mean like Pat Robertson lying about lifting 2000 pounds with a leg press because he drinks an  energy shake he wants to sell you? Or do you mean like how the Roman Catholics tried to hide the sexual abuse of children going on among their priests?

Yes, but they all felt tremendous pressure while doing those things.

Date: 2006/06/10 17:17:22, Link
Author: qetzal
afdave, I just have one question for you.

A while back, you said you believe God exists and that the Bible is literally correct because you were convinced by the evidence. Right?

So my question: what evidence would convince you the Bible is not literally correct, or that God does not exist?

Date: 2006/06/15 14:07:39, Link
Author: qetzal
Quote (PuckSR @ June 15 2006,11:00)
Ok, well another eventful night last night.  Either I got too drunk, or me and God spoke again.  I asked him some of the are the responses.

Ask him if he can make a burrito so hot that even he can't eat it.

He said that was stupid.  Why would anyone make burritos so hot that they couldn't be eaten.  They are delicious.

Can you please tell Him that my personal favorites are carne asada burritos from Roberto's, especially the one in Del Mar ('cause you can eat them on the beach). Was He the one who taught Roberto how to make such great burritos? I bet He was!

Date: 2006/06/17 05:54:18, Link
Author: qetzal
Quote (Occam's Aftershave @ June 17 2006,10:07)
This thread is an excellent case study so I'll give you an example.

Skeptic says:

The sky is blue!

Ok, now have at it.

No, here is a much more realistic example:

YECharlie says "Hi, I'm new here at ATBC and I just wanted to tell you that anyone who believes the sky is blue is a brainless sheep who has been led astray by those evil atheist scientists trying to keep God from his rightful place in the schools.  The sky is really paisley.  I know this because my Bible tells me so, and the Bible is the inerrant Word of the Lord!!  Sure I've seen your 'evidence' about light wavelengths and Rayleigh scattering, but those are only 'just so' stories to prop up your science religion.  Besides, we all have the same data, we just interpret if differently, and my interpretation is the only correct one.  Change your beliefs to match mine OR YOU WILL SURELY BURN IN HE11."

That's what we normally get around here.

Or there's this example:

Quote ( skeptic says in the opening post to Reinventing Evolutionary Theory @ May 23 2006,22:48)
Current evolutionary theory is fatally flawed because we lack the ability to perform experiments, collect data, and make predictions.

Can we develop an experiment that can be tested and repeated to reveal the mechanism driving evolution?

Random mutation is inadequate as a sole mechanism for diversity.

Organisms are much too responsive to the environment for diversity to be driven by random interactions.

The environment is much to dynamic to support the slow development required by random mutation.

Proteins must be self-organizing, but is this process molecularly driven or at the sub-atomic level?

Interestingly, skeptic was answered politely for several rounds, until it became clear that he would not engage in intelligent discussion.

Date: 2006/06/17 12:22:30, Link
Author: qetzal
Quote (skeptic @ June 17 2006,16:57)
So based upon this line of thinking, half the nation is a wash and deserved to be insulted and minimized regardless of what they say because of what they may believe.  They're just not worth the effort anymore.

In case anyone buys skeptic's baloney, go take a look at the thread he started, called "Reinventing Evolutionary Theory..." Notice that he came in with a bunch of ludicrously false statements. Yet he was not immediately insulted or minimized. He was told that his statements were false, and that it was clear that he didn't really understand evolutionary theory at all. The insults didn't start until long past the time that his trollishness became apparent.

Date: 2006/06/18 06:26:56, Link
Author: qetzal
Quote (skeptic @ June 18 2006,09:10)
Now if we go back to the emergence of life and we can all agree that it may have happened individually in many different locals at many different times then we would have to conclude that in order reach the a common descent scenario then all of these forms must have died out or converged and then diverged again to generate the present life forms we see today.  Is this likely?

A priori, who knows? But in light of the evidence, it is virtually certain that if life arose multiple times, it went through some sort of bottleneck at an early stage, such that the ancestry of all extant organisms can be traced back to a single interrelated group of organisms. The alternative, of course, is that life arose only once, and everything can be traced to that single event.
Given the fact that conditions were favorable for the emergence of life and the proliferation of life, why would it not continue to happen?

How do you know conditions were favorable? Maybe life emerged only once, because conditions were not so favorable.
I wouldn't reserve PE for an orgins scenario but for a continuing diversity scenario.

AFAIK, you still haven't explained what you really mean by PE. For instance, someone asked if you thought it was possible that mammals and fishes do not share a common ancestor. What was your answer?
Given the time and technology, if we converted the current tree of life into a genetically-based one wouldn't it get more complex and what patterns would emerge out of that?

If? That's been happening for quite a while now. I believe all sorts of interesting patterns are being observed, but none that call common descent into question.
PE would be represented as multiple common ancestors, more extinction, and some convergance throughout the tree. (I'm working on some diagrams to demostrate this).

How long ago did these multiple common ancestors exist, in your opinion? If you mean a few billion years ago, fine.
Anyway, this whole exercise is foundational to my biggest problem with the current theory and that is random mutation.  I don't believe them to be random at all.  Everything in chemistry and biochemistry seems at odds with random mutation.  This planet has conditions that are favorable to life and biomolecules have exploited that favorability for billions of years.  I'm interested in the mechanisms behind that exploitation.

Depends on what you mean by random. Mutations are decidely nonrandom in many ways. As one example, an average G:C base pair is more likely to mutate into an A:T base pair than into a T:A base pair.

When people talk about 'random' mutations in the context of evolution, they mean that the nature and frequency of mutation does not depend on the subsequent effect on fitness. In other words, the chance of a given mutation does not depend on whether that mutation will be 'good' or 'bad' for the organsim's survival or reproduction. Note that this is not some philosophical belief. It's what the evidence shows. People have tried very hard to show that mutations might some times be 'directed.' So far, they've all failed.

If you want to have a real discussion, you need to be more specific with your terms. In what sense do you think that mutations are nonrandom? What do you really mean by parallel evolution? Will you ever explain yourself? Or is this thread always going to be an on-line version of one of those rambling, drug-induced 'what-if' sessions that most of us left behind in college?

Date: 2006/06/18 16:49:42, Link
Author: qetzal
Quote (skeptic @ June 18 2006,21:05)
Now tell me with your full knowledge of chemistry and biochemistry where you see a support for randomness.  No one word answers here, I want you to think about it and tell me what you know or think you know.  I think you'll find the task a bit harder than some violent insult impling that you know what you're talking about.

Mutations are random in the sense that their nature and frequency is unrelated to their effect on fitness.

Did you not see where I wrote this two posts above you? Is it too hard for you to understand? It's OK if you need it explained in simpler terms. We all know now that you're not really a biochemist as you once claimed.

Date: 2006/06/19 14:22:07, Link
Author: qetzal
Quote (ericmurphy @ June 18 2006,23:12)
With respect to "random mutation," I think you're getting hung up on the "random" part. As I said quite a few pages ago, it's unlikely that mutations are "random" in the mathematical sense, i.e., all mutations having exactly equal probability of occurring.

In fact, it's extremely well documented that mutations are not random in that sense (as any biochemist should know).

As ericmurphy says, they are 'random' in the sense of unguided. Non-teleological. The types and frequencies of mutations are not determined by their effect on fitness.

These are not philosophical committments. This is not some blind Darwinian dogma. These are the only reasonable interpretations of the available facts.

So once again, I challenge skeptic to explain what he means when he says he thinks mutations are not random. And once again, I expect he will not answer.

Date: 2006/06/19 18:56:21, Link
Author: qetzal

First, thanks for attempting to clarify what you mean. I'm glad to see my expectation was wrong. Now regarding your post:

Quote (skeptic @ June 19 2006,20:39)
Random mutation, meaning that the mutation that occurs has no bearing upon the fitness of the result,...

That's backwards. Rather, the relative fitness of the mutation (more precisely, the relative fitness of an organism harboring the mutation) has no bearing on whether the mutation occurs.
...implies that a mutation occurs (good, bad or neutral) and is only fixed if the animal survives and prospers but the initial impact of the mutation is unknown. Does that sound close to what you're saying?

Closer, anyway. The mutation's potential impact on fitness is not 'known' to the organism at the time the mutation occurs. If that's what you're saying, OK.
We know that different parts of the genome mutate at different rates.  Some genes are conserved at greater frequency.  Is it true that these tend to be beneficlal genes?

You seem to be confusing two different things. One is the frequency of mutations in a given gene. The other is the likelihood that mutations in that gene will accumulate in a population.

It's true that mutations may occur at different rates in different genes. It's also true that some genes are more conserved in a population than others, and that this will generally be true for beneficial genes.

But this is not because the organism somehow ensures that beneficial genes are less likely to mutate. It is because a mutation in these genes is more likely to be detrimental or lethal to the organism. Organisms containing mutations in beneficial genes are less likely to survive and reproduce than organsims that lack such mutations. That's why those genes are more conserved in the population. (I agree with ericmurphy that 'beneficial genes' is not really an appropriate term, but I can live with it for the sake of this exchange.)
My hypothesis is that mutations are encouraged or favored in response to pressure s (call them selective, if you like) in order to encourage diversity as a means of survival.

This is a bit vague. It's true that mutational frequency can increase in response to certain 'pressures.' If you stress bacteria in certain ways, the mutation rate will increase. However, the data shows that you do not selectively increase the frequency of beneficial mutations. People have tried to find such an effect. They have so far failed.
The consequence of this in a parallel sense is that under similar circumstances, similar animals evolve along similar paths because the mechanism driving mutation is generic.

The mechanism 'driving mutation' does not determine the evolutionary path. That's determined by things like selection and drift. When similar animals evolve along similar paths, it's because they are subjected to similar selective forces, not because there is some mechanism causing similar mutations in each species. That's what the data indicates.
We could have the emergence of three independant branches in the tree of life because they started off in the same environment and were workin out of the same tool kit, so to speak.

But where do these independent branches emerge from? If you're talking about distant branches of the same tree, that's fine. Dolphins are only distantly related to fish, but they share certain body characteristics because they have to survive in the same general environment. But dolphins are ultimately related to fish. They share a common ancestor. They are not totally independent branches on different trees. That's what the data indicates.
 The convergence I suggested would arise if two similar species are close enough that their germ plasma is compatible and their offspring are fertile, examples are lion + tiger and more recently grizzley + kodiak.

Not sure of your point here. FWIW, this kind of hybridization only occurs between species that diverged from a common ancestor relatively recently. That's why their germ plasms can still be similar enough to allow hybridization.

This is not surprising. In essence, evolutionary theory says that new species arise when one interbreeding population of organsims splits into two reproductively isolated populations. There are a lot of ways this can happen, but it's not a sudden, all-or-none event. It happens over a period of time. Tigers and Lions are examples of species that are mostly, but not completely, reproductively isolated. You could say that the speciation process is not quite complete. Presently, they can still occasionally interbreed, and the hybrid female offspring are generally fertile. (Male hybrids are generally sterile). At some point in the future, this limited ability to interbreed will probably be lost (assuming they don't both become extinct first).

The fact that closely related species like lions and tigers, or camels and llamas, can sometimes interbreed is actually evidence in support of general evolutionary theory. It fits with what we know about speciation. On the other hand, species that are physically similar but not closely related never interbreed. Examples include dolphins and fish, or sea snakes and eels. This is also evidence in support of evolution.
To answer an earlier question: animals and fish could have developed independantly at just show the similarities due to the same paths (for a time) of evolution.

Well, absent any data, I suppose that's a possibility. Unfortunately, we have quite a lot of data that conflicts with that possibility. Given that data, the chance that mammals and fish do not share a common ancestor is essentially nil.

Date: 2006/06/20 01:46:00, Link
Author: qetzal

That's what I was trying to say. Re-reading my post, I see it wasn't so clear. I was trying to explain, for skeptic's sake, the distinction between the rate of mutations *occuring* in a given gene of a given cell of a given an individual organism, versus the rate at which mutations in that gene become fixed in the population of organisms.

Skeptic's references to hydrophilic/hydrophobic and electrostatic interactions clearly refer to mutational events themselves. He seems to think that the biochemical mutation rate largely determines whether a gene is more or less conserved during evolution. Of course, this is not so.

Beneficial genes was skeptic's term. I assumed it was his way of describing genes where an inactivating mutation significantly impairs fitness.

Date: 2006/06/24 13:44:18, Link
Author: qetzal
I'm not up to date on a lot of what the authors cover (esp. the role of membranes as stress sensors for the heat shock response). Nonetheless, there are a lot of incorrect statements in that paper.

Nowhere, however, in these or subsequent formulations of evolutionary change resulting from accumulated genetic modification is the cellular “target” of inferred mutation identified.

Huh? The cellular target of mutation is DNA, by definition. Do they mean that no one can specify the location of the exact mutation(s) that led to some phenotypic feature? Even that's not necessarily true.

Nevertheless, intermediates between living pro- and eukaryotes do not exist, variation within species reflects fluctuating frequencies of existing features, and the fossil record does not document seamless transformation of lineages.

Intermediates between prokaryotes and eukaryotes aren't expected to exist. Nor do we expect the fossil record to be complete and seamless. This is just a silly statement.

Current evolutionary theory assumes various molecular phenomena. For instance, under a constant mutation rate, new phenotypes should emerge gradually, because, as Morgan (1916) argued, the chance of a mutation affecting a trait would be increased by an earlier mutation affecting the same trait.

Current evolutionary theory doesn't claim this all. And why are the authors disputing a 90-year-old reference? If they want to show how current theory is inadequate, shouldn't they cite current theory?

Frequency of mutation is a physical phenomenon that depends on the structure and mechanism of DNA replication, which is altered only by exposure to physical and chemical mutagens.

Not true (unless "physical and chemical mutagens" is interpreted much more broadly than normal). Is temperature a physical mutagen? What about if you starve a cell of an essential amino acid? Is that a physical mutagen?

Detectable mutation is the result of both a base substitution in a DNA sequence and an effective repair
mechanism (a compromise between low and high efficiency of repair) that brings it to a fixed, constant, and very low rate of change....

Obviously, there are other mutations than just base substitution. Very sloppy writing.

Date: 2006/06/26 05:59:25, Link
Author: qetzal
Quote (skeptic @ June 25 2006,23:05)
Interesting line of reasoning, so the idea is that this is a low quality of material that has been published.  The reason for this seems to be that some of the statements the authors make are disturbing in light of the current theory (past also, as some references are towards Darwin).

No, my reason for considering this a low quality work is that it contains numerous statements that are unequivocally wrong.

The most charitable interpretation I can see is that perhaps the authors know better, but they didn't word things correctly, or didn't qualify what they were trying to say. That still speaks very poorly of their scholarship.

As to the substance of their idea, they appear to be proposing a particular model of how 'stress' may increase mutation rates, resulting in more rapid evolution.

The first part - increased stress -> increased mutation rate - isn't too novel. That's known to happen under at least some conditions in some organisms. Does it happen generally in all organisms, and by the model they suggest? I don't know. Given the many other errors in their paper, I'm not inclined to take their word for it, but I don't know enough to reject it either.

Even if it does, I'm not sure it would automatically lead to more rapid evolution, especially in sexually reproducing metazoa. Among other things, there would have to be a mechanism where stress on the organism as a whole led to increased mutations in the actual gametes.

And even if that happens, there's no proposed mechanism to somehow target mutations to sites or genes where a change might be beneficial. I don't think even the authors are claiming that.

Date: 2006/06/27 15:12:15, Link
Author: qetzal
Quote (skeptic @ June 27 2006,14:06)
I don't at all think this article implies a contradiction to evolution (Darwinian or otherwise).

Then what did you have in mind when you titled this thread "Reinventing Evolutionary Theory?"

Date: 2006/06/28 11:30:11, Link
Author: qetzal
I seem to recall Rev. Dr. Lenny is an amateur herpetologist. He may know whether this happens in any other snakes, but I don't know that he ever reads these boards. Someone may need to make an off-topic comment to him on Panda's Thumb.

Date: 2006/07/09 13:55:26, Link
Author: qetzal
I've seen suggestions that two populations could be called different species whenever they show greater than X% genetic difference. I don't see the value in that though.

It seems silly to object to the reproductive isolation definition, just because there are some cases that are incompletely isolated. Sort of like objecting to the distinction between green and blue, just because there are some hues that are in between.

Date: 2006/07/10 11:13:30, Link
Author: qetzal
Quote (jeannot @ July 10 2006,05:54)
Quote (qetzal @ July 09 2006,18:55)
I've seen suggestions that two populations could be called different species whenever they show greater than X% genetic difference. I don't see the value in that though.

I've never heard of that....

To be clear, I can't say whether this has been seriously proposed by any evolutionary biologists. Only that I recall seeing someone suggest it somewhere. It may well have been in a comment here or at PT, and may even have been offered as a deliberate strawman (i.e. to show that a purely genetic definition of species is unworkable).

Date: 2006/07/21 18:48:20, Link
Author: qetzal
I thought the regulars here might enjoy this amusing and topical music video by the New York Dolls:

Dance Like a Monkey

Endorsed by His Noodliness, as you'll see.

Date: 2006/07/23 15:51:58, Link
Author: qetzal
The whole idea of the "selfish carbon" doesn't work, because there's really nothing that will change either the lifetime of an individual carbon atom, or the number of carbon atoms on earth. At least, nothing related to living organisms. The amount of carbon increases by tiny amounts as carbonaceous meteorites impact earth, but that still doesn't fit the original proposal.

I guess water molecules are a bit different, since plants convert water plus CO2 plus light into carbohydrate plus O2, but that goes the wrong way. If anything, life should result in a net decrease in water. The 'unselfish water molecule' perhaps?

In any case, how do you define an individual water molecule. They exchange hydrogen nuclei (protons) with other molecules all the time, so what makes a given molecule unique? Just the oxygen atom? Now you're back to the same issue with carbon - life can't change the number or lifetime of individual oxygen atoms.

How about the 'selfish carbohydrate'? Life definitely increases the number and variety of carbohydrates on the planet. Is a plant just a carbohydrate's way of making another carbohydrate?

I don't think so.

Date: 2006/07/25 15:06:34, Link
Author: qetzal
Quote (skeptic @ July 25 2006,18:52)
I see religion vs religion.

Only because that's what you want to see.

From the moment you came here, you have been asked to provide evidence for your claims. In almost every case, you provided none.

In contrast, many others on this site provided you with evidence to show that your claims were wrong, and that standard evolutionary theory is by far a better explanation for what we observe.

Of course, you already know that science is about evidence and observation, right? Because you're a biochemist, right?

Bullsh1t! You're no more a biochemist than i am a walrus.

You see religion vs. religion because you are fundamentally self-deceiving, or fundamentally dishonest. Or both.

Date: 2006/08/05 10:03:20, Link
Author: qetzal
Quote (skeptic @ Aug. 04 2006,22:24)
Bacteria are so successful because they are just about the most versitale things on Earth.

Bacteria are successful in niches where it's advantageous to be single celled and have a very short generation time. They're not successful in niches where it's better to be complex and multicellular.

To the extent that bacteria are 'more successful' than metazoa (if such a thing is even meaningful), it merely reflects that there are more niches suitable for bacteria than for metazoa.

In other words, you've got it pretty much backwards.
Bacteria acquire mutations incredibly quickly and a good example of that is antibiotic resistantance.

An individual bacterium does not 'acquire' mutations incredibly quicker than metazoan cells. The mutation rates per base pair per cell division are roughly comparable. The difference is that every bacterium is an individual organism, which means that population sizes can be enormous, organismal replication rates can be very high (up to 2-3 times/h), and every mutation in every daughter cell has a chance to be positively selected if it provides an advantage in the current environment.

Because of those factors, newly favorable mutations can indeed become fixed in a bacterial population very quickly (relative to metazoans). But that does not mean that bacteria are not somehow dramatically better at generating favorable mutations on a per cell basis.
And if I remember correctly the organism with the greatest number of chromosomes is a bacteria, I'll double-check that to be sure.

Sorry, no. Unless, like so many of your statements, you're using your own private definition of "number of chromosomes."
In short, I'd rethink this idea of "accidental" because its just not what we actually see.  I'll put together some references to try to support this point.

In the process, I hope you'll clarify what your friggin' point actually is. Please explain what you think is the difference between 'accidental' and 'non-accidental' mutations.

Date: 2006/08/06 09:36:47, Link
Author: qetzal
Quote (Flint @ Aug. 06 2006,12:19)

Maybe it's the way you phrase things that's causing the problems.

Mutations happen. Organisms have *absololutely no control* over either the frequency or the type of mutaton.

I think that's arguable, Flint. One could consider the bacterial SOS response as a sort of inducible way to increase mutation rate. Whether the increased mutation rate is actually a selective advantage, or merely a byproduct of overcoming otherwise lethal DNA damage, I'm not sure.

If nothing else, there are very specific mutational events that are certainly controlled. For example, pili expression in E. coli is controlled by regulated, site-specific inversion of a particular DNA sequence. Then there are the recombination and somatic hypermutation processes involved in antibody maturation.
The pattern of mutations doesn't correlate with benefit or survival or utility.

Except in very specific cases (such as the pili and antibody examples above), I agree.

Quote (skeptic @ Aug. 06 2006,11:33)
Look at it this way, what evidence indicates that mutations occur purely by accident, and lets leave out mutagenic events due to radiation, etc (for now)?

Hard to answer when you won't clarify what "by accident" means to you. But, if you're asking 'what is the evidence that the frequency of a specific mutation does not depend on its effect,' look up the classic experiments by Luria & Delbruck, and Lederberg & Lederberg.

More recently, Cairns thought he had demonstrated 'adaptive' mutation. He used E. coli that had with a mutation in a lac gene, so they couldn't grow on lactose. When he put them on medium with only lactose, they seemed to preferentially 'fix' the mutation in the lac gene, allowing them to grow again.

However, further study showed that the effect is really due to a general increase in mutations during starvation. The cells do not appear to have some mysterious mechanism that lets them target mutations to the lac genes when lactose is the only available sugar.

Of course, we can't rule out the possibility of 'directed' mutations in every situation, or in every organism. But given evidence against directed mutations in testable systems, and no evidence for directed mutations, the rational conclusion is clear. Science, remember?

Date: 2006/08/06 11:41:55, Link
Author: qetzal
Quote (Flint @ Aug. 06 2006,16:15)
Apply a careful reading. The bacterial SOS response is NOT a way to increase either the type or frequency of mutation. It's a way to let down the safeguards against those mutations that happen. It's not clear to me (and what little I've read indicates otherwise) that organisms can *cause* specific mutations. All they can do is *accommodate* specific mutations IF they occur. Have I misunderstood?

So if starving bacteria mutate faster, does this mean that they exercise some control over the type or frequency of mutation, or only over the degree to which mutations are permitted to 'take' rather than be error-corrected out?

OK, I see your point. Sorry I misunderstood before.

You're saying that SOS response doesn't cause mutations per se, it just allows more errors to occur during repair replication, and/or corrects fewer of them.

Fair enough. Still, SOS is an inducible response that is regulated by the cell. If SOS has been evolutionarily selected to have a greater than 'normal' error rate, then in some sense the cell is still actively controlling its overall mutation rate, is it not? (Again, I don't know whether the higher error rate during SOS is a feature or an unavoidable consequence, so maybe it's a moot point.)

At minimum, regulated recombinational events like the E. coli fim system are controlled mutations, albeit hardly relevant to skeptic's point (whatever that is).

Date: 2006/08/06 13:18:13, Link
Author: qetzal

Very well put. I'll give you 10:1 on getting any intelligible response from skeptic.


I've seen the arguments about an optimal error rate on average. But the error rate during SOS repair is significantly higher than the error rate during exponential growth (when SOS is not active). Are you aware of any reference that says the higher rate during SOS induction is actually optimal for those conditions? That would be nice to see.

Date: 2006/08/27 05:11:46, Link
Author: qetzal
Easy: C.

ID certainly shouldn't be taught in science class. Typically, ID makes no scientifically testable claims. In that case, it's not science. In the rare cases where there have been testable claims related to ID, they've either been wrong or not different than what TOE predicts. There is no sense in which ID is a valid scientific alternative to TOE.

ID shouldn't be taught in philosophy or humanities either. At least, not as a valid philosophy. While it's true that ID's claims are philosophical not scientific, ID is dishonest. It dishonestly claims to be science, when it's real goal is to force religion into the classroom.

The only way I can see teaching about ID in a classroom is to analyze its use in the 'culture wars.' That could be appropriate in a suitable university level humanities class.

To summarize, ID has no place in public school, because it's not science and it's dishonest. Our kids deserve better.

Date: 2006/08/27 08:33:40, Link
Author: qetzal
Quote (Mark Frank @ Aug. 27 2006,12:49)
Actually I would vote for (b). Note that "teaching X" in a philosophy class is quite different from "teaching X" in a science class. All sorts of views are covered in a philosophy class, some of which are much nuttier than ID (solipism for instance) and ID raises all sorts of quite deep issues about probability, scientific explanation, and the relationship between religion and science. After all the argument from design has been covered in philosophy classes for centuries.

Teaching the argument for design in a philosophy class is fine, but skeptic asked about teaching ID. That's different.

ID proponents claim that ID is science. If that were so, why would you teach it in philosophy class? Does anyone teach evolution in philosophy class? I doubt it.

OTOH, if ID is really philosophy pretending to be science, why teach it that way in philosophy class? If you consider it equivalent to a legitimate philosophical argument from design, just teach that argument directly. Teaching it under the pseudoscientific guise of ID makes no sense.

The truth is that ID is neither science nor philosophy. It's politics. Religiously & philosophically motivated, to be sure, but politics all the same.

Date: 2006/08/28 16:48:24, Link
Author: qetzal
I stopped following this thread a long time ago, but seeing that there are now over 5000 posts, I have to ask: shouldn't AFDave win some sort of award for being stupid in more subjects than anyone in history?

In how many topics has he proven to be a complete moron so far? My list, no doubt highly incomplete (& please feel free to flesh it out):

evolutionary biology
cultural anthropology
nuclear physics

What's the antonym of polymath? Whatever it is, AFDave is definitely the poster child. He is more stupid on more topics than any other ID/creationist I've ever seen. DaveScot, JAD, LarryF, GOP, BlastFromThePast, Dembski, and the rest can't hold a candle to AFDave. They are not fit to untie his sandals, if I may coin a phrase. They must be sooooo jealous.

Date: 2006/08/29 18:32:13, Link
Author: qetzal
Quote (skeptic @ Aug. 29 2006,22:55)
A proposed mechanism of directed mutation via external stimuli has nothing to do with the experiment you're describing.  Mutations occur through multiple mechanism and I am just looking at one.  The ENU experiment exploits another.

It sure would help if you'd explain what your proposed mechanism of directed mutation actually is, rather than what it's not.

In fact, molecular modeling would assess the binding probabilities of ENU along the genome and rank the genes based upon nucleophilic nature.

Please tell me you aren't seriously proposing to rank entire genes based on nucleophilic character. Please.

Date: 2006/08/30 12:22:59, Link
Author: qetzal
Quote (skeptic @ Aug. 29 2006,22:55)
If I were to make predicts of the ENU experiment I would not us my model, I would use the molecular modeling techniques that I described and I'm betting the would reflect the actual data closely as the current molecular modeling approximations are quite good for simple or well-understood systems.  

I gather you think you know something in this area? In that case, please explain how you can tell that one gene is more nucleophilic than another. Heck, just explain what you think that even means.

Prediction: you won't, because you can't. You know just enough to think you can discuss these things intelligently, but not nearly enough to realize how silly such statements are.

Care to prove me wrong?

Date: 2006/09/01 15:58:20, Link
Author: qetzal
Quote (skeptic @ Sep. 01 2006,08:56)
getzal, a quick approximation of nucleophilicity could be obtained by calculating the LUMO energy.  This is a molecular level descriptor and not as precise as needed for this example.  Since electron density is essentially what we're refferring to an examination of atomic frontier orbital energies would work.  Given this experiment, the complication arises from the supercoiling and how that would affect the relative accessability of the bases regardless of nucleophilic character.  This does present an interesting experiment.  One could look  at the genes in question and map the nucloephilic character of the bases and compare that to the mutation frequency and also compare between genes.  The calculations are straightforward it just comes down to a matter of computer time and computation power.

I literally laughed out loud when I read this. You actually think you can calculate the LUMO energy of entire genes, and use that to predict relative mutability? OMG WTF BBQ!

Date: 2006/09/01 18:27:53, Link
Author: qetzal
Quote (skeptic @ Sep. 01 2006,22:53)
hate to break it to you but real science does go on in some parts of the world.

Yeah, but you're not involved in any of it, Mr. I Can Calculate the Nucleophilicity of an Entire Gene.

Honestly, skeptic, if you would stop pretending to know way more than you do, we might even have an interesting discussion.

Date: 2006/10/04 13:51:55, Link
Author: qetzal
Perhaps this is a mistake, but....

Re: Paley's claims of guts to gametes, Walter Doerfler has published a fair number of papers claiming that you can administer large amounts of DNA to mice, and subsequently detect said DNA in the bloodstream, spleen, & some other tissues, that it can become integrated into mouse DNA, and can even be transmitted to fetuses.

See the first 6 or 7 references here.

Not that this provides any support for acqusition of new traits via ingestion of foreign DNA. I'm not aware that anyone other than Doerfler has confirmed these findings. And even if they're true, only small fragments are typically observed in these mice, and only after adminstering quite large amounts of a relatively short DNA sequence. Also, I don't think Doerfler has ever shown DNA transfer to gametes. Finally, folks interested in gene therapy have looked for possible vertical transmission of exogenous DNA administered IV and subQ. AFAIK, it's never been observed. (You can certainly detect such DNA in gonads, but it appears not to reach the gametes themselves.)

Date: 2006/10/05 15:06:52, Link
Author: qetzal
Quote (The Ghost of Paley @ Oct. 04 2006,20:08)
Quote (Chris Hyland @ Oct. 03 2006,16:48)
Im confused, either you have a mechanism wherby DNA ingested by humans can be passed to the gametes or you don't.

This has always been a strawman version of my glorious hypothesis that discredits what remains of the evidence for the amoral ontology of evolutionism. In short, I do not or never have claimed that organisms can acquire the characteristics of other organisms from eating them. I merely claim genetic testing results proving that chimpanzees or mushrooms are my distant cousins are confounded by DNA coming from food, like what happened in the case of our slimy, Scandanavian friend I discussed a couple of posts ago. Since the Xenoturbella worm dined on only two kinds of molluscs, the evolutionists eventually caught on and were able to separate them. Humans eat all sorts of things. How many alien DNA fragments are picked up by the Gel electrophoresis machine? The thing is only capable of separating them, and not telling us exactly from whence they came. Heck, you would have to unravel the diet of every human tested through cross-checking with all the possible things she could eat!

Sorry, Paley. I haven't read much of this thread, so if you aren't claiming "guts to gametes," fair enough.

Unfortunately, your idea that ingested DNA confounds our ability to discern genetic relationships is quite wrong.

Are you aware that we have essentially complete sequence info for humans and chimps? For ingested DNA from food to confound things, it would have to be integrated into the human or chimp DNA. It would be really easy to identify these foreign sequence by simple comparison of the human and chimp sequences. They're just not there. Not to any significant degree.

Date: 2006/10/19 13:21:47, Link
Author: qetzal
Quote (heddle @ Oct. 19 2006,16:35)
As I'll describe it (for the gazillionth time) fine tuning + one universe --> God designed the universe.

That is not a reasonable (i.e. based on reason) or rational argument.

I'm willing to accept that fine tuning is an observation in need of explanation. Your argument would be reasonable if there were only two possible explanations: multiple universes, or God did it. Unfortunately, there is one more explanation: "something else caused it." Just because we can't currently imagine what that something might be doesn't mean we can reasonably reject it and conclude God did it.

Of course, it's your perogative to reach that conclusion if you wish, but it's not a reasoned conclusion.

Date: 2006/11/04 12:15:33, Link
Author: qetzal
Quote (argystokes @ Nov. 02 2006,23:59)
Good grief, when I perused that first chapter, I assumed it was aimed at early highschoolers.  Apparently I was wrong:
College level ID textbook to be released March 1, 2007 (chapter 1 available online)
by scordova on November 2nd, 2006 · No Comments

The Design of Life

   …this book is poised to become the authoritive textbook on the theory of intelligent design.

Keep reading →

Filed Under: Intelligent Design

Then again, I suppose that any college that would use this tripe in their curricula would be on about the level of Pensacola Christian College.

So, will this book finally explain what holds the clouds up?

Date: 2006/11/04 13:24:22, Link
Author: qetzal
Quote (Ichthyic @ Nov. 01 2006,00:42)
Francis Collins thinks that morality and empathy, including altruism, are traits that distinguish humans from other animals.

I agree that based on behavioral evidence, it seems very likely that some animals have empathy. Similarly, I think there are plenty of animal species whose behavior is at least as "moral" as our own. (Or, perhaps more accurately, their behavior is no more immoral than humans.)

I tried to think of any traits that really are qualitatively unique to humans. At first I thought our use of symbolic written language might be one. But, IIRC, wasn't there a chimp that learned to communicate through abstract symbols? Of course, the chimp didn't invent the language, but it did (apparently) have the capacity to learn a symbolic language with syntax.

As far as I can tell, that only leaves one significant qualititative difference between us and all other animals - religion.

Not sure what that really means, but it strikes me as interesting.

Date: 2006/11/05 08:07:11, Link
Author: qetzal
Quote (skeptic @ Nov. 05 2006,11:19)
Taking your example, let's examine the nature of knowledge with is based upon human reason and accept that it is purely human knowledge.  Beyond that constraint it may have no real explanatory power which is something we may never know unless we were to encounter other beings with comparable levels of communication.

That's wrong. Our "human" scientific knowledge allows us to accurately predict future events and observations. That's what explanatory power really boils down to.

If non-human intelligences exist, their non-human knowledge is going to make the same predictions as ours would. Assuming the starting conditions are equivalent, human knowledge is not going to accurately predict one outcome at the same time that non-human knowledge accurately predicts another. (Not unless you reject the concept of objective reality.)
I am not sure that animals experience altruism even though we describe the behaviors that we see according to our concepts and label it as altruism.

You're still missing the point. Animals behave altruistically. How can you argue that humans are uniquely altruistic, when certain animals behave in ways that clearly meet the observational definition of altruism?

If your claim is that only humans "experience" altruism, because only humans have the capacity to articulate altruism as a motive, then it isn't the altruism that sets us apart. It's our cognitive and communicative abilities. In that regard, we differ only quantitatively from animals, not qualitatively.

Date: 2006/11/05 08:18:03, Link
Author: qetzal
In the case of irreducibly complex organisms, taking away any one part causes it to die.

Ever seen a man with one leg? Proof positive that humans are not irreducibly complex.

This guy sounds dumber than AFDave. [shudder]

Date: 2006/11/05 10:54:59, Link
Author: qetzal
Quote (skeptic @ Nov. 05 2006,15:32)
I would disagree on these grounds, the two sets of predictions may agree if both we and the other beings described the world in the same way and if we both were correct.  Otherwise, you run into a problem where the other being doesn't even agree on the premise of the predictions or our theory is more correct and we arrive at correct predictions and they do not or vise versa.


Your claim was that knowledge based on human reason was purely human knowledge, and may have no explanatory power beyond that.

Sure, our "knowledge" may have no explanatory power if we're wrong. But that's because the "knowledge" is wrong, not because it's human.

If the other being doesn't agree on the premise of our predictions, then either one of us is wrong, or we're talking about two different things. Once again, any limitation in that case has nothing to do with our knowledge being human.

It may be more accurate to say that we describe animals' behavior as altruistic.  Which is to say that animals appear to act in an altruistic way, as we define altruism, but their actual motivations are unclear to us.

So in other words, it's only "true" altruism if we know the actor's motivations? Are you familiar with the "no true Scotsman" fallacy?

Still, you admit that some animals appear to behave altruistically. Which means that it's wrong to claim that altruism is unique to humans. The available evidence at least shows that animals may experience altruism, even if you insist that more information is needed to be sure.

Date: 2006/11/09 20:15:03, Link
Author: qetzal
Quote (skeptic @ Nov. 09 2006,19:14)
2) someone is looking for a scientific evaluation of Moral Law?

I think I'll be laughing about this for hours; if anything, you guys sure are amusing.

Further proof that you are not the open minded skeptic you think you are, but a closed-minded person who's unwilling to question your preconceived assumptions.

Consider. If it's true that some higher supernatural being or consciousness (e.g. God) exists, it's easy to him/her/it as the source of morality. Fair enough.

But what if there is no such being or consciousness? Where does morality come from then? Suppose philosophical materialism is right? Then morality can only be a result of some naturalistic process. In that case, evolution seems the logical candidate, no?

This is not meant to argue that philosophical materialism is, in fact, correct, or that morality must be the result of evolutionary processes. It's merely to show that it's a logical and reasonable possibility. And, if it's correct, then morality is most certainly subject to scientific evaluation, however laughable that seems to you.

But I have no doubt you'll come up with some convoluted defense of your statement, so you can hold on to your cherished self-image of open-mindedness. Mean time, I see no further point in engaging your comments.

Date: 2006/11/16 21:42:20, Link
Author: qetzal
Quote ("Rev Dr" Lenny Flank @ Nov. 16 2006,21:26)
Alas, fellow Rev, it's not about you, you, you . . . . Here, it is all about Paley, Paley, Paley.  As you have already seen, he has an irresistable compulsion to make himself the center of every thread.  Not to mention his weird compulsion to post photos of men in leather.

I think he's just compensating for his small penis and his confusion/shame over his sexual identity.  (shrug)

Don't be so sure. How do you know RevTragic isn't also GoP?

GoP's already admitted that "he" was actually two different people posting under one ID. I doubt he/they would consider sock puppetry "beyond the pale." (Sorry!;)

Date: 2006/11/21 22:26:29, Link
Author: qetzal
Quote (Robert O'Brien @ Nov. 21 2006,01:07)
Was the Ford Pinto, with all its imperfections revealed in crash tests, not designed?


Dunno. What holds up the clouds?

Date: 2006/12/14 17:49:02, Link
Author: qetzal
No question about it: GOP is full of s**t.

Date: 2007/01/11 22:42:12, Link
Author: qetzal
Great post, Dr. Hurd!

One minor quibble, which I only point out so you can correct when you do an update. The section on chirality mentions nucleic acid bases in several places. The bases themselves are not chiral, of course. It's the attached sugars that are chiral. (The term for a base plus a sugar is a nucleoside. If a phosphate is also attached, it's a nucleotide.)

Date: 2007/03/03 22:19:15, Link
Author: qetzal
Quote (skeptic @ Mar. 03 2007,19:55)
Funny that she bothers you guys so much...I guess you just don't understand her humor.

You think she's funny? I think she's a misanthropic attention whore who will say anything, no matter how hateful, in a pathetic attempt to stay in the spotlight. But that's just me.

Even so, the linked "story" isn't much different than some of the vile crap Coulter spews. Coulter may be despicable, but that's no reason to stoop to her level.

Date: 2007/03/04 00:59:42, Link
Author: qetzal
Quote (skeptic @ Mar. 04 2007,00:06)
Ann Coulter, Whoopi Goldberg, Chris Rock, George Carlin ( especially George Carlin), they're all the same.  I just find it amazing that people take Ann seriously enough to be offended.  Hey, but maybe that's just me. (chuckle)

Coulter doesn't offend me. I think she's pitiful. Literally.

I feel the same way about people who somehow think Coulter is insightful, or even (amazingly) funny. It takes a certain smallness and meanness of spirit to think that the bile Coulter spews is funny.

I'm truly sorry for you.

Date: 2007/03/04 10:20:04, Link
Author: qetzal
Quote (Stephen Elliott @ Mar. 04 2007,05:39)
Or could this be an example of co-evolution that may result in co-dependent systems?

That seems reasonable to me. Presumably the monkeys were frugivores while they still had dichromatic vision. Monkeys with better color vision (i.e. trichromacy) would presumably be more efficient in finding fruit, giving them a survival advantage over other monkeys.

At the same time, fruits that are more brightly colored are more likely to have their seeds widely dispersed. That should give them a survival advantage over other fruit plants.

I'm just speculating though. As a lowly molecular biologist, I don't have advanced expertise in evolutionary biology.

Date: 2007/03/04 12:21:36, Link
Author: qetzal
Quote (Stephen Elliott @ Mar. 04 2007,11:54)
But in the scenario given, why don't we see many white fruits? They would be easier to spot by both dichromatic and trichromatic (probably even tetrachromatic) frugivores.

Good question. I don't have any good answers. There are naturally occuring white flowers, so obviously it isn't because plants somehow can't make white organs.

Maybe an all white fruit is actually disadvantageous? Maybe it would tend to get overlooked because it looks like a patch of bright light?

It might be interesting to try to simulate what white vs. brightly colored fruits in a forest would look like to an animal with dichromatic & trichromatic vision. Maybe the intuition that white would stand out better is incorrect.

IIRC, there are flowers that look white to us, but are multi-colored in the UV wavelengths that their pollinators (e.g. bees) can see.

That's the best I can come up with off the top of my head. Maybe someone who actually knows what they're talking about will chime in with a better answer.


Date: 2007/03/04 15:43:23, Link
Author: qetzal
Quote (Stephen Elliott @ Mar. 04 2007,15:38)
I guess that I am the only one here that finds Anne Coulter sexually atractive then?

No, Bachem Macuno thinks so, too.


Date: 2007/03/04 22:19:23, Link
Author: qetzal
Quote (skeptic @ Mar. 04 2007,22:06)
Angry, I must disagree.  The entire theme of this thread is that she shouldn't be allowed to speak, period!

You never do get tired of saying idiotic things, do you? Where did anyone, anywhere in this thread say that Coulter shouldn't be allowed to say the things she does?

Do you understand the difference between "Coulter is wrong to say those things," and "Coulter shouldn't be allowed to say those things?" I'm surprised you have such difficulty in comprehension, you being a biochemist and all.*

*Footnote for the comprehension challenged: This sentence is sarcasm. I'm not really surprised at all.

Date: 2007/03/05 11:27:19, Link
Author: qetzal
What about bioluminescent fruits? Or bioluminescent plants in general. Are there any (not counting the man-made ones)?

If animals can harbor bioluminescent bacteria in light emitting organs, why couldn't plants do the same? If they can why don't they?

Sorry for going off on a tangent, but the question of 'why aren't there any white fruits' has tweaked my imagination.

Date: 2007/03/12 18:37:02, Link
Author: qetzal
Quote (The Ghost of Paley @ Mar. 12 2007,11:33)
And I'm skeptical that most of these mutations will be beneficial or even neutral, because they might be working against the historical selective forces that "chose" religious societies over nonreligious ones.

It's not clear that religiousness was ever directly selected for. Didn't you read the recent posts on spandrels?

Quote (The Ghost of Paley @ Mar. 12 2007, 15:08)
The question becomes, "How can we minimise harm?" I don't know the answer either, but a society predicated on an ethical, life-affirming philosophy seems like a good place to start.

Religion is not necessarily a requirement for such a philosophy.

warfare for instance. Have nations fought each other for religious reasons? Certainly. But if your hypothesis was true, we should have seen a net reduction in bloodshed in the more secular 20th Century.

Only if you assume there were no confounding factors. That's hardly the case. Societies and technologies have both changed enormously since the 1900s. It's ludicrous to ignore those changes and only cite increased secularism.

I doubt you could ever tease out all the confounding variables, but if you were going to try, you'd do better to compare more versus less secular societies in a given time period. At least then you could attempt to control for relative wealth, technology, etc.

If you take that approach today, my guess is the more religious societies will not look so good by comparison, but I freely admit it's purely a guess.

Date: 2007/03/17 18:41:13, Link
Author: qetzal
Quote (skeptic @ Mar. 17 2007,10:50)
That's crap and lazy thinking...To most here, religion and specifically Christianity, is the root of all evil and for the them to even entertain any other concept is beyond their ability.


This is just an example of how atheists try to justify their belief with some moral higher ground and how Christians try to label atheists as little satans.  Until we get beyond that, there simply is no discussion.

Lessee: sweeping generalizations? Check. Blatant projection? Check. Crap and lazy thinking? Absolutely.

Skeptic, you're a riot.

Date: 2007/04/03 18:46:09, Link
Author: qetzal
Quote (The Ghost of Paley @ April 03 2007,14:52)
Mr. Elliot:

OK Paley, I'd like an example.

Fair enough.

[Meandering off-topic anecdote about skeptics being rude omitted]

There you go, Louis. Proof positive that most skeptics have a hidden agenda to abolish all religion. After all, they booed and reacted negatively. Viscerally so, even! How can you possibly argue with that?


Date: 2007/04/04 09:17:58, Link
Author: qetzal
Paley is such an amusing (if transparent) tool.

Louis asked:

Not every atheist/skeptic/secularist has some hidden anti-religion agenda. In fact in my experience (oh let's play duelling anecdotes, that's really rational! Not) this is a very rare (perhaps very vocal) occurrence. Mostly skeptics/secularists/atheists want exactly what I've described: a liberal secular state, and I mean liberal in the "not-authoritarian" sense not the economic sense, and "secular" in the "not privileging religion" sense. This can include right wing (small state) govts, left wing (heavy state) govts and a plethora of possibilities around them. I defy you to prove this "hidden agenda" nonsense of yours.

Paley's reply (offered only after a hilariously childish insistence that someone else had to ask him, pretty please, to answer): a long-winded anecdote about skeptics behaving rudely. By his own admission, the point of his little story was:

Nice way to miss the point, which was about how irrationally the crowd was acting.

Funny. I thought the point was to provide proof that most atheists have a hidden agenda to abolish religion. Clearly, somebody missed the point.

Date: 2007/04/04 13:24:05, Link
Author: qetzal
Quote (Stephen Elliott @ April 04 2007,11:47)
EDIT: I forgot to ask. What is this thread about?

Let me 'splain. [pause] No, there is too much. Let me sum up.

Proposition: atheists are dangerous to society and want to abolish all religion.

Evidence: some of them were rude at a meeting.


Date: 2007/04/04 15:53:13, Link
Author: qetzal
Quote (eddiep @ April 04 2007,09:43)
I hope I don't come off as a concern troll, this is just an issue I've been interested in for a long time....

Specifically, how do we account for those things that are not made up of matter and energy?

The question is interesting, but I don't see why it should be a concern. At least, not in the sense of being incompatible with naturalism, if that's what worries you. We can't really account for things that are made up of matter and energy either. We simply observe that they exist.

Date: 2007/04/04 16:05:19, Link
Author: qetzal
Quote (The Ghost of Paley @ April 04 2007,15:34)

Now who's trolling?

Let me explain this once more: I do not respond to Lenny and Louis's posts. If you knew the whole story, you would know why.

Says the guy(s)/gal(s) who claimed to be two people posting under one account, deliberately arguing outlandish positions s/he/they didn't really believe in.


Date: 2007/04/04 19:37:58, Link
Author: qetzal
Quote (stevestory @ April 04 2007,19:24)
Why do people so easily believe things?

In a case like this, I think there's a desire to believe because it makes for a cool "fact" to tell one's friends. Knowing interesting things makes you seem more interesting and knowledgable to others.

And how does this sort of thing show up among creationists or evolutionists?

For some people, there's the additional motivation that some "facts" confirm what we want to be true. Most of us are more willing to believe things that already fit our preconceptions.

Date: 2007/04/05 16:53:56, Link
Author: qetzal
Quote (Louis @ April 05 2007,03:38)

It's just staggering that this level of dishonesty is tolerated in anything that is even remotely supposed to be a civilised and respectful discussion. After all, is it not an insult to the other participants in a debate or discussion that one lacks even the scintilla of respect for them required by honesty and basic intellectual rigour?

That's why I've vowed not to attempt any sort of rational argument with GOP. I promised myself that right after he confessed his trolling. What's the point of discussion with someone who deliberately argues absurdities?

I admit fell off the wagon for one post at the beginning of this thread, but I promise it won't happen again. I do, however, reserve the right to ridicule GOP's childish antics from time to time. After all, what's the world coming to if you can't bait a troll on his own thread?


Date: 2007/04/06 20:38:50, Link
Author: qetzal
Quote (Louis @ April 05 2007,08:33)
Hi Eddie,

Ah the old "is the purple you see the purple I see" question!

It's a doozy. To the best of my knowledge we can say nothing about the ultimate expression of this question. What we can say is that the frequencies of light that I recognise as purple are the same that you recognise as purple and that the bits of my brain and eye that trigger when I see a purple object are the same bits of your brain that trigger when you see the same purple object. Does the colour purple I see in my brain look the same to you? I can never know. In a sense it's a meaningless question.

I think the only reasonable answer is yes, we do see the same thing.

We're all receiving light of the same wavelengths. Our brains process the signals from our retinas, and have learned to label that particular set of signals "purple." We don't really see purple in our brains, and it doesn't matter if the exact neural pathways are non-identical between you and me. We're still responding to the same wavelengths of light, and labeling them the same way. That's the only meaningful sense in which we "see" any color.

It's not really different than the example of "5" except of course that there's more room for individuals to disagree on the boundaries of "purple."

Date: 2007/04/07 09:03:39, Link
Author: qetzal
Skeptic, you should try harder to keep your arguments straight.

First you said:
Quote (skeptic @ Mar. 30 2007,17:18)
Ogee,  "strong" atheism is not merely the acknowledgement that a null condition exists.  It is an affimative statement that a previously held belief is false.  It is a deliberate statement of faith that requires belief and then leads one to make decisions or act according to these tenets.

In other words, according to you, "strong" atheism is a religion.

But then you said:

Quote (skeptic @ April 06 2007,17:46)
Over here there are concerted efforts to remove religion by the "strong" atheists and if I take you to be correct, you're not seeing those same movements.

And as evidence, you offered:
Quote (skeptic @ April 06 2007,21:50)
GCT, school prayer, "one nation under God", "In God we trust".  Three specific examples.  

You guys can continue under this delusion that a secular society is simply one in which religion has no favored status, as you put it Louis, but that is simply not the case in the US.  In this country some religions enjoy favored status in a variety of areas and at the same times are discriminated against.  Again, this means nothing towards my overall point.  I'm just trying to raise this conversation above the level of "atheist bad/religion good and religion bad/atheist good."

If strong atheism is a religion, as you claim, then trying to remove government sponsored references to God is not trying to remove religion, is it? It's merely an attempt to ensure that the "religion" of strong atheism (as you see it) has equal protection.

By your own argument, it makes no sense to say "religion bad/atheist good."

Date: 2007/04/07 11:57:00, Link
Author: qetzal
Quote (ofro @ April 06 2007,21:48)
Anything that involves the human brain for physical observation, however, is much less certain.  There is no guarantee that a physical sensation made by one individual’s body’s sensors/receptors is processed and perceived is the same as that by another individuals.  In fact, there can be significant differences among different individuals.   An extreme case to make it obvious:  the ultimate color perception of a “normal” and a red/green colorblind individual.  The physical input (light of a certain wavelength) is the same, but the primary light-detecting machinery (the set of color-sensitive cones of the retina with their color-specific opsins) differs between normal and color blind individuals.

Things also differ in the neural processing machinery of a signal.  For example, there is a condition called synesthesia .  Just to mess up the “5” example a bit, in grapheme-color synesthesia, an individual actually senses a color when seeing a number.

I agree color perception is more complicated, and I purposely ignored colorblindness, synesthesia, etc. for simplicity.

My basic point is just this: if you and I agree which things are purple and which are not, I think we are "seeing" the same color by definition. I think the idea that purple might somehow "look" yellow to me, even though I call it purple, is meaningless.

Date: 2007/04/07 21:54:56, Link
Author: qetzal
Quote (skeptic @ April 07 2007,21:42)
GCT, you just can't read.  A seperation of state from the church exists not the other way around.

Wow. Are you channeling GOP? You're in geocentrism/guts-to-gametes territory now.

What exactly do you think you're saying? The state has to be separate from the church, but the church doesn't have to be separate from the state?

This is one of the most surreal statements I've read on this board.

Date: 2007/04/08 08:11:31, Link
Author: qetzal
Please answer the question. What does this mean:

Quote (skeptic @ April 07 2007,21:42)
 A seperation of state from the church exists not the other way around.

Date: 2007/04/09 09:38:09, Link
Author: qetzal
Quote (Louis @ April 09 2007,09:13)
So you're doing what I predicted and running away, obfuscating and demonstrating that you cannot support your claim?

Louis, are you psychic? How could you possible guess he'd do that?!!!1!


Date: 2007/04/09 13:08:02, Link
Author: qetzal
Quote (Louis @ April 09 2007,10:53)
Quote (qetzal @ April 09 2007,16:38)
Louis, are you psychic? How could you possible guess he'd do that?!!!1!


Nah, I just looked up Skeptic's biographical entry in my copy of "The Big Book of Online Cowards, Anti-Intellectuals, Liars, Idiots, Blinkered Pseudo Creationist Shills, and Personages of Low Intellect" and read off a litany of his standard tactics.

{whips out pipe, slippers, and old man costume}

Ya see youngin, when you've been at this lark for as many years as I have, you'll learn to see the patterns that fools make. It's easy for the likes of Skeptic to make claims, but the minute they are asked to back them up they turn tail an run. The best description one can give is that of a Pooflinger. What many like Skeptic do is appear on a thread or board, fling poo around liberally and then refuse to support any of it in the hope that some sticks. It's one sign that you have a troll on your hands. By no means definite proof, but certainly indicative.

Claims like this, for instance?

Quote (skeptic @ May 23 2006,17:48)
Current evolutionary theory is fatally flawed because we lack the ability to perform experiments, collect data, and make predictions.

I think I see what you did here. It's like you took observations of previous events (e.g. skeptic's past posts), used them to form some sort of, I don't know, intelligent guess about something (e.g. skeptic is a troll), and you could predict future events accordingly! Wow, that is sooo cool!

You should invent a catchy name for that process. Seems like it could be useful.

Date: 2007/04/09 19:04:17, Link
Author: qetzal
Quote (skeptic @ April 09 2007,15:52)
...and qetzal can continue to fail to understand that the Constitution is a restriction upon government not upon people.

Oh, I understand just fine. Don't go blaming me because you write an incoherent sentence and refuse to explain what the heck you really mean. :-D

Let me make a suggestion. If you phrase something badly, and people call you on it, try this. Just say, "Sorry, I wan't clear. What I meant was ____" It's really easy. I have to do it myself far too often.

Oh yeah, and you can continue to believe that "strong atheism" only wants religion to occupy a non-favored position in society.  I'll just continue to enjoy the humor along the way.

You know, I would agree with you if your point was that(some) strong atheists want to abolish religion. What fraction, I have no idea. (Although numerically, I'd bet there are far more people in the US who want to abolish atheism and all non-Christian religions.)

One other thing for you to consider, if you're able. Some people are religious and strong atheists at the same time! Not everyone who wants to practice their religion in peace believes in a god.

Date: 2007/04/24 23:03:16, Link
Author: qetzal
Quote (stevestory @ April 24 2007,20:56)
You can tell me it's a nice Sumatra, but if it's actually a lightly-roasted Kenya AA, one sip and it's going down the sink.

(And don't tell me some people prefer a nice lightly-roasted Kenya, Costa Rica, or Guatemala. There's no such thing, and those people are perverts.)

Finally! Truth is revealed at AtBC.

You, sir, are my new diety.

Date: 2007/04/25 21:07:01, Link
Author: qetzal
Quote (Arden Chatfield @ April 25 2007,11:56)
My old creaky metabolism will no longer tolerate my drinking coffee all day.  :(

Saint stevestory preserve me from such a fate. I'm useless without my 10 cups a day. ;-)

Date: 2007/04/25 21:15:28, Link
Author: qetzal
Quote (Wesley R. Elsberry @ April 25 2007,18:17)
And when it is hot out and the bank account is looking parched, too, Miller Genuine Draft is still beer.


Date: 2007/05/06 19:49:21, Link
Author: qetzal
Quote (The Ghost of Paley @ May 06 2007,16:11)
I am not saying the Second Law is inconsistent, I am saying that it MIGHT be because WE DO NOT HAVE ENOUGH INFORMATION YET. In my opinion, we CANNOT claim that the Second Law is inconsistent with abiogenesis for the very same reason that we cannot be reasonably sure that it is consistent, because THE DEMONSTRATION OR CALCULATIONS HAVE NOT BEEN DONE YET.

What's funny about all of this is that I'm perfectly willing to admit I'm wrong. ALL THAT NEEDS TO BE DONE IS TO POINT ME TO PAPER(S) THAT SHOW HOW THE FORMATION OF NUCLEIC ACIDS IS A SPONTANEOUS PROCESS.

And you wonder why people consider you a troll.

Do you honestly think there may not have been enough energy available in the prebiotic Earth to drive NA formation? Do you think it's such an uncertainty that we need to calculate whether it's possible according to SLOT?

Either you have NO understanding of SLOT, or you're being disingenous. Again. I wonder which? (Not that they're mutually exclusive.)

A non-troll might reasonably ask whether there are plausible specific mechanisms to explain how NA's may have formed abiotically. But to suggest that the process might be impossible based on the SLOT is ignorant and/or trollish. (And yes, it is a standard creationist argument, despite your attempt to recast it as merely a 'possible' problem.)

Date: 2007/05/19 13:20:00, Link
Author: qetzal
Quote (guthrie @ May 19 2007,10:50)
lkeithlu- the technical term is "belief tank".

How about "dogma tank?"

Date: 2007/05/21 21:24:57, Link
Author: qetzal
Interesting post, but I don't agree with all of it. My thoughts:

Celebrating the death of somebody you disagreed with pretty much makes you a dick.

Not necessarily. Depends on the magnitude and cause of the disagreement. Stalin, for example, was a pretty disagreeable fellow, and I don't think celebrating his death makes you a dick.

Furthermore, suggesting people were celebrating Falwell's death simply because they disagreed with his opinions is a bit disingenuous. In my opinion, Falwell was an evil, hateful, immoral, selfish, self-aggrandizing prick, and the world is better off without him. That's not to say he deserved to die, nor that he had no redeeming qualities at all. I didn't celebrate his death, but I certainly wasn't unhappy about it.

1. You Can Do Terrible Things in the Name of Either [Christianity or Atheism]

Yep. Ditto Islam, Buddhism, Scientology, Agnosticism, etc.

2. Both Sides Really Do Believe What They're Saying

To a point. I agree that many people on both sides really do believe what they're saying. At the same time, I believe that many religious leaders are in it for the power and personal glory. A lot of what they say is simply about furthering those goals, and has little to do with truly believing what they say. Falwell was definitely in that class (IMO).

For whatever reason, this does not seem to be a common problem with leading atheists.

3. In Everyday Life, You're Not That Different

Agreed. (Although the part about living "as if the absolute morality of some magical lawgiver were true" is a little over the top.)

4. There Are Good People on Both Sides

Absolutely agreed.

5. Your Point of View is Legitimately Offensive to Them

This should be "Your point of view may be legitimately offensive to them." Personally, I'm not in the least offended by someone telling me I'm going to H*ll, because I'm quite convinced there's no such place. For the same reason, I don't think it's legitimate for a Christian to be offended if I say I don't believe they're going to Heaven. If they're certain they are, my statement should seem merely ignorant and wrong to them, not offensive.

I do think it's legitimately offensive if a Christian tries to impose his/her religion on me. For example, here in Georgia, it's illegal to sell liquor on Sundays. Why? Because Christians don't like it. I find that legitimately offensive (although a very minor offense). At the same time, it's legitimate for a Christian to be offended if an atheist tries to interfere in his/her religions practice. So, for example, I think it would be legitimately offensive to force Christian shop owners to sell liquor on Sunday against their beliefs.

6. We Tend to Exaggerate About the Other Guy;


7. We Tend to Exaggerate About Ourselves, Too

Agreed (except for the part about no God = no free will, which is quite wrong).

8. Focusing on Negative Examples Makes You Stupid

I agree it make you look stupid (which I assume is what was meant). It has the additional disadvantage of making your 'argument' easy to refute.

9. Both Sides Have Brought Good to the Table

Agreed. But then there's this:

Seriously, what did you think the creationism thing was about? It's about keeping humanity sacred. They think that once you dash the idea of a created humanity, then there'll be nothing to stop strong humans from treating weak ones as cannon fodder.

And logically, there won't be anything.

This is also wrong.

10. You'll Never Harass the Other Side Out of Existence

Agreed. As for the overall message - be tolerant and courteous, I completely agree (even if I admit I don't always live up to that goal).

Date: 2007/05/25 20:43:07, Link
Author: qetzal
Quote (shi @ May 25 2007,15:01)
Definition of a Tard: A person who underestimates the tardness of a chimp desendent who really only cares and knows nothing other than to produce as many desendents as possible.

Wait. You mean we're actually underestimating your tardness?

Dude. Do they have mental health professionals in your reality? 'Cause you need to consult one, ASAP.

Date: 2007/05/25 21:09:24, Link
Author: qetzal
Quote (Louis @ May 24 2007,03:56)
But the capability of our immunes system to produce antibodies that are specific is inherent in the DNA, and can provide an (estimated) 10 to the 11th different antibodies.  But these are nor specific to anything before they are made - the body ends up producing more of the ones that work.

To an extent this is why the analogy with bioactive secondary metabolites works, their formation is also encoded in the organisms DNA. The analogy isn't about which specific antibodies or metabolites are made but that for relatively little cost a very diverse set can be produced.

Louis, I'm curious. You're comparing diversity in secondary metabolites to diversity in antibodies.

With antibodies, there are mechanisms to generate diversity (e.g. VDJ recombination) plus mechanisms to preferentially amplify expression of "successful" antibodies (e.g. clonal expansion of B-cells).

Are there parallels to this for secondary metabolites? In other words, can some organisms preferentially select which metabolites to produce, depending on which one(s) will be most beneficial in a given setting?

Date: 2007/05/25 21:36:36, Link
Author: qetzal
Quote (Ichthyic @ May 25 2007,16:54)
all current phylogenies put marsupials as branching off earlier than placental mammals.

I think this is the main thing here that is meant here by the term "primitive".


also, I would wager (without knowing for sure) that marsupial immune systems differ in certain ways that would include fewer components.

Here's one account of why marsupial immune systems have been considered primitive (source):

[U]nsuccessful attempts to isolate T cell derived cytokines in the laboratory has led some authors to suggest that the marsupial immune system is 'primitive' and does not possess the level of complexity demonstrated by eutherians such as humans and mice. The fact that some T cell driven responses are also aberrant adds to this argument. Marsupials appear to have delayed skin graft rejection [18] and antibody class switching [19], together with an apparent lack of an in vitro Mixed Lymphocyte Response [20].

Also, I don't see how the branching of marsupials from placental mammals says anything about which is more 'primitive.' They branched from one another, so both groups go back to to the same point in time. The only way marsupials can be considered more primitive than eutherians is if they retain more characters of the last common ancestor.

At least, that's my understanding.

Date: 2007/05/26 09:22:50, Link
Author: qetzal
Quote (Louis @ May 26 2007,05:34)
[T]he point wasn't about the similarity of their mechanisms or their nature, but the fact that (after the initial genetic investment, if you get my drift) that the cost of production of a diverse set of products (be they antibodies or metabolites) was relatively cheap.


OK, but what makes the cost of secondary metabolites relatively cheap (at least, in the view of those who support that argument)?

I re-read your opening post, but it didn't seem very clear on this. At one point you mention high substrate tolerance in certain enzymes. Is the point that some individual enzymes can produce relatively diverse secondary metabolites by accepting a broader than normal range of substrates?

Date: 2007/05/28 00:06:13, Link
Author: qetzal
I liked "Evolution Tree" versus "Creation Orchard."

Date: 2007/05/30 20:03:43, Link
Author: qetzal
Quote (Ichthyic @ May 29 2007,21:58)
Quote (ScaryFacts @ May 29 2007,21:56)
Back on topic:  Does anyone know if the "tours" are guided by real people (who can take questions) or are just driven along by a group of "World of Tomorrow" style pre-recorded messages?

"Welcome, to the world of tomorrowwwww!"

do they have the "Whalers on the Moon" exhibit, I wonder?

Why not? If The Flood caused the Grand Canyon, no reason there can't be whales on the Moon. (Who says the flood waters couldn't rise high enough to put whales on the Moon?!!1!)

Maybe we could sic The Crushinator on Hammie's Playhouse?

Date: 2007/05/30 22:13:12, Link
Author: qetzal
Quote (Ichthyic @ May 30 2007,21:09)
Quote (qetzal @ May 30 2007,20:03)
Quote (Ichthyic @ May 29 2007,21:58)
Quote (ScaryFacts @ May 29 2007,21:56)
Back on topic:  Does anyone know if the "tours" are guided by real people (who can take questions) or are just driven along by a group of "World of Tomorrow" style pre-recorded messages?

"Welcome, to the world of tomorrowwwww!"

do they have the "Whalers on the Moon" exhibit, I wonder?

Why not? If The Flood caused the Grand Canyon, no reason there can't be whales on the Moon. (Who says the flood waters couldn't rise high enough to put whales on the Moon?!!1!)

Maybe we could sic The Crushinator on Hammie's Playhouse?

btw, my earlier post was a shameless reference to futurama, which i was reminded of by the "world of tommorrow" phrase.

they had an episode where fry goes to the moon...

and they've made it into a thempark (ala disneyland), complete with a hugely distorted history including a recurring theme of "whalers on the moon" being the ones primarily responsible for exploring the moon to begin with.

yeah, silly, I know, but if you saw it, you'd immediately recognize the parallels with Hammy's new crapseum.

ARRR, here, matey:

I think even Fry, if he wandered into Hammy's crapseum, would have said the same thing he did in that clip:

"This is stupid"

which means a lot, coming from Fry.

Watchin' the Big Piece of Garbage episode right now.


Fry (after using the Smelloscope to smell Saturn (strawberries!) and Jupiter (pine needles!)): Just don't make me smell Uranus!

The Professor: Fry, they renamed it to get rid of that joke once and for all.

Fry: What do they call it now?

The Professor: Urectum.

Sorry. We now return you to your regularly scheduled creo-bashing.

Date: 2007/06/01 19:56:52, Link
Author: qetzal
Quote (Steviepinhead @ June 01 2007,19:40)
Ahm gettin moor eddicated all teh tiem.

Spellins a reel strawng pint.

You're being taught by a Moor?


Date: 2007/06/03 12:03:52, Link
Author: qetzal
Quote (Ftk @ June 02 2007,23:16)
It's time to put Darwin to the test...

That's been done already.
[H]ow did this information arise?

Incomplete list: base substitutions, insertions, deletions, duplications, translocations, transpositions, horizontal transfer, aneuploidy, polyploidy. Alkylating agents, UV light, polymerase stuttering, template switching, error-prone repair, non-disjunction, unequal crossing-over. Natural selection, sexual selection, random drift, co-evolution. Etc.
And, is it possible for it to have evolved without the aid of intelligence?


Feel free to pass these answers along to your buddies at Baylor. Might save them some time.

Date: 2007/06/16 12:31:03, Link
Author: qetzal
Quote (VMartin @ June 16 2007,09:53)
Probably - again - you didn't read my previous post completely. There was a quotation of abstract from a scientific journal.  You probably din't make any own research to find out and disprove my "bald assertion" when mammalian orders evolved.

At least five lineages of placental mammals
arose more than 100 million years ago, and most of the modern orders seem to have diversified before the Cretaceous/Tertiary
extinction of the dinosaurs.

Amolecular timescale for vertebrate evolution
Sudhir Kumar & S. Blair Hedges

Probably you didn't read your own citation completely. This paper offers evidence that mammalian orders appeared less abruptly than previously thought. Here's their final paragraph (emphasis added):
Our molecular timescale for vertebrate evolution will be useful in calibrating local molecular clocks and in estimating intraordinal divergence times more reliably, especially in groups with poor fossil records. Molecular times also provide an independent measure of the tempo and mode of morphological change. For example, the sudden appearance (in the Early Tertiary fossil record) of mammalian and avian orders, which show large morphological differences, has been taken to imply rapid rates of morphological change at that time(14,24). Now, the possibility of 20–70Myr of prior evolutionary history relaxes that assumption and suggests a greater role for Earth history in the evolution of terrestrial vertebrates(12,25). An accurate knowledge of divergence times can help to direct the search for ‘missing’ fossils and test hypotheses of macroevolution.

Date: 2007/06/25 19:54:25, Link
Author: qetzal
Look again. It's actually "ALL BOLLOCKS."

Except for the hyper-bunnies. They're clearly real.

Date: 2007/06/26 19:18:00, Link
Author: qetzal
My tastes run more toward the cheesy horror flicks, so I'm thrilled to hear they're included. Sure hope I can pull up a burning log and join in.

Dagon is definitely a top candidate.

Any one see Night of the Cicada?

How about Attack of the Tree Monster? (Yes, the monster was a man in a tree suit, shuffling awkwardly about. Classic.)

I don't have a favorite movie over all, but my single all-time favorite scene is the one in Species where tentacles come out of what's-her-name's nipples. I still giggle every time I think of that scene!

P.S. Death Race 2000 was OK, but it can't hold a candle to Dagon.

Date: 2007/06/26 20:55:22, Link
Author: qetzal
Quote (Ichthyic @ June 26 2007,19:30)

ever see "Day of the Triffids"?

(the marine biologist was the hero in that one).

Oh, yes. Seawater.

How about Attack of the Killer Condom.

And of course, The Crawling Eye.

Another one (title escapes me) was about a sort of intelligent parasite called an Eomer (sp?). A biggish worm like thing that injected some kind of additive substance directly into your brain. Once you were hooked, you would do anything it wanted to avoid the withdrawal. Naturally, what it wanted was to eat teenage girls. The best scene was where the Eomer was hiding in the addicted guy's pants, and the girl starts giving him oral sex. You can guess the rest.

I'll think of more.

Date: 2007/06/27 17:27:05, Link
Author: qetzal
After last night's post, I remembered Lair of the White Worm. Seems I wasn't the only one.

Another 'scientist as hero' movie is Day of the Locust. Giant grasshoppers attack New York, IIRC. The hero (an entomologist, I presume) plays amplified grasshopper noises to lure them all out to sea to drown.

Then there's one called The Swarm (I think). Killer Africanized bees attack Houston. Everybody hides out in the Astrodome.

Date: 2007/06/28 20:57:27, Link
Author: qetzal
Has Cube already been mentioned?

Date: 2007/06/29 22:28:10, Link
Author: qetzal
Does anyone remember one involving creatures that dissolved your bones? They looked sort of like giant amoeba, 2-3 feet across, with a tentacle that came out and grabbed their victims. The tentacle would inject something that dissolved the bones, then they'd suck out the resulting liquid. Horribly, the victims were left alive, albeit temporarily.

I remember seeing it decades ago on Creature Feature, but I have no clue what it was called.

Date: 2007/07/02 22:05:34, Link
Author: qetzal
I don't suppose there's an opening for Wisecracking Sidekick?

Date: 2007/07/20 22:59:18, Link
Author: qetzal
Quote (skeptic @ July 19 2007,21:11)
Nothing like that.  I want to represent mutations within a computer simulation so I need a generalized rule or set of rules to do so.  Raw data is not exactly, although somewhat, helpful in this regard.  I hope you see what I'm getting at.

I think your question is too general. There are too many kinds of mutations, and their frequencies are dependent on circumstance and context.

In some cases, you can specify simple rules. E.g. for base substitutions, transitions usually outnumber transversions. I don't recall the relative percentages off-hand, and again it would depend on the circumstances, but you could find such numbers if you wanted.

But if you want a general set of rules for modeling substitutions and small deletions/insertions and large deletions/insertions and inversions and duplications and translocations and transpositions and etc., I think you're out of luck.

One other thing to keep in mind. We can only derive rules on mutations by sequencing, and we can only sequence mutations that are recoverable. There's no guarantee that recoverable mutations are representative of which mutations actually occur.

Date: 2007/07/21 00:58:24, Link
Author: qetzal
Quote (skeptic @ July 21 2007,00:15)
My final goal is to develop a minimal gene organism model and use it for simulations to test toxins, environmental changes, population dynamics and so on.  The organism would be hypothetical so I'd want to generalize specific data as much as possible and that may not be too easy.

Sounds pretty ambitious. I doubt the requisite knowledge exists to accurately model such things, but I wish you luck with it.

Date: 2007/07/22 15:51:08, Link
Author: qetzal
Quote (VMartin @ July 21 2007,04:15)
The evolution is teleological process aimed for perfection and emergence of human.

This is perfection? Homo sapiens?

Ho. Lee. Cr*p. How could anyone, no matter how delusional, think that man = perfection?

If I actually believed evolution was teleological and aimed at perfection, I'd be dead certain it wasn't finished yet.

Date: 2007/08/01 21:14:46, Link
Author: qetzal
Maybe RedDot would care to select one specific claim to argue?

It's probably impossible to avoid a dozen or so different people arguing against RedDot, but at least the dogpile (or bundle) could be confined to one topic.

Date: 2007/08/01 22:51:04, Link
Author: qetzal
Quote (RedDot @ Aug. 01 2007,22:03)
If pathogen virulence increasing in the presence of antibiotics is the best you have, then you're a long way from your stated goal.  Both papers make lip service only to evolution.  Neither have an actual prediction of what will happen when a particular pathogen is introduced to a particular antibody.

So, since they lack that particular prediction, that shows they make no evolutionary predictions at all?
Evolutionary theory specifically states that enviromental pressure will cause an organism to gain information in the way of new genes or more specific proteins.

Actually, no, it doesn't.
 However it is just not the case.  Here are some examples for you:

Citing a few examples of loss-of-function mutations doesn't prove that gain-of-function doesn't happen. Besides, half your examples are wrong. An SOS response is not a loss of function. Neither is reducing the affinity of 23S RNA for erythromycin.
Where mutations are oberved, these mutations result in the loss of pre-existing cellular systems/activities, such as porins and other transport systems, regulatory systems, enzyme activity, and protien binding.  Such losses are never compensated, unless resistance is lost, and cannot be held up as valid examples of evolutionary change.

Really? Shall we take your example of actinonin? Try Googling "actinonin +resistance". Very first hit:

"Reducing the fitness cost of antibiotic resistance by amplification of initiator tRNA genes."

You keep swinging, you're just not making any contact.

Date: 2007/08/01 23:07:38, Link
Author: qetzal
By the way - this:
The ToE demands that proteins can form naturally and spontaneously.

is quite wrong.

The ToE really has nothing to say about where the first proteins, nucleic acids, or living cells came from. It's only concerned with the diversification of life after it arose.

Even if we knew for a fact that the first life was purposefully created, the ToE would still be the only legitimate scientific theory for how that first life led to what we see today.

Date: 2007/08/05 21:13:08, Link
Author: qetzal
Quote (RedDot @ Aug. 05 2007,20:46)
I was at Mammoth Cave National Park last week.  My wife and I were taking a tour through one of the large chambers that had been dissolved from the surrounding limestone.  Both of us marveled at how much water it would have taken to cut such a chamber.  The literature in our hands told us millions of years through a slow trickle of water flowing through what were at one time tiny cracks.  However to our eyes we could only see the jagged effects from millions of cubic meters of water violently tearing away the rock.  Both can be valid observations.  One can be true, or both could be false.  Since no one was there to witness the event, no one can really be sure.  Oh, we both can speculate, and we both will see what our worldview demands that we see.  But that does give one side the right to state that the other's observations are not "science".

This is always my favorite: the "different interpretations of the evidence" argument.

Here's the problem, RedDot. Initially, perhaps, one could argue the chamber might have been carved slowly, by small amouns of water acting of millions of years, or rapidly, by large amounts of water acting all at once.

Thing is, we don't have to be content with that ambiguity. We can use science to figure out which option is correct. We simply ask, "If it took millions of years, what should we expect to see now? Or, if it happened all at once, say ~ 4000 years ago, then what should we expect to see now?"

Then we go out and actually look for the answers. And guess what? We see things that are consistent with the "slowly over millions of years" option, and inconsistent with the "all at once 4000 years ago" option. And we see that over, and over, and over again.

What do you think we should conclude from that:

A) It happened slowly over millions of years.

B) It happened all at once 4000 years ago, but God made it look like it took millions of years.

[edited to fix italics tags]

Date: 2007/08/09 20:34:07, Link
Author: qetzal
Quote (IanBrown_101 @ Aug. 09 2007,20:25)
Essentially, he argues, the universe is a closed system, therefore everything (very slowly, I don't think he's a 6000 year old universe nut) is decending towards entropy, and all viable energy is being used up. Therefore either something created the universe a fixed time ago, and it's been going downhill ever since, or something held back the actions of thermo prior to it coming into effect.

Even if that proves the universe had a beginning (and I'm not sure it does), it doesn't prove that the universe was created by something supernatural.

Unless, of course, his definition of supernatural is whatever accounts for the universe having a beginning.

Date: 2007/08/09 20:47:40, Link
Author: qetzal
It's just the old "everything has to have a cause" BS.

Date: 2007/08/09 20:54:33, Link
Author: qetzal
The thermo is irrelevant.

He says, "the universe is a closed system. It must have had a beginning."

I say, "So what? 'The universe had a beginning' does not prove 'the universe was created by something supernatural.'"

Unless, as I said above, his definition of 'supernatural' makes it true by tautology.

Date: 2007/08/11 10:02:24, Link
Author: qetzal
Quote (Stephen Elliott @ Aug. 11 2007,09:21)
By the way. The fact that he acknowledges that we don't know if the Universe is infinite or not might be likely line of attack to get him to acknowledge that you are in the "gaps" area of argument.

No, don't go there. As Louis pointed out again, and I have been saying from the second comment, the cosmology and thermodynamics are irrelevant. They're smokescreens, diversions.

This guy wants to get into a big argument over whether the universe is infinite, and what SLOT implies about entropy if we extrapolate backward to some beginning. He wants to draw your attention away from his central logical fallacy, which is this:

The universe has certain properties, therefore it was created by something supernatural.

It's a non sequitur. The conclusion doesn't follow from the premise. So of course he wants to argue over the truth of the premise. If you're busy doing that, he hopes you won't notice that true or false, his premise doesn't support his conclusion.

Date: 2007/08/12 09:11:27, Link
Author: qetzal
Quote (IanBrown_101 @ Aug. 11 2007,16:27)
His latest is telling me that for something to break the natural laws, it must be supernatural, and if the laws didn't apply pre big bang, the laws governing the state must be supernatural, since today's natural laws didn't hold sway (I'm paraphrasing).

That was in reply to me telling him that they didn't have to be supernatural.

Now he's just begging the question (i.e. assuming the conclusion):

1.  Supernatural is defined (by him) as anything that is unexplainable by physical laws as we currently understand them.

2.  The beginning of the universe is unexplainable by physical laws as we currently understand them.

3.  Therefore, the beginning of the universe was supernatural.

To which I say, sure! So what?

If he wants to define supernatural that way, then I agree the beginning of the universe was supernatural - according to that definition. However, that does not support taking a further step to claim the universe was created by some intelligent, purposeful God.

From what you've posted, I'm not even sure that's where he's headed. He sound more like a smart but immature high school kid who gets his kicks arguing with empy rhetoric.

Date: 2007/08/12 09:14:51, Link
Author: qetzal
Quote (Louis @ Aug. 12 2007,08:16)
Why do these bozos think this shit works?

Probably because it does work among the faithful.

Date: 2007/08/20 20:30:19, Link
Author: qetzal

I just want to know what The Mind is, and how it differs from the (or a) mind.

Is it one thing? Some all pervasive consciousness that permeates the universe? And if so, how is The Mind related to God? I assume it's not the same as God, or there'd be no reason to call it The Mind. (Does The Mind = the holy ghost?)

Or do we each have a Mind? And if so, how is it different from our minds?

Date: 2007/08/30 18:53:51, Link
Author: qetzal
Quote ("Rev Dr" Lenny Flank @ Aug. 30 2007,17:53)
Science simply is not universally applicable. It simply cannot answer ethical, moral or aesthetic questions.

Lenny, as you've said repeately, science can't provide objective, universal answers to these questions because they don't HAVE objective, universal answers. You seem to be claiming that science isn't universal because it can't do what's logically impossible - i.e., answer questions that are inherently unanswerable. I confess that makes little sense to me.

Which means that if religion limits itself to those questions that science can't answer, then there simply is no inherent conflict between science and religion.

But, as you yourself point out, religion can't answer those questions either (because they have no answer). So, isn't this equivalent to saying that science and religion don't conflict as long as religion does nothing?

Date: 2007/09/05 01:29:08, Link
Author: qetzal
Quote (skeptic @ Sep. 03 2007,08:22)
Bill, I was struck by one similarity in your argument. ?God is a spiritual or non-physical or meta-physical agent that in some way interacts with the world, by definition. ?If God exists and is undetectable via this interaction then it stands to reason (lol) that souls would fall into this same situation.


You seem to be suggesting that something can interact with the physical universe, yet be entirely undetectable. Is that right?

How is that not a logical contradiction? Doesn't "interaction" imply that the physical universe is somehow affected? In other words, wouldn't the physical universe be different after an interaction than it was before? And if the physical universe changes as a result of interaction, wouldn't that change be detectable (at least in principle)?

Aside to Louis: I've been mostly lurking this thread since the beginning. My sympathies to you; it's been both fascinating and repulsive. I haven't read anywhere near everything you've written, but what I have read seemed quite clear and unambiguous, and I'm frankly baffled at the way some have responded.

Date: 2007/09/05 08:49:23, Link
Author: qetzal
Quote (skeptic @ Sep. 05 2007,08:10)
Getzal, that's a tough question. ?To actually answer that I'd have to have absolute knowledge of the entire universe. ?I would say that by definition those interactions would be undetectable by methods that we consider to be science but I in no way know how that is.

OK, so far, so good. You are saying something can interact with the physical universe, yet be undetectable (I don't agree, but I appreciate the straightforward answer to this part.)

So can you answer the second part? Let me restate.

Do these interactions result in *any* objective change in the physical universe? If so, how can they be undetectable in principle? (Note: not undetectable given current or forseeable scientific limitations; rather, undetectable regardless of any objective knowledge or technology that could ever be attained.)

If not, in what sense are they interactions at all?

One example that I hesitate to offer but it does put the idea of interaction in perspective is those people that claim to be able to talk to the dead or have out of body experiences. ?Personally, I don't place much on these claims but who's to say and it points to the kind of interaction that we may need to be looking at not a measurable, observable on.

But in fact, if such interactions really occur, they do have an effect on the universe: they change the beliefs/statements/actions of the people who (supposedly) have such interactions.

Date: 2007/09/05 18:49:24, Link
Author: qetzal

In one post, you said:

I would say that by definition those interactions would be undetectable by methods that we consider to be science but I in no way know how that is.

I took this to mean that you believe some things (e.g. God) can interact with the universe yet be undetectable in principle.

But then you said:

There is an impact upon the universe if only in the Minds of those experiencing the interaction. ?But again I can not describe or quantify this even though as you say in principle it must be true.

Now it seems (to me) that you're saying the opposite. Interaction does result in objective impacts on the universe.

Have you changed your mind, have I misinterpreted, or other?

BTW - just because we can't currently describe or quantify an interaction scientifically doesn't mean it is beyond the realm of science in principle. I hope you agree with that.

So again I will ask, do you believe that something can interact with the universe, such that it has an observable effect on the physical universe, yet be forever beyond the reach of science? Yes or no will do for a start. Then, if yes, and if you are able, please explain what sort of interaction would fit that category. (If you believe it but are unable to explain any further, that's OK with me, too.)

Date: 2007/09/18 18:04:32, Link
Author: qetzal
By coincidence, the gravity travels faster than light thing was re-debunked last week by Mark Chu-Carroll on Good Math, Bad Math (hosted by the highly recommended ScienceBlogs).

Date: 2007/09/20 23:12:37, Link
Author: qetzal
Quote (BWE @ Sep. 20 2007,17:06)
Quote (supersport @ Sep. 20 2007,17:01)
Quote (improvius @ Sep. 20 2007,15:47)
Quote (supersport @ Sep. 20 2007,16:20)
from where did the spine come from?  What was the cause of the emergence of the spine?

It's a chemical reaction to the predator.  You'd have learned this if you spent 10 minutes on Google.

You're not done yet.....what released these chemicals...and why...what signal called for their release??


That's my guess.

Nope. Weren't me.

We're talking water fleas, right? Could've been Neptune (or Poseidon or whatever he's calling himself these days).

Date: 2007/09/21 14:28:33, Link
Author: qetzal
All these questions about spines and chemicals are easily answered if one simply reads the paper that C.J.O'Brien linked just yesterday.

The chemicals are released when fish digest Daphnia that they have eaten. In other words, the chemicals are digested Daphnia. Those chemicals get released into the water where the fish and the Daphnia live. The Daphnia can detect these chemicals and 'recognize' them (in a non-anthropomorphic way) as a signal that there are Daphnia-eating fish around.

It's rather like when you eat asparagus. One of the digestion products has a distinct odor. You release it into the environment when you pee. If someone is nearby at the time, they can smell it and recognize that you've been eating asparagus. You didn't purposely release the chemical in your urine. It's just an unavoidable consequence of eating and digesting asparagus.

Anyway, the chemicals trigger developmental changes in the Daphnia that result in spines (or bigger spines). I think it's clear that appearance of the spines is not based on a contemporaneous mutational event. The Daphnia already have the ability to respond to the chemical signals by growing the spines.

One could ask why Daphnia don't have spines all the time. My guess is that there's an energetic cost to growing and maintaining the spines, and that it's advantageous not to grow them if they aren't needed for defense. That's admittedly speculative on my part, although it's testable (and may have been tested, for all I know).

SS seems to think that, just because some morphological changes occur in response to environmental cues, therefore all morphological changes occur in response to environmental cues. Why he thinks that's a logical conclusion is beyond me.

Date: 2007/09/21 18:05:42, Link
Author: qetzal
I don't think ss should be a pariah either, unless he's done something I'm not aware of.

I think there's a good chance he's a troll, as alleged. If there's more evidence of that, I'd like to see it posted here. Even then, I wouldn't support this action. We can always choose to ignore him, and to date, I'm not aware that he's been disruptive on any other threads.

If he's done something more egregious than what we've seen on this thread, can the mods please explain?

If not, I respectfully request he be given back his posting priveleges.

Not because I think he's posting anything of value, but because I want this board to maintain the highest standards of tolerance. GOP was much more deserving of being banned, but wasn't. Let's please not stoop to UD's level in this case, either.

My $0.02.

Date: 2007/09/25 00:23:28, Link
Author: qetzal
Quote (JAM @ Sep. 24 2007,23:51)
Disruption of intra-neuronal cytoskeletal structures impairs cognition, such as tangling of the tau MAP linking MTs in Alzheimer’s disease (Matsuyama and Jarvik, 1989, Iqbal and Grundke-Iqbal 2004).

This is an irresponsible case of stating hypothesis as fact. It's not yet known whether the plaques and NFTs of AD cause cognitive impairment or are the effects of a more subtle mechanism that causes cognitive problems. It's one of the major issues in AD research, and claiming that it is already solved is ludicrous.

Hameroff seems to do that rather a lot. Consider this claim:

To gauge how single neuron functions may exceed simple input-output activities, consider the single cell organism paramecium. Such cells swim about gracefully, avoid obstacles and predators, find food and engage in sex with partner paramecia. They can also learn; if placed in capillary tubes they escape, and when placed back in the capillary tubes escape more quickly.

A quick PubMed search suggests this is arguable at best:

Behav Neurosci. 1994 Feb;108(1):94-9.

Is tube-escape learning by protozoa associative learning?

Hinkle DJ, Wood DC.

Department of Behavioral Neuroscience, University of Pittsburgh, Pennsylvania 15260.

The ciliate protozoa, Stentor and Paramecium, have been reported to escape from the bottom end of narrow capillary tubes into a larger volume of medium with increasing rapidity over the course of trials. This change in behavior has been considered an apparent example of associative learning. This decrease in escape time is not due to a change in the protozoa's environment, their swimming speed, frequency of ciliary reversals, or the proportion of time spent forward or backward swimming. Instead, most of the decrease results from a decrease in the proportion of time spent in upward swimming. However, a similar decrease in upward swimming occurs when the task is altered to require escape from the upper end of the capillary tubes. Because the protozoa exhibit the same change in behavior regardless of the reinforcing stimulus, tube-escape learning is not associative learning.

PMID: 8192854

Skimming through some of the links on Hameroff's site, he seems to repeatedly oversimplify unsettled questions in ways that conveniently fit his preferred hypothesis. As one more example, he states that gaseous anesthetics work by binding to hydrophobic pockets in proteins, and argues that this supports his model of superposition of states in tubulin. Here again, a quick search suggests that this is just one possible model of how such anesthetics work.

None of this is actual evidence against Hameroff's claims, of course, but I'm always more suspicious of someone who's willing to employ such dubious arguments.

Date: 2007/09/25 11:03:47, Link
Author: qetzal
Quote (Thought Provoker @ Sep. 25 2007,09:43)
We don't think of it that way because we are conditioned to expect flipped coins to "randomly" come up heads or tails even when we flip them in the exact same manner. The same would be true if we used a perfectly repeating mechanical device to flip the coin. Assuming the coin was perfectly balanced, the results would not be a pattern. A perfectly repeatable (deterministic) setup is impossible because quantum level effects are non-deterministic.

You may be interested to learn that this is not true. Not that this really speaks to your main point, of course.

You might ask what quantum level effects have to do with Intelligent Design.

First of all, it goes to show that magic-like effects can be scientific. There is also reason to believe quantum effects where instrumental to function in early life on Earth (front loaded?).

I expect quantum effects are instrumental to function of everything, living and non-living. I fail to see how that ties in to ID.

Recently, it was discovered that photosynthesis uses quantum mechanics. Photosynthesis is an extremely old biological mechanism.

When you get down to it, doesn't every chemical reaction use quantum mechanics? I imagine thermonuclear fusion uses quantum mechanics, and that's a much older 'mechanism.' What should we infer from that?
DNA is being used as building blocks for quantum computers and the DNA structure and “code” is optimal for processing search algorithms.

Optimal how, and compared to what? Any citations? Are you suggesting this implies something related to ID?  
DNA/RNA defines what is or isn’t considered a living organism.

Not really. At present, everything we know that's arguably living contains DNA and/or RNA, but lots of people think that life without DNA or RNA is at least theoretically possible.
Finally, the Penrose-Hameroff Orch OR model of consciousness hypothesizes that consciousness is an artifact of quantum processing in microtubules. Microtubules are instrumental in living structures and organisms that appear to be aware of their surroundings.

Microtubules are found in pretty much all eukaryotes, are they not? That doesn't prove much. Lipids are also instrumental in living structures, but I don't think that's evidence that consciousness is an artifact of quantum processing in lipids. (Note - I realize there's more to the microtubule hypothesis, and I'm not attempting to refute it here. I'm only pointing out that the ubiquity of microtubules in eukaryotes tells us nothing about their role in consciousness.)
Personally, I have serious criticisms concerning the apparent motives and past actions of the ID Movement, but it would be a mistake to dismiss all challenges to orthodox thinking as simply an appeal to the metaphysical because it may turn out that the magic is real.

Agreed. However, please note the key difference between QM and ID - evidence. As you acknowledge in your post, we can set up conditions where these seemingly magical QM effects can be conclusively demonstrated. We can state what observations are expected in certain situations, according to QM.

ID does none of that. It makes no claims about what we should observe. It offers no demonstrations or concrete evidence. It merely claims evolution is inadequate, therefore ID.

I don't reject ID because it seems too magical or counterintuitive. I reject it because it makes no claims, offers no predictions, and has no useful explanatory power.

Date: 2007/09/25 18:48:55, Link
Author: qetzal
Quote (Thought Provoker @ Sep. 25 2007,17:00)
Associating it with ID isn't that hard.  ID proponents have a very flexible definition of "Intelligence".  And, to them, design practically means "not random". My ideas are supportive of MikeGene's front loading.

No offense, but I don't think you've provided any evidence of such support. Not here, anyway.

As far as I can see, your 'argument' on this thread boils down to: "If QM is real even though it seems supernatural, then ID and front loading could also be real even though they seem supernatural." That's not a valid argument, and I don't think it supports ID any more than it supports pixies and fairies.

Have I missed something?

Date: 2007/09/25 22:02:49, Link
Author: qetzal
How many unsupported assertions are you prepared to cram into one post?  
Quote (Thought Provoker @ Sep. 25 2007,21:25)
The purpose of our teleological universe is to be internally consistent.
The wavefunction is purposeful design.
Whether via anthropic principle or divine whim, life may be necessary to make the teleological universe complete.
If the universe needs something to be consistent, than interconnected quantum effects will make it happen and time order isn’t a restriction.
While quantum effects are inherent in both living and non-living material, living material is inherently more flexible.
MikeGene’s front loading is essentially looking for a preponderance of clues that a future need was satisfied by a past feature.

Retrocausality would be something that interconnected quantum effects would demonstrate.

The ability to imagine or assert something is not evidence for its reality.

Date: 2007/09/26 00:58:45, Link
Author: qetzal
Quote (Thought Provoker @ Sep. 25 2007,22:34)
Hi qetzal,

If you have heard a better pro-ID presention, I would like to know where.

I would even be interested in knowing about any that matched this one.

Oh, I agree yours is as good as any and better than most. For what that's worth. ;-)
Ok, let's play the game...

"The purpose of our teleological universe is to be internally consistent."

This is a falsifiable statement.  It is being tested each and every day.  It the universe should suddenly quit being consistent we will know it.  Then again, maybe we won't.

No, "The universe is internally consistent" is a falsifiable statement. The fact that the universe is (so far) internally consistent does not demonstrate that consistency is the universe's purpose. It's the assertion of purpose that I object to, not the statement about consistency.
"The wavefunction is purposeful design."

This follows from the first statement and the reference to Anthropic principle that you skipped over.  Your problem may be in the word "design".  I had indicated earlier that design, for all practical purposes, means non-random.

No, my problem is with the adjective "purposeful." It implies conscious intention in the design, an intention that you have not justified.
"Whether via anthropic principle or divine whim, life may be necessary to make the teleological universe complete."

You did notice the word "may", right?  I provided an example of how it "may" be necessary.

Exactly. It may be necessary, or it may not. It's just a statement of possibility. Which is fine, as far as it goes, but that doesn't support anything one way or another.
"If the universe needs something to be consistent, than interconnected quantum effects will make it happen and time order isn’t a restriction."
I posted three long comments explaining this one.

But you haven't justified that the universe needs something to be consistent. So, again, this is really just a statement of possibility.
"While quantum effects are inherent in both living and non-living material, living material is inherently more flexible."

Don't like the word "flexible"?  How about more utilitarian?

I don't accept either. You haven't defined what flexible or utilitarian mean in this context, or shown how living material is more flexible/utilitarian, or shown how greater flexibility/utilitarianism relates to quantum effects, or tied that putative relationship to the overall ID hypothesis.
"MikeGene’s front loading is essentially looking for a preponderance of clues that a future need was satisfied by a past feature."

Are you demanding citations and references to MikeGene's works?

No. I wasn't objecting to that sentence by itself. I quoted it because your next sentence refers to it. (Although I will note, in passing, that most people mean something much more specific by "front loading." If I eat that banana in my office tomorrow, my future hunger will have been satisfied by my past purchase of a banana. Would MikeGene consider that front loading?)
"Retrocausality would be something that interconnected quantum effects would demonstrate."

Interconnected via space and time, means interconnected via space and time.  Time is just another dimension that extends in two directions.

Right. So if the purpose of the universe is to be consistent, and if the universe needs life to be complete, and if interconnected quantum effects allow for retrocausality, then that's consistent with a weak version of ID that boils down to "life was inevitable."

Sure. If we posit those ifs and that version of ID, I agree. It's consistent. So what? To me, it seems like your whole point is to find a way to argue that some version of ID could be true, based on QM. If so, then you've succeeded. I, for one, will happily concede that certain versions of ID could be true, at least hypothetically.

But hypothetically, there could also be a teapot in orbit around Mars. If I claim (without empirical evidence) that the universe may require a celestial teapot to be internally consistent, does that make the teapot's existence significantly more likely?

Date: 2007/09/27 13:29:36, Link
Author: qetzal
Quote (Thought Provoker @ Sep. 26 2007,16:01)
What I have been presenting here is what I call the Third Choice.  A choice other than the status quo and an unidentified Intelligent Designer.

Many ID proponents claim ID isn’t about God.  I am giving them the opportunity to stand by their words.  Here is an ID hypothesis with scientific justification.  The reactions to it are informative.

Once again, I disagree that you've provided any scientific justification. To me (and to most working scientists, I suspect), scientific justification means some reasonable level of empirical data that supports the hypothesis. I don't think you've provided that at all.

Instead, you've taken some observations about QM, made a series of assumptions, and shown that life is inevitable ("retrocaused") under those assumptions. The problem with that is one can show virtually anything with the right set of assumptions. I don't consider it scientific justification unless there's some evidence to support the assumptions.

Now, maybe I still don't grasp what your Third Choice really says. So let me try to boil it down, and you can tell me if I've got the gist.

1.  Particles can be quantum entangled. This is demonstrated.
2.  Based on (1), you propose that the universe is interconnected across all of space and time due to quantum effects.
3.  For reasons that aren't clear to me, you further propose that living things (perhaps specifically intelligent living things) are required for the universe to exist.
4.  Thus, life developed because it had to. The requirement for (intelligent?) life at some point in space-time 'retrocaused' life to begin developing at some other point(s) in space-time.

Is that approximately right? If not, feel free to correct my errors. If so, isn't this essentially just the Strong Anthropic principle?

Regardless of the above, I don't consider your ideas to be equivalent to front loading. Here's why.

In 'traditional' front loading, all of the 'information' needed to generate every possible future organism was loaded into the first organism. Proponents generally argue that it was all encoded into the DNA, but most of it was repressed. The key point is that it was all inherent in that first organism.

You're arguing (I think) that the information needed to generate every possible organism was loaded not into the first organism, but into the universe itself. That's fundamentally distinct. You may choose to call that front loading, but it's not compatible with front loading as it's commonly understood.

Date: 2007/09/27 16:39:36, Link
Author: qetzal
Quote (Thought Provoker @ Sep. 27 2007,15:39)
I understand that MikeGene and Krauze of Telic Thoughts are credited for pushing the Front Loading meme for a long time.  I can't speak for them, but I have noticed they have rejected similar characterizations of "traditional front loading" in past comments.

Whether or not the Third Choice is considered part of the rubric called "Front Loading" isn't up to you or me.  It is up to those proposing the Front Loading hypothesis.

Labels aren't important, ideas are.

Well, this is what MikeGene posted on 9/24/07:

For years, I have been trying to flesh out the conceptualization of front-loading evolution at the origin of life. A working hypothesis has been that the first cells (uni-cellular life forms) were front-loaded with information that would facilitate the evolution of multi-cellular life.


Isn't that pretty much what I said?

In contrast, your version doesn't postulate front loading of information into the first cells per se. It postulates that the information is part of the overall wavefunction of the universe, right?

I agree that concepts are what matter, but when the same label is used to refer to two different concepts, confusion is inevitable.

Regarding RecA, you're in my sweet spot now! I agree it's an amazing protein. But being multifunctional and forming nucleoprotein filaments is not evidence that it's front-loaded. Not unless you're going to claim that it's "too complex to have evolved naturally."

Whether recA is an "evolution gene" depends on what that means. It's a central player in a lot of DNA repair and recombination processes. Where there's repair/recombination, there's mutation. Where there's mutation, there's potential evolution. If that's all that's required to meet MikeGene's idea of an "evolution gene" then recA fits the bill.

On the other hand, if MikeGene thinks RecA somehow directs evolution in a teleological way, he's wrong.

Date: 2007/09/27 16:42:14, Link
Author: qetzal

I forgot to add - even though I think your ideas are mostly BS, props for getting RecA protein versus recA gene right!


Date: 2007/09/27 18:40:35, Link
Author: qetzal

Thanks for the reply (and the previous ones). It's nice to discuss this with someone who responds to the questions that are asked, even if we may disagree on the answers.

Quote (Thought Provoker @ Sep. 27 2007,17:22)
Hi qetzal,

Thank you for your comment and thank you for providing the link.  As you pointed out, MikeGene said...

"A working hypothesis has been that the first cells (uni-cellular life forms) were front-loaded with information that would facilitate the evolution of multi-cellular life." (emphasis mine)

I have noticed MikeGene is pretty careful with his words.  The word "facilitate" makes a big difference IMO.  Life's use of quantum mechanics facilitates the evolution of multi-cellular life.

Maybe, but in distinguishing MikeGene's (et al.) version from yours, I'd place the emphasis here: "A working hypothesis has been that the first cells (uni-cellular life forms) were front-loaded...."

MikeGene is more careful with his words than I.  If I said the Third Choice is a Front Loading hypothesis then I was mistaken.  I have asked, MikeGene has not said one way or the other.  I have my opinion, but it is only my opinion.

BTW, I am of the opinion that this is an ID Hypothesis based on the lose definitions used, but I could be wrong about that.

Fair enough.

I'm glad to hear from a knowledgable source.

You can read MikeGene's paper for itself.  I won't speak for MikeGene.

I'll try to look over his post(s) tonight. Can't promise though.

I look at the recA gene and, especially, the RecA protein as being in the unique position of having great influence over the evolution process in what MikeGene referred to as "deep time".  Pencils balanced on their tips could fall in any direction. I gentile breeze might not make a difference that is immeadiately noticable.  But if there are a lot of pencils over a lot of time, the pencils might be biased to tip a certain way.

Sorry, I don't follow that.

I understand the RecA protein acts very much like a microtubule (I am counting on your expertise to argue this point if applicable).  That is a rather convienent coincidence.

I don't really think so. There are similarities, of course. It forms filaments assembled from monomers, but it does so by assembling around DNA. Given its function of catalyzing strand exchange during recombination, and the linear nature of DNA, that's not particularly surprising.

There are other proteins that form filaments in a generally similar way. Coat protein from tabacco mosaic virus is a good example, and that's a case where there's no reason to invoke any quantum computing.

The simple explanation is that assembling monomers into helical filaments is a convenient way to generate long filaments from proteins. That's really the common theme I see. RecA needs to make linear filaments to coat linear DNA and promote strand exchange. TMV coat protein needs to make linear filaments to coat viral RNA. Tubulin needs to make linear filaments to provide structural support to the cell. Other geometries could also work, but they would be less efficient.

I am not suggesting some human-like intelligence designed it that way.  Think of it as some unknown evolutionary advantage to having a quantum computer in charge of this highly important function.

Except that you're pretty much begging the question. You've decided that quantum computers exist in biology, and you're using that to justify the hypothesis that RecA is a quantum computer. I see no evidentiary basis to do that.

And thanks for noticing the recA gene and RecA protein.  I feel my efforts weren’t wasted.

You're welcome! I tend to be a bit anal about that kind of thing, so I'm one to notice.

Date: 2007/09/27 22:47:54, Link
Author: qetzal
Quote (Thought Provoker @ Sep. 27 2007,19:49)
It's no longer a question of whether life directly utilizes quantum mechanics but how and in how many ways.

AFAIK, that's been clear for quite a while. After all, life depends on chemistry, and chemistry depends on physics. I believe it's old news that chemical bonds and chemical reactions have quantum mechanical aspects.

The work on quantum coherence in photosynthesis sounds pretty interesting. I readily admit I don't have the physics to evaluate their research. Still, I highly doubt that their work gives us much reason to think that life is capable of quantum computing.


From a paper (essay?) titled Bio-quantum computing...

Sorry, but this guy's a crank. There is NO evidence that DNA works as an antenna to transmit gene signals at a distance. His quantum physics language sounds highly bogus to me, but like I said, I don't have the background to really critique it. I DO have the background to critique his biology, and it's crap.

For instance, his reference (9) in the passage you quoted is to another of his essays. In that, he says things like this:

We know that from the point of view of bio-electrical behaviour, the closed and stable DNA is
considered a bio-polymer ; hence it does not conduct any electromagnetic field as in a wire. Rather,
when DNA is open via the enzyme (DNA-polymerase) into two anti-parallel half chains and after is
closed again from side to side with the binding protein activities, the DNA chains become polarised
and depolarised. During the opening and closing, the DNA can emit quantum particles ("Gene-
Ons") corresponding to the double helix polarization in “bi-polarons”, interacting with “biophonon”
emission. These last are generated by the breaking of hydrogen bonds of the sequences, of
A-T and C-G couplings. Therefore, such quantum particles generated by the opening of the DNA
helicoidal molecular chains, and by the breaking of the h-bonds, can communicate a quantumspectrum,
based on a series of "Gene-Ons". This spectrum has an exact correspondence with
quantum–pulses to the coding information of the gene because it is emitted at the same time that the
gene is copied by the RNA.

Trust me, that is complete and utter BS. DNA is a biopolymer at all times, not just when it's "closed and stable." DNA polymerase doesn't open the helix; helicases do that. The chains don't get polarised and depolarised, and in fact, there's a better chance of DNA conducting electromagnetic fields when it's closed than when it's opened, because of the base stacking that occurs in the double helix. "Gene-ons" are completely imaginary, and, oh yeah, genes don't get copied by RNA.

From a paper (essay?) titled Quantum Algorithms and the Genetic Code...

OK, this one seems more legit. Again, most of it is physics-speak that I can't critique. However, there's at least one big red flag in the biology:

Enzymes are able to create superposed states of chemically distinct molecules. This is an active task. Various nucleotide bases differ from each other only in terms of small chemical groups, containing less than 10 atoms, at their Hydrogen bonding end. To convert one base into another, enzymes have to be repositories of these chemical groups which differentiate between various nucleotide bases. Enzymes are known to do cut-and-paste jobs with such chemical groups (e.g. one of the simplest substitution processes is methylation, replacing ?H by ?CH3, which converts U to T). Given such transition matrix elements, quantum dynamics automatically produces a superposition state as the lowest energy equilibrium state. (Note that the cut-and-paste job in a classical environment would produce a mixture, but in a quantum environment it produces superposition.) It is mandatory that the enzymes do the cut-and-paste job only on the growing strand and not on the intact strand. Perhaps this is ensured by other molecular bonds.

Enzymes do not convert one base into another during replication. It sounds like he thinks enzymes generate a superposition of the 4 possible bases during replication, and that superposition collapses down to the one correct base that pairs with the opposite strand. That's just wrong.

A few other things are problematic:

It is obvious why DNA replication always takes place in the presence of enzymes. If base-pairing were to occur by chance collisions, it would occur anywhere along the exposed unpaired strand.

No, the reason it requires enzymes is that the phosphodiester bond won't form spontaneously under normal, uncatalyzed conditions. Base pairing can occur by chance collisions, but it doesn't lead to a backbone linkage.

As long as quantum coherence is maintained, the replication process is reversible. This can easily explain the error-correcting exonuclease action of the polymerase enzymes.

No, because the exonuclease activity is separable from the polymerase activity. It resides in a separate domain of the protein.

Maybe his arguments about quantum search algorithms have merit. I don't know. They're not obviously BS, like the previous links were. But I'm still suspicious, because it's clear that he's making at least some fundamental errors regarding the biology, and I can't judge how those impact his quantum models.

Date: 2007/09/27 23:46:01, Link
Author: qetzal
Quote (Thought Provoker @ Sep. 27 2007,23:20)
Hi qetzal,

Yea, I only skimmed the first paper.  I will take your word on it.

The second paper is Patel in 2001.

Did he improve his biology in the 2007 paper?

Well, the discussion of how the genetic code may have evolved is provacative. I know that this is an active area of investigation, but I haven't followed it, so I can't say whether his ideas are reasonable. I don't see any glaring errors in that part, for what that's worth.

However, he still seems to be advancing the idea of superposition of all four bases during DNA replication:

Grover’s algorithm needs certain type of superpositions, and catalytic enzymes can stabilize certain type of superpositions. Do the two match, and if so, what is the nature of this superposition? The specific details of the answer depend on the dynamical mechanism involved. The requisite superposition is of molecules that have a largely common structure while differing from each other by about 5-10 atoms. I have proposed two possibilities [Patel (2001a); Patel (2006b)]:

(1) In a quantum scenario, wavefunctions get superposed and the algorithm enhances the probability of finding the desired state. Chemically distinct molecules cannot be directly superposed, but they can be effectively superposed by a rapid cut-and-paste job of chemical groups (enzymes are known to perform such cut-and-paste jobs). Whether this really occurs, faster than the identification time scale [t-sub-b] and with the decoherence time scale significantly longer than [h-bar]/[omega-sub-0], is a question that should be experimentally addressed. It is a tough proposition, and most theoretical estimates are pessimistic.

(2) In a classical wave scenario, all the candidate molecules need to be present simultaneously and coupled together in a specific manner. The algorithm concentrates mechanical energy of the system into the desired molecule by coherent oscillations, helping it cross the energy barrier and complete the chemical reaction. Enzymes are required to couple the components together with specific normal modes of oscillation, and long enough coherence times are achievable. This scenario provides the same speed up in the number of queries Q as the quantum one, but involves extra spatial costs. The extra cost is not insurmountable in the small N solutions relevant to genetic languages, and the extra stability against decoherence makes the classical wave scenario preferable. (Once again note that time optimisation is far more important in biology than space optimisation.)

Unless I grossly misunderstand what he's proposing, option (1) above is completely untenable, and it's disturbing to me that he still offers it for consideration, having had 6 years to learn that basic biochemistry rules it out. It makes me wonder about the validity of everything else he says.

I'm not sure what he's suggesting in option (2), so I can't say if it's compatible with known molecular biology & biochemistry or not.

Date: 2007/09/28 16:22:06, Link
Author: qetzal
Quote (Arden Chatfield @ Sep. 28 2007,14:51)
Quote (C Gieschen @ Sep. 28 2007,14:15)
God was the observer and His log is readily available to anyone reading His word.


Arden -

Does this mean... Blammo is God?!

Date: 2007/09/30 18:23:02, Link
Author: qetzal
Quote (Thought Provoker @ Sep. 30 2007,11:44)
Hi K.E.,

You wrote...
You seem to be arguing that our brains are quantum computers. For that to be true the processing power available from such a device of that size would be orders of magnitude larger than Deep blue.

Maybe you haven't understood the magnitude of woo being presented here.  This isn’t just human brains.  Microtubules are present in practically everything we think of as living.  If Hameroff is right, quantum computers in microtubules explains why life appears to be aware if its surroundings.  From this Hameroff paper (essay?)….

To gauge how single neuron functions may exceed simple input-output activities, consider the single cell organism paramecium. Such cells swim about gracefully, avoid obstacles and predators, find food and engage in sex with partner paramecia. They can also learn; if placed in capillary tubes they escape, and when placed back in the capillary tubes escape more quickly. As single cells with no synaptic connections, how do they do it? Pondering the seemingly intelligent activities of such single cell organisms, famed neuroscientist C.S. Sherrington (1957) conjectured: “of nerve there is no trace, but the cytoskeleton might serve”. If the cytoskeleton is the nervous system of protozoa, what might it do for neurons?

We did this one already. It doesn't hold up. See my previous comment here.

Date: 2007/09/30 21:03:08, Link
Author: qetzal
Quote (Thought Provoker @ Sep. 30 2007,19:26)
Hi qetzal,

First of all, I was talking about awareness, not learning.

Two, your article was a counter balance, it made the learning point equivocal not dead.  We are talking about single celled organisms here.  Your example is the equivalent of saying it wasn't taught to play checkers because it always loses.

Here is a 2006 reference...
Previous attempts to condition a 1-celled organism, paramecium, by either classical or instrumental procedures, have yielded equivocal results. The present experiments were designed to determine whether the use of positive reinforcement provided by DC electrical stimulation at the cathode, which had previously been shown to be attractive to paramecia, could be used to train these organisms in a discrimination learning task. The results indicate that such learning did take place.

We have all seen the kind of activity that occurs in a drop of pond water.  It is hard to watch and not question how single-celled life can do what it does.

Re 'two,' I disagree. My point is (and was in the previous thread) that Hameroff makes unsupportable claims. He states unequivocally that paramecia can learn. The reality is that the data is arguable AT BEST, and the specific example he cites is wrong.

When somone overstates the evidence on a claim that I CAN check, I am less likely to believe them on claims that I can't.

Re 'first of all,', awareness* is easily explained by classical mechanisms. If you choose to believe that it's really due to quantum computing by microtubules, that's up to you. But there's no need whatsoever to invoke such things to explain how protozoa behave.

*Note added in edit: I mean "awareness" as exemplified by the behavior of single-celled organisms. I don't mean to claim that human consciousness is easily explained by classical mechanisms.

Date: 2007/10/01 16:12:35, Link
Author: qetzal
Quote (Thought Provoker @ Oct. 01 2007,08:15)
Hi qetzal,

You wrote...
I mean "awareness" as exemplified by the behavior of single-celled organisms. I don't mean to claim that human consciousness is easily explained by classical mechanisms.

We may be finding ourselves on opposite sides of the fence from the usual ID positions.  Typical ID proponents generally consider humans special; I don't (unless the idea of the evolutionary equivalent of runaway cancer makes the cancer "special").

I don't see a clear demarcation for awareness in living organisms.  Humans are aware, chimpanzees are aware, worms are aware.  Life, in general, is aware.  Some even argue that plants are aware.

My embrace of the concept of common descent is potentially another thing that sets me apart from typical ID proponents.  If awareness is an inherited trait, what is the common ancestor that first exhibited awareness?  I suggest an animal with a pair of light-sensitive pits linked to a hormonal signaling system has inherited this awareness trait and natural selection has already begun improving its effectiveness.  The Vernanimalcula guizhouena is precambrian.

I suggest human consciousness is only the tip of the iceberg of the "hard problem".

A dispassionate analysis of the situation would suggest that the awareness trait is wide spread in living organisms on Earth and, therefore, appeared extremely early on the evolutionary tree, possibly at the Origin of Life regardless of how incredulous it seems.

It would be ironic if "Darwinists" started responding with an argument from incredulity.  :O

I agree with much of this. Based on your examples, I think we agree that being aware can mean something as simple as being able to sense the environment and react accordingly, yes?

I'm not at all incredulous about the first organisms having basic awareness in this sense. In fact, they almost certainly did have it, or they would not have survived.

Still, I'll repeat that there's no need to invoke quantum computing to explain awareness at that level. Simple classical mechansims involving sensor circuits and motor circuits connected by positive and negative feedback loops can reproduce behaviors consistent with basic awareness.

As I recall, some pretty interesting "behaviors" have been generated with entirely mechanical/electrical circuits in simple robots. I'll try to find some links if I can. You could also look at how some flagellated bacteria use a combination of tumbling and straight line swimming to move up or down chemical gradients. These kinds of behaviors do not require any quantum computational explanations.

Regarding human consciousness, I wasn't trying to advocate a clear demarcation versus more basic awareness in 'simpler' organisms. I don't consider humans special either. I was merely acknowledging that we don't know enough about consciousness to explain it yet.

Date: 2007/10/02 13:30:17, Link
Author: qetzal
Quote (Thought Provoker @ Oct. 02 2007,10:36)
Hi K.E.,

I quoted Dembski for the purposed of explaining why I feel the Third Choice hypothesis meets the definition of "design" as outlined by a prominent ID Movement leader.

OK, but why? Dembski isn't notorious because he advocates design per se. (Evolution can also be said to "design" organisms). He's notorious because he advocates intelligent design.

Here is Discovery Institute's definition of ID:
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

I didn't think your Third Choice idea required guidance by an external intelligence. Am I wrong?

Date: 2007/10/03 22:39:16, Link
Author: qetzal
Quote (Thought Provoker @ Oct. 03 2007,20:56)
As I have indicated before, I'm open to the idea that quantum computations could be the result of microtubules, actin or pixie dust.  It is a detail as far as the Third Choice hypothesis is concerned.

No offense, TP, but this is a very telling statement. Specifically, it tells me that you have already decided that quantum computations must be involved. Now you just need to decide where and how they're taking place.

That's faith, not science. If it were science, the first step would be to ask, "Are quantum computations involved? Is there data to support this? If not, is it possible to generate such data?"

Date: 2007/10/04 10:12:45, Link
Author: qetzal
Quote (Thought Provoker @ Oct. 04 2007,08:49)
[T]he basic conflict is generally about randomness verses a designer.

Too many people get sidetracked by the word "randomness." It gives the wrong impression of what the theory of evolution (TOE) says. (Cf. the 'tornado in a junkyard' metaphor.)

In reality, much of what happens according to the TOE is decidedly non-random. The TOE merely holds (among other things) that there is no intended outcome, no external agency that guides evolution toward some prespecified goal.

Thus, I think it's more useful to say this conflict is about non-teleological versus teleological claims, or undirected versus directed outcomes.

There is a lot of ground between these two extremes. What would it take to convince both sides that a middle ground hypothesis that presumes neither randomness nor a designer is not only plausible but likely?

Adequate empirical evidence. E.g. TOE predicts X, ID predicts Y, your Third Choice (TC) predicts Z. Perform a study to determine which of X, Y, or Z is actually observed. If the results are Z & not-X & not-Y, that's evidence in support of TC.

All I've seen so far is arguments for why TC could be true. Even if I accepted those arguments as valid, that would merely establish TC as a possibility. It wouldn't be a reason to accept it.
I have previously presented the concept that there is no such thing as randomness in a post titled The Magic of Intelligent Design. This post has appeared in Telic Thoughts and in After the Bar Closes. For a proposed design agency, I have offered the orchestrating properties of quantum effects generally outlined in the Penrose-Hameroff model called Orchestrated Objective Reduction or Orch OR for short.

What would it take to convince either side that quantum effects are interconnected?

That's already scientifically accepted.
How about seven decades of physicists performing experiments demonstrating non-local behavior and paradoxical behavior that can only be explained if nature is “entangled” at the quantum level?

Yes, this is why quantum effects are accepted at the quantum level. This doesn't establish the degree of
interconnection required in your proposal. (Or in Penrose-Hameroff's, as best I can tell.)
What would it take to convince either side that life is directly dependent on quantum effects?

Given that life depends directly on chemistry, and quantum effects play an integral role in chemistry, this is already established as well.
What would it take to convince either side that evolution is under the control of interconnected quantum effects?

Adequate empirical evidence.
What if it turned out the DNA search function is a quantum algorithm that requires quantum-like superposition?

Even that were true, wouldn't support the claim the evolution is under the control of interconnected quantum effects.
From Patel's Quantum Algorithms and the Genetic Code…
Replication of DNA and synthesis of proteins are studied from the view-point of quantum database search. Identification of a base-pairing with a quantum query gives a natural (and first ever!) explanation of why living organisms have 4 nucleotide bases and 20 amino acids. It is amazing that these numbers arise as solutions to an optimisation problem. Components of the DNA structure which implement Grover’s algorithm are identified, and a physical scenario is presented for the execution of the quantum algorithm. It is proposed that enzymes play a crucial role in maintaining quantum coherence of the process.

From Patel's Towards Understanding the Origin of Genetic Languages…
The initial and final states of Grover’s algorithm are classical, but the execution in between is not. In order to be stable, the initial and final states have to be based on a relaxation towards equilibrium process. For the execution of the algorithm in between, the minimal physical requirement is a system that allows superposition of states, in particular a set of coupled wave modes.

As we discussed on the previous thread, at least some of Patel's proposals for how DNA replication might involve quantum superposition effects are clearly incompatible with known biochemistry. As far as I can tell, the rest are purely speculative at best.
There is more support for the possibility of life's direct dependence on interconnected quantum effects for functions like cellular awareness (i.e. consciousness) as an artifact of quantum computation in microtubules. "Bio-quantum physics" appears to be an emerging science. While it is still speculative, that is not the point.

The question is… What would it take to convince ID/Darwin extremists to agree on a scientific hypothesis that supports neither philosophical agenda?

Actually, the fact that it's still speculative is exactly the point. Without data that supports the speculation, there's no reason to accept it. Especially not when we already have a theory that does a damn good job of explaining what we see (the TOE, of course).

BTW, a quantum mechanical explanation can be thought of as a tool of an intelligent designer just as much as the result of a non-teleological universe that occurred “randomly” from multiple universes. However, these are metaphysical concerns, not scientific ones.


Date: 2007/10/04 13:23:45, Link
Author: qetzal
Looks like maybe TP is right after all!


Hat-tip: The World's Fair.

(Please excuse my irreverance. I couldn't help myself!)

Date: 2007/10/04 16:35:23, Link
Author: qetzal
Quote (Henry J @ Oct. 04 2007,14:01)
Beyond A 'Speed Limit' On Mutations, Species Risk Extinction
Cambridge, Mass. - October 1, 2007 - Harvard University scientists have identified a virtual "speed limit" on the rate of molecular evolution in organisms, and the magic number appears to be 6 mutations per genome per generation -- a level beyond which species run the strong risk of extinction as their genomes lose stability.

iirc, the average mutation rate for the coding section in humans is what, 1 or 2 per generation?


Two qualifications on this paper:

1) It's actually 6 mutations per essential part of the genome per generation. As best I can tell, the "essential part" in their model corresponds to the coding sequences for proteins that are essential to survival.

2) Their model assumes organisms reproduce independently. In other words, the calculated speed limit is only applicable to asexually reproducing organisms. Indeed, the authors compare their models only to empirical data from viruses and prokaryotes.

Date: 2007/10/04 17:46:01, Link
Author: qetzal
Quote (Thought Provoker @ Oct. 04 2007,16:06)
Engineers are like that too.  They tend to go with what works.  Provide a mechanistic explanation that makes sense (i.e. a model) and they will run with it.  I have plenty of experience with PhD types providing lists of why a proposed design won't work.  However, when they refuse to offer an alternative we have to go with the best we got.  The funny part is when the project is successfully completed, the PhD types still maintain they were right and provide plenty or reasons why.

Yes, and note what the engineers did - they performed an empirical test by putting the design into practice, thus providing evidence to support their hypothesis that the design was sound. As you rightly point out, we can't always trust that our theories accurately reflect reality. That's why we insist that theories be supported with evidence.
Penrose's quantum interpretation (OR) makes sense and answers all of the quantum observations like GHZ states.

But you've just illustrated so clearly, we can't always trust our theories even when they're supported by lots of evidence. Yet you want us to accept Penrose's theory based on no evidence. Can't you see the disconnect there?
The Penrose-Hameroff Orch OR model is a fall out of this.  Consciousness has to be tied to interconnected quantum effects.  Consciousness can't be purely algorithmic.

Why? How do you know? You sound suspiciously like those PhDs who insist things must be a certain way.
Dr. Hameroff takes this a provides a detailed model of how this could work.  I understand it well enough to go with its basic concept.  Do you have an alternative model?

Hameroff's model focuses on how microtubules and microtubule networks might engage in quantum computing. I'm not qualified to evaluate the quantum aspects, but even if they're plausible, how does Hameroff support the claim that they lead to consciousness? As far as I can tell, it's just an appeal to apparent mysticism. Quantum effects seem mystical, consciousness seems mystical, one must cause the other. Not a very compelling argument.

Please note - I don't reject Hameroff's ideas out of hand. I admit they seem a bit wacky to me, but it's too far out of my area of expertise. I just refuse to accept his ideas in the absense of adequate supporting evidence.
There is no reason that the future couldn't effect the past for similar reasons that the sun can effect the Earth.

In other words, you're arguing it's possible. But not everything that's possible is real.
Are you ready to agree there is no such thing as randomness (or at least that it is a metaphysical presumption)?

You're missing the point. We're not arguing whether randomness exists per se. We're saying that evolution isn't random. The TOE is not equivalent to randomness a la the tornado in a junkyard. Not by any stretch.

In fact, perhaps you should take heart in this. You originally asked:
What would it take to convince both sides that a middle ground hypothesis that presumes neither randomness nor a designer is not only plausible but likely?

The answer is that TOE is a middle ground hypothesis. It doesn't invoke a designer, yet it doesn't claim that organisms arose by anything akin to "random assembly of a 747 from a pile of junk" either.

Dilemma solved! Of course, it was solved even before you asked the question, but I suppose your asking now could have retrocaused the solution in the past. ;-)
To BWE - Other than arguing against randomness, what I am saying isn't in direct conflict with the ToE.  I am suggesting an enhancement that might explain why living organisms like Vernanimalcula guizhouena are more complex than expected.

On what basis is V. guizhouena more complex than expected? Are you trying to suggest that it's 'too complex' to have evolved 'naturally' in the available time period? Do you have any evidence to support that, or is it based merely on personal incredulity?
While I hesitate to speak for MikeGene, I think it is safe to say he has a similar position.  Front Loading is an enhancement, not a challenge.

That's not correct. Front loading is directly contradictory to the TOE as we know it.

Date: 2007/10/04 22:19:20, Link
Author: qetzal
Quote (Thought Provoker @ Oct. 04 2007,20:56)
Hi qetzal,
You wrote...
In other words, you're arguing it's possible. But not everything that's possible is real.

This is probably a philosophical difference.  I have a strong sense that, in this universe, if it can happen it does happen.  I think Penrose has a similar philosophy.

Well, if that's your view, I can see why evidence is mostly irrelevant to you. But do you really believe that? If it's merely possible that microtubules perform quantum computations, then they do?
Hawking and Penrose figured out Black Holes could happen.  They presumed Black Holes existed long before evidence was found.

Not so. They figured out that, based on our best understanding of physics, black holes must form under certain conditions. I trust you see the difference?
Did you know natural occuring laser light was found on Mars? link

Yes, and....?
I think the trick to physics is trying to figure out what isn't possible under what conditions.  It may be the trick to biology too.

I guess that's not entirely unreasonable, at least as a way to distinguish what's possible from what's not. It's still necessary to generate evidence, to distinguish what's merely possible from what's actually true. Keep in mind that our ability to determine what's really impossible is no better than the quality of our current theories. And we already apparently agree that it's unwise to assume those are infallible.
You wrote...
That's not correct. Front loading is directly contradictory to the TOE as we know it.

You might want to talk to MikeGene about his opinion on that.

Here is my comment on Vernanimalcula guizhouena.

Yes, I saw it. I didn't respond at the time, but I will now. You wrote:
Alright, I will admit the Vernanimalcula guizhouena probably had to hand out "I am deaf" cards to any verbalizing organisms running around, but all and all, for it's time the Vernanimalcula guizhouena were intellectual giants. That time was 600 MILLION YEARS AGO!

As a champion of a Third Choice I will point out the challenge of this for the other two choices. First of all, what evolutionary pressures would there be to cause such a complex creature to evolve? How much complexity is needed to eat microbes? How complicated do early organisms have to get before it is admitted they just might be more complicated than expected?

Do you realize that the first life probably arose almost 4 BILLION years ago? (Believe it or not, there are fossils of these cells.) That leaves ~ 3 billion years to go from the first cells to V. guizhouena, versus only 600 million to go from V. guizhouena to H. sapiens. I think that puts things in more perspective.

Evolutionary pressures that might lead to V. guizhouena are easy to imagine. If you're the biggest organism around, it's rather hard for all the littler things to eat you. The ability to sense light could also have lots of value. Helps you find where all the photosynthesizers are hanging out, in case you need a snack, for example.

And of course, the raw material for developing light sensors had been around for a few billion years. How hard would it be for a photon-absorbing photosynthetic pigment to get co-opted for use as a photon-absorbing sensory pigment? Seems entirely plausible to me.

You seem to be applying very different standards here. For Penrose & Hameroff, mere plausibility is all you require. Is there a reason why you set the bar so much higher for poor old V. guizhouena?

Date: 2007/10/04 23:03:22, Link
Author: qetzal
Quote (Thought Provoker @ Oct. 04 2007,20:56)
You wrote...
That's not correct. Front loading is directly contradictory to the TOE as we know it.

You might want to talk to MikeGene about his opinion on that.

OK, I read a bit more of Mike Gene's stuff, and I tentatively retract my objection, at least as regards his version of front loading.  To be honest, I'm still not clear what the essence of his version is. But in its loosest form, it appears to be simply that evolution of new traits is partly constrained (and therefore partly determined) by previously existing traits.

That is indeed entirely compatible with the current TOE. New traits don't evolve out of nothing. They arise by modification of what's already there.

If that's all Mike Gene's version of front loading says, I have no problem with it. I'm not sure how it's an extension, but I confess there's a lot there I didn't try to go through.

I do note, however, that he repeatedly refers to a designer. If a designer is detectably involved in his version of front loading, then my objection stands - that's incompatible with the current TOE.

Date: 2007/10/04 23:28:20, Link
Author: qetzal
Quote (Thought Provoker @ Oct. 04 2007,22:53)
Going from V. guizhouena to humans seems trivial compared to going from basic chemicals to V. guizhouena, even at 5 times the duration.

That's not what I said. Life didn't go from basic chemicals to V. guizhouena in ~ 3 billion years. It went from early cells to V. guizhouena in that time. Presumably, those early cells were already much more than just "basic chemicals."

The more surprising thing, as you imply, is the suggestion that it took "only" ~0.7-1 billion years for the first cells to arise. If that's true, then I don't see any reason to be impressed by V. guizhouena's complexity.

I am impressed.  Do you mind if I mention your qualified admission on Telic Thoughts?

No problem, but I'd prefer that you link to my comment, so there's less chance of misconstruing my meaning.

Date: 2007/10/05 10:52:56, Link
Author: qetzal
Quote (Thought Provoker @ Oct. 05 2007,10:25)
What would it take to resist the ID/Darwin polarization?

For a start, ID proponents would need to do one of two things.

1) Act like scientists: generate positive hypotheses based on ID, make predictions based on those hypotheses, design experiments to test those predictions, perform those experiments, interpret the results as objectively as possible, and report it all in the peer-reviewed literature.


2) Admit that ID isn't science, admit they have no plans to ever treat it as science, stop claiming it's a valid scientific alternative to the TOE, and stop pretending that "evolution is wrong; evolution can't explain X" constitutes a scientific theory.

I don't believe the current leaders of the ID Movement will ever do either of those.

I also don't expect that option 1 would actually generate evidence in favor of intelligent design, but I agree that it might lead to new insights.

Date: 2007/10/05 10:55:40, Link
Author: qetzal
Doesn't work for me, using IE7. Gives a message saying "No canvas (try it in Firefox instead)."

Date: 2007/10/05 16:46:22, Link
Author: qetzal

That sounds like a potentially fascinating symposium. I would love to discuss any or all of those questions. (Not that I'm knowledgable in any of those areas, you understand.)

However, I'm not sure where to start. Assuming you've had time to at least skim through the journal, maybe you can tell us which question(s) generated the most interesting responses?

Date: 2007/10/06 20:33:05, Link
Author: qetzal
Hi TP,

Are you planning to franchise these? Somehow, Third Choice, ID Version makes me think of Law and Order, SVU!   :-D

Regarding TC/IDV, I'm curious about the proposed intelligence. Do you consider it to be intrinsic to (or coincident with) the universe, or does it have some sort of external existence outside the universe?

I ask because points 3 & 6 together seem potentially contradictory - the universe has an intelligence that purposefully designed the universe.

Or does this fall under point 8?

BTW, I don't see how this can work:

Empirical evidence of design comes from the hypothesis' predictions like expectations that conscious decisions are effected by future events (Libet)

How would you ever demonstrate that a decision made today was affected by an event that has not occurred?

Date: 2007/10/08 09:10:33, Link
Author: qetzal
Hi TP,

I have to say that I get a bit frustrated with some of your posts. You tend to state things as fact when they are often merely conjecture. For example:

The observed reality shows that going in retrocausal circles is what the universe does at the quantum level. The universe is full of interconnected feedback loops. An infinite number of circles existing in Einsteinian/Minkowskian space-time.

I don't have a problem with conjectures and wild 'what if' statements, but it's helpful to be clear that they are conjectures. At least, it would help me. ;-)

Anyway -

I don't think your proposed experiments to show retrocaused actions make much sense. If you flash a light and then the subjects move a toggle, the light flash can't have retrocaused the movement, because it came first. The focus on reaction times and Libet limits don't change that.

You could ask people to move the toggle before the light flashes. Then you'd be doing standard precognition tests, which, AFAIK, have always failed miserably (as long as they were properly controlled).

The idea of comparing a quantum random number generator to an algorithmic one seems workable. Conventionally, assuming each generates a suitably "random" sequence, subjects' responses to them should be indistinguishable.

I think that's one of those experiments where you'll almost certainly get the conventional result, but if you did see a reproducible difference in subject response to the quantum sequence, (and if artifacts and experimental biases could be ruled out), it would be very hard for conventional science to explain it.

Date: 2007/10/10 18:40:47, Link
Author: qetzal
It has been speculated by anthropologists-- including C. Owen Lovejoy of Kent State University and Helen Fisher of Rutgers University--that sex is partially separated from reproduction in our species because it serves to cement mutually profitable relationships between men and women. The human female's capacity to mate throughout her cycle and her strong sex drive allow her to exchange sex for male commitment and paternal care, thus giving rise to the nuclear family.

This arrangement is thought to be favored by natural selection because it allows women to raise more offspring than they could if they were on their own.

There must be more to it than that. Why do so few species engage in recreational sex? (Are there any other examples beyond humans and bonobos?) Why are there species that pair-bond strongly in the complete absence of recreational sex?

Critiques aside, I think the parallels between bonobo and human sexuality are fascinating and have enormous value for understanding human behaviors.

Regarding Homo versus Pan, I doubt there's any right answer. Unlike species, where reproductive isolation is at least a semi-objective criterion, what constitutes different genera is pretty much arbitrary, is it not?

Date: 2007/10/11 17:53:45, Link
Author: qetzal
Quote (JohnW @ Oct. 11 2007,16:33)
Quote (qetzal @ Oct. 10 2007,16:40)
There must be more to it than that. Why do so few species engage in recreational sex? (Are there any other examples beyond humans and bonobos?) Why are there species that pair-bond strongly in the complete absence of recreational sex?

I don't have a reference (and if you think I'm going to google "animal recreational sex" from my office computer...) but I think dolphins and porpoises are pretty enthusiastic in this field.

Yeah, I think you're right. (But I'm not about to Google it right now either!)

If that's true, it raises some interesting questions. The three species that engage in recreational/social sex are among the most intelligent known species.

Does that mean recreational sex is restricted to smart creatures? (Insert conservative/liberal or scientist/creationist joke of choice here.)

Date: 2007/10/15 11:19:31, Link
Author: qetzal
Hi, TP.

Sorry to have been absent from the conversation. Real life intervened.

Anyway, your last several posts are emblematic of the problems this discussion has suffered from the beginning: reckless extrapolation, misrepresentation of data, assuming facts that aren't established, etc.

Quote (Thought Provoker @ Oct. 13 2007,14:36)
Before we review the evidence of living things directly using quantum physics, we need to discuss the concept of decoherence.

As has been stated repeatedly, we know living things use quantum physics. Evidence that photosynthetic complexes use quantum tunneling is not sufficient to support a claim that living things use quantum superpositions of entire proteins to perform quantum calculations. Based on what you've provided to date, as well as everything I've read from Hameroff, Patel, etc., that evidence is entirely lacking. It's pure speculation.

Not that there's anything wrong with speculation per se. But it's ludicrous to use such abject speculation as a basis for claiming that quantum computation in microtubules is the likely basis for consciousness. Absolutely ludicrous.

Quote (Thought Provoker @ Oct. 13 2007,14:36)
It is reasonable to presume that tubulins are capable of being in quantum position since similar sized fluorofullerenes exhibit quantum behavior.

No, it isn't! It's ludicrous to presume that a 1634 amu fluorofullerene exhibiting wave-like behavior in a carefully isolated system means that a 110,000 alpha/beta tubulin heterodimer is capable of quantum superposition in any useful sense in the midst of a living cell.

Did you note how the authors boasted that their fluorofullerene was twice as massive as the previous largest molecule to show such effects? Twice. Yet you want to presume similar effects in a molecule more than sixty-seven times larger! In a cell, yet.

Quote (Thought Provoker @ Oct. 13 2007,14:36)
DNA provides another possible example of life directly using quantum effects. Patel is refining the model (Grover's algorithm) of the search function inherent in the DNA...

Patel's model is pure speculation, as well as almost certainly wrong. He wants to claim that the cell uses a quantum search function during DNA replication. For that, he needs some sort of superposition of the four different bases, during the "search" to determine which base should be added next.

His original idea was that enzymes would somehow rapidly "cut and paste" functional groups to create an effective superposition of A, G, C, and T. From a biochemical, molecular, and enzymatic perspective, that is just laughable.

Now he apparently realizes that idea is dead wrong, so he's 'refining' the model. But he hasn't even developed a complete model yet, much less provided a realistic link to the known biochemistry of DNA replication.

So, to use Patel's 'model' as a "possible example of life directly using quantum effects" is just more wild extrapolation.

In reality, quantum superposition a la Patel almost certainly plays no role at all in selecting bases during DNA replication. But even on the remote chance that it did, it still wouldn't mean DNA is a quantum computer in any useful sense. At most, DNA would be 'quantum computing' which base to pair with the opposite strand. Big deal.

Quote (Thought Provoker @ Oct. 14 2007,22:59)
I don't understand your fundamental objection to presuming long quantum coherence times for isolated biomolecules.  Here are the two states of tublin dimers...

The peanut-shaped tubulin dimer switches between two conformations in which the alpha monomer flexes 30 degrees from vertical alignment with the beta monomer. These are referred to as open and closed states (Figure 8, Melki et al 1989, Hoenger and Milligan 1997, Ravelli et al 2004).

Here is the Ravelli 2004 paper showing the two different tubulin dimer configurations.  Ravelli used the terms "curved" and "straight" instead of "open" and "closed".

This is a good example of why I am highly skeptical of Hameroff. Note how he states without qualification that the tubulin dimer switches between two conformations. He even cites three papers to support his claim.

However, when you actually read the papers, things aren't quite as simple. Melki proposes a curved state that occurs in subunits that are not part of an intact microtubule. Hoenger and Ravelli each show curvature cause by other molecules binding to tubulin (kinesin and ncd for Hoenger; colchicine and RB3 for Ravelli). Ravelli even states:

Quote (Ravelli @ et al.)
It shows the interaction of RB3-SLD with two tubulin heterodimers in a curved complex capped by the SLD amino-terminal domain, which prevents the incorporation of the complexed tubulin into microtubules.

So, what we really have is a series of reference showing that tubulin can adopt curved structures when it is not part of a microtubule. Yet Hameroff is quite happy to cite them as evidence that tubulin can switch between states within a microtubule. That's disingenuous. And, as we discussed on the previous thread, overstating the evidence is a recurring theme with Hameroff.

It's fun to play "what if" and wonder if there's some connection between consciousness and quantum effects. There's nothing wrong with imagining wild hypothetical scenarios where this might even be true. But it's silly to pretend that such imaginings make it likely, and it's self-deceptive to think that wild extrapolations of known observations constitute evidence.

Date: 2007/10/15 21:55:10, Link
Author: qetzal
Hi TP,

Thanks for the reply (and especially for the Python link!), but I think perhaps you did miss the overall point.

Regarding tubulin:

I wasn't claiming that tubulin dimers don't exist in two (or more) states while part of a microtubule. My point was that Hameroff claimed they clearly did, but the references he cited didn't support his claim. It's poor scholarship to claim that tubulins can be straight or curved in microtubules, and cite references that only show curved states outside tubulins.

Hameroff should have done one of two things. Either cite references that support two states within microtubules, or say that there might be two states within microtubules.

If that was the only case where Hameroff appeared to overstate the evidence, I wouldn't gripe. Unfortunately, it's not. Hopefully you recall that we discussed this on the previous thread. From everything I see, Hameroff shows a recurring pattern of claiming things are a certain way (that coincidentally fits with his hypothesis), when the available or presented data only shows that things could be that way.

People who do that repeatedly don't get the benefit of the doubt from me.

Which leads us the the real issue. I'm not really interested in disputing specific factual claims like "tubulins exist in two or more states in microtubules." That was given as just one example of the fundamental problem.

What I'm really objecting to is the overall rhetorical approach of overstated evidence, unreasonable extrapolation, unwarranted presumptions, and unsupportable claims of likelihood.

You keep citing Hameroff as if he's all but proven quantum superposition in microtubules. The fact is, that's entirely speculative. Your latest cite is more of the same - claims that tubulins might exhibit quantum coherence, along with designs of experiments that might test those claims, but no actual data.

You repeatedly cite Patel as evidence that DNA is 'likely to be' a quantum computer. In fact, Patel is almost certainly wrong, and even if his general idea has some grain of truth, the computing power he's attempting to claim is trivial. How much computation is involved in deciding if A, G, C, or T should be added opposite a given base during DNA replication?

You've cited the photosynthesis study ad nauseum, but the fact is that it has almost no relevance to what you're really trying to show.

I respectfully suggest you admit to yourself the following truth: quantum computing by microtubules may be an interesting speculation, and it may fit well with your belief in quantum interconnectedness, but at present it is virtually pure speculation. The data that's been cited so far doesn't begin to provide actual support for this claim. And until someone gets around to actually performing experiments that directly test these claims, they will remain pure speculation.

Date: 2007/10/16 00:24:38, Link
Author: qetzal
Quote (Thought Provoker @ Oct. 15 2007,22:48)
Hi qetzal,

You know I am an engineer and not a scientist, right?

That being said.  In 1951, two inexperienced young scientists put together a highly speculative model for the genetics.  The model was humiliatingly wrong.  The two were chastised and told to quit working on it.  However, they were stubborn and after "borrowing" data obtained by more experienced scientists, they got lucky and this time the model they put together resulted in them eventually being awarded the Nobel Prize.

The two scientists, of course, were Watson and Crick and the model was DNA’s double helix.

Nice tale. Points for using Watson and Crick instead of Galileo.

Here's another. Once upon a time, there was a brilliant chemist, biochemist, crystallographer, and molecular biologist, all wrapped up in one. He was a pioneer in quantum mechanical treatments of chemistry. He won the Nobel Prize for his work on the nature of chemical bonds. Later, he won the Nobel Peace Prize for his efforts against nuclear testing. He's the only person to be the sole recipient of two Nobels.

The scientist, of course, is Linus Pauling. The list of fundamental discoveries that he made is mind-boggling. And after decades of brilliant accomplishment, do you know what idea he championed at the end of his career? Orthomolecular medicine - the idea that mega-doses of vitamin C could cure colds and cancer. He became so thoroughly enamored of this idea that he apparently forgot the #1 rule in science: data rules.

He was convinced he was right. Thus, anecdotal data that fit his convictions was offered as proof. Data that contradicted him was dismissed as the result of incompetence or even fraud.

I saw him give a talk on vitamin C when I was in grad school. It was quite sad.

The lesson? Ideas in science aren't judged on the people who propose them. They're judged on the data that supports them.

Stuart Hameroff is 60 years old.  He has been working on this for his entire professional life.  Do you think he really cares whether or not you give him "the benefit of the doubt"?

Sir Rodger Penrose probably cares even less.

I don't expect either of them to care what I think. As scientists, I *do* expect them to care about basic scientific principles, such as providing data to support your hypotheses, and fairly distinguishing fact from conjecture.

Jack A. Tuszynski, Avner Priel, Arnolt J. Ramos, Horacio F. Cantiello, Nancy J. Woolf, Vahid Rezania, Michael Hendzel and others might care.  They are the ones doing the experiments.

Great! Let's see some of their results! I'm quite tired of the hand-waving and speculation. What do their experiments actually show?

I find Orch OR interesting for a couple of reasons.  First of all, it makes for a good hypothetical in the ID/Darwin debates.  Would either side accept this as a reasonable hypothesis?

I get the impression that you see this as partly a philosophical debate. Personally, I couldn't care less about the philosophy. I accept the ToE because it's supported by evidence and accurately predicts what we see. I reject ID because it isn't, and it doesn't.

If you show me that Orch OR accurately predicts things that conventional models don't, I'll be much more interested. Until then...

Second, it is thought provoking both for others and for myself.

Yeah, it's been a more interesting discussion than the typical ID bilge. But for me, it's now pretty tapped out (absent some data...?).

Third, it feels right.  The details aren't as important as the fact that things fit together.  Too many questions have gone unanswered for too long.  Orch OR goes a long way to answering the big ones.

Hand-waving doesn't really answer any questions. In fact, it's usually just a way to avoid really answering, so we can pretend that the answers we like are true.

If anyone can show that Orch OR accurately predicts things that other models can't, then it will be fair to say that it answers questions. Until then, it's just castles in the air.

Besides, SteveStory said he was looking to provide you guys with something more substantial than the cotton candy opponents you a used to dealing with.

Now if you would rather argue with AfDave....  

AFDave?!! OK, Uncle! You win!


Date: 2007/10/16 12:40:48, Link
Author: qetzal
Careful, Rich. Woden's gonna be pissed if he hears you claiming Wednesday. (Unless you're him? In which case, glad to see you've given up the whole war thing.)

Date: 2007/10/16 15:55:45, Link
Author: qetzal
Hi TP,

You wrote:

Quote (Thought Provoker @ Oct. 16 2007,13:26)
Hi qetzal,

Please pardon me for threatening you with AfDave but the point was to put things into perspective.  I'm just an engineer trying to make sense of things.  That, and having some fun being a quasi-troll.

You wrote...
I get the impression that you see this as partly a philosophical debate. Personally, I couldn't care less about the philosophy. I accept the ToE because it's supported by evidence and accurately predicts what we see. I reject ID because it isn't, and it doesn't.

If you show me that Orch OR accurately predicts things that conventional models don't, I'll be much more interested. Until then...

It is the "until then..." where the philosophical battle takes place. What are the default presumptions?  I am not challenging established ToE principles, neither is Mike Gene.

OK, in retrospect, I realize my comment actually does relate to my philosophy. Let me clarify.

I don't care about the implications of ToE, ID, or your Third Choice (TC) vis-a-vis philosophies like materialism, naturalism, teleology, etc. My philosophical bias is for models that accurately predict empirical observations. Those models can be materialistic or non-materialisic, teleologic or non-teleologic. I don't much care about that, as long as they are accurate and predictive.

So, I don't reject ID because it implies the universe is teleologic. I reject it (in most forms) because it either makes no predictions or wrong predictions.

I'm highly skeptical of your proposals because I see little evidence to support them, and I don't see that they predict reality better than ToE and other, more conventional models. At least, not in those cases where I know the conventional models well enough to judge.

If, however, you showed me that your models (&/or Hameroff's, Penrose's, Patel's, etc.) predict observation in ways that other models can't, I will happily re-consider the validity of your models. The same goes for ID. (Of course, I'm looking for useful predictions. We can debate what that means, but typical ID claims like "Stuff is complex" and "Darwinism can't explain X" don't make the grade.)

What is your presumed answer for the GHZ states described in the opening post to this thread?

What do you mean? To the extent that I understand it, I accept that quantum entanglement occurs under certain conditions. If GHZ accurately describes how that operates, I'm fine with it.

What is your presumed answer for the source of Gamma EEG waves?

Well, I'm not a neurologist, so I don't have a presumed answer. Which doesn't mean there isn't a perfectly good explanation, just that I don't know it, and I'm not interested enough to look it up.

What is your presumed answer for how single-celled organisms can avoid obstacles, find food and engage in sex?

OK, this is closer to my expertise. Let's take finding food. This is an example of chemotaxis - movement in response to a chemical gradient. Bacteria typically swim towards chemoattractants (incl. food), and away from chemorepellants (e.g. harmful compounds). They can do this by mixing two kinds of swimming: runs and tumbles. Runs are relatively long periods of roughly straight line movement. Tumbles are short periods where the cell randomly re-orients.

When bacteria move up an attractant gradient, they are seen to have longer runs and fewer tumbles. When they get 'off course' (i.e. if they're not moving up the gradient any more), they're more likely to tumble and change direction. Changing the duration of runs and the frequency of tumbles like this lets them take a so-called random walk approach towards the source of the attractant. As long as they're moving in the right direction, they tend to keep going. If they go in the wrong direction, they're more likely to stop and try a different direction.

Note - when they change direction, they don't automatically re-orient towards the source. Re-orientation is (apparently) random. If, by chance, they end up pointing in the right direction, they'll keep going. Otherwise, they'll soon change direction again.

Note also - once they reach the food source, they're at the maximum point of attractant concentration. Any direction they move is away from the gradient. So, they minimize the length of their runs, and tumble frequently. In this way, the just sort of mill about in the region of highest food concentration.

So, how do they control runs and tumbles? They have receptors on the surface that bind attractants (and repellants). Binding causes a conformational change in the receptor, which extends through the membrane to the inside of the cell. The altered receptor interacts with other proteins. This changes the level of phosphorylation on a protein called CheY. When CheY is phosphorylated, it binds to certain flagellar proteins. This causes the flagella to rotate clockwise. Because of the unsymmetrical shape of the flagella, CW rotation causes tumbling.

When CheY is un-phosphorylated, it doesn't bind the flagellar proteins. In that case, the flagella rotate counterclockwise. Again, because of flagellar shape, CCW rotation causes runs.

Here is a review that provides more detail (see first section).

Note that nothing in this whole scheme requires any quantum superposition of proteins, or quantum calculation by the cell's DNA or tubulin-like proteins. There's no need to invoke any ill-defined awareness in the cells, quantum interconnectedness, or retrocausation. If someone can show how those things increase the accuracy of the model, great. At present, however, they don't appear to be relevant.

I suggest that many have a philosophical bias towards explanations that presume solid matter is operating in a universe of Euclidean Geometry where time always marches forward like a frame by frame movie (i.e. “Materialism”).

Perhaps, but I don't. My bias is against models that don't increase our explanatory power, and don't increase our ability to predict observations. As an aside, I think your definition of Materialism is rather different than the usual one.

“Materialism” is a philosophical outlook.  I think it is outdated considering what we know from quantum physics.  The Many Worlds interpretation is a desperate attempt to hang on to the security blanket of presuming solid particles actually exist.

I am not suggesting God or even Intelligent Designer(s) should be presumed.  A lot of people have complained that my philosophical leaning is “Naturalism” which, to some, is just as bad as “Materialism”.

We can’t escape our biases.  We all have them.  But I suggest in this case, you might be attempting to presume a biased position that you have no right to claim should be considered the default ("conventional models").

Well, hopefully I've at least clarified what my philosophical position is. I'm not saying it's objectively right, or that you should adopt it as well. However, I will say that it's more or less a default position for science.

I am an engineer putting together my model.  You put together yours and we will compare them.  Ok?

Depends. A model for what? There's a model that I currently accept for how bacteria find food. (At least, that's one way they do it; there are undoubtedly others.) If you have an alternative, we can discuss how it they compare.

However, if you're looking for my proposed model of consciousness, I don't have one. That doesn't mean I have to accept yours or Hameroff's. I'm perfectly content with the fact that we don't have an adequate model for consciousness yet.

Date: 2007/10/17 10:20:09, Link
Author: qetzal
Allow me to pick a troubling nit:

Quote (JonF @ Oct. 17 2007,08:06)
Quote (C Gieschen @ Oct. 16 2007,20:47)

So let me get this straight, according to the tree of life, we are all just animals.


Saying we are "just" animals is a sneaky way to imply that evolution claims we're no better than any other animal. That our lives have no more intrinsic value than any other animal's. Such as a spider's.

Evolution doesn't say that. It says we are animals. Whether we are better, worse, or equal in 'value' to any other animal is a judgement that is independent of evolutionary science.

Date: 2007/10/17 14:12:38, Link
Author: qetzal
Quote (C Gieschen @ Oct. 17 2007,11:40)
I don't see how it does not follow regarding the death question.  If we are just animals, then what is the reason to not behave like animals?

We already do. We behave like human animals. See Occam's Toothbrush's post above for why that doesn't mean random acts of violence.

Besides. Think of all the things that humans do routinely: lie, cheat, steal, rape, murder, wage war, etc. Judged solely on actions, humans are a lot less moral than many other animals. Behaving like "just animals" would be an improvement!

Rather a sad situation for someone who considers humans to be God's favored creation.

Date: 2007/10/18 20:25:22, Link
Author: qetzal
Speaking of Kevin Spacey, definitely see "Seven."

"L.A. Story" is also must-see.

Date: 2007/10/23 20:59:35, Link
Author: qetzal

If you're still around, you might appreciate this.

I don't have an immediate opinion on the paper in question, but it has this much going for it:

This theory naturally explains recently observed marked increase in dominance duration in binocular rivalry upon periodic interruption of stimulus and yields testable predictions for the distribution of perceptual alteration in time.

Date: 2007/10/31 19:07:29, Link
Author: qetzal
Quote (Richardthughes @ Oct. 31 2007,16:12)
Quote (jeannot @ Oct. 31 2007,15:57)
Misleading thread title.  :(

I read "lateral gene transfer".  :O

Twas a pun. Memes, memetics... you know..

No, no...not a pun...What's that thing that spells the same backwards as forwards?

Date: 2007/12/27 23:03:17, Link
Author: qetzal
Quote (VMartin @ Dec. 27 2007,14:36)
Quote (Alan Fox @ Dec. 27 2007,14:08)
But they are wrong, because descending of testicles has meaning beyond any neodarwinian paradigma.

Well, you've got my attention, now. Please do tell, Martin. The meaning of descending testicles is...

You know, some outdated theory no one cares anymore. Something like German mysticism. Polarity of mammalian bodies, two centres. Head and reproduction organs on the opposite side of the body. Centre of individuality and centre of species proliferation as opposing principles which are now displayed. Maybe not worth of mentioning for you.

But this time darwinists have not better stance with the cooling sperms bullshits.

Yes! Yes! I see it now!

Polarity of bodies! Head and reproduction organs on opposite sides! That's why testicles are outside the body. Just like ovaries.... Wait. Hmm.

Dammit! It was clear there for a second. of individuality...opposing principles...wave both hands about out of both ends of the body....

Nope, I've lost the thread. Can you explain it again, V?

Date: 2008/01/01 09:36:06, Link
Author: qetzal

If you think logic requires that the universe has a cause, and you call that cause God, what caused God? Is/was there an Ur-God? And an Ur-Ur-God? Ad infinitum?

Or, if God doesn't need a cause, why does the universe?

Date: 2008/01/20 09:57:35, Link
Author: qetzal
The obvious, experimentally supported, explanation is that interconnected quantum effects is the fundamental organizing force of the universe.

In practical terms, what does this mean? It sounds like a quantum version of determinism. Is that what you're suggesting?

Date: 2008/01/20 19:33:42, Link
Author: qetzal
Quote (Thought Provoker @ Jan. 20 2008,10:41)
Hi qetzal,

You wrote...
In practical terms, what does this mean? It sounds like a quantum version of determinism. Is that what you're suggesting?

Yes and no.

Would a Mandelbrot Set be considered deterministic even if its equation was unknowable?

Not "unknown", but "unknowable".


Quantum effects are artifacts of one giant multidimensional wave function in the space-time geometry that is our universe.

So you're saying everything is part of a single wave function, so all is predetermined. Yes?

Date: 2008/01/30 18:34:57, Link
Author: qetzal
Quote (Kristine @ Jan. 30 2008,17:15)
The local fish-wrapping that calls itself a newspaper had the "woman with the highest IQ in the world" with her own column for a while. She took questions from the audience. What a twit! That did not last long, either. :D

You mean Marilyn vos Savant? She still does that - in her weekly column in Parade (the Sunday 'magazine' that comes with most big city newspapers).

Kind of an odd shtick for the 'woman with the highest IQ in the world.'

Date: 2008/02/06 21:04:56, Link
Author: qetzal
Quote (Louis @ Feb. 06 2008,11:46)
P.S. One particular investigation did cause us to revise the estimate to: boobies, boobies, boobies. However the issue of priority raised its ugly head again. We were very drunk. Anyway, without arguments over priority it would be impossible to form really bitter schisms and divided sects. That would lead to harmony, and where's the fun in that?


Date: 2008/02/21 17:30:01, Link
Author: qetzal
I'm not convinced that either the Australopithecines or the Neaderthals have proved their case. I therefore volunteer for a randomized, double-blindfolded, two period cross-over study to evaluate which of the two females is superior.

Date: 2008/02/27 20:17:03, Link
Author: qetzal
Let's remind ourselves and Kevin what the Discovery Institute says the "theory" of ID is (link):

The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

[T]he dominant theory of evolution today is neo-Darwinism, which contends that evolution is driven by natural selection acting on random mutations, an unpredictable and purposeless process that "has no discernable direction or goal, including survival of a species." (NABT Statement on Teaching Evolution). It is this specific claim made by neo-Darwinism that intelligent design theory directly challenges.

In other words, Kevin, ID isn't just about where the universe came from, or even where the first life came from. ID claims that evolution cannot account for the current diversity of life, no matter where the first life form came from, and that an intelligence must have repeatedly intervened.

This claim is directly contrary to the actual evidence, which shows that evolution can account for existing diversity, existing biological complexity, etc.*

ID is like claiming that the first humans in North America must have been teleported here, because the existing explanations involving land bridges are impossible.

*Of course, the fact that evolution can account for biology is not proof that evolution does correctly account for biology, but that's beside the point here.

Date: 2008/03/04 11:46:20, Link
Author: qetzal
Quote (BWE @ Mar. 03 2008,22:05)
Hmmm. Socrates, I see you got better. I guess we all see who gets the last laugh. I do have a question about something you put there in the midst of that brilliant essay (we creationists have to stick together you know).
This is not only extremely rare, but physically impossible.

Which one? I'm confused.

Both, silly! It's physically impossible, but it has happened extremely rarely. Rarely meaning once, ~ 6000 years ago when goddidit. Physical impossibility is no problem for the Big Guy, you know.


Date: 2008/03/13 21:48:44, Link
Author: qetzal
Quote (Assassinator @ Mar. 13 2008,19:17)
What's wrong with asking certain things? Why can't we question God, what in God's name is wrong with that?

We can. The problem is that he never answers. At least, not in any objectively discernable way.

The question is why doesn't answer? A simple and obvious explanation is that there is no omniscient, omnipowerful, omnipresent personal god. But of course, that answer is not acceptable to a believer, so believers need a different answer.

Hence, "We're not capable of understanding; God answers in his own way; God's plan is incomprehensible to mortal man; etc."

Date: 2008/03/14 17:28:44, Link
Author: qetzal
Quote (skeptic @ Mar. 14 2008,07:53)
No, getzal, it's simpler to say that we don't know why he doesn't answer and not make any assumptions beyond that.

That's not what you said earlier.
Quote (skeptic @ Mar. 12 2008,07:37)
In fact there's an entire Book to the point that you're not going to know why because you're incapable of understanding it.

Quote (skeptic @ Mar. 12 2008,23:20)
no God doesn't tell Job that I'm bigger than you, he says I can't tell you because you just wouldn't understand.  it is beyond human capacity.

"God doesn't answer because we aren't capable of understanding" is not equivalent to "We don't know why God doesn't answer." (Begging the question of God's existence to begin with.)

P.S. It's "qetzal" - with a "q" not a "g." As in "qetzalcoatl" (or "quetzalcoatl" if you prefer).

Date: 2008/04/02 22:16:20, Link
Author: qetzal
Communication certainly exists in bacteria. Here's a briew review of one type of bacterial communication - quorum sensing.

Art as form of cognitive play with pattern sounds like a good description to me, but who am I to judge?

Edit: I'm not so sure that art and storytelling are really adaptations though. Communication is certainly an adaptation, and trying to understand the world and communicate that understanding to one's relatives is likely an adaptation as well. Communicating via metaphor, fiction, and artistic representation probably arise out of those adaptations, but may not be strictly adaptive in themselves.

Date: 2008/04/02 22:43:21, Link
Author: qetzal
I have my work badge on one of those retractable clip thingys; I could use it as a garrote in a pinch.

I can also highly recommend guthrie's weapon #1. It's generally served me well.

But really, my favorite weapon is 100 billion or so cerebral neurons. I try to keep those ready for use at all times.

Date: 2008/04/18 17:42:47, Link
Author: qetzal
Quote (Leftfield @ April 18 2008,14:08)
I think the best way to resolve the whole question is to put Dr. Herrmann, kairosfocus and a monkey in a locked room with three typewriters and not let them out until they produce a sane and intelligible paragraph. :p

When the monkey does it, does Dr. H. get out too?

Date: 2008/06/04 19:29:26, Link
Author: qetzal

Do we also teach "strengths and weaknesses" of gravitional theory? How about plate tectonics? How about strengths and weaknesses of the idea that enzymes catalyze reactions?

This 'strengths and weaknesses of evolutionary theory' business is highly disingenuous, and you know it. It's fair to teach a bit about strengths and weaknesses of every scientific theory. It's NOT fair to specifically single out evolutionary theory for special attention to its 'weaknesses.' Especially since we all know the motivation for doing so is the religious beliefs of those pushing for this approach.

Also, your "both sides have an agenda" claim is crap. At most, a tiny minority of pro-evolution advocates wants it taught because of religious reasons (i.e. because they think it will promote atheism). Conversely, essentially EVERYONE who's trying to water down the teaching of evolution is doing so for religious reasons.

Date: 2008/06/11 08:17:56, Link
Author: qetzal
Quote (skeptic @ June 10 2008,22:32)
please pay attention, there is no need for the legislation and bias is in the eye of the beholder.  Both sides see bias on the other.  The idea is not to address the bias but eliminate the ability to claim it exists.

You don't seem to understand. As far as the "other side" is concerned, the weakness of evolution is that it contradicts their religious belief of special creation. That's never going to change. (Barring the miraculous discovery of new evidence.)

Your proposal to adopt the "strengths and weaknesses" claim isn't going to eliminate the problem, because evolution will still contradict special creation. Religious fundamentalists want evolution "taught" in such a way that it doesn't contradict their belief (e.g. as "just a theory" or really watered down or, preferably, not at all). Unless you do that, the problem remains. In fact, it's worse, because you've gone along with the idea of legislating how a subject is taught due to religious beliefs.

The motivation for this legislation is religious. Specific religious beliefs should never dictate what is taught in public high school, nor how it is taught. Such legislation should be opposed and defeated.

Date: 2008/07/16 20:20:51, Link
Author: qetzal
Quote (Louis @ July 16 2008,09:39)
There is one tiny thing I wish to take issue with: This "before brushing your teeth" stuff. Any chance you could mention this action to some of my more personal hygeine challenged colleagues? Some of them are very eminent scientists, and also quite frequently wrong and humble about it, but one does wonder if smelling like a dead badger is part of the package.


Maybe it's akin to evolutionary traits like the peacock's tail. Along the lines of, "I'm such a badass scientist that I can be successful even while smelling like a dead badger. Better not challenge me at the next departmental meeting!"


Date: 2008/07/25 16:51:15, Link
Author: qetzal
Here's a very interesting abstract from Cell. Ran across it on one of the xkcd Science forums.

Drummond & Wilke (2008), Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution. Cell 134:341-352.

Strikingly consistent correlations between rates of coding-sequence evolution and gene expression levels are apparent across taxa, but the biological causes behind the selective pressures on coding-sequence evolution remain controversial. Here, we demonstrate conserved patterns of simple covariation between sequence evolution, codon usage, and mRNA level in E. coli, yeast, worm, fly, mouse, and human that suggest that all observed trends stem largely from a unified underlying selective pressure. In metazoans, these trends are strongest in tissues composed of neurons, whose structure and lifetime confer extreme sensitivity to protein misfolding. We propose, and demonstrate using a molecular-level evolutionary simulation, that selection against toxicity of misfolded proteins generated by ribosome errors suffices to create all of the observed covariation. The mechanistic model of molecular evolution that emerges yields testable biochemical predictions, calls into question the use of nonsynonymous-to-synonymous substitution ratios (Ka/Ks) to detect functional selection, and suggests how mistranslation may contribute to neurodegenerative disease.

I knew that codon usage correlated with gene expression levels, but I had no idea that evolutionary rates did as well! Unfortunately, I won't have full text access 'til I'm back on work on Mon. Can't wait to read it!

Date: 2008/07/29 00:23:53, Link
Author: qetzal
I had a chance to read the Cell paper I mentioned a few days back. I thought it was fascinating, and I highly recommend it.

Basically, it appears that a number of things correlate with mRNA levels across species from E. coli, yeast, worms, flies, mice, to humans. These include the fraction of optimal codon usage (i.e., the fraction of codons that correspond to the most abundant tRNA for that amino acid), the evolutionary non-synonymous substitution rate, the synonymous substitution rate, and even the relative rate of transitions to transversions.

The authors use principal component analysis to argue that all of these are related to one main underlying feature. They then argue that this feature is the need to minimize translation errors that lead to protein misfolding. In essence, they argue that misfolded proteins are cytotoxic, presumably in rough proportion to their abundance.

For low abundance proteins, occasional misfolding contributes little to the total cytotoxic burden in the cell. But for high abundance proteins, even rare misfolding may be detrimental. Thus, they argue, highly expressed genes need to use optimal codons to minimize translation errors. Even synonymous substitutions in a highly expressed gene can be detrimental, because they will tend to change an optimal codon to a suboptimal codon. This will increase the rate of translational error, resulting in more misfolded proteins, and greater cytotoxicity.

They go on to show how all of the observed correlations with gene expression level can be explained by this underlying mechanism. They do simulated evolution studies in silico that reproduce the observed correlations, but only if they include a cost associated with protein misfolding. Then they go a step further and suggest that this effect shows tissue specific features in complex organisms. For example, they suggest that neural tissue may be particularly sensitive to cytotoxicity from misfolded proteins (think Alzheimer's, Parkinsons, CJD, etc.). They note that brain-specific genes appear to evolve relatively slowly as a group, and explain how their hypothesis accounts for this.

The authors suggest that, if they're right, this has wide ranging implications for our understanding of evolution. Among other things, we would need to take into account how this affects synonymous vs. non-synonymous substituion rates when estimating divergence based on molecular data.

Here's what I really liked about this paper. 1) It proposes a new mechanism that has fundamental implications for how evolution works and is constrained. (At least, it's new to me; an editorial in the same issue of Cell seems to think it's potentially quite important as well.) 2) It provides a unifying explanation for a number of seemingly unconnected observations. (It even provides possible insight into the mechanisms of type 2 diabetes!) 3) The authors make multiple predictions based on their proposal, all of which can be tested experimentally.

To me, this is a stellar example of how science really works. The contrast with ID is stark.

Date: 2008/07/30 21:10:42, Link
Author: qetzal
OK, I really don't have much of interest in my backyard these days. Am I allowed to indulge my inner geezer & reminisce?

We lived in southern Illinois for a year in junior high. There were probably 20 chipmunks living in the back yard. We'd hand-feed them peanuts; they got quite tame. We gave them all names and learned to recognize them on sight.

We had a great horned owl that nested in the woods behind us. I climbed an adjacent tree to see the chicks, and the female strafed me. Almost fell out of the tree.

There were also flying squirrels. We discovered them when we heard little chirps in the trees at night. At first, we couldn't see what was making the noise, but it didn't sound like a frog or cricket. Took a while before we saw the dark shapes gliding from tree to tree.

Best was the time we caught a coatimundi in the field across the street! Turns out it was an escaped pet from down the street, but still.

Those were the days, I tell you! (Get off my lawn!)


Date: 2008/08/07 08:32:17, Link
Author: qetzal
Quote (lcd @ Aug. 07 2008,07:10)
What I'm looking for is science evidence that will back up my faith.

So yes all you ATHEISTIC EVIL NAZI-MARXIST WANNABES I'm looking for evidence to give to more than a few people I know and teach them a few things.

In other words, you want evidence that can be selectively made to fit your pre-determined belief, and that can be used to dishonestly* convince others of that belief.

(*Dishonestly because it selects only the 'favorable' evidence, and implies that unfavorable evidence doesn't exist.)

Did I understand you correctly?

Oh, well. At least you're being 'honest' about your plans to be, er, dishonest.

Date: 2008/08/28 22:24:25, Link
Author: qetzal
Quote (Lou FCD @ Aug. 28 2008,21:32)
For the moment though, we have no evidence of disembodied telic entities, ghosts, or leprechauns pushing the termites around. We're sticking with the substance in the ink hypothesis for the moment.


Maybe you should check for quantum coherence in their microtubules. I'm sure TP can help you with experimental design.  :D

Date: 2008/09/04 22:27:03, Link
Author: qetzal
Quote (Daniel Smith @ Sep. 03 2008,19:09)
By "lab tested" I mean something that is tested period.  For instance, if two sets of genes are known, and are said to be from a common ancestor, it should be possible to extrapolate the common ancestral gene (and intermediate genes) via computer simulation.  Then you should be able to test the resultant genes for viability by altering and inserting the DNA into the living organisms.

Been done. Multiple times. Here's just one example:

J Mol Biol. 2007 Jun 15;369(4):1060-9. Epub 2007 Apr 5.

Extremely thermophilic translation system in the common ancestor commonote: ancestral mutants of Glycyl-tRNA synthetase from the extreme thermophile Thermus thermophilus.

Shimizu H, Yokobori S, Ohkuri T, Yokogawa T, Nishikawa K, Yamagishi A.

Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.

Based on phylogenetic analysis of 16 S and 18 S rRNAs, the common ancestor of all organisms (Commonote) was proposed to be hyperthermophilic. We have previously tested this hypothesis using enzymes with ancestral residues that are inferred by molecular phylogenetic analysis. The ancestral mutant enzymes involved in metabolic systems show higher thermal stability than wild-type enzymes, consistent with the hyperthermophile common ancestor hypothesis. Here, we have extended the experiments to include an enzyme of the translation system, glycyl-tRNA synthetase (GlyRS). The translation system often shows a phylogenetic tree that is similar to the rRNA tree. Thus, it is likely that the tree represents the evolutionary route of the organisms. The maximum-likelihood tree of alpha(2) type GlyRS was constructed. From this analysis the ancestral sequence of GlyRS was deduced and individual or pairs of ancestral residues were introduced into Thermus thermophilus GlyRS. The ancestral mutants were expressed in Escherichia coli, purified and activity measured. The thermostability of eight mutated proteins was evaluated by CD (circular dichroism) measurements. Six mutants showed higher thermostability than wild-type enzyme and seven mutants showed higher activity than wild-type enzyme at 70 degrees C, suggesting an extremely thermophilic translation system in the common ancestor Commonote.

Note that it doesn't just show that the inferred ancestral sequence works. It shows that the inferred ancestral sequence has specific properties predicted based on evolution!

Date: 2008/09/06 10:16:39, Link
Author: qetzal
Quote (Daniel Smith @ Sep. 05 2008,18:28)
This is exactly what I've been looking for.  Thank you for posting that qetzal.  I only wish I could read the whole paper.  You say that experiments like these have been done multiple times: if you have any more links to papers such as this (preferably the full paper), I'm interested and would appreciate your posting them.

Thanks again.

You're welcome.

I found this quite quickly at PubMed by searching the phrase "ancestral sequence" (including the quote marks).

Not all the hits are what you want, but many are, and some have free full text links. See the little paper icons to the left of each hit? The ones with a green or orange bar at the top have free full text links.

Try other search phrases or word combos. Try using the Limits tab. You can limit searches to title words, even restrict your search to papers with free full text links if you want.

Also, if you find one reference you like, try using the "Related Articles" link to the right of it.

(Apologies if you're already familiar with PubMed.)

Date: 2008/09/06 12:38:56, Link
Author: qetzal
Quote (Amadan @ Sep. 06 2008,11:54)
This seems like the right place to ask this question.

I'm trying to find a suitable moniker for the Republicans' Happy Couple. The need for this struck me as I was looking at PTET's excellent, sneering coverage of it all.

"Captain Geritol and Polar Barbie"?
"ditto and Igloo Barbie"?
"Fossil Man and Gospel Mama"?
"President POW and The Moose-Meat MILF"?

Your thoughts (FTK, it's in the dictionary)  and suggestions, please.

Let's see. Who do we know that likes to give other politicians nicknames?

I know! Let's get Georgie!

Date: 2008/10/21 19:58:26, Link
Author: qetzal
Personally, I wasn't very impressed with it.

Too many opinions stated as facts, such as:

Regardless of the timing, we know we are in serious overshoot and that the total human footprint (whatever enormity it is) must get smaller.

Arguably true, but not well supported by the article.

Humanity has probably been in overshoot of the Earth's carrying capacity since it abandoned hunter gathering in favor of crop cultivation (~ 8,000 BCE) and it has been running up its ecological debt since that time.

Really? The human population at 8000 BCE was already beyond carrying capacity? That's pretty hard for me to believe, and definitely not supported by anything in the article.

I also think it's exceedingly unrealistic in its prescription:

The best suggestion so far to produce Rapid Population Decline (RPD) is for the collective global human family to adopt a One Child Per Family (OCPF) 'modus operandi/philosophy'. Even with general acceptance of RPD and OCPF, the human population decrease that is necessary to achieve a sustainable solar energy-dependent culture, will take several centuries. Governments, as they become convinced that RPD is necessary, may choose monetary incentives, tax breaks and/or penalties to achieve general acceptance of OCPF or some other RPD program.

Achieving RPD through OCPF would require unprecedented worldwide control over human reproduction, especially if the goal is a world population comparable to 8000 BCE. I don't see that happening any time in the forseeable future, and I think it's foolish to argue for such a 'solution.'

Date: 2008/10/22 12:43:20, Link
Author: qetzal
Quote (Erasmus @ FCD,Oct. 22 2008,09:07)

if carrying capacity is defined as the author uses it then I suspect he may have a point.  a major platform of his argument is that technological innovations have artificially increased carrying capacity K (or perhaps more precisely, have given the illusion of an increased K).  Thus soil fertility, as humans have known it for about 10,000 years, is a product of ecological process and not technological process, then the limiting factors on soil fertility define carrying capacity.

I agree that agriculture enabled much higher populations. But the statement suggested that we began exceeding carrying capacity pretty much as soon as we developed agriculture.

I doubt that's true. Moreover, we should hope it's not. Otherwise, the rapid population decline the authors propose is going to have to take us all the way down to pre-agricultural levels. I think that's impossible to achieve governmentally. Among other things, you won't be able to maintain the necessary world-wide government. Long before you reached such low population levels, the government would become fragmented and regional. Inevitably, some regions would then return to positive population growth, and the authors' implied sustainability point would never be reached.

I don't know what the capacity of Earth really is, given our current and near-future technology. If it's within a factor of ~10 of our current population, then perhaps we can self-regulate world-wide birth rates to achieve and maintain that level. If it's substantially lower, as the authors seem to imply, then IMO, we're headed for a major crash.

Date: 2008/12/05 14:53:54, Link
Author: qetzal
Quote (stevestory @ Nov. 30 2008,12:21)
could drinking heavy water extend your life?

The sidebar at the end of that article contains the following quote:

"Every single atom in the DNA of the brain of a 100-year-old man is the same atom as when he was 15 years old," says Shchepinov (BioEssays, vol 29, p 1247).

That's a stunningly incorrect claim, especially from someone who supposedly has expertise in isotope effects and their potential impact on free radical damage.*

If that quote is accurate (I can't access the original citation), it wouldn't encourage me to trust much of what Shchepinov says.


*For one thing, some of the protons (H atoms) on the DNA bases are sufficiently acidic to exchange with water at appreciable rates. Plus there are many spontaneous acid/base catalyzed reactions that alter the atoms in DNA, including cytosine deamination and depurination, to name two that are especially prevalent.

More important, the guy claims that the isotope effect will help us live longer by slowing damage from free radicals. Surely he realizes that free radical damage often changes the atoms in an affected biomolecule. Does he think DNA in the brain is somehow exempt from such alterations?

I sure hope that's a misquote.

Date: 2009/01/06 17:04:56, Link
Author: qetzal
Quote (stevestory @ Dec. 29 2008,16:29)
This is really distressing news about drugs and studies. Assuming it's true, of course, and that the author isn't some crank.

Having worked on new drug development for some years, I think most of Angell's criticisms in this article are on target. I haven't agreed with some of her previous opinions on pharma, and there are some minor bits in this one that I think are wrong, but I agree with her main points: conflicts of interest and publication bias are serious problems that affect how drugs are prescribed in the US and result in significant detriment to patients.

Date: 2009/06/01 16:24:27, Link
Author: qetzal
Was hiking this weekend at Huntsville State Park (north of Houston) & saw two otters in the lake. They were going down beneath the water lilies and coming back up with crayfish in their mouths. They'd hold their heads up above the water while they crunched on a crayfish, then head back down for another.

Sadly, my wife had taken the camera out of town with her. I didn't even realize otters lived around here!

Date: 2009/06/02 09:22:53, Link
Author: qetzal

I saw them from the boardwalk marked "1" at the top of
this map (warning: pdf). It's basically the northernmost part of Lake Raven, about where Alligator Branch enters.

The lake is shallow there and fairly thick with water plants. I had stopped to watch a great blue heron that was standing motionless among the lilies. I had it in view in my binoculars when I saw some movement among the lilies nearby. At first I thought it was just a smaller water bird, but then saw an otter poke its head up, and then saw a second next to it.

I was pretty surprised to see otters, as I hadn't heard they lived here. But the only other aquatic mammal even close would have been nutria, and these weren't nutria.

Afterwards, one of the park rangers confirmed that they do get a few otters in the lake, but she said they were "few & far between."

Date: 2009/07/28 20:49:30, Link
Author: qetzal
Quote (Perfectly Candide @ July 26 2009,12:44)
I have seen it claimed that humans are born on average with 175 mutations.

I agree with midwifetoad that this sort of argument isn't going to persuade the typical YEC. Many of them won't be able to follow the probability calculations anyway.

But as to the number of mutations per generation, this came up in a recent discussion over on the xkcd forums, where I posted some supporting references. See here.

Bottom line is that current data apparently suggests a slightly lower number, around 130 new mutations per zygote. Which means it would take even longer to accumulate all the mutations we have.

But that's all moot, 'cause God zapped 'em there after Eve made Adam eat that apple, so mutation don't have nuthin to do with it.  :p

Date: 2009/09/01 20:56:07, Link
Author: qetzal
Quote (jeannot @ Sep. 01 2009,10:57)
Quote (afarensis @ Aug. 28 2009,19:19)
Quote (Erasmus @ FCD,Aug. 28 2009,13:34)
they're still just mice.


wake me up when one gives birth to a dog-cat.

I'm holding out for a fishungulant myself - part barracuda, part moose, and all Sarah Palin!

Talking about hybridization, there's a bizarre paper on the early edition of PNAS.

"Caterpillars evolved from onychophorans by hybridogenesis"

Yes, you read it right. (for your info, onychophorans are not even arthropods)
I find it quite disturbing. The author (Donald Williamson) proposes that some larvae and their adults do not have a shared ancestry, but that larvae (namely caterpillars) were acquired by hybridization with distant taxa.
Although the hypothesis is testable, it seem extremely far-fetched, and in any case, not tested in the paper. So the title is highly misleading.
This reminds me of some JAD's paper, the guy does not seem to like Darwin either.

How could such paper pass through the editorial board?  

Must be because it's PNAS, and it was communicated by Lynn Margulis. PNAS gives academy members special rights to communicate papers and more-or-less bypass 'normal' peer review. From the PNAS Info for Authors page:

An Academy member may “communicate” for others up to 2 manuscripts per year that are within the member's area of expertise. Before submission to PNAS, the member obtains reviews of the paper from at least 2 qualified referees, each from a different institution and not from the authors' or member's institutions. Referees should be asked to evaluate revised manuscripts to ensure that their concerns have been adequately addressed. The names and contact information, including e-mails, of referees who reviewed the paper, along with the reviews and the authors' response, must be included. Reviews must be submitted on the PNAS review form, and the identity of the referees must not be revealed to the authors. The member must include a brief statement endorsing publication in PNAS along with all of the referee reports received for each round of review. Members should follow National Science Foundation (NSF) guidelines to avoid conflict of interest between referees and authors (see Section iii). Members must verify that referees are free of conflicts of interest, or must disclose any conflicts and explain their choice of referees. These papers are published as “Communicated by" the responsible editor.

I assume Margulis is an NAS member. Still, it's pretty bizzare that she would agree to communicate such nonsense, or that she was able to find two qualified referees to agree that it should be published!

Date: 2009/09/18 13:56:51, Link
Author: qetzal
Remember the PNAS paper that argued that caterpillars and butterflies used to be different species? Jeannot first linked it here.

Turns out PNAS is changing their submission policies so that papers like this can no longer avoid standard peer review. See this post at Sandwalk for more details.

Date: 2009/09/18 17:17:58, Link
Author: qetzal
I think they couldn't reject it as long as Margulis could submit two favorable reviews. I don't have access to the Science article, but Larry Moran at Sandwalk quotes it as saying the following:

He {Williamson} also says he knows that Margulis sent his paper to a half-dozen academy reviewers. Williamson says that he thinks they were all positive reviews, but Margulis told Scientific American last week that she canvassed six or seven reviewers to find the two positive reviews necessary to push the paper through.

Sounds like their hands were tied under their existing policies, which is no doubt why they're changing them.

Date: 2009/12/12 01:22:01, Link
Author: qetzal
For my 50th birthday a few weeks ago, my wife took me to Costa Rica. We stayed at a rental villa owned by some friends. (Very close to where dhogaza was, between Cartago & Paraiso.)

Here are some wildlife pics. Please excuse the extreme and obvious amateurism of the photographer!

I caught his little guy (gal?) running across the volcanic sand at Volcan Irazu. Don't know what kind of lizard this is.

White nosed coati (Nasua narica) that was cruising the parking lot at Volcan Irazu, hoping to beg and/or steal something to eat.

Brilliant blue bug seen at Braulio Carillo National Park.

Another lizard, this one from Braulio Carillo. Again, don't know what kind.

Collared aracari (Pteroglossus torquatus, Braulio Carillo).

Terciopelo, aka fer de lance (Bothrops asper), also from Braulio Carillo. It was coiled right on the edge of the trail, but I didn't even see it. I literally stepped right over it. My wife saw it as she stopped to look at something else. And that was after I'd been assuring her we were extremely unlikely to see any snakes! Good thing I didn't step on it!. They're supposed to be pretty aggressive, but this one was very docile. Even when prodded with a (long) stick, it merely slithered into the bushes.

Green vine snake (Oxybelis fulgidus; rear-fanged, mildly venomous). This guy was crossing the trail further along at Braulio Carillo. He kept his body very straight and elongated as he crossed, with very little serpentine motion. Also, his tongue was stuck out straight like that the whole time we watched him.

There are a few others I’ll try to post soon.

ETA: Alas, no. No quetzals. Sigh.

Date: 2009/12/13 13:53:28, Link
Author: qetzal
Quote (Lou FCD @ Dec. 12 2009,07:37)
They're awesome shots, qetzal! I think I'd have wet my boxers, having realized I'd just stepped over a Fer-de-Lance.

I didn't realize that’s what it was until later that evening, when I had a chance to look it up. Even then, it was pretty sobering to think about!

According to Wikipedia, Bothrops asper is one of four different species that are sometimes called “fer-de-lance.”

Quote (Kattarina98 @ Dec. 12 2009,08:16)
You did what????

Well, in my defense: 1) I didn’t know it was a fer-de-lance at the time. 2) I wanted to get a shot of its belly, since that sometimes helps with identification:

And 3) I was in complete control at all times. If he had made the slightest move toward me, I was quite prepared to sprint screaming in the opposite direction. And from the way he slunk off, I think he knew it:

The ranger station at Braulio Carillo had a huge colony of golden orb weaver spiders (Nephila clavipes). I don’t know how well you can see in this shot, but there were dozens of big females and who knows how many small males inhabiting an enormous complex of interconnected webs. The whole thing was probably 10ft wide by 8ft high by 6ft deep!

Here’s a close up of one of the larger females:

A few days later, we drove south to the Boruca Indian reservation. On the way, we saw this sign:

I was hoping to see some wild monkeys, but if that’s the kind of freaky, Island-of-Dr.-Moreau-looking monos they’ve got, I’m glad there weren’t any cruzan la via near me!

On the dirt road to the Boruca, we saw this laughing falcon (Herpetotheres cachinnans) sitting on top of a dead palm:

And this scorpion (maybe Centruroides margaritatus?):

The last morning, as we were headed to the airport, we managed to get a shot of a blue-crowned motmot (Momotus momota). (It was back-lit, and I haven’t learned how to compensate for that, so I had to increase the brightness a lot to make it visible in the image; that’s why the pic looks so washed out.)

Date: 2009/12/14 20:42:51, Link
Author: qetzal
Quote (dhogaza @ Dec. 14 2009,18:20)
Qetzal ...

White nosed coati (Nasua narica) that was cruising the parking lot at Volcan Irazu, hoping to beg and/or steal something to eat.

Wow, that was probably one of the coatis we saw at Volcan Irazu.  When we were there, one of the little bastards darted into the little cafe/store there, jumped up and started eating someone's food (the someone went screaming in the opposite direction, it was really quite hilarious).

We were there November 3rd ... you weren't the clueless tourist feeding them, were you? (just kidding)

Yeah, he (?) definitely looked like a regular. In fact, we had bought a couple of T-shirts in the gift shop, and when we set them down on the picnic bench, he suddenly rushed up and started ripping into the bag! He was clearly hoping there was food inside.

But no, that wasn't us on the 3rd. We were there in mid Oct.

Date: 2010/02/09 22:28:42, Link
Author: qetzal
Quote (Joy @ Feb. 09 2010,16:30)
My only thought on abiogenesis is that I would like to believe life is intentional rather than accidental. It struggles too mightily to stay alive - even when it knows it's doomed, at this end of the scale - as if it had purpose. A reason to be.

Perhaps. Another explanation is that any kind of life that doesn't struggle mightly to stay alive and reproduce doesn't exist for very long, and doesn't leave any descendents for us to observe.

The advantage of this explanation is that it doesn't require any higher-order knowledge by life. No knowledge that it's 'doomed' or that it has a purpose. Kind of hard for me to see how bacteria could know they were doomed or had a purpose, especially a few billion years ago when they were the only life in existence.

Note: I'm not claiming this as evidence against a purpose to life. Only that it's not evidence for a purpose.

That fits nicely into my metaphysical views.

Do you consider that a reason to believe it?

Date: 2010/02/10 12:07:25, Link
Author: qetzal
Quote (Joy @ Feb. 09 2010,23:35)
Note: I'm not claiming this as evidence against a purpose to life. Only that it's not evidence for a purpose.

That's why I qualified the statement to "this end of the scale." While all life forms we know of act/react to stimulus (process information) and display some signs of volition - jury's still out on viruses as life forms - not all life forms are 'conscious'. According to the Hameroff-Penrose model, there is a numerical quantification for the appearance of that phenomenon.

I'd argue in favor of all conscious life forms having 'purpose' (to include self-purpose), even if it seems trivial to us.

So only conscious life necessarily has a purpose, but that purpose might be nothing more than 'survive and reproduce.' Is that what you're saying? If so, how does that support your belief that life is intentional? As I already noted, the 'purpose' of surviving and reproducing can be readily explained without supposing that the first life arose through intentional agency.

Quote (Joy @ Feb. 10 2010,10:02)
Just have to chuckle sometimes at the stubborn refusal of biologists to credit anything to physics.

Weren't you the one arguing that life requires more than just a specific arrangement of atoms? Seems to me that's the ultimate refusal to credit physics.

But I'll guess that you're referring more to stuff like Penrose-Hameroff, right? The thing is, biologists are more than happy to credit physics when the empirical evidence supports it. Last I knew, Penrose, Hameroff, and others like them were still at the hand-wavy speculation stage, with their ideas about quantum consciousness, Orch-OR, et al. I'm not aware that they've developed any significant evidence to support such ideas.* If they ever do, I'm confident that biologists will take more notice.

Might still take a while, of course, due to differences between disciplines, inertia, etc. But saying that biologists refuse to credit physics strikes me as either ignorant or disingenuous.

*If you think otherwise, feel free to provide a link. But please, no links about how microtubules might do this or might collapse that. If there's evidence that they really do that, and that it is related to consciousness, great - let's see it. Otherwise it's still hand-wavy speculation, and isn't (yet) deserving of significant credit from anyone.

Date: 2010/02/10 14:22:53, Link
Author: qetzal
Quote (Joy @ Feb. 10 2010,12:25)
Judging from the number of dumb assumptions and inane assertions I've seen so far in this thread....

Joy, are you familiar with the parable of the mote and the beam?

Date: 2010/02/10 17:14:07, Link
Author: qetzal
Quote (Joy @ Feb. 10 2010,16:05)
As I already noted, the 'purpose' of surviving and reproducing can be readily explained without supposing that the first life arose through intentional agency.

Survival and reproduction are trivial considerations of 'purpose' beyond any given individual's ability to contribute to the gene pool (intentionally or not). Possibly pertinent to the process of evolution, not necessarily pertinent to the 'purpose' of life itself.

My question was whether "survive and reproduce" was sufficient to constitute "purpose" as you define it. Your failure to actually answer is duly noted.

Once more, I don't know how "first life" arose and honestly don't give a shit because it affects my life not at all. In fact, that unanswerable question affects no one's life in the here and now (except a handful of abiogenesis researchers). So I sure don't know why any of you believe it's some sort of effective religion-slayer. Mere Dueling Metaphysics. Ho, hum.

I never said anything about abiogenesis being a religion-slayer. Also, weren't you just admonishing us about making dumb assumptions? Your double standard is duly noted.

In any case, I only raised the question because you said:

I would like to believe life is intentional rather than accidental.

If you no longer give a shit, that's fine with me.

Since you're uninterested in research on PCCs [MTs/MAPs*] I guess you'll just have to wait on something that grabs your attention. And much of the active research is in the proprietary realm these days anyway. Guess Big Pharma knows a promising direction when it sees one. Lord knows we've all been waiting on the "Really Good Drugs" all our adult lives... §;o)

When did I ever say I was uninterested in any of that? More dumb assumptions, I guess.

As for your links, are you actually suggesting that they support Orch-OR or any other quantum consciousness type claims? Guffaw!

The first one attempts to explain the effects of gravity on assembly of microtubules. The second is a computer model of how the C-terminus of tubulin might behave. Neither one provides any test of its ideas. More importantly, neither one provides evidence to support Orch-OR or anything similar. That you offer them as such suggests you really don't understand what you're talking about. Either that, or you're just hoping I'll be cowed by a couple of random papers about microtubules.

Also, if you think pharma is pursuing microtubules because they believe in quantum consciousness, you're seriously deluded.

Feel free to continue with your buffoonery. I've had enough.

Date: 2010/02/11 17:45:16, Link
Author: qetzal

I don't claim any particular insight into metaphysics. Definitely not my area of expertise. But for the sake of discussion, my thoughts are these.

If we define "purpose" as something like "a function or outcome anticipated by some intentional agent," then I see no reason to believe that the universe has a purpose. However, I also think possible that the universe could have a purpose without any of us being able to discern as much.

Is life and consciousness required for purpose? I think that depends. Again, if we're going to define "purpose" as above (which I think is the intuitively obvious definition), then there has to be some intentional agent involved. Even then, however, I see no obvious requirement that a universe with purpose must contain life and consciousness. The intentional agent that defines the universe's purpose could be outside the universe itself. In that case, the universe would only need to contain life and consciousness if that's what the outside intentional agent demanded. Obviously, we would (probably) have no way to know about any of that.

Even if we somehow concluded that life and consciousness are required for whatever purpose the universe is supposed to have, I don't see how that supports a metaphysical presumption that life is more than just a collection of materials. Maybe the purpose of the universe is to entertain the outside intentional agent, and he is only entertained if the universe contains life and consciousness. In that case, why would life need to be more than matter?

Date: 2010/02/12 17:30:22, Link
Author: qetzal
TP, you originally wrote:

Is life and consciousness a necessary precondition for purpose?

If so, it would lead to a metaphysical presumption that somehow life is more than just a collection of material and chemicals.

As written, it sounds to me like you are actually claiming that the first statement logically implies the second. If so, I disagree. However, if your point is only that many people arrogantly assume that life is more than material, then I agree.

In many games (e.g. World of Warcraft) there are AI objects programmed with the “intent” of killing player characters.  A similar example is a Windmill with the “intent” of pumping water.  Do these things only quality as having purpose because a special clump of matter imbued the non-living thing with this special characteristic?

Like you said, it depends on how one defines purpose. If purpose is defined as something that only conscious living organisms can have, then people can have it and windmills can't.

FWIW, I doubt that "purpose" really exists in the sense that most people seem to mean it. That is, people may (or may not*) have intent, but I doubt that people (or anything else) have a purpose in the sense of some duty or goal or expectation that has been established for them by some outside intentional agency (e.g. God).

*You've noted the issues of randomness, determinancy, & free will, but that's much further down the rabbit hole than I care to fall today.

Date: 2010/02/14 13:47:17, Link
Author: qetzal
Quote (Thought Provoker @ Feb. 12 2010,19:47)
It was my intent to suggest the first statement (purpose requires living consciousness) would lead to a presumption living consciousness is something special.

It would be a logical default position, IMO.

Special? I wouldn't say that. All it means is that living consciousness is essential for purpose. (And from my perspective, that's really just a matter of definition anyway.)

It wouldn't imply that living consciousness is somehow 'special' as far as the universe or a hypothetical god is concerned, if that's what you're suggesting.

Date: 2010/02/14 14:14:27, Link
Author: qetzal
Quote (Reciprocating Bill @ Feb. 08 2010,22:32)
As I read Robert Pennock, he equates the "natural" in "methodological naturalism" with those phenomena that are within the reach of the empirical sciences.

I agree with this. In fact, I don't like the term 'methodological naturalism' at all. It's misleading, IMO, because there's too little agreement on what 'naturalism' and 'natural' mean.

Can science investigate the supernatural? Some say sure; for example, science can investigate the possible existence of ghosts, or the healing power or prayer. But others say no, science can't investigate the supernatural, because anything truly supernatural is outside of the realm of science by definition.

Thus, I think it's confusing to say the science practices methodological naturalism, or that it confines itself to studying the natural. Rather, science confines itself to the study of things that can be observed empirically, objectively, reliably, predictably, etc. I'm not sure what single word best captures all of that, but 'natural' is not it.

From that perspective, science can study ghosts or gods or pixies if any of them have observable, predictable effects that we can detect empirically. If they don't ever have such effects, science can't study them.

Of course, if something has no observable, predictable effects that we can detect empirically, even in principle, does it even exist for us? I would argue it probably doesn't, but that's a different discussion.

Date: 2010/02/15 10:56:27, Link
Author: qetzal
Quote (Thought Provoker @ Feb. 14 2010,14:50)
It probably comes down to semantics and stating the obvious.  If consciousness is required for intent then consciousness is a special quality because it is required for something to have intent.

I did not mean in-the-image-of-God type special.

OK, but I still don't know why you say that consciousness is a special quality. I get the impression that your use of "special" implies more here than simply "required for something to have intent." If so, could you please elaborate?

As for your subsequent questions, I agree that many living things are conscious to some degree, at least as we usually define that term. I don't think there is any clear threshold between conscious and non-conscious. It's a continuum, as fnxtr said. From your list, I'd say that consciousness and intent definitely exist in humans, monkeys, & dogs. Definitely not in viruses or bacteria. Almost certainly not in ants.

As I've already said, however, I don't think that consciousness is "special" in any fundamental way. It's an exceedingly interesting phenomenon, of course, but I'm certainly not convinced it's some sort of essential underlying property of the universe.

Thus, if someone wants to argue that ants and bacteria are also conscious in some way (perhaps because they define "conscious" somewhat differently than I), I'd say OK, that's interesting, but so what?

Date: 2010/02/15 14:11:17, Link
Author: qetzal
Quote (Thought Provoker @ Feb. 14 2010,21:41)
I generally don't like it when people try to create their version of reality, especially when it involves worshipping deities.

However, every now and then, I realize that believing a lie or being overly optimistic is exactly what is needed.

Honest question: are you trying to make a point about methodological naturalism or anything else relevant to this thread's topic? If so, I'm afraid I'm missing it.

(Note - I don't object to banter, if that's all you're doing. For whatever reason, I keep thinking your statements imply more than you may have intended. No offense meant.)

Date: 2010/02/15 17:25:50, Link
Author: qetzal
Quote (Thought Provoker @ Feb. 15 2010,15:25)
So, do you presume consciousness (the ability to have intent) is algorithmic or not?

Algorithmic, I suspect. However, I'm not sure I adequately understand everything that might be implied by the term 'algorithmic.' So, to answer another way, I think it will some day be possible for humans to create 'from scratch' entities that have consciousness and intent that are not fundamentally distinguishable from the consciousness and intent that humans or other animals possess now.

Even if consciousness and intent arise from quantum effects in some 'special' way, and even if that means they are non-algorithmic, I still expect that they are properties that arise automatically from certain arrangements of matter and energy. If you create the appropriate arrangement of matter and energy de novo, I expect it will be conscious and have intent.

I assume there is nothing 'magic' about consciousness. It doesn't require some sort of soul bestowed by a deity. The mind is what the brain does, and all that.

I'm not absolutely committed to any of that, though, because we simply don't understand mind or consciousness very well. If someone could present strong evidence in favor of mind-body duality, for example, I'd be willing to reconsider.

Date: 2010/02/20 21:32:01, Link
Author: qetzal
Quote (Lou FCD @ Feb. 20 2010,14:29)
I just got my acceptance letter to UNCW. I'm kind of tearing up. It's dumb I guess, but there you go.

Very, very hearty congrats, Lou!

Date: 2010/02/22 15:46:12, Link
Author: qetzal
Quote (BWE @ Feb. 21 2010,21:30)
I've never managed to get a single quality assignable to god out of a believer....

That's easy: existence!

I suppose next you'll be complaining about the definition of existence. Sheesh!


Date: 2010/02/24 10:05:22, Link
Author: qetzal
It all boils down to two fundamental problems:

1. ID is not supported by the scientific evidence.

2. To date, pretty much every attempt to teach ID has been motivated by the desire to sneak religious creationism back into science class.

Both of those are excellent reasons it should not be taught as science in public classrooms. It could accurately be taught as an example of the so-called 'culture wars,' except I don't think any cdesign proponentsists want it taught that way.

Date: 2010/02/24 17:30:34, Link
Author: qetzal
Quote (Joe G @ Feb. 24 2010,10:47)
All experiments and observations support baraminology.

There isn't any experiments that support universal common descent via an accumulation of genetic accidents.

Yep, he's right. I did an experiment today where I labeled some protein. You know what I found? Baraminology!

How fitting that Joe G's avatar is a cartoon character. Are we sure he's not a poe?

Date: 2010/02/25 17:30:49, Link
Author: qetzal
Quote (Thought Provoker @ Feb. 25 2010,16:20)
Do you think Roger Penrose needed empirical evidence before he was convinced Black Holes existed?

I realize this doesn't really matter for your overall point, but yes, Penrose needed and had empirical evidence before he was convinced black holes existed. He needed evidence about the behavior of matter and gravity.

Everything in science is based on empirical evidence. Even when someone postulates something that has never been observed, it's still based on things that have been observed.

Date: 2010/02/25 21:39:15, Link
Author: qetzal

I fear you learned the wrong lesson from that experiment. It's never about knowing the answer before you run the experiment.

Fuzzy models are fine in many situations, especially if they help to generate better hypotheses. However, fuzzy models are only good if they adequately fit the empirical evidence. If your model insists on A but the evidence clearly shows B, the evidence wins. (That's one of my presumptions.)

Date: 2010/03/26 17:06:40, Link
Author: qetzal
Quote (lkeithlu @ Mar. 26 2010,16:25)
Ooooohhh you bad guys are in trubble now. They are meeting in their secret lair, planning to inflict the ultimate smackdown on all of you with their super-secret-ID-mechanistic-dot-connecting-dr-dr-dr-theory. You should be shaking in your boots. Just you wait.

More fart-noise videos? Dolls with nooses around their necks?

Date: 2010/03/28 12:21:11, Link
Author: qetzal
We seem to have a red-shouldered hawk* nesting near us. It (or one of them?) perches on our back fence occasionally.

*Red-shouldered seems likeliest, based on this site. The call is certainly identical.

Date: 2010/03/29 08:53:50, Link
Author: qetzal
Actually, we're north of Houston.

I'm guessing these hawks show geographical variation then?

Date: 2010/03/29 18:23:32, Link
Author: qetzal
Quote (Thought Provoker @ Mar. 29 2010,17:29)
On the positive side, I wasn't aware C.S.Lewis was the creator of the "Lord, Liar, or Lunatic" trilemma.  At least I learned something new.

Not surprisingly, Lewis is guilty of a false trichotomy. A more complete version would be Bart Ehrman's tetralemma:

"Lord, Liar, Lunatic, or Legend"

Date: 2010/03/30 20:35:34, Link
Author: qetzal
After all, the evolution controversy reaches into the very heart of both faith and science.

Except that it doesn't. It reaches into the heart of certain faiths that insist that humans are extra-special independent creations of God.

But so what? Should we also conclude that the heliocentrism controversy reaches into the very heart of both faith and science, just because certain (mostly-extinct) versions of faith insisted that the Sun revolved around the Earth?

Quite frankly, I'm amazed that Collins can be a good scientist when he obviously has such dismal ability to reason. My guess - he's not actually a good scientist, so much as a good science administrator.

Date: 2010/03/31 18:15:54, Link
Author: qetzal
Quote (Doc Bill @ Mar. 31 2010,15:52)
Ever since they turned on that thing I've been unable to find my car keys.

Coincidence?  I think not.

You're right - I can't find your car keys now either!

Date: 2010/03/31 18:51:01, Link
Author: qetzal
Well I'm not gonna look there!


Date: 2010/04/07 09:14:26, Link
Author: qetzal
Anaerobic multicellular animals!

Here's the abstract:

Several unicellular organisms (prokaryotes and protozoa) can live under permanently anoxic conditions. Although a few metazoans can survive temporarily in the absence of oxygen, it is believed that multi-cellular organisms cannot spend their entire life cycle without free oxygen. Deep seas include some of the most extreme ecosystems on Earth, such as the deep hypersaline anoxic basins of the Mediterranean Sea. These are permanently anoxic systems inhabited by a huge and partly unexplored microbial biodiversity.

During the last ten years three oceanographic expeditions were conducted to search for the presence of living fauna in the sediments of the deep anoxic hypersaline L'Atalante basin (Mediterranean Sea). We report here that the sediments of the L'Atalante basin are inhabited by three species of the animal phylum Loricifera (Spinoloricus nov. sp., Rugiloricus nov. sp. and Pliciloricus nov. sp.) new to science. Using radioactive tracers, biochemical analyses, quantitative X-ray microanalysis and infrared spectroscopy, scanning and transmission electron microscopy observations on ultra-sections, we provide evidence that these organisms are metabolically active and show specific adaptations to the extreme conditions of the deep basin, such as the lack of mitochondria, and a large number of hydrogenosome-like organelles, associated with endosymbiotic prokaryotes.

This is the first evidence of a metazoan life cycle that is spent entirely in permanently anoxic sediments. Our findings allow us also to conclude that these metazoans live under anoxic conditions through an obligate anaerobic metabolism that is similar to that demonstrated so far only for unicellular eukaryotes. The discovery of these life forms opens new perspectives for the study of metazoan life in habitats lacking molecular oxygen.

Link to full text

Link to some commentary

Link to more commentary

HT: The Scientific Activist

Date: 2010/05/22 12:21:56, Link
Author: qetzal
As a communication engineer I know - with 100.000000000%
certainty - that this is impossible.

Nowhere in the vast field of engineering is there any such
thing as "the percentage of the time that corrupted data is
helpful instead of harmful."

It's ALWAYS harmful. Always. Copying errors and data
transmission errors never help the signal. They only hurt

Excellent disproof by sledgehammer. But empirical disproofs aren't even needed. This is simply logically false. The only way that modifying data can ALWAYS be harmful is if you assume the data starts out PERFECT. But as any competent engineer knows, data is rarely (if ever) perfect.

Of course, we know what kind of person assumes that all organisms were initially created perfect.

Date: 2010/06/21 22:17:03, Link
Author: qetzal
Does anyone else think that Denyse O'Leary is secretly Anne Elk (or vice versa)? Or is that just me?

Date: 2010/07/21 13:26:06, Link
Author: qetzal
Quote (Kattarina98 @ July 21 2010,04:45)
The article says they have discovered a new species found only in this glacial lake - that means the species can't be older than 10 000 years.

I hate to be pedantic,* but since this is the Science Break thread, I feel compelled to point out that the above species could actually be very old and merely died out everywhere else after colonizing that lake.

*OK, yes, I actually enjoy being pedantic, to the frequent annoyance of my wife.

Date: 2010/08/17 22:17:38, Link
Author: qetzal
Quote (Zachriel @ Aug. 17 2010,12:35)
Quote (socle @ Aug. 17 2010,12:13)
Quote (Zachriel @ Aug. 17 2010,11:59)
Sometimes Joe G is just plain funny.


Here's part of my response to that, still in moderation:

Sheik:  The short answer is, you can't hold the empty set in your hands. It's like I'm talking to a materialist here. :D The empty set is an abstract entity.

Joe G: But how big does the box have to be in order to hold nothing?

Not by weight, but by volume!

What if the contents have settled during shipping?

Date: 2010/08/23 11:33:13, Link
Author: qetzal
Quote (Zachriel @ Aug. 23 2010,07:15)
Or is he confused...?!


Date: 2010/11/30 16:01:30, Link
Author: qetzal
Quote (Thought Provoker @ Nov. 24 2010,13:10)
DNA = Quantum Computers?

Some 2010 papers on that...

DNA Replication via Entanglement Swapping

The relevance of continuous variable entanglement in DNA

Enol Tautomers of Watson-Crick Base Pair Models Are Metastable Because of Nuclear Quantum Effect

EDIT - fixed title of third paper

Interesting papers; thanks for the links!

However, I'm not sure what they have to do with quantum computers. They describe how quantum effects may be important in base pairing, replication, & duplex stability. I don't see the relevance to quantum computing, other than perhaps "computing" which bases should pair with one another.

Date: 2010/11/30 19:54:27, Link
Author: qetzal
Thought Provoker,

Sorry, I still don't see how any of that suggests that DNA is any sort of quantum computer.

BTW, we discussed that Patel paper in a previous thread. I can't speak to the math, but the biochemistry & molecular biology are incredibly wrong. Makes it hard for me to take any of the rest seriously.

Date: 2011/01/13 21:55:17, Link
Author: qetzal
Quote (Seversky @ Jan. 13 2011,17:42)
Quote (Richardthughes @ Jan. 13 2011,13:38)
DNA teleportation WTF:

Sounds like a variant of Jacques Benveniste's claims about water 'memory'.

Not teleportation. Just plain old vanilla cross-contamination in their PCR. (The only other conceivable explanation is deliberate fraud.)

Montagnier has previous published claims wherein highly diluted DNA supposedly emits "electromagnetic signals" when placed inside a special apparatus. According to that paper, the apparatus was based on a design by none other than Jacques Benveniste!

Not sure if this device is the same one, but it sounds similar.

Sadly, it seems that Montagnier has gone down the same path as Pauling and Duesberg - once-brilliant scientists who become cranks in their old age.

Date: 2011/01/22 22:11:20, Link
Author: qetzal
Quote (Kris @ Jan. 22 2011,21:18)
Virtually every day some scientist comes up with some new theory or hypothesis or speculation or inference about something and many of them are not testable with empirical evidence and are no more provable or falsifiable than ID or creation by an intelligent entity.


Why aren't you guys bitching about those so-called theories, hypotheses, speculations, or inferences?

Because even if you were right about all these scientists making unfalsifiable claims, they don't insist that their ideas should be given equal time in public schools, or that their ideas are just as well-supported by the facts as bona fide scientific theories like evolution.

Just to let you know, it's not only Judeo-Christians who think there is or could be a creator and/or designer. Just ask some American Indians, for example.

They're welcome to think it as much as they like. As long as they're not trying to get their opinions taught as legitimate scientific theories, or trying to force others to pretend their opinions are anything more than that, their beliefs don't bother me at all.

Date: 2011/01/23 08:48:34, Link
Author: qetzal
Quote (MadPanda @ FCD,Jan. 22 2011,22:29)
There you go, being all reasonable and stuff.

I'm sorry - was that wrong? Should I not have done that?


Date: 2011/01/23 19:12:00, Link
Author: qetzal
Quote (Louis @ Jan. 23 2011,09:10)
It's intolerance like that that makes you worse than Hitler you baby eating atheist Darwinist persecution loving bastard.

{shakes fist}


Guilty on all counts. Oh, except the baby-eating. I'm baby-meat-intolerant. It's so embarassing to have to ask for beef or pork when everyone else at the secret atheist Darwinist Nazi barbecue is enjoying sweet, succulent baby.

Date: 2011/01/24 10:43:08, Link
Author: qetzal
Kris writes:
Quote (Kris @ Jan. 23 2011,21:54)
Why not just remove such a hypocritical, dishonest rule and replace it with a truthful one like: *Attacking religious beliefs is the only purpose of this site. Anyone who does not regularly attack religious beliefs and the people who adhere to them will be insulted, attacked, ridiculed, and probably banned.*

Dale_Husband responds:
Quote (Dale_Husband @ Jan. 23 2011,22:32)
Because that's not true. We don't necessarily attack Christianity itself, only Christians who are delusional about what science is or should be.

Kris then quotes the above exchange verbatim, and replies:
Quote (Kris @ Jan. 24 2011,02:43)
Dale, your responses are so far off track and so irrelevant to what I said that they're not worth responding to, except by saying this:

You're a moron.

Seriously? You don't think Dale's response was relevant to your statement? Perhaps you need to take a breath and actually read what people are saying.

P.S. To the best of my knowledge, I have never "regularly attack[ed] religious beliefs and the people who adhere to them." Yet strangely, I've never been "insulted, attacked, ridiculed, [or] banned." Not by the PT regulars or moderators, anyway.

Date: 2011/04/04 19:54:36, Link
Author: qetzal
It's getting to be all birds, all the time around here! For a brief respite, here's a little fella (or gal?) that was on our gazebo the other day. Green tree frog (Hyla cinerea cinerea), I believe. Not much of a photo, esp. since it was taken with my iPhone, but I liked the pose.

Date: 2011/05/29 11:50:22, Link
Author: qetzal
This little green anole (Anolis carolinensis) managed to get caught by the tail in the web of a basilica orbweaver (Mecynogea lemniscata).

After snapping a few pics, I helped him (her?) wriggle free. Probably ruined the orbweaver's big Memorial Day family reunion. ("Sure! Everybody come to my web this year. We'll do lizard!")

Last month, I had the great pleasure of seeing a bald eagle at the lake near our house north of Houston. I saw it several times, but the only pics I could get were from far away - either perched on the opposite side of the lake or soaring. These were taken at maximum zoom, and have also been cropped and enlarged 6-fold. They're very low quality, but we don't get many eagles around Houston, so I was still really happy to get them!

Date: 2011/08/21 12:52:59, Link
Author: qetzal
I'm pretty sure it's a type of moth.

ETA: Looks like it's probably a plume moth. What's that bug is a great site I know for these kinds of questions.

Date: 2011/11/11 11:26:30, Link
Author: qetzal
I hope you'll pardon me for jumping into an ongoing discussion.

Quote (Southstar @ Nov. 11 2011,08:56)
Okay I get it but supposing we do some tests on generations of Drosophila, cause they're quite easy to breed and we can do a nice time lap test on them.

But instead of doing it out in the open we do it in in a lab, where the happy flies have really eveything they need. Esentially what we are doing here is eliminating natural selection.

Actually, no. You'd just be changing the selective pressures, because you've altered the environment. Any genotype/phenotype that gave a fly an advantage in this new lab environment would still be selectable (and selected). You could argue that it's artificial (human-caused) selection instead of natural selection, but that's really just semantics.

Quote (Southstar @ Nov. 11 2011,10:09)
What it boils down to is that, in the absense of natural selection, do speices evolve randomly.

Yes. It's called genetic drift. Even when there's no selective pressure at all, a certain fraction of new mutations will get fixed in a population over a given period of time. Depends on breeding population size and mutation rate.

Date: 2011/11/14 20:14:18, Link
Author: qetzal
I was confused by this passage from the penultimate paragraph of Bard's review:

Complex systems have properties that cannot be pre- dicted, albeit that they can be understood with hindsight, and it may well be that the network for some trait (e.g. bone growth or pigmentation pattern) in the offspring has quantitative properties that are very different from those of the parents, not because of new mutations but because the novel mix of the rate constants will yield a trait that is an outlier of the normal distribution (known as a sport in breeding circles). As a result, the offspring may be able to colonise a novel environment far better than its peers. Equally important, this variant will naturally be heritable because it derives from the kinetics of the network (minor variation) rather than additions or losses to the proteins that comprise them.

I understand and agree that a novel combination of existing alleles could result in the offspring having a novel phenotype due to particular network interactions. But how would that novel phenotype be heritable? If it depends on an unlikely combination of alleles, it's not likely to recur in the subsequent generation.

And even if it did result in selective fixation of the relevant combination of alleles, how does that go beyond existing evolutionary theory?

I feel like I must be missing something, but I'm not sure what.

Date: 2011/11/16 11:26:11, Link
Author: qetzal
Quote (Dr.GH @ Nov. 16 2011,07:07)
Quote (midwifetoad @ Nov. 16 2011,00:24)
Shapiro plays at  being L'enfant terrible, but he doesn't seem stupid enough to assert that variation anticipates need.

He seems to take an extreme position on evolvability and seems to assert that there are mechanisms to increase certain kinds of mutations as a response to stress.

There are in bacteria. Under heat stress, or antibiotic attack, error checking during DNA replication is turned (nearly) off in bacteria (and archaea?) generating huge mutation rates.

This could be why bacteria are so successful. But, this approach would obviously destroy any metazoans.

There are certainly mechanisms that increase mutation rates under stress. But is there evidence that such increased mutation is actually adaptive? Or is it merely an unavoidable consequence of things like needing to relax proofreading in order to replicate damaged DNA?

Shapiro definitely thinks it's adaptive. He even goes so far as to claim that:

Large-scale genome-wide reorganizations occur rapidly (potentially within a single generation) following activation of natural genetic engineering systems in response to a major evolutionary challenge. The cellular regulation of natural genetic engineering automatically imposes a punctuated tempo on the process of evolutionary change.

This does seem to flirt with ideas like front loading and purposeful evolution. Perhaps he's merely being excessively metaphorical, but I don't see any sense in which individual organisms can be properly described as responding to evolutionary challenge.

He also ignores the seemingly insurmountable issue of how such mechanisms could apply to large organisms. Individual cells in our bodies might respond to stress in some of the ways Shapiro suggests, but there's no known mechanism to allow "successful" responses in a somatic cell to be transmitted to the germ cells.

Date: 2011/11/17 12:39:00, Link
Author: qetzal

Your friend Ioseb may claim to be a scientist, but he(?) doesn't sound like he knows what he's talking about. He mentions "Malaria or HIV plasmoid." No such things. Malaria is the disease caused by a parasite called Plasmodium. HIV is a virus. Neither one is a plasmid, which is a form of self-replicating DNA.

He says Sequence A produces Protein B through replication, transcription, and translation. Wrong! Replication is not involved in going from DNA sequence to protein. Replication of Sequence A just gives you more copies of Sequence A.

As for this:

Please note that the modification of a nucleotide is an extremely rare event, 2 nucleotides are immensly rare, 3 are astronomicaly rare, 4 are next to impossible.

The average human baby's DNA contains ~100 new mutations that weren't present in either of it's parents (

Plus he's still dodging your question of how to quantitatively measure information in a DNA sequence. He says it's based on the number of kilobase pairs and the number of mutations, but that's hand waving. Which has more information, in his opinion - sequence 1: AAAAAAAAAAAA, or sequence 2: ATGACCGACTAG? They're the same length, so do they have equal information? What if the first base of each is mutated to a C. How much has the information in each sequence changed? Just one A-to-C mutation in each, so it must be the same amount, right?

Sorry, but Ioseb is talking gibberish.

Date: 2011/11/20 09:50:50, Link
Author: qetzal
I enjoyed these bits from Luskin's article:

If the trait evolved multiple times independently, then why do so many plants still lack such a "lantern" protective shelter?

Ah, yes. The old 'if evolution is true, how come humans haven't evolved wings' ruse. Just because a trait evolves and is selected for in some species doesn't mean it should be selected for in every species.

After noting that some proponents of neo-Darwinism make unfalsifiable appeals to unknown selective advantages, [Lonnig] concludes that neo-Darwinism is not making falsifiable predictions and finds that this "infinity of mostly non-testable explanations (often just-so-stories) itself may put the theory outside science."

So if a "Darwinist" appeals to unknown selective advantages, he's guilty of making unfalsifiable predictions and being unscientific. But it's totally fine for an IDist to appeal to an unknown designer, right? At least the Darwinist is appealing to a mechanism that's proven to exist.

Date: 2011/11/20 11:03:19, Link
Author: qetzal
Quote (Glen Davidson @ Nov. 20 2011,10:01)
Intelligence is proven to exist, too, and to produce functional structures.

It's just that God's intelligence is very different, so you'd expect his designs to be very different as well.

So the analogy holds.  I mean, except for God's intelligence being so unlike any we've ever seen, and the functional structures being a great deal different from anything we've produced.

Glen Davidson

Intelligence is proven to exist, but an intelligent designer is not. Plus, which is worse - a scientist appealing to unknown selective advantages? Or an IDist appealing to the unknown/unknowable motives of an unknown/unknowable/undemonstrated designer?

Not that consistency in argument was ever Luskin's forte.

Date: 2011/11/20 11:51:33, Link
Author: qetzal
Quote (Southstar @ Nov. 20 2011,10:21)
Ioseb: Anyway here's how it's done let me explain it to you since you and your friends are stupid beyond belief. We look at the position of the nucleotied and/or the aminoacid within biological molecules these have always a precise physical, chemical and structural significance. These represent specific information, all that needs to be done is to count the nucleotides and the aminoacids in the sequence so as to determine the intrinsic complexity.

This is the measure of information I'm talking about.

Wrong. The vast majority of proteins include amino acids that are completely superfluous to their structure and function. They can be replaced with other amino acids or even deleted with no effect. So no, you can't just count amino acids, because number of amino acids doesn't directly correspond to function, complexity, information, meaning, or anything else he's suggesting.

Regarding your stupid quiz let me show you and your ignorant friends how real biology is done.

Let's take three sequences the first two are your invented sequences. The third is a real sequence. (See scientists use real things not like the ones you make up).


See now sequence 3 has the same probability of being genereated by chance as the other two, but it is a real RNA sequence starting with a codon (AUG) and the codons for translating amminoacids valinm lisin and glicin.

So if we make the assumption that this sequence codifies in the begining a protiene, it would not contain only information of the random sequence of letters but it would also contain information (contained in the example in the first triplet regarding) reagarding the amminoacid start, the same for each triplet which together contains a specific information which can be chemical/physical or structural. This is INDESPENSIBLE for the function of the protiens produced.  

Now my sequence is the only one of the three that permit the formation of a protiene

Really? I guess Ioseb didn't notice that Sequence 2 is simply the DNA version of the following:


Note that it also contains the AUG start codon (which codes for methionine), followed by codons for threonine (ACC) and aspartate (GAC). Even better, Sequence 2 includes a stop codon (UAG), with is also INDISPENSIBLE for function.

Now do you understand the information I'm talking about.

I understand it a lot better than Ioseb does. That's clear.

So now I've proven to everyone that information exists and it can be seen.

Congratulations to Ioseb for "proving" what no one was disputing. We all agree that information exists. We even agree that it can be measured, as long as you're careful about precisely defining the kind of information you're measuring.

The issue is not whether information exists. The issue is Ioseb's (and others') claim that information can't be increased by evolution. To wit:

Ioseb said: well see you evolutionists suggest that we have passed form simple organisms to complex organisms. Read your silly theory. From bacteria to humans. So according to the theory we have moved from less complex organisms to more complex organisms. In accordance with this there must have been a increase in biological information humans have many more functions than bacteria. So we had to have new functions that had to develop naturally (not in your stupid PS2 game), new functions would have led to new organs and new life forms.  

Please show me a peer reviewed paper that shows increase function has lead to anything...
Actually show me a peered reviewed paper that shows that functions can increase

Easy: Richard Lenski's demonstration that E. coli can spontaneously evolve the ability to use citrate as an energy source.

Of course, Ioseb may object that demonstrating evolution of such a relatively simple new function is a long way from demonstrating that fins can evolve into legs and wings. And it's true that we don't (yet) understand the details of how that could happen. But we haven't yet had the luxury of running controlled evolutionary experiments over the course of several million years. What we have done is proven that evolution really happens on observable scales, and that it's consistent with the reams of data from molecular phylogenies & the fossil & geological record going back billions of years.

What has Ioseb shown? Can he provide any shred of positive evidence for a designer (or whatever else he thinks accounts for biological complexity)?

To the readers of this forum: I think that we can rest assured that science, the real science has and will triumph over this blinded and evil idea.

And here we see a clue to Ioseb's real objection to evolution: it's "evil." And what makes it evil? Could it be because it contradicts Ioseb's religious beliefs? Naaah.

P.S. What's your interest in trying to "break this down?" If you're just trying to understand how Ioseb's arguments are flawed, or you're trying to convince others how he's wrong, fair enough. But if you're hoping to convince Ioseb that he's wrong, forget it. It's not gonna happen.

Date: 2011/11/20 16:39:27, Link
Author: qetzal
Quote (OgreMkV @ Nov. 20 2011,15:29)
Then we would know what he means by 'information' wouldn't we?

You're assuming he has a coherent meaning....

Date: 2011/11/21 16:16:58, Link
Author: qetzal
If your opponents won't even accept that evolution can generate new functionality without intelligent intervention, I suggest you not get sucked into a discussion of abiogenesis. Although there are some great hypotheses about abiogenesis, the evidence base is still virtually nothing compared to what's been proven for evolution.

Date: 2011/11/24 18:01:26, Link
Author: qetzal
Just FYI, it's not that the studies belong to the universities. It's that the papers are often published in for-profit journals. Such journals don't typically provide free full-text access because they're trying to make money.

Not that that makes Ioseb's argument any less ridiculous.

Date: 2011/11/27 14:44:19, Link
Author: qetzal
Quote (Southstar @ Nov. 27 2011,10:18)
[Ioseb] is arguing that, the paper proves beyond doubt that there are hardly any gain of FCT mutations. So evolution can't occur. So it's all wrong.

Simply showing that gain-of-FCT mutations are uncommon proves nothing of the sort. For Ioseb to make his case, he'd need to show that gain-of-FCT mutations occur too infrequently to support the rate at which new phenotypes have appeared over the past few billion years. Behe doesn't do that in his paper, and I'm confident Ioseb can't do it either.

In any case, focusing on gain-of-FCTs is a red herring. If modification of an existing function leads to a new function, it's still a new function. Especially if the modification involves gene duplication so that the original function is maintained as well. So Ioseb's (and Behe's) challenge is actually much greater: show that the combined rate of M+G mutations isn't enough to support evolution of existing diversity.

Date: 2011/11/28 14:56:31, Link
Author: qetzal
Quote (OgreMkV @ Nov. 28 2011,09:21)
I've designed an experiment to cause a star to nova... but I never can get funding for some reason.

Perhaps you don't have sufficient preliminary data in your applications. Try including this next time.

P.S. Marty, if no one else has addressed your specific questions by this evening I'll try to take a few stabs, time permitting.

Date: 2011/11/28 19:58:20, Link
Author: qetzal
Quote (Southstar @ Nov. 27 2011,10:18)
Quote (OgreMkV @ Nov. 26 2011,08:44)

Some help needed to fight behe's silly work.

Okay I have made the following case against this paper presented by the Tards. but before I write it down I want to check with you guys if I'm on track. I don't want to mess this part up.

here is the link to the paper:
Ioseb is using the paper in the following way:

He is arguing that, the paper proves beyond doubt that there are hardly any gain of FCT mutations. So evolution can't occur. So it's all wrong.

Here are my accusations:

1) The paper is limited in that it only analises bacteria and viruses. No eukyrots are analised. So how the hell can you say that it applies to life in general.

I don't think this is a compelling argument on your part. First, the paper does include eukaryotes. All the mutations discussed in Table 1 are in human genes. Second, even if the paper does focus mostly on prokaryotes, they still comprise the longest extant lineage, dating back some 2 billion years, and a huge range of distinct functions first arose in prokaryotes. So if Behe's analysis really presented a fundamental problem for evolution, even just in prokaryotes, that would be a significant issue. Fortunately, his analysis does no such thing.

2) The paper is limited to artificial experiments in which the process of natural selection has been removed. The only natural case examined was malaria.

I don't think this is a good criticism either. Even if most of the experiments involved selection in a lab environment, it's still a matter of some organism adapting to a new environment. The only real issue with lab-based studies, IMO, is that they're only able to assess evolution over periods of years to (at most) decades. They're not capable of directly observing the slow accretion of mutations and new functions that take place over thousands to billions of years. Naturally, the kinds of changes we see over ~ 10 years will look trivial compared to what can happen in 10 million years.

3) Concerning the case Gain of FCT function i found a comment on a critic site:

stating that: "The construction by mutation of a new promoter, intron/exon splice site, or protein processing site are gain-of-FCT mutations. Also included in this category is the divergence by mutation of the activity of a previously duplicated coded element.” In other words, mutations in this category produce new genes, parts of genes, or confer drastic new capabilities on genes by adding new splicing sites.

Also note that because almost no bacteria or viruses have introns in their cellular genes, it’s impossible to even see one class of this mutation in lab experiments on these groups.

a) What does this last paragraph mean?
b) How does this relate to FCT gains?
c) Is there evidence to support this?

Eukaryotes often have their protein coding sequences broken into separate bits called exons, with non-coding sequences called introns in between each exon. Bacteria don't usually do this - their protein coding sequences are typically uninterrupted. Some types of FCT gains involve rearrangement of introns and exons. Since bacteria don't usually have those, they can't generate that type of FCT gain.

All that said, I don't think this is a good criticism either. As noted above, bacteria have unquestionably developed new functions over evolutionary time. Really complicated structures like ribosomes, flagella, replication complexes, transporter proteins, etc., etc., all arose in prokaryotes first. So one way or another, bacteria must have developed novel functions over time.

4) Behe states regarding Lenskies experiments:
If the phenotype is due to one or more mutations that result in, for example, the addition of a novel genetic regulatory element, gene-duplication with sequence divergence, or the gain of a new binding site, then it will be a noteworthy gain-of-FCT mutation.

Do we have examples of gain-of-FCT mutations in experiments similar to Lenskies?

Behe's paper already lists some mutations that he classifyies as gain-of-FCTs. See Tables 2 & 4.

5) Is there a specific reason that has arisen in other papers as to why most of the experiments lead to loss of FCT? I would answer that it is only due to the experimenters removing natural selection from the equation. Would I be right?

No, it's almost certainly because loss-of-FCT mutations are much more common than gain-of-FCT mutations. I can't readily offer a citation, but it's widely accepted that the vast majority of mutions in a protein coding sequence, for example, will either be neutral or deleterious to protein function. Only a few will enhance function or generate new functions (assuming we can agree on what a 'new function' really means). I don't think it's surprising that there will often be cases where a loss of FCT provides a selective advantage.

6) The work is based on three organisms, prokaryotes, viruses and hemoglobin?
Eukyrotes are not included in the study. Or does table 1 automatically include eukyrotes?

Table 1 exclusively lists human mutations that provide malaria resistance, so yes, it's about eukaryotes.

7) Plasmodium falciparum (malaria) is a eukyrote but the genetic mutation that is being studied is of Hemoglobin not of the malaria. Is this correct?

Hemoglobin and other genes in humans, yes.

8) Isoeb makes the following case: The adaptation to Malaria is the sickle cell. Which is obviously due to FCT loss and leads to premature death.  Only on extremely rare occasions do we get gain of FCT by Chloroquine Complexity Cluster or C Harlem. How rare is this gain let me tell you with C Harlem where the are two conections sites in the plasmid: it required 10^40 organisms to get this mutation. Seeing as there is only one known case.

Want to know how many organisims are estimated to have been around since start of life on the planet? 10^40.
Do you know how may conection sites ther are in a cell 10.000.

Okay point one: I would say that he's making the stupid probability error again so I just fight this with the "evil killer dust bunny".
Point two: What has this got to do with anything???

I have to guess with this one, because Ioseb is talking gibberish. I have no idea what "connection sites" are supposed to be, and plasmids have nothing to do with either chloroquine or malaria resistance.

A quick google of "C harlem" reveals that it's a particular hemoglobin variant where the B chain has two different amino acid substitutions. Most likely, Ioseb is trying to make the argument that it's nearly impossible for both of those mutations to have arisen simultaneously in one person, given the known mutation rate and the likely number of humans that have ever existed.

If so, there are two huge flaws in his argument. The first is his assumption that no other single or double mutations would have afforded malaria resistance. But in fact we know that's wrong, as Behe's own Table 1 shows. Thus, it's not a question of the probability of getting exactly those two mutations at some time during human evolution. It's a question of how many possible combinations of mutations would confer resistance, and whether it's reasonable that at least some of them could have arisen by chance during human evolution.

The other huge flaw is that Ioseb seems to be assuming that both mutations would have to arise at the same time in the same person. But that's obviously wrong. Nothing prevents one mutations from occurring and spreading through the population, before the second mutation occurs. And here's the kicker: it turns out that one of the two mutations in hemoglobin C harlem is the same mutation seen in conventional sickle cell disease. And we already know that lots of people have only that one mutation, and that that mutation alone confers malaria resistance. So it's easy to imagine that the sickle mutation happened first and spread to many individuals due to conferring resistance. The second mutation could have happened at some later date. Maybe the second mutation adds some additional selective advantage. (I didn't see anything about that either way in my brief search.) If so, that would be a perfect example of how evolution often works - incremental advantages adding on to previous ones.

8) Ioseb calls my attenton to this site:
Saying that you see another study say exactly the same thing.

I looked at it and could find nothing of the sort...

Well, the first sentence of section 16.5.1 reads: "Making random changes in a gene is quite likely to stop it working, but very unlikely to give it a novel function." So Ioseb's point is probably again that gain-of-FCT mutations are uncommon. I already addressed this in my previous post: yes, but so what? Just because gain of function mutations are less common doesn't mean they don't happen (as even Behe acknowledges), and it doesn't mean they're too rare to support evolution. If Ioseb thinks they are too rare, he's going to need a lot more evidence than Behe's paper to make his case.

9) My main argument is that okay so he saw loss of FCT functions in controlled environments in a few species of bacteria and virus (except the malaria) sooo what?

Exactly. Evolution clearly requires gain-of-FCT mutations, so if we never saw such mutations in lab studies, that might raise some questions. But we do see such mutations, so that's all fine. The fact that we see more loss-of-FCT mutations isn't a problem for evolution.

Thanks for your imput on this


You're welcome. I hope that's helpful.

Date: 2011/12/01 20:18:27, Link
Author: qetzal
Quote (Southstar @ Nov. 30 2011,13:38)
[quote=qetzal,Nov. 28 2011,19:58][/quote]

Thank's for this it was really useful!

Just a consideration, is it possible that oraganisms left to themselves, without the pressures of natural competative selection would automatically tend toward loss of function.

After all they would just be responding to the new situation which requires less complex machinery.

What are your thoughts on this?


Well, like others have said, you can never completely escape from selection. Even if all resources were infinite, there would still be selection against mutations that cause death or infertility.

That said, there are lots of examples where organisms have lost functions that were no longer essential. A very well known example is that humans and related primates have lost the ability to synthesize vitamin C.

In some cases, there may even be advantages to not making something that's no longer needed.

Date: 2011/12/07 21:03:12, Link
Author: qetzal
Quote (Southstar @ Dec. 07 2011,09:57)
The objection made to this article is that there is no proof of novel genetic material in the study. Actually in all fairness it does state "Tail clips taken for DNA analysis confirmed that the Pod Mrcaru lizards were genetically identical to the source population on Pod Kopiste."

So one could assume that the mutations are only induced by the enviroment and are not genetic based?

Mutations are genetically based, by definition. And the DNA analysis did not confirm the the lizards were genetically identical. It only confirmed that the PM lizards were genetically indistinguishable from the PK lizards by the method employed. The test was only designed to show that the lizards collected on PM were, in fact, descendents of the original 5 pairs of PK lizards that were introduced to PM. That test was not designed to identify possible mutations in the PM lizards that might account for the observed physical differences.

another thing I have replied to this saying that the development of the Cecal valve which is only been developed on the lizards of one island can only be produced with an increase of the amount of genetic material. Would this be correct?

Or would it be possible that these genes were somehow latent and were only expressed when the animal turned to a heavier herbivourous diet?


No, I don't think you can't say the the development of cecal valves could only occur with an increase in the amount of genetic material. Remember that these lizards are descended from a total of 10 original lizards. So, any particular gene locus could have been present in multiple different versions (alleles) in the founding population. As the population expanded, those alleles would have reassorted into many combinations that weren't present in any single founding lizard. In addition, most traits are influenced by combinations of lots of genes and loci. So the appearance of cecal valves might not involve any new mutations. It might just involve new combinations of alleles that already existed individually in the founding population.

The fact that these traits appeared in only ~ 30 generations suggests to me that reassortment and selection of existing alleles is probably a significant factor here, though it's possible there were novel mutations as well.

Note that this is not really the same as saying that the genes were somehow latent, though your anti-evolutionist acquaintences may try to claim as much.

Date: 2011/12/08 16:29:38, Link
Author: qetzal
Quote (oldmanintheskydidntdoit @ Dec. 08 2011,08:21)
Quote (Southstar @ Dec. 08 2011,08:12)
but it's so little and so rare that it isn't enough to drive evolution.

The question to ask them is what is the number that's required to allow evolution to operate?

If they don't know then on what basis do they say it's "too little"?

It would be interesting to go back to Behe's paper, count up all the things that even he concedes are "gain-of-function" mutations in lab experiments, and calculate how many organisms evolved through how many generations to get that number. Then roughly extrapolate how many new functions you'd expect from an entire Earth full of organisms evolving over several billion years.

Even with very conservative assumptions, I guarantee the number will be staggeringly high. I'm sure Ioseb and his ilk would find a way to object, but it might take them aback temporarily.

Not that I think such calculations would have any real relevance. But that's what Ioseb et al seem to value, and I doubt they realize what their own approach would show.

Date: 2011/12/12 09:39:31, Link
Author: qetzal
Quote (Southstar @ Dec. 12 2011,05:32)
Okay the conversation has reached a point, where a few people have asked:

Give us the smoking gun,  show us an example of evolution that:

1) Envolves a new spieces that can no longer reproduce with the parent spiecies.
2) In which the new spieces has novel DNA
3) In which the mutation cannot in any way be classed as epigenetics

Why the insistence on new species with "novel DNA?" As has already been noted above, speciation doesn't have to involve the appearance of brand new genes. And again - mutations can never be classified as epigenetics. Mutations are changes in DNA sequence. Epigenetics is changes in gene activity that are not caused by changes in DNA sequence.

I suspect what your opponents are really objecting to is not speciation, which merely requires reproductive isolation. I think they're disputing that evolution can produce new genes and new functions.

If so, you're never going to be able to cite a lab study showing the complete evolution, from scratch, of some complex new structure like an eye. Evolution doesn't work fast enough to observe that directly.

In fact, you might remind them that that's their hypothesis - that some "intelligent designer" can supposedly create new functions and whole new creatures in an instant. Where's their evidence for that?

It's true we can't watch a mouse-like animal evolve into a bat-like animal in a lab. But we can observe mutations that alter gene functions. We observe the appearance of novel genes and novel biochemical functions. We observe transitions throughout the fossil record that are consistent with gradual evolution, not with instantaneous design. We observe genetic relationships between organisms, and between functions, that are very consistent with the fossil record. We can even observe related genes in different species, infer a likely evolutionary path from an ancestral organism, predict the likely gene sequence and function that ancestral organism should have had, make that predicted ancestral gene, and show it has the predicted function!

So, while it's true that we can't observe everything about evolution, it's very much false that belief in evolution is just as much faith as is belief in ID.

Date: 2011/12/13 07:21:56, Link
Author: qetzal
Why does there have to be "novel genetic material" and what does that actually mean? If a series of mutations altered existing genes and led to some new function, would that count as new added genetic material?

Date: 2011/12/13 07:48:06, Link
Author: qetzal
But again, what counts as "new genetic material" as they (or you) define it?

Date: 2011/12/13 13:15:57, Link
Author: qetzal

I still want to know what they consider "new genetic information." Which of these would qualify, in their opinion?

A) a mutation in an existing gene that has no effect on gene function
B) a mutation in an existing gene that modifies the existing function (eg maybe changes gene expression levels, or changes catalytic rates of an enzyme encoded by the gene)
C) a mutation in an existing gene that creates a new function (eg the encoded enzyme can now act on a different substrate, or the encoded protein can now bind to a different DNA sequence)
D) an existing gene that gets duplicated, with no change in the DNA sequence
E) a gene that gets duplicated with some sequence change that either modifies gene function (E1) or creates a new function (E2)
F) duplication of a large stretch of the genome, without or with modified or new functions
G) duplication of the entire genome (polyploidy)
H) introduction of DNA from an outside source, such as integration of viral DNA into the host's chromosome
I) appearance of brand new genes that didn't previously exist in that organism and weren't somehow introduced from an outside source.

Date: 2011/12/13 16:22:44, Link
Author: qetzal
Quote (Southstar @ Dec. 13 2011,14:28)
That's a damn good question, I'll bet that they say that you should look at behe's paper as to what he calls gain of function mutations.

Behe's paper doesn't say anything about whether those gain of function mutations involve novel genetic information. Are these people saying gain of function is the same as novel genetic info?
Simply he states that has clearly been proven in a peer reviewed paper by Behe that there is only a very remote possibility of gain of function therefore 0 possibility for it to be the cause of biodiversity.

Behe's paper acknowledges that gain of function mutations (GOFs) happen. It claims they're rare compared to modification or loss of function mutations. Behe does not show or even argue that GOFs are too rare to explain biodiversity.

Anyone who argues "remote possibility therefore zero possibility" is either ignorant or disingenuous.

To this lot a second group of people on the forum have asked for: (I) appearance of brand new genes that didn't previously exist in that organism and weren't somehow introduced from an outside source.
Further to (I) they asked that it would be good that these genes had a phenotypic effect.

Then this second group is asking for proof of a nonsensical notion. Evolution doesn't work that way. It's like claiming there are cats and dogs, but to prove evolution we should produce a dat.

Date: 2011/12/14 06:47:24, Link
Author: qetzal
Once again, Marty. Behe's paper only attempts to show that gains are much less common than modifications and losses. It does not show that gains are too rare to support evolution. It doesn't even address that question. Behe's paper is irrelevant to what these people are claiming.

Date: 2011/12/15 11:58:40, Link
Author: qetzal
Quote (Southstar @ Dec. 15 2011,09:33)
But isn't it skewed? I mean okay he does point out the limits of the paper calling them possible objections, but still it's all the stuff that he doesn't consider that's worring,like that the historical evidence from eukaryotes genome shows that most of the kinds of mutations that would have been important could not have occurred in the experiments.

No! Frankly, I don't understand why you and/or Ioseb keep saying this. All Behe claims to show is that G is much rarer than M+L. That is NOT THE SAME as showing that G is too rare for evolution to work, or that the kinds of mutations needed for evolution couldn't have happened.

If you want to argue that G is too rare to support evolution, you need to show that the observed rate of G is low compared to the rate needed for evolution! Comparing it to the rates of M+L is NOT RELEVANT!

Date: 2011/12/18 09:58:36, Link
Author: qetzal
Quote (Southstar @ Dec. 18 2011,08:48)
In a formal debate you would get no points for that argument. Don't get me wrong I do agree with you in every point but:

1) You have not shown that the articles are "unscientific"

We've hashed Behe's article to death. It's not horribly unscientific (though is categories of loss, modification and gain are pretty subjective), but we've explained repeatedly how his paper doesn't show what it's proponents claim. Wesley linked to discussions of Axe's paper, showing why it's a crock. Quite a few other ID papers have been extensively debunked in various places as well. At some point, it becomes a game of junk-paper whack-a-mole.

2) the measure of citation for items which are on the cutting edge of science might be expected to be low and is in any case really a subjective measure of the value of a study.

Not so. Every scientist wants to be on the cutting edge. If this stuff were perceived as actually cutting edge, it would get more citations, not less. True, citation rates are not an objective measure of importance, but they are a very good indication of whether other scientists consider important.

3) If I write a theory of the spaghetty flying monster that explains string theory with the use of Zibibop power. Someone with a normal mind has got to denouce the fact that I've lost it especially since I have an organisation that supports the SFM and that I call myself a respectible scientist.

No. Nobody has any obligation to say a word about it. You're theory would be bogus either way. If enough people started believing you, and that affects others, then perhaps respectable people will start to denounce you. And that's exactly the case with ID & "scientific" creationism. Respectable scientists (like Elsberry) have taken the time to denounce this stuff as the crap that it is.

4) If you're ignoring something you either don't know that it exists or if you do it just means that you:
a) Can't find the time to call it rubbish (shameful)
b) Can't find a reason to call it rubbish (verry worring)
c) Can't find a problem with the item and just don't know what to do with it, which would not mean that it is not useful but that you can't understand it. (I believe that this is not the case with the Bio-complexity articles which are in fact junk).

It's not being ignored. It has been called rubbish, and the reasons that it's rubbish have been given repeatedly.

5) Just because google scholar / pub-med do not indicate results it does in no way demish the particular value that a study may have.

True, but it's another indication that the study is not considered valuable.

I'm not quite sure what you're expecting here. Even if the NAS came out with a list saying "These journals and these papers are junk," so what? ID proponents would claim conspiracy, just like they have already. The real issue is whether these papers and claims hold up to scientific scrutiny, and they don't.

Date: 2011/12/18 11:24:54, Link
Author: qetzal
No, I don't have any links that specifically denounce Bio-complexity org, nor do I have links that specifically deconstruct those papers by Axe. Axe's past work has already proven to be wrong (see Elsberry's link above). Behe's paper has already proven not to show what Ioseb and company claimed it showed.

At some point, it becomes a waste of time. People like Ioseb never admit any error, they just point to something new and say, "Well, can you disprove this?" After a while, it becomes tiresome dealing with people who don't discuss in good faith.

Date: 2011/12/24 15:52:58, Link
Author: qetzal
Quote (Southstar @ Dec. 23 2011,09:42)
Another thing did Lenski ever get round to finding the origin of the CIT+ mutation, was it epigenics or a two step indipendant mutation.

Epigenetics. It doesn't mean what you seem to think it means.

A mutation is a heritable change in the DNA base sequence. Epigenetics cannot, by definition, involve a change in the DNA sequence. Instead, it involves things like base modification (e.g. methylation) or alteration of the pattern of histones binding to DNA. So it's non-sensical to ask if the origin of the CIT+ mutation could be epigenetics. Just so you understand the terminology.

What you're really trying to ask is whether the CIT+ phenotype (i.e. the observed ability to use citrate as an energy source) is due to a mutation or due to some epigenetic change. I don't know the answer for a fact, but I can almost guarantee that it's due to mutation. E. coli does utilize things like methylation and histone-like proteins, but I'm not aware of any case in E. coli where an epigenetic change could cause the appearance of something like the CIT+ phenotype.

Note that I didn't bother to see if Lenski has identified a mutation responsible for the CIT+ phenotype. I'd guess that he has, but I'll let you hunt that down yourself.

Date: 2011/12/27 14:45:20, Link
Author: qetzal
Quote (Robin @ Dec. 27 2011,08:31)
So the sound is sort of like (phonetically) "hoechhh-hoechhh".

An owl with a bad chest cold?  ;)

Date: 2012/01/02 09:34:23, Link
Author: qetzal
Quote (Southstar @ Jan. 02 2012,04:28)
Rather chance is used to express that we don't know what mutations will arise.

And, perhaps more importantly, that mutations arise independently of their observable effects. In other words, there is no purposeful direction to which mutations occur. The mutational process is random with respect to phenotype.

Evolution, in contrast, is highly non-random, because the chance that a given mutation will be passed down to future generations does depend on phenotype.

Date: 2012/12/07 21:19:35, Link
Author: qetzal
Is that a legless lizard? Can't quite see the head clearly enough.

Date: 2012/12/12 23:46:58, Link
Author: qetzal
Yeah, I couldn't be sure I was seeing external ear openings in the original, but they look pretty clear in the head shot. So definitely a legless lizard, not a snake.

Date: 2012/12/13 08:29:59, Link
Author: qetzal
Viewed from my iphone, at least, the head shot is much clearer. No doubt a function of how it's being displayed, not the photo itself.

Date: 2012/12/13 14:37:43, Link
Author: qetzal
Quote (OgreMkV @ Dec. 13 2012,12:51)
That's very useful information.  However...

I am NOT going to go around lifting up the skirts of these things to try and figure out if it's a legless lizard or a snake.  ;)

Yes, much easier to look for external ear openings. Snakes don't have 'em. Also, lizards can move their eyes in their sockets. Snakes can't.

Remind me at some point to tell you the story of the spotted snakes.

Let's see - what's the proper straight line here. How about, "Were they spotted all over?" :)

Date: 2013/01/28 08:20:32, Link
Author: qetzal
Principle #9: Check if the author deliberately misrepresents others' views.

Caroline Crocker, paraphrasing Brian Alters to illustrate Principle #6 (emphasis in original):
Only 50% of the American public "believe" in evolution. Could only be for one of three reasons. 1) Scientific illiteracy, 2) Religious illiteracy, or 3) The activity of the "large...powerful...very effective" anti-evolution industry. Brian Alters, Chapman U,

What the article actually said (emphasis added):
Alters gave three main reasons for widespread misconceptions about evolution in the United States.

(Also, Principle #10: Beware the ellipses!)

Date: 2014/01/17 21:56:43, Link
Author: qetzal
Keep in mind that each individual can have a mutation. So if you had 100,000 children born in each new generation, you'd expect one new mutation per 3000 bp per generation in the population overall.

I'm sure the actual math is more complicated, but I don't know the details.

Date: 2014/01/18 08:41:03, Link
Author: qetzal
It's also worth noting that the initial human population didn't all start with a single MHC allele. MHC traces far back in the mammalian lineage. (Mice have them, for instance.) So the first humans would have had a range of MHC alleles that they inherited from their pre-human ancestors, and they would have inherited a range from their primate ancestors, and so on.

Again, I know it's more complicated, since there are population bottlenecks and alleles get lost etc. but you get the idea.

Date: 2014/01/18 17:07:53, Link
Author: qetzal
Quote (Friar Broccoli @ Jan. 18 2014,16:08)
I am interested in assuming 8 alleles 4500 years ago (or two 6,000 years ago) and establishing that it is impossible.

Sure, you can show it's impossible based on the natural processes we know of. But how do you plan to show that it's impossible to someone who believes in a being that created all life less than 10,000 years ago?

The best you'll manage is to elicit a response like "It's not impossible for God!"

Date: 2014/01/23 11:57:07, Link
Author: qetzal
Quote (Soapy Sam @ Jan. 22 2014,16:00)
Obviously, since the MHC is involved in distinguishing self from non-self, I had to artificially raise variation in it as the human population expanded, so that individuals would not all get confused as to who was who.

All the best,


Nice to see a creationist "explanation" with some detail for a change!

Date: 2014/08/22 10:27:45, Link
Author: qetzal
Well, he did say he was substantially illiterate about DNA!

Date: 2015/01/16 11:53:57, Link
Author: qetzal
Quote (cryptoguru @ Jan. 16 2015,9:09)
My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.

Quote (cryptoguru @ Jan. 16 2015,10:33)
[A] living cell is a computer, not analogous to a computer, but IS a computer.

Perfect. Lenski already demonstrated new functions being added to the genome using E. coli, which are living cells, and therefore ARE computers.

You're welcome.

Date: 2015/01/17 12:32:54, Link
Author: qetzal
Quote (cryptoguru @ Jan. 16 2015,19:14)
No, not begging the question, I'm merely pointing out that Lenski's results don't show anything either way ... you can claim it's evolution, but I can claim that what he observes is part of its original programming, as the bacteria is still E. Coli ... it may have adapted and changed to resist death, because we know that is part of the inherent functionality of bacteria, they swap genetic code with other bacteria. Like a computer virus, the code is mostly concerned with reproduction and not any complex functionality. We embed all sorts of randomisation algorithms into computer viruses to make them harder to identify by the host and harder to stop ... this is engineered resistance. I'm claiming that all the research so far does not contradict that explanation. And in fact, if anything the experiment has proved that nothing has changed in millions of years of evolution. If evolution is so easy and happens everywhere to every organism world-wide to some degree, why are they still E. Coli and not Bananas or Dolphins or Pygmy Elephants? (that one's for Kevin)
This is why I ask for a simple model, that models the core features of the proposed theory of evolution.

Actually, what you asked for was this:
My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.

You didn't ask for a model that shows E. coli turning into bananas or dolphins. You asked for a model that shows new functions and information being added, and you've been given multiple examples. If what you really want is a model that turns E. coli into bananas, then you're right. We're not currently capable of modeling evolution on that scale. But as others have pointed out, not being able to model something on a computer is not strong evidence that it doesn't happen.

Also, I'm curious. Were you just being mocking, or do you really understand so little about evolution that you think it means bacteria should turn into bananas (or any complex multicellular organism) over a few decades? Because if it's the former, then it suggests you're not interested in honest discussion. And if it's the latter, then your understanding of evolution is so poor that rational discussion is probably impossible. Of course, the two aren't mutually exclusive.

But hey, it's possible that I'm wrong on both counts. I'm a scientist; I believe in empirical evidence. So show me some evidence that you understand what evolution actually claims, and that you're willing to discuss the validity of those claims honestly.