Joined: Jan. 2006
6)). In both cases, mere similarity between the contents of the alleged copies and the originals was not considered compelling evidence of copying. After all, both chemistry textbooks were describing the same body of chemical knowledge (the books were designed to "function similarly") and both directories listed members of the same industry, so substantial resemblance would be expected even if no copying had occurred. However, in both cases errors present in the "originals" appeared in the alleged copies. The courts judged that it was inconceivable that the same errors could have been made independently by each plaintiff and defendant, and ruled in both cases that copying had occurred. The principle that duplicated errors imply copying is now well established in copyright law. (In recognition of this fact, directory publishers routinely include false entries in their directories to trap potential plagiarizers.)
Now I have read both articles in their entirety, but before Dr. Max even gets into the details of gene "mistakes", there is one very large item jumps out at me. The analogy seems very clever, but there is a huge assumption that is made which I consider to be invalid and to me this destroys the whole analogy. See what you think and please correct me if I am wrong.
OK. Are you ready? With the plagiarism case, we are talking about printed words in a well-known language. In the GLO gene case, we are talking about genetic "words" in a poorly-understood language. I hope I don't have to cite the recent literature to prove to you how poorly we understand the genetic language. If you do a Google Scholar search, you will see numerous articles talking about pseudogene and "junk DNA" function and how much we are learning and how much there is remaining to be learned. Here's just one with an appropriate comment from Woodmorappe ...
Balakirev, E.S. and Ayala, F.J., Pseudogenes: are they ‘junk’ or functional DNA? Annual Review of Genetics 37:123–151, 2003. The very title of this article would have, only a few years ago, been almost on a par with the following: ‘The Earth: is it spherical or flat?’
Are you with me so far? I don't want to lose anyone. Again, I am saying that ...
With the plagiarism case, we are talking about printed words in a well-known language. In the GLO gene case, we are talking about genetic "words" in a poorly-understood language. This is a big, big difference.
Notice again that Dr. Max's whole argument rests on the following ...
In both cases, mere similarity between the contents of the alleged copies and the originals was not considered compelling evidence of copying ... The principle that duplicated errors imply copying is now well established in copyright law.
Do you see where I am going? Dr. Max is assuming that the state of the GLO gene in humans and apes is an error and with our as yet limited knowledge of gene function, genome function as a whole, pseudogene function discoveries, and "not-junk-after-all" discoveries about "junk DNA", this seems to be an enormous unwarranted assumption. If, in fact, this GLO gene turns out to have some function, then Max's whole argument fails, because now the gene would be rightly interpreted as part of the correct informational content analogous to the correct informational content in the textbooks.
To emphasize this point, consider a passage of text from a language which you do not know, but I do (my dad's jungle tribe for whom he is a Bible translator). In this case, I am playing the role of the hypothetical "Designer" and you are playing the role of the genetic researcher trying to unlock the code. Let us say the above plagiarism case involved the following text ...
ORIGINAL TEXT: Twaihsom me thakwa xatkene roowo pono komo ahnoro. Yipinin yaw so tko xakne Kaan. Ero ke Tumumuru tak nimyakne rma okwe twaihsom mera tak ehtome so. Waipini ro me xa matko naxe Noro pona enine komo.
ALLEGED PLAGIARIZED TEXT: Twaihsom me thakwa xatkene roowo pono komo. Yipinin yaw so xakne Kaan. Ero ke Tumumuru tak nimyakne okwe twaihsom mera tak ehtome so. Waipini ro me naxe Noro pona enine komo.
While a word by word comparison of the above text gives some evidence of plagiarism, i.e. they are similar, you cannot conclude this positively if we use the court case guidelines because you do not know the language so as to be able to detect errors.
Now I DO know the language, so I can identify an error, namely that the word "cewnaninhiri" which means "only begotten" (it is John 3:16) is left out of both texts.
So we see that for Dr. Max's argument to be valid, we have to know the language which obviously, genetic researchers do not yet very well.
Now there is something else interesting here. This text of John 3:16 could be rendered in a number of different ways and yet communicate the same meaning. For example, we could say ...
Yipinin yaw so xakne Kaan roowo pono komo poko. Ero ke Tumumuru tak nimyakne okwe twaihsom mera tak ehtome so. Waipini ro me naxe Kaan pona enine komo.
I know the language well enough to know that this would communicate the same message, but with different structure.
Now, back to biology. It is my theory that this is exactly the situation which we will find in the genomes of various organisms as we understand more and more about them every year. I predict that we will find that the genetic code is a very real language, complete with "words", "sentences", "phrases", "paragraphs", and different ways of saying the same thing.
Now, here is something else ...
How do you explain the similarity of the GLO gene "defects" of humans and guinea pigs? (you knew I was going to go here, didn't you) Apparently, something like 36% of the substitutions are the same when compared to the functional rat GLO gene. If we assume that there is some pro-simian ancestor that has a functional GLO gene, then it would appear that humans are more closely related to guinea pigs than to this pro-simian ancestor. This would seem to defy the evolutionary scenario. How do you explain this?
OK. There's some food for thought. Now pick me apart.
Oh ... and here the quote from Balakirev and Ayala for you
Annual Review of Genetics
Vol. 37: 123-151 (Volume publication date December 2003)
First published online as a Review in Advance on June 25, 2003
PSEUDOGENES: Are They "Junk" or Functional DNA?
Evgeniy S. Balakirev1,2 and Francisco J. Ayala1
1Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697-2525; email: email@example.com
2Institute of Marine Biology, Vladivostok 690041,
Russia and Academy of Ecology, Marine Biology, and Biotechnology, Far Eastern State University, Vladivostok 690600, Russia; email: firstname.lastname@example.org
Pseudogenes have been defined as nonfunctional sequences of genomic DNA originally derived from functional genes. It is therefore assumed that all pseudogene mutations are selectively neutral and have equal probability to become fixed in the population. Rather, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity. Pseudogenes are involved in gene conversion or recombination with functional genes. Link to article
And here's one I like from Dr. Max that confirms what us YECers so often say about mutations ...
Mutations causing genetic diseases and malformations are generally so detrimental to the organism's survival and reproductive success that in the wild--i.e. in the absence of modern medical science--they would tend to be "weeded out" by the pressure of natural selection. Rarely, mutations can be beneficial to an organism: these rare cases form the basis for evolutionary adaptations that improve the "fitness" of an organism to its environment.Link to article
And now, while you all are busy refuting me on this thread, I will hop back over to the "Creator God Hypothesis" thread and dive in again ...
It appears that no one accepts the evidence for a Creator I have given so far, so we will explore that some and find out why ...
See you there ... :-)
Then, you notice a paragraph of about 400 characters that's identical in both samples. It's not in the same place in both texts, but it is absolutely identical down to the individual character. You even note that at the end of the fifth sentence, there's an extra period. You have no idea what any of the text means, but is there any doubt, at this point, that one sample was in fact at least partially copied from the other? Is there any possible doubt that both articles share a common provenance?
You don't need to know anything whatsoever about the language to make this determination, Dave. And it is far from true that biologists know nothing at all about the genetic code. In fact, they may not know what all the "paragraphs" (i.e., genes) in the genetic code mean, but they sure know what the "words" (i.e., codons) mean.
Are you saying that this is what has been found? I did not understand that from the findings of the authors below ...
My knowledge of this
All we really know is that ... (a) it is somewhat similar to the functional rat GLO gene (149 out of 647 substitutions when comparing humans to rats, 96 out of 647 substitutions when comparing guinea pigs to rats),
comes from this
Inai, Y., Ohta, Y. and Nishikimi, M., The whole structure of the human non-functional L-gulono-ã-lactone oxidase gene—the gene responsible for scurvy—and the evolution of repetitive sequences thereon, J. Nutritional Science and Vitaminology (Tokyo) 49(5):315–319, 2003.
Apparently we do not have a situation of identical sequences if I am reading this correctly. Or maybe there is another study that I could not find which states that the human and ape GLO genes ARE identical?
Again ... IF we find the GLO gene sequences identical (or very close) in apes (I think we only have rat, human and GP currently), why does this prove common descent of apes and humans? We do not KNOW that the human (and presumable ape) manifestation is in fact an "error" because we don't know the genetic language well enough yet. All we know is that BOTH apes and humans cannot synthesize Vitamin C. It is and ASSUMPTION to say that "see it's because their GLO gene is broken." How can you say that? Maybe that's was never intended to BE a GLO gene in the first place. You don't know because you don't know the language well enough yet.
My bet is that when we DO learn the language well enough, we will see it has a purpose far different that Vitamin C production.
Here's another analogy ...
Do you think that "The dog is barking" and "The dog is barfing" means that the second sentence is somehow "broken"?? Of course not. They are both valid sentences but they mean ENTIRELY different things.
Also, in our language, the same words can mean two different things in different contexts, i.e. "bark" (dog) and "bark" (on a tree).
I really think Dr. Max is making a bad analogy and assuming too many things.
Can you tell me what a "frameshift mutation" is?
Can you tell me the significance of a frameshift mutation?
Somewhat familiar ... I can read up on it quickly if I need to ...
But go ahead ... why is that significant here? I honestly want to understand this
Yeah. Look at the cytochrome c gene.
I thought were talking about the GLO gene which supposedly formerly allowed Vit C production in primates, but now is broken and does not anymore. Why do you mention Cytochrome C genes?
What if "The dog is barking" and "The dog is barfing" were two sentences from two different novels that were 95+% similar?
You seem to be forgetting the Vitamin C stuff happens in that kind of context.
No I'm not forgetting. But OK. Let's write a "novel" describing how to make a pine tree and another "novel" that describes how to make an oak tree. OK?
HOW TO MAKE A PINE TREE
Start with a 50 foot long piece of soft wood. Add some rough bark. Poke it upright in the ground. Add some kinda straight branches that angle down. Add leaves that are thin and poky. Etc. Etc.
Voila! Pine Tree!
HOW TO MAKE AN OAK TREE
Start with a 50 foot long piece of hard wood. Add some semi-rough bark. Poke it upright in the ground. Add some kinda crooked branches that angle up. Add leaves that are broad and smooth. Etc. Etc.
Voila! Oak Tree!
Now ... notice they are 95% (or so) similar? Do they share a common ancestor? No. I assembled them in my backyard with raw materials following these highly detailed instructions. (I didn't really, but I could have)
The burden of proof for Common Descent seems to me to be much more difficult that the burden of proof on Common Design.
Wrong again, pine breath! You are the common ancestor of both.
Hey watch it, oak breath ... I am the common DESIGNER of both :-)
It's hard to judge as you haven't presented any evidence for common design.
This is what the ID movement is all about. Stay tuned! And tell your friends to quit throwing fire bombs and at least listen .... then make judgment.
That's the hard part -- even getting people to listen --because most people are so set in their thinking.
Well ... I'm quitting until evening ... so I guess I'm gonna start losing now by default.
Good morning everyone--
We are getting close to wrapping up this thread and I feel it is an important thread because the differences between apes and humans are in fact immense, and whether you realize it or not, there are many major issues riding on the answer to the question, "Common Descent or Common Design?"
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.
However, IF Common Design is true, then this raises a whole string of potentially life changing questions. What is this Designer like? Is it one Designer? Or many? If He designed ME, does he want anything from me? The Creation myths are well known ... could there be any truth to any of them? After all, there is one in particular that speaks of a Creator God who will someday hold humans accountable for their actions. Could there be any truth to this? 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 for which evidence continues to mount?
I think it was Renier (can't remember for sure) who said that he "used to be a YEC fundy" but is no longer because of the Vitamin C issue.
Just to recap yesterday ... Talk Origins has two relevant articles that I found
(1) Plagiarized Errors and Molecular Genetics
Another argument in the evolution-creation controversy
by Edward E. Max, M.D., Ph.D.
(2) 29+ Evidences for Macroevolution, Part 2: Past History
Copyright © 1999-2004 by Douglas Theobald, Ph.D.
Prediction 2.3: Molecular vestigial characters
Abstracts for the 3 articles referred to by the second article are as follows:
Abstracts from Talk Origins: 29+ Evidences - Vitamin C Pseudogene
1: J Biol Chem. 1992 Oct 25;267(30):21967-72. Related Articles, Links
Guinea pigs possess a highly mutated gene for L-gulono-gamma-lactone oxidase, the key enzyme for L-ascorbic acid biosynthesis missing in this species.
Nishikimi M, Kawai T, Yagi K.
Institute of Applied Biochemistry, Yagi Memorial Park, Gifu, Japan.
Guinea pigs cannot synthesize L-ascorbic acid because of their deficiency in L-gulono-gamma-lactone oxidase, a key enzyme for the biosynthesis of this vitamin in higher animals. In this study we isolated the L-gulono-gamma-lactone oxidase gene of the rat and the homologue of this gene of the guinea pig by screening rat and guinea pig genomic DNA libraries in lambda phage vectors, respectively, using a rat L-gulono-gamma-lactone oxidase cDNA as a probe. Sequencing analysis showed that the amino acid sequence of the rat enzyme is encoded by 12 exons and that all the intron/exon boundaries follow the GT/AG rule. On the other hand, regions corresponding to exons I and V were not identified in the guinea pig L-gulono-gamma-lactone oxidase gene homologue. Other defects found in this gene homologue are a deletion of the nucleotide sequence corresponding to a 3' 84-base pair part of rat exon VI, a 2-base pair deletion in the remaining exon VI-related region, and nonconformance to the GT/AG rule at one of the putative intron/exon boundaries. Furthermore, a large number of mutations were found in the amino acid-coding regions of the guinea pig sequence; more than half of them lead to nonconservative amino acid changes, and there are three stop codons as well. Thus it is clear that the guinea pig homologue of the L-gulono-gamma-lactone oxidase gene exists as a pseudogene that randomly accumulated a large number of mutations without functional constraint since the gene ceased to be active during evolution. On the basis of the neutral theory of evolution, the date of the loss of L-gulono-gamma-lactone oxidase in the ancestors of the guinea pig was roughly calculated to be less than 20 million years ago.
J Biol Chem. 1994 May 6;269(18):13685-8. Related Articles, Links
Cloning and chromosomal mapping of the human nonfunctional gene for L-gulono-gamma-lactone oxidase, the enzyme for L-ascorbic acid biosynthesis missing in man.
Nishikimi M, Fukuyama R, Minoshima S, Shimizu N, Yagi K.
Institute of Applied Biochemistry, Yagi Memorial Park, Gifu, Japan.
Man is among the exceptional higher animals that are unable to synthesize L-ascorbic acid because of their deficiency in L-gulono-gamma-lactone oxidase, the enzyme catalyzing the terminal step in L-ascorbic acid biosynthesis. In the present study, we isolated a segment of the nonfunctional L-gulono-gamma-lactone oxidase gene from a human genomic library, and mapped it on chromosome 8p21.1 by spot blot hybridization using flow-sorted human chromosomes and fluorescence in situ hybridization. Sequencing analysis indicated that the isolated segment represented a 3'-part of the gene, where the regions corresponding to exons VII, IX, X, and XII of the rat L-gulono-gamma-lactone oxidase gene remain with probable deletion of the regions corresponding to exons VIII and XI. In the identified exon regions were found various anomalous nucleotide changes, such as deletion and insertion of nucleotide(s) and nonconformance to the GT/AG rule at intron/exon boundaries. When the conceptual amino acid sequences deduced from the four exon sequences were compared with the corresponding rat sequences, there were a large number of nonconservative substitutions and also two stop codons. These findings indicate that the human nonfunctional L-gulono-gamma-lactone oxidase gene has accumulated a large number of mutations without selective pressure since it ceased to function during evolution.
Biochimica Biophysica Acta, International Journal of Biochemistry and Biophysics,(ISSN: 00063002) 1999 Oct 18;1472(1-2):408-11. Related Articles, Links
Random nucleotide substitutions in primate nonfunctional gene for L-gulono-gamma-lactone oxidase, the missing enzyme in L-ascorbic acid biosynthesis.
Ohta Y, Nishikimi M.
Department of Biochemistry, Wakayama Medical College, Japan.
Humans and other primates have no functional gene for L-gulono-gamma-lactone oxidase that catalyzes the last step of L-ascorbic acid biosynthesis. The 164-nucleotide sequence of exon X of the gene was compared among human, chimpanzee, orangutan, and macaque, and it was found that nucleotide substitutions had occurred at random throughout the sequence with a single nucleotide deletion, indicating that the primate L-gulono-gamma-lactone oxidase genes are a typical example of pseudogene.
The first article above compares the functional rat GLO gene with the supposedly homologous guinea pig GLO gene and finds significant differences. They say "Thus it is clear that the guinea pig homologue of the L-gulono-gamma-lactone oxidase gene exists as a pseudogene that randomly accumulated a large number of mutations without functional constraint since the gene ceased to be active during evolution."
The second article does the same comparison for rats and humans and concludes ... "These findings indicate that the human nonfunctional L-gulono-gamma-lactone oxidase gene has accumulated a large number of mutations without selective pressure since it ceased to function during evolution."
The third article does the same comparison among humans, chimpanzees, orangutans, and macaques, and it was found that "nucleotide substitutions had occurred at random throughout the sequence with a single nucleotide deletion, indicating that the primate L-gulono-gamma-lactone oxidase genes are a typical example of pseudogene."
Dr. Max draws on these findings and compares the situation to a copyright court case. His argument is that since apes and humans have the same "errors" in the "broken GLO gene", this shows that apes and humans have a common ancestor.
Now this has one HUGE assumption which appears to me to be entirely unwarranted. now maybe it is warranted, but no one gave me any reasons that it should be yesterday
DR. MAX's HUGE ASSUMPTION
The apparently homologous "GLO gene" in humans, primates and guinea pigs used to function to produce Vitamin C, but now no longer does. As such this constitutes a "broken gene" caused by random mutation. My question is ... why do you assume these 3 organisms EVER had a functioning GLO gene? Maybe this gene DOES HAVE a function which we just don't know about. After all, we are seeing a dramatic reversal in the area of pseudogenes. Scientists are all of a sudden finding all kinds of purpose for them. Do a Google Scholar search to see this.
Does anyone have any good arguments for why this is a good assumption to make?
Because Dr. Max's whole argument rests on this being a valid assumption. If it is not valid, then his whole argument fails.
OK ... now tell me ... why is this assumption valid?
(By the way, Tom Ames, I didn't see that frame shift mutations have anything to do with this discussion, but please correct me if I am wrong)
Thanks to Tom Ames for clarifying one point -- I thought you were bringing up something that was relevant to our discussion of the supposedly "broken GLO gene", but apparently I was mistaken.
Maybe it's time for a review again. I'll put it in bold so no one will miss it ... then I'll repeat it a few days from now for the slow ones
THINGS THAT ARE NOT AF DAVE'S GOALS
(1) Get a biology degree
(2) Become a genetic engineer
(3) Get an advanced science degree
(4) Become a biochemical researcher
(5) Pretend I know more about biology than you
(6) Become a geologist
(7) Become an astrophysicist
OK? ... again, I appreciate all the admonitions to get this or that degree or go buy this or that book ... but it's not necessary ... there are plenty of competent researchers like Mr. Nishikimi out there who give me the data I need, and of course I do have YOU ALL to keep me straight.
And I should point out that you guys do a great job of knowing biology and the workings of DNA and transcription and chromosomes and all these wonderful details.
Your problem is NOT your comprehension of the data or in understanding the mechanics of how things work. You are even quite good at explaining this stuff -- Incorygible did a great job explaining the transcription thing. Spent a lot of time on it too, I understand.
Your problem is simply your interpretation of data and your sometimes faulty logic. I don't fault you for this ... it's understandable because of the overwhelming power of your Darwinian worldview. You have been fed a steady diet of Darwinism since you were very young and it wields much power over your minds (much like a religion) and while this is not a problem for most of the things you do, it makes you fall into saying some illogical things when you start trying to explain your view of origins.
THINGS THAT ARE AF DAVE'S GOALS HERE AT PANDA'S THUMB
(1) Find out firsthand why Darwinists believe humans and apes have a common ancestor and evaluate if this is reasonable. We're making good progress here.
(2) Find out firsthand why Darwinists are apparently losing the PR game in the USA. I find it strange that Darwinists have been so unsuccessful in convincing the public of their views because of the virtual monopoly that Darwinists hold over schools, museums, magazines, the media, etc.
(3) Present my evidence that supports a Designer, followed by evidence for YEC, the Flood, the inerrancy of the Bible, etc.
(4) Help as many open-minded folks as possible who read my threads walk through all of my "SEVEN STAGES IN THE EVOLUTION OF A FORMER DARWINIST."
Again, these are ...
SEVEN STAGES IN THE EVOLUTION OF A FORMER DARWINIST
STAGE 1: ToE advocates are becoming frustrated because their explanations are sounding more and more like pro-geocentrism and pro-flat-earth arguments as time goes on.
STAGE 2: The Ship of Darwin has hit an iceberg and a few brave souls are jumping into life boats before it sinks. See www.dissentfromdarwin.org
STAGE 3: And now, ordinary amateur scientists like me are jumping in the fray and shining the light on their weak arguments.
STAGE 4: Frustration ensues, followed by name calling, arrogant and belittling comments, talk of censorship, and the like.
STAGE 5: This is turn fuels more doubts in people minds. ("Why would that guy resort to name calling? Doesn't he have any GOODS?" etc.)
STAGE 6: Which in turn fuels more frustration and mental anguish. And so the cycle goes until finally for some ... in a desperate moment ... possibly in the middle of the night ... or out on a peaceful lake while fishing ...
STAGE 7: THE LIGHT BULB COMES ON! (Trumpets) And one more Darwinist is rescued from the darkness of error.
Now that we have that clarified, the present issue that we are discussing is ...
THE SUPPOSEDLY BROKEN VITAMIN C GENE IN HUMANS AND APES
Again, some of you need to re-read yesterday's posts because someone made the same mistake today which was made yesterday, namely, someone today was basically saying ...
"Of course humans and apes have a broken Vitamin C gene. Isn't that obvious? Wouldn't it be obvious if there were some tires and broken car pieces laying on the side of the road that we were viewing a broken car?"
YES with the car. NO with the genes.
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. This has to be your assumption if you say it is "broken" now, and the fact is that you do not know this. Also, you are assuming that you (or the genetics researchers, rather) know enough about the genetic language to even recognize an error. My contention is that we (genetic researchers) know SO LITTLE about any genomes, that we cannot assert that this gene or that gene is broken.
Please tell me that you guys ARE aware of all the new information coming in about "junk DNA" that apparently isn't junk after all (the gene we are discussing IS one of those genes, right?)?
You guys are the biology experts ... you should know this.
So am I clear now? You guys did very well on the Chimp Chromosome thing, but on this thread, it seems you don't have much understanding of this particular issue and many of you apparently have not even read the relevant articles.
Do you really want me to go away from this thread thinking you guys are confused about this issue? Because right now, that's what I think. Remember, one of my goals is to try to determine why Darwinists have been only mildly successful in selling their views on the open market. Your arguments on this thread so far help me understand why this is.
Maybe you can think about some of this tonight and redeem your arguments tomorrow.
Remember, you guys did good just last week on the chromo thing ... I know you guys can give me some substance on this thread as well.
Again, this is really simple ... all you have to do is present evidence of WHY you are so sure that humans and apes formerly had a functioning GLO gene, but now do not. Simple, right? Sleep on it ... it'll probably come to you.
(Oh, and BTW ... I think Atheists are very good, moral people ... it's the long term trend of society that worries me, but we'll get to that elsewhere ...)
Have a good night and I'll see you in the morning!
Argystokes said ...
Let me see if I can add something to the conversation.
You've been arguing that what appears to be a broken GLO in primates may not be in fact broken at all, but is rather a designed stretch of DNA that performs some unknown function (we'll call this "pseudo-GLO"). You haven't stated it explicitly, but I think we can infer that this putative function has nothing to do with Vitamin C synthesis (seeing as primates and guinea pigs can't do it). That is, pseudo-GLO has a function entirely distinct from regular GLO.
If pseudo-GLO has a distinct function, we could use the framework of common design (as well as common descent) to predict that pseudo-GLO would be found in organisms that have functioning GLO. This is because there is no reason to predict that a gene unrelated to Vitamin C would only be found in GLO-deficient species.
So there are two possible scenarios:
(1) Pseudo-GLO is found throughout the animal kingdom (either ubiquitously, randomly, or in nested hierarchies). This type of scenario, where a species has a functional gene and a pseudogene is not uncommon.
(2) Pseudo-GLO is only found in species unable to synthesize vitamin C.
It seems to me that a design hypothesis would only predict scenario (1), for reasons discussed above. Common descent would predict either scenario (2), or scenario (1) with nested hierarchies of Pseudo-GLO (this would be the result of a duplication of GLO followed by the inactivation of one of the copies, which still persists in the population). Seeing pseudo-GLOs (especially those that look very much alike) randomly throughout the animal kingdom would certainly be a surprise to me (I can think of a mechanism by which it might occur, but we won't get in to that). Ubiquitous pseudo-GLO would strongly imply that it has an important function, but would not really support either common descent or common design over the other.
I haven't done the research to find out which is the case, but there should be sufficient online tools to find out which is the correct scenario. With the relatively low number of genomes sequenced, it is probably not possible right now (using good ole look-it-up-online methods) to differentiate between the subscenarios of scenario (1).
I'm willing to look up the information for you (assuming you don't know how to do a BLAST search) if you're willing to concede that scenario (2) does not logically fit with a special creation model.
So how's about it, Dave? Shall we do some science?
This is an excellent discussion here. I like the terminology you use to keep everything clear. You are correct that I have lately focused on the question "Why are researchers so sure this is a broken gene?" I think this is a legitimate question to ask (but I could be wrong) in light of statements like this from Watson (co-discoverer of DNA) in 2003 ...
‘The most humbling aspect of the Human Genome Project so far has been the realization that we know remarkably little about what the vast majority of human genes do.(Watson, J.D., DNA: The Secret of Life, Alfred A. Knopf, New York, p. 217, 2003.)
and we are obviously learning much about pseudogenes as the following title suggests ...
PSEUDOGENES: Are They "Junk" or Functional DNA?
Evgeniy S. Balakirev1,2 and Francisco J. Ayala1
1Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697-2525; email: email@example.com
2Institute of Marine Biology, Vladivostok 690041,
Russia and Academy of Ecology, Marine Biology, and Biotechnology, Far Eastern State University, Vladivostok 690600, Russia; email: firstname.lastname@example.org
And the answer may well turn out to be that it is in fact a broken gene, when more is known. But if the answer is "Yes, it IS broken", then there is another question which immediately follows. I mentioned this early on and we never explored it. The next questions would be these ... "Did it break independently in humans and apes? Or did it break in our ape-like ancestor and get transmitted to both apes and humans as Dr. Max asserts?" Is it not just as plausible that both ape and human GLO "broke" independently? Design hypothesis predicts similarity in the the two genomes also, but for a different reason than common descent advocates. It seems to me that it is quite probable that IF apes and humans did in fact at one time have functional GLO, the functional genes would have been quite similar (is it not true that OTHER functional genes found today in apes and humans are similar?)and the large differences b/t apes and humans that we see today would have also been seen at that time in the past. This scenario also seems to me to be supported by the 2003 Inai study comparing guinea pig and human pseudo-GLO. Guinea pigs and humans are obviously not in sister groups, but they both have pseudo-GLO, which actually has 36% "identicalness" according to the report. Are we to conclude that humans are more closely related to guinea pigs who (like humans) have pseudo-GLO, than to pro-simians who have functional GLO? It seems that the guinea pig-human pseudo GLO similarity all by itself falsifies common descent for apes and humans.
So I think the following possibilities exist ...
(1) Pseudo-GLO is NOT "broken GLO" and is found throughout the animal kingdom (either ubiquitously, randomly, or in nested hierarchies). This type of scenario, where a species has a functional gene and a pseudogene is not uncommon.
(2) Pseudo-GLO IS "broken GLO" and is only found in species unable to synthesize vitamin C ... this is because the gene "broke" in the ape-like ancestor, then this "broken gene" was copied throughout the evolutionary path to humans. If this is true, however, you would still need to explain how the gene broke independently in the guinea pig ancestor, but wound up in modern guinea pigs looking "36% similar" to modern human pseudo-GLO. You have the problem of the appearance that humans are more closely related to guinea pigs than to the pro-simians! (who have functional GLO)
(3) Pseudo-GLO IS "broken GLO" and is only found in species unable to synthesize vitamin C ... this is because all animals were designed with a functional gene, but now some have independently lost function because of mutations.
I realize that at this point, I have not given positive evidence for the Design Hypothesis regarding apes and humans, because that was not my goal on this thread. I have only pointed out that Dr. Max's assumptions -- (a) this is a broken gene and (b) if it is broken, this proves common descent -- are unwarranted assumptions.
This whole thread started because someone (I think Renier) said he used to be a YEC advocate, but abandoned it because of this issue which he thought was a closed case. If nothing else, I think I have shown that it is definitely not a closed case.
As for which of the above 3 scenarios is true, I obviously do not know yet. It does appear that (2) is not consistent with the evidence that we DO have. My suspicion is that (3) will turn out to be the correct one when more is known. Either (1) or (3) appears to be consistent with the Design Hypothesis.
ps Once again could you confirm or deny that you don't think we can infer any of this stuff as we didn't see it happen.
I confirm that we can indeed infer many things in spite of the fact that we did not see it happen with our own eyes. In fact, this is my exact argument on my other thread where I INFER a the idea of a Super-Intelligent Engineer from "apparently engineered" biological "machines." I also INFER an Intelligent "Parameter Setter" from the "apparent precise setting" of the many parameters required for life in the Cosmos in which we find ourselves.
1- This is ironical, coming from someone taking the Bible as evidence for his hypothesis.
Again, if you read my threads, you will see that Bible is a source for plausible hypotheses. It is not "evidence" to support them. My evidence comes from scientific observation of nature.
It's not an assumption. It's a tested hypothesis that follows from the theory of evolution. It's been cross-checked in thousands of organisms and it fits neatly with all the data. I asked you to explain why Nishikimi could expect to find gulo-homologous sequences in humans, orangs and guinea pigs, if not because of common descent. No response.
Are you saying that the analysis proposed by Argystokes has already been done? I know of GLO being analyzed in a few primates, guinea pigs and humans, but thousands of organisms?
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?
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. We need to be very careful in our quotes and our logic. I believe these types of assumptions, rushes to judgment, and lack of sound logic are precisely why Darwinists are painting themselves into a corner which will ultimately be an embarrassment to them. We have already seen the embarrasment to Darwinists of their failed predictions in the fossil record. Darwinists predicted continuous transitional forms in the fossil record. Creationists predicted ubiquitous gaps. Creationists were correct. Darwinists predicted true "vertical evolution" (or macro-evolution), but leading evolutionary scientists have now admitted that no true vertical evolution from one kind of organism to a more complex kind has ever been observed in all human history. Creationists predicted that any "evolution" would be lateral or downward and this has been confirmed. Creationists also predicted the limited variation that we see in natural and artificial selection, but Darwinists try to use this as evidence for their failed predictions of true vertical evolution, when in fact it is better evidence for "designed adaptability" put in the originl created "kinds" by the Creator. Since all this and many other things outlined by Denton and others have been embarrassing and unanswerable by Darwininsts, they are now repeating the same logical mistakes at the molecular level. I predict the results will be the same. And if that were not enough, they are calling Creationists and ID people stupid for questioning their theories!!
After all, it could be that the Flying Spaghetti Monster created us with his noodly appendage.
I admit this is a logical possibility. I challenge you to find evidence which supports it.
AFDave: Your smugness is quite grating. I assume you're doing that on purpose, no? It always amazes me how the preachiest christians lack what I would have thought would be the "zeroth commandment" of christianity: humility.
Have I not demonstrated humility by "eating crow" graciously about the chimp chromosome issue? I think what you perceive as smugness here is in reality a little bit of satire and poking fun at a theory. I am trying very hard to use innovative tools to jar people's thinking. I think Darwinists are so steeped in logical fallacies that it takes something rather jarring to make them wake up and see the errors.
I think that idea sounds a little screwy, but it does seem to me that some junk DNA won't be the vesigial stuff we are predicting. Supposedly 90 percent of our genetic material is this junk DNA, but our bodies don't support 90 percent junk organs -- or vestigial organs -- why would our DNA?
My point exactly. I am not familiar with the "fractal" theory or whatever it was. I do not claim to have an idea about what all that "junk DNA" does. It will be fun to investigate it though.
No, dave. It's not an assumption. It's an inference, based on evidence. There's a difference.
Thank you for agreeing with me (and Meyer) that INFERENCES to the Best Explanation are valid. This is exactly what I am doing on my other thread to try to explain a Creator.
I just performed a quick BLAST of GULO (exon 10), and the homology between human and chimp is 97%.
No surprises there, right?
So you want the original article? ... I can probably have it on Monday or Tuesday ...
Are you saying you will agree with me if I give it to you?
It's not even necessarily true on that 'one little piece of DNA'. Whats the sequence similarity for the GLOs? We just know in this discussion that two are broken. It's absolutely idiotic to use this single fact to infer things about common descent.
Steve! My buddy! You and I agree on something ... I KNEW it would happen sooner or later.
That's what I've been trying to say ... Dr. Max's article on T.O. uses this as evidence of common descent for apes and humans. My point has been all along that this assertion is not warranted with just this little bit of knowledge that we have.
But I'm also not saying it proves Common Design. It obviously doesn't, but it at least argues that either one is a possibility.
Again, the whole thing started with Renier saying "Look ... Dr. Max has proven common descent with this Vitamin C thing" which I think he has not.
afdave, that's just retarded! And you're quote mining. steve is talking about that so called 36% similarity being poor evidence of our relatedness to rats.
Aw come on ... you mean Steve isn't agreeing with me here? Bummer ...
Oh well ... gotta keep trying! Gonna happen sooner or later ...
I AM interested in hearing the outcome of the big Saturday night event ... "Max vs. Woodmorappe"
Faid? Any more analysis from your corner?
Why do you ask? Got anything to share?
I thought you were going to show why Dr. Max of Talk Origins is correct and Woodmorappe of AIG is wrong on this "Vitamin C gene" issue.
That's what we were talking about ...
There it is. They [AIG] don't do science, they do apologetics. They don't do any scientific research for themselves--the best you can say is that they are armchair critics.
Armchair critics ... er, yes ... sort of like you, right?
It's funny that Evos think that Creos should "do their own research." That would be like me saying "PT and TO people shouldn't quote researchers like Nikimishi and Inai ... they should do their own research!!"
Pretty silly argument, now, isn't it?
Yeah, I thought so ... you can take it back if you like ... I won't embarrass you by quoting you further.
So Dave, since 36% of similarity between the broken GLO genes in guinea pigs and human are very low and support our view, what is your interpretation?
My view is that Dr. Max made an unwarranted assertion by saying that "GLO mistakes" were copied from the common ancestor of apes and humans. I think the GLO situation we have in humans and apes today could just as easily support Common Design Theory.
Of course, it is fine for him to have that interpretation if he chooses. I just think we know too little to be dogmatic as he seems to be.
Renier said that basically this was a closed case for him and was the very issue that made him abandon the YEC position.
Separate issue: the guinea pig thing
This is interesting, but I'm not saying anything dogmatic about it. I really don't understand enough about it and I would value Jeannot's analysis of the AIG article. Jeannot, do you also have the Inai article that AIG quotes?
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?
Faid said ...
Dave, we're referring to AiG and all their proclaimed experts, like Woodmorappe, not you. You reply by referring to us.
And AiG does not quote scientific research that supports Genesis (because there isn't any, and they cannot come up with any), so they take existing scientific research and try to twist and distort its data to their liking. They're liars, dave.
I was not referring to you. What I said was ...
That would be like me saying "PT and TO people shouldn't quote researchers like Nikimishi and Inai ... they should do their own research!!"
My point was that people like Dr. Max on Talk Origins use other people's research (Inai, Nikimishi, etc.) and draw conclusions ... why shouldn't AIG do the same? Obviously they are going to have different conclusions because they hold a different world view. This is not lying. You have not shown me one lie they have told. You have shown me that Dr. Wieland was uninformed about transcription direction being unimportant. And I agreed with you. But you have not shown me that they lie.
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.
I do understand all this, yes. I think my understanding is correct that human and ape genes are about 95% (or 97) similar. My assumption would be that the inactivated GLO gene would likewise be approximately 95% (or 97 or whatever it really is) similar also. Is this correct? Or am I to understand that human and ape GLO is 100% IDENTICAL? Can someone confirm this for me?
If the former is true, then to me it is clear that Dr. Max's assertion that this proves common descent is an OK guess, but it doesn't close the case. One could just as easily say that apes and humans are separate designs and the GLO broke independently in each. Why should we think it would not? Apparently it did also break independently in guinea pigs.
And again, the 36% thing to me is a side issue. What I am trying to show is simply that Renier said that Dr. Max said that the broken GLO in humans is exactly 100% the same as in apes. Enter Dr. Max's copyright case. And yes, IF this is the situation we in fact have, then I would agree ... it looks like common descent.
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.
Creationism HAS provided many detailed explanations of the available data and has accurately predicted many things, including ubiquitous gaps in the fossil record and the inability to induce "good changes" or "vertical evolution" in fruit flies by "speeding up the evolutionary timescale." It has predicted a certain "fixity of kinds" and "downward evolution" (not "upward") (note we are using MY terminolgy here in which humans are "at the top" of the hierarchy and single celled organisms are at the bottom--this is my convention, of course, but I believe it to be a good convention which in many ways can be a useful organizational tool) which in fact has been observed--i.e. our bodies continue to accumulate more and more harmful mutations and the bacteria are winning, among other things. It hypothesized that coal does not require millions of years to form, but can be formed quite quickly. This has now been shown. It hypothesized that sedimentation such as that seen in the Grand Canyon is not formed gradually over millions of years, but is formed catastrophically. This has now been proven at Mt. Saint Helens where there is a "miniature Grand Canyon which was not there before 1980. Creationism and the idea of the the Curse has the only sensible description of human nature which lines up with what we actually observe. And many other things which we have already begun to get into on my "Creator God Hypothesis" thread.
According to common design, the creator would have put broken copies of a gene in each species, copies that reflect the current phylogeny, built with coding genes. Why would he? A broken gene is not part of a design, it's useless.
You said you would readily accept any evidence for common descent. I don't think you are sincere. What kind of proof would convince you?
Please see above. Can you confirm that the broken GLO gene is 100% identical to the broken ape GLO gene? If so, then I think you have something.
And what are your thoughts on the fact that AIG only referred to the 36% homology between guinea pigs and humans, but forgot to mention the 97% identity between us and chimpanzees? Silly mistake again?
No. Just irrelevant to their discussion. The whole Inai paper discussion (I think) is intended to show that "Guinea pigs GLO gene broke independently. Why shouldn't apes and humans GLO gene ALSO break independently? They may be trying to say something further than this also when they get into the pro-simian discussion and 36% etc., but I don't really follow that part of their argument. They freely acknowledge elsewhere that there is great similarity in ape and human genes, so it is clear they are not trying to obfuscate. They may think it will come in a bit less--maybe 90%--when more is known, but even if it stays at 95-97, this does no damage to their idea that apes and humans DO NOT share a common ancestor. A house builder builds many houses that look similar--97% similar probably--but this is obviously because of a Common Designer, not Common Descent.
By the way, the 36% 'similarness' number comes from 47 out of 129 substitutions, i.e. 47/129=0.36. I do have the complete Inai article, and they themselves say "A high percentage of the same substitutions in the total substitutions (36%) indicates that there were many hot spots for nucleotide substitution throughout the sequences examined." (Journal of Nutritional Science & Vitaminology, 2003, Vol. 49, Issue 5,p. 316). This does not lead to any profound conclusions for me ... how about you?
I did not see anything in this article which would confirm 100% identicalness of human GLO to ape GLO. Possibly some other article has this?
I keep asking, and you keep not answering: what, in the "common design theory", would have led Nishikimi to expect to find gulo homologs in humans and guinea pigs?"
To me it is quite conceivable that a Designer designed functional GLO genes in all the distinct "originally created kinds." The fact that Human Designers make similar structures to perform similar function should have led Nishikimi to expect to find homologues in the natural world as well. I don't think the genes have to be identical to be functional. Just as several different codons can code for a particular protein (I think that's correct, right?--help me all you genetics experts). Similarly, in the English language, I can say I'm going to go grocery shopping in a variety of different ways ... "I'm going to go buy some food" and "I'm gonna drop by Safeway and restock our vittles" and "I'm going to go to town and get our pantry restocked" all communicate the same idea but with very different words. There is no reason in my mind to think that the situation in genetics is any different than this.
Apparently the fossil evidence, DNA sequence analysis, chromosome structure, and a coherent theory are not enough. What kind of proof would convince you?
100% identicalness of the GLO gene between apes and humans would be a good piece of evidence to me. The whale evolution sequences presented to me are very unconvincing. The chromosome thing is the best one I have been given yet, but again, considering the above discussion, why couldn't a Designer have used the '2A and 2B' chromosome info that he used for apes, modified it slightly by fusing it and a few other changes, then inserted this into the human genome? Or vice versa. Maybe He used Human chromosome 2, split it into two and put it into the chimp genome as 2A and 2B. When an artist creates two pieces of artwork, they may be very similar, and the artist may reuse certain pieces of one in creating the other. Certainly software 'artists' do this. I've done this myself many times. Why write a second program entirely from scratch when you can reuse some code snippets and save yourself some time? Again, I am not saying here that I can prove this definitely happened. I am just saying that it is perfectly plausible and exactly what we should expect from a Designer. Some kind of 'upward evolution' (my definition of upward -- humans at the top, one-celled organisms at the bottom) in fruit flies would be impressive. I think these experiments try to 'fast forward' evolution. But all I've ever heard of is dead fruit flies, deformed fruit flies, etc. Never 'advanced' fruit flies with major increased abilities.
Jeannot said ...
Anyway, the percentage of identical substitutions between human and chimp is certainly well above 36%.
I would expect it to be around the same as the general genetic similarity -- 95-97%. This would be consistent with Design Theory.
To check that, we should gather several sequences from rodents, primates (and maybe other mammals), if available, and build a maximum likelihood our parsimony phylogeny. The three sequences alone (rat, guinea pig and human) won't do.
Agreed. Does anyone have a paper comparing human and chimp GLO, for example? Is it 100% identical? Or 95-97% as I predict.
...You know, it's a good thing creationists like Dave drop by from time to time and try to "enlighten" us: It helps us refresh things we had forgotten, learn things we didn't know, have constructive debates (such as this) we'd normally not have, and in the end appreciate science even more.
See ... even ugly, flea-bitten dogs are good for something ... to throw rocks at, kick when your mad, etc. :-)
Faid said ...
Did I mention that this is fun?
Well ... at least I am contributing entertainment value to everyone if nothing else ... think of me a side show at the carnival that you didn't have to pay for!
I wonder why AFDave isn't hear setting you all straight about your convergences and your BLASTs and what have you.
Oh, I was there alright. I actually read these posts on my Blackberry at church during the boring announcements. I just have never tried posting from my Blackberry.
From what I hear, he's busy posting over at his newfound haven at UD right now. But I'm sure he'll be back...
Oh yes. I'll be back. I wouldn't call UD a haven. Those guys all agree with me. What fun is that? I just thought I'd better spread the word about that fun quote from TO before someone at TO changes it to sound ... er ... less supportive of Creos.
And he has a website:
He gets Warren Buffet quoting Jesus:
But he doesn't seem to know that Warren Buffet is an atheist, like Bill Gates and George Soros.
Oh I know he is. That's irrelevant to me. I posted this in response to a friend that maintains that you shouldn't be quoting Jesus at work. My response was "Well, why not? Warren Buffet does!"
While you are at my blog site, you guys HAVE to try my "Mist, Ghost or Computer Graphics?" link ... but turn your speakers up loud.
When did the split occur Dave? around the time of pharoah? Oh right you don't think there WAS a split. Interestingly, you sparked a conversation between two people who DO know what they are talking about and got some interesting info.
Of course. I like it when this happens. BTW, I did see your questions and I have good answers, but I'm on a particular train of thought and would like to answer them in my own sequence. Did you read the latest page on my "God Hypo" thread?
Dave, no one understand why you want GLO to be 100% identical between human and chimps, since that's precisely what evolution doesn't predict. This pseudogene is not selected, so it can freely accumulate mutations at a high rate.
I just thought this was the whole premise of Dr. Max's argument -- that a mistake was copied identically from the common ancestor to apes and also to humans.
If this is not the case, then he does not have an argument, in my opinion.
He does not have an argument, in my opinion, if the error is not copied 100%. Remember the copyright case that Dr. Max made an analogy to?
If we are just talking about the same difference as with other genes, then this is just as easily explained by common design as common descent.
Everyone else--I'll look at your points in the morning.
OK. It's time for a review.
Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far
The Daily Wingnut