Antievolution.org - Antievolution.org Discussion Board -Topic::Thread for Cryptoguru

Posted: Jan. 16 2015,09:09

Hi Kevin,

thanks for the introduction.

I'm going to pose the following definition/algorithm of biological evolution, please feel free to disagree and post what you think it actually is.

Here are some assumptions:
1) DNA is a self-replicating computer code, a list of instructions that is used by a cell to build a specific organism by a very complex and highly non-linear process that involves transcription and translation.
2) DNA is randomly mutated at the level of nucleotides (i.e. the letters of the programming code, not the functional/gene level)
3) Natural selection is not an intelligent entity, therefore it cannot evaluate the performance of an organism. It is the name given to the process whereby more suitable organisms survive and others die ... achieved by a selective pressure being applied to the environment (e.g. availability of food/water, predators etc.)

Evolution is:
1) take an organism and let it replicate
2) random mutations should be introduced to the offspring DNA.
3) a selective pressure is applied to the environment the organisms live in
4) less fit organisms will die before replicating due to the pressure
5) most fit organisms will continue to replicate and mutate
6) eventually new functions and traits will emerge

Biological Evolution is presented as a scientific law, it is simple to define, so should be simple to model

My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.

caveats:
- Mutation can't simply combine functions in different arrangements. Mutation must occur on the code that defines the functions themselves, and affect the ability of the organism to build itself, to function and to replicate.
- the selective process can't include measuring properties of the organism to remove them from the population, the selective process must rely on organisms dying off due to the environmental factors. (e.g. energy)

It may sound subtle ... but breaking these laws means that you're not modelling biological evolution, you're performing functional optimisation. This is VERY different, as the degrees of freedom of the problem have been limited so that a solution is either stochastically highly likely or definite.

So far I have seen no model that satisfies the conditions to be a true model of biological evolution. I am not doubting that there are numerous models that show the seeming emergence of complexity. However, when you limit the problem to randomly selecting functions to solve a problem, if the problem space is well defined and the functional space is limited then you are simply performing a stochastic search .. this is NOT evolution. You are not inventing functions out of nothing, you are finding the best way to perform a pre-determined function.

I assert that it is impossible for a truly random mutation process to create new functionality if that functionality doesn't exist already in component form.
EXAMPLE
Given all the parts for a clock in sensible quantities it is reasonable to assume that randomly choosing components until you get a functioning clock through an optimisation algorithm is completely achievable.
Blind Watchmaker Evolution
However, if you didn't define the component parts and allowed random shaped parts to be randomly mutated as well as selected and combined through a similar optimisation algorithm, you would never expect to get a working clock. (this is what biological evolution is claimed to do)

I know of AVIDA, but it uses 26 predefined functions to combine to solve optimisation problems ... it doesn't mutate the code that defines these functions or how they're executed. It also doesn't model real-world selection.

I am a computer modeller and Mathematical Biology researcher, so I'm writing my own code which I believe will demonstrate the proposed mechanism more accurately ... I will share (with source) when it's done.

I am interested in an intellectual discussion here, not a creationist-bashing flame-war ... if you don't have any scientific answers that hold up to scrutiny please don't just post insults as though that's going to help. And please don't just make unsubstantiated claims, back them up with logic or research that can be shown to be applicable to this issue.

Cheers

Crypto

JonF

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Posted: Jan. 16 2015,09:22

Define "adding information".

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Joined: Mar. 2008

Posted: Jan. 16 2015,09:33

Quote

- Mutation can't simply combine functions in different arrangements. Mutation must occur on the code that defines the functions themselves, and affect the ability of the organism to build itself, to function and to replicate.

Well that's not exactly what happens in biological evolution. It is rare for the infrastructure of translation to change. It would seem that the likelihood of a mutation being tolerated is inversely proportional to its effect on the cell infrastructure.

That's a rather sloppy way of saying that vital functions are highly conserved.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

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Posted: Jan. 16 2015,09:33

Many things are simple to define but appallingly complex, if not impossible, to model. Fluid flow is one vast field where there are simple descriptions and definitions of phenomena that resist modeling.
The same goes for economics.
The same goes for such iterative functions as produce the Mandelbrot and Julia sets, as well as a host of other similar phenomena. I add these because while we can 'model' them by virtue of producing the simple equation and iteration process involved, we cannot, in principle, predict what will be the result at any given point. Models are not perfect predictors, nor is that their purpose.
Finally, let us note that the current absence of a model does not say anything about the possibility of ever modeling any particular phenomenon. What we can say is that, in principle, it is impossible to assert that any given model can be predictive of real-world results, regardless of how many models are, in fact, predictive of such results.

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Posted: Jan. 16 2015,09:46

Quote

However, if you didn't define the component parts and allowed random shaped parts to be randomly mutated as well as selected and combined through a similar optimisation algorithm, you would never expect to get a working clock. (this is what biological evolution is claimed to do)

If you intend to model evolution (possibly with the intention of demonstrating that life cannot arise "spontaneously," Your component parts will be expressed as chemistry.

Before wasting your time, please solve the problem of emergence. Demonstrate that you can predict, for example, the properties of water by deriving them from the properties of hydrogen and oxygen.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

damitall

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Posted: Jan. 16 2015,09:51

I believe that Dr Elizabeth Liddle ("Febble", and "Pingu") has ideed modelled the addition of new information in an computer simulation of evolutionary process - at least that type of information known to IDists as "CSI" or any one of a number of related acronyms.

I can't be arsed to look it out, but an intelligent search of The Skeptical Zone should reveal it.

It certainly caused an outbreak of the malice and vituperation to be expected from IDists with no answers

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Posted: Jan. 16 2015,09:55

Quote (cryptoguru @ Jan. 16 2015,10:09)

...
Here are some assumptions:
1) DNA is a self-replicating computer code, a list of instructions that is used by a cell to build a specific organism by a very complex and highly non-linear process that involves transcription and translation.

Questionable definition -- it is almost certainly question-begging, if not entirely incorrect, to assert that DNA is a 'computer code'. To do so is to take metaphorical language and reify it to the point where the specific phrase becomes meaningless.

Quote

2) DNA is randomly mutated at the level of nucleotides (i.e. the letters of the programming code, not the functional/gene level)

OK, but this obscures the fact that function is tied to specific DNA arrangements. Note, too, that those arrangements include physical folding and proximity to other DNA fragments.

Quote

3) Natural selection is not an intelligent entity, therefore it cannot evaluate the performance of an organism.

Half true, half radically false. Yes, 'Natural Selection' is not an intelligent entity, but this is because it is not an entity at all. It is a process. The distinction matters. Whether this process can, or need be, called 'intelligent' really depends on what your operational definition of 'intelligence' is. I know researchers who take a stance towards intelligence that includes processes such as natural selection within the scope of intelligent behavior. I know others who reject that judgement. You appear to be taking an anthropomorphic, physicalist (i.e., embodied) approach to intelligence such that 'natural selection', not having a body (or a soul?) cannot be 'intelligent'. What's your operational definition of 'intelligence' such that you can support your assertions using the term?

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It is the name given to the process whereby more suitable organisms survive and others die ... achieved by a selective pressure being applied to the environment (e.g. availability of food/water, predators etc.)

Correct but misleading. What natural selection does is always negative. It weeds out failures. The failures are always with respect to the organism's current environment and is only usefully evaluated at the group level.

Quote

Evolution is:
1) take an organism and let it replicate
2) random mutations should be introduced to the offspring DNA.
3) a selective pressure is applied to the environment the organisms live in
4) less fit organisms will die before replicating due to the pressure
5) most fit organisms will continue to replicate and mutate
6) eventually new functions and traits will emerge

Biological Evolution is presented as a scientific law, it is simple to define, so should be simple to model

See my previous reply.

Quote

My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.

Why the insistence on a computer model? Lenski et al have performed this over tens of thousands of generations in the lab and verified the process. What more is required?
How is gene duplication not an increase of information in an organism? Trivially, the information of the number of genes, and therefore DNA base pairs, has changed, in fact, increased.

Quote

caveats:
- Mutation can't simply combine functions in different arrangements. Mutation must occur on the code that defines the functions themselves, and affect the ability of the organism to build itself, to function and to replicate.

Why?

Quote

- the selective process can't include measuring properties of the organism to remove them from the population, the selective process must rely on organisms dying off due to the environmental factors. (e.g. energy)

Weasel-worded and a distinction without a difference.
If it's done in a computer model, measurement will happen, albeit properly the measurement does indeed need to be of survival(reproduction)/failure(to survive and to reproduce). How else do you propose to determine the whether selection occurred at all in a computer model? Randomly? That is invalid for ecosystems due to the inherently constrained nature of the 'change space'. See below.

Quote

It may sound subtle ... but breaking these laws means that you're not modelling biological evolution, you're performing functional optimisation. This is VERY different, as the degrees of freedom of the problem have been limited so that a solution is either stochastically highly likely or definite.

As I said before, weasel-worded. A distinction without a difference. Natural selection is a functional optimization. And the work has been done in the lab that verifies it.

Quote

So far I have seen no model that satisfies the conditions to be a true model of biological evolution. I am not doubting that there are numerous models that show the seeming emergence of complexity. However, when you limit the problem to randomly selecting functions to solve a problem, if the problem space is well defined and the functional space is limited then you are simply performing a stochastic search .. this is NOT evolution. ...

No, that is simply confused.
The problem, in part, is that the random changes are inherently constrained by the laws of physics, chemistry, and thermodynamics. The 'change space' is not infinite although it may be unimaginably large. The ever changing 'problem space' against which the specific changes which occur are evaluated is also inherently constrained by the laws of physics, chemistry, and thermodynamics. It is not infinite even if it might be unimaginably large.
Neither the 'change space' nor the 'problem space' is free to vary perfectly randomly.
There is also the factor of time. Either space may hold relatively constant while the other space changes at a greater or lesser rate. Both spaces may change relatively quickly or slowly. Neither space may vary much. Over varying spans of time, these temporal factors matter tremendously.

cryptoguru

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Posted: Jan. 16 2015,10:06

My field of research originally was fluid mechanics, lately I've applied that to biological chaotic flows. I've written a LOT of programs that model fluids. We can accurately model the components of fluid flow (as well as chemical reactions with them), sure it's complicated but we can do it ... and we can compare them to real-world observations. (Watch any Disney 3D animated movie). We can model complex environmental interactions too ... it's done everyday and applied to thousands of useful real-world problems.

The definition of evolution is simple and it's implementation is simple too ... a self-building, self-replicating entity is mutated so that the code that runs it is mutated at an atomic (nucleotide) level. That's easy to model, I can write code to do that in a couple of hours ... my point is the other models that are used as "proofs" of the theory evolution do not prove anything, they simply solve optimisation problems, which is not the same thing.

JonF: "adding information" - new and novel functions that didn't exist before that solve a problem that wasn't solved previously.

midwifetoad: I'm not just asking that vital functions be conserved I'm asking that the overall net effect is improvement after mutation occurs on the definition of the code that is being run. DNA is an information system, it defines the process by which something is built ... we are mutating THAT. Not simply selecting between functions.

midwifetoad: the properties of water are observed, we understand the physics and chemistry behind them. We don't need to model things from atoms ... but we do need a model that reflects the theory to test the theory is sound, we don't have that with evolution.

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Posted: Jan. 16 2015,10:19

Quote (cryptoguru @ Jan. 16 2015,11:06)

... That's easy to model, I can write code to do that in a couple of hours ... my point is the other models that are used as "proofs" of the theory evolution do not prove anything, they simply solve optimisation problems, which is not the same thing.

Why and how not?

Evolution is the solution of an optimization problem. Optimize the reproductive success of ever changing, in constrained ways, collections of organisms in an every changing, in constrained ways, environment.

As to 'easy to model, I can write code to do that in a couple of hours', well, no you can't. Not and model all the factors involved in physically functional (in all senses) genes or chromosomes. If you could, we'd have a trivial solution to the folding problem, and we don't. Physical structure is inherently bound to a wide variety of factors impacting the existence and functionality of specific DNA segments in situ. Slight changes to chemical structure can have anywhere from minor to overwhelming impact on the physical structure, and vice versa. Your 'couple of hours effort' model is so flawed as to be meaningless for an actual simulation of the reality you are attempting to assess or reject. It provides essentially zero guidance to what can and does happen in the living environment in the chemical, physical, and thermodynamic realities constantly at play at the level of DNA. You might as well be solving the 3 body problem by recourse to the behavior of balls swung on the end of strings.

Also, I note you ignored a couple of my key points in your rejoinder: the success of any number of computer molding strategies says nothing whatsoever about the in principle solvability of all problems with computer modeling strategies. This has been proven as well as demonstrated, countless times in countless fields.
Nor does the present absence of any particular model or computer simulation speak to the in principle possibility or lack thereof of a future model.

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Posted: Jan. 16 2015,10:19

It has already been noted that you are reifying a metaphor. DNA is not a computer program, It is a molecule.

The map is not the territory. Dawkins' Weasel does not prove evolution (although it would be interesting if it didn't work).

Now if you, in your brilliance, can model the HOX gene and can model how variations in form and body plan can be made by varying the timing of developmental events, you might have something useful.

But what will be demonstrated if you fail to model biological evolution? I can write a program that doesn't work.

I'm trying to get a grip on your hypothesis. What are you trying to demonstrate?

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

cryptoguru

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Posted: Jan. 16 2015,10:33

Quote

if not entirely incorrect, to assert that DNA is a 'computer code'

I've been over this ground on the other site.
DNA is a computer code ... a living cell is a computer, not analogous to a computer, but IS a computer.
This is a true statement because it fulfils the definition of a computer as a Turing machine.
This is also proved by the fact that we use the living cell as a computer ourselves now
DNA computing - Wikipedia
There are LOTS of evolutionists who attest to this fact.

The reason you're avoiding this definition is because you want to keep it mysterious and difficult to pin down.

Quote

OK, but this obscures the fact that function is tied to specific DNA arrangements. Note, too, that those arrangements include physical folding and proximity to other DNA fragments.

I don't see how what I said contradicts that? I'm just speaking in generic terms.

Quote

You appear to be taking an anthropomorphic, physicalist (i.e., embodied) approach to intelligence such that 'natural selection', not having a body (or a soul?) cannot be 'intelligent'.

I think you're jumping the gun here, I'm not claiming Natural Selection is powerless to do anything, I'm just asserting that it is not like a god ... it can't measure and evaluate, it's not magic. It is simply the process of filtering organisms that don't work in their environment. It's not the Grim Reaper going around choosing who to kill. Therefore modelling processes that attempt to model natural selection as though it is intelligent are incorrect.

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Correct but misleading

Again, I complete agree with your definition there ... I am not trying to be sneaky. Nothing I said disagrees with your understanding of natural selection, unless you think it IS magic.

Quote

Lenski et al have performed this over tens of thousands of generations in the lab and verified the process

Lenski has demonstrated E. Coli doing exactly what E Coli is programmed to do, it adapts (this is true of all viruses and bacteria) ... this does not demonstrate new features. They've performed an equivalent of millions of years of evolution ... where's the more complex life-forms? They're still bacteria!

Again ... a computer model should be able to at least prove the theory is possible.

Quote

The problem, in part, is that the random changes are inherently constrained by the laws of physics, chemistry, and thermodynamics

You're grasping at straws ... random mutations are random. Natural selection is purely the ability for the organism to keep on reproducing. It can fail to do that for many reasons e.g. competition for food, disease etc
But the process is simple

Quote

If it's done in a computer model, measurement will happen, albeit properly the measurement does indeed need to be of survival(reproduction)/failure(to survive and to reproduce). How else do you propose to determine the whether selection occurred at all in a computer model? Randomly?

I completely agree ... but we should be doing as you suggest measuring survival and not measuring for example how fast something goes. If we want to measure speed competition, we need to let the organisms have speed and see which survive, not calculate speeds and set an arbitrary threshold ... does that make sense to what I'm saying now?

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Posted: Jan. 16 2015,10:37

Quote (cryptoguru @ Jan. 16 2015,09:09)

My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome. [emphasis added]

Whether or not you, yourself, are a Creationist, cryptoguru, this challenge of yours is (whether you realize it or not) the hoary old mutations can't create new information argument beloved of Creationists, just dressed up in computer terminology. So please, tell us if you will: What does "new information" look like? Given an arbitrary string of nucleotides, and a mutation which alters that string of nucleotides, how can you tell whether or not the post-mutation version of that string contains any "new" information?

cryptoguru

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Posted: Jan. 16 2015,10:43

midwifetoad:

I explained to you why it is a computer program. You call DNA a double helix, it is a definition of it's shape. A computer program is a definition of its function.
You need to understand the definition of a computer.
Nature article on cell being Turing machine

I'm not trying to model the WHOLE of proposed biological evolution ... what nonsense are you suggesting?

I'm modelling the key components ... a key component is the code that is executed by the cell's operating system is mutated, which gives the possibility of it crashing (death) ... this is what we observe through genetic mutations.

I'm suggesting we model the core tennets of evolution ... existing models do not do this.

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Posted: Jan. 16 2015,10:51

When you build such a model that works, I'll be impressed.

Explain why I should be impressed by a model that fails.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

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Posted: Jan. 16 2015,10:52

Avida.

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"You can't teach an old dogma new tricks." - Dorothy Parker

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Posted: Jan. 16 2015,10:55

Quote

I explained to you why it is a computer program. You call DNA a double helix, it is a definition of it's shape. A computer program is a definition of its function.

The word program is a metaphor. You cannot determine the limitations of DNA from the limitations of a computer program.

Just as you cannot determine the existence or non-existence of a landscape feature from a map.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

Doc Bill

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Posted: Jan. 16 2015,10:55

Greetings, NotGuru, we meet again!

Perhaps a full disclosure of your real purpose is in order. I present to you NotGuru's Agenda:

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I paint evolution (non-science) as faith ... because it is.
It's an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who've wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

You still don't address any of the gaping black holes that I've pointed out.

I'm thinking this one is a Gary Gaulin clone, but super tard charged. If you don't mind I'll duck out and get some popcorn.

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Posted: Jan. 16 2015,11:03

Quote (cryptoguru @ Jan. 16 2015,09:09)

My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.

Certainly. Dr. Lenski used the Avida program to show the evolution of new functions.

The cover page is The Evolutionary Origin of Complex Features

The detail is line of descent.

For "new informaiton" you will need to tell us how you are calculating the quantity of information present. Evolution can increase both Shannon and Kolmogorov information. Are you using a different measure?

rossum

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The ultimate truth is that there is no ultimate truth.

OgreMkV

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Posted: Jan. 16 2015,11:18

Perhaps, he will listen to you guys. I've said all this already.

crypto, perhaps you should explain, in detail why AVIDA does not do what the writers of the software say it does... and show that it does in the paper I provided you.

This ought to be entertaining.

We desperately need a popcorn smiley.

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Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

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Posted: Jan. 16 2015,11:47

Quote (cryptoguru @ Jan. 16 2015,11:33)

Quote

if not entirely incorrect, to assert that DNA is a 'computer code'

I've been over this ground on the other site.
DNA is a computer code ... a living cell is a computer, not analogous to a computer, but IS a computer.

Prove it. Don't assert it, prove it.
You can't because there simply are no significant respects in which it is true.
The entire realms of thermodynamic effects and of self-assembly, with constrained errors, and self-repair, with constrained errors, simply have no equivalent in computers. At all.
This metaphor is wildly less accurate and wildly less appropriate to the cases at hand than 'natural selection'.
So, once again, prove it. Don't assert it, don't point me to garbage sites where you've also asserted it.
It's a simple proposition, it should be simple to prove, without abstracting away all the differences that make a difference.

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This is a true statement because it fulfils the definition of a computer as a Turing machine.

A computer is a Turing machine. Are all Turing machines computers? Proof please.

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This is also proved by the fact that we use the living cell as a computer ourselves now
DNA computing - Wikipedia
There are LOTS of evolutionists who attest to this fact.

Irrelevant and absurd. We can use strings and beads as calculating machines, this does not mean that strings and beads are calculators.

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The reason you're avoiding this definition is because you want to keep it mysterious and difficult to pin down.

No. And offensive.
We're 'avoiding' this definition because it is not a definition and because it is incorrect. It is analogy run amuck.

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OK, but this obscures the fact that function is tied to specific DNA arrangements. Note, too, that those arrangements include physical folding and proximity to other DNA fragments.

I don't see how what I said contradicts that? I'm just speaking in generic terms.

And the genericity is where you go wrong. The same set of DNA patterns operate, or fail to operate, depending on the physical arrangement of other DNA patterns, which are dynamic over time.
That you don't understand this fundamental fact demonstrates that you are unprepared to make the claims you are in fact making.
Do you even know what the folding problem is? Or why it matters, and matters particularly in this problem space?

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You appear to be taking an anthropomorphic, physicalist (i.e., embodied) approach to intelligence such that 'natural selection', not having a body (or a soul?) cannot be 'intelligent'.

I think you're jumping the gun here, I'm not claiming Natural Selection is powerless to do anything, I'm just asserting that it is not like a god ... it can't measure and evaluate, it's not magic.

Disagreement without basis. No one is claiming it is, or 'is like' a god (for one thing, it is not fictional or mythical, it does not operate by miracles, and it can be seen in action in controlled and well-defined tests, none of which can be done with any god ever proposed). It is, in the sense it which you are using it here, a description of a process of evaluation, of measurement. It measures, it evaluates, reproductive failure. That's all it has to do.
We have operational definitions. It appears you do not.

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It is simply the process of filtering organisms that don't work in their environment. It's not the Grim Reaper going around choosing who to kill. Therefore modelling processes that attempt to model natural selection as though it is intelligent are incorrect.

Quote

Correct but misleading

Again, I complete agree with your definition there ... I am not trying to be sneaky. Nothing I said disagrees with your understanding of natural selection, unless you think it IS magic.

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Lenski et al have performed this over tens of thousands of generations in the lab and verified the process

Lenski has demonstrated E. Coli doing exactly what E Coli is programmed to do, it adapts (this is true of all viruses and bacteria)

Can you say 'begging the question'? You appear to be arguing that cells/organisms are programmed by asserting as one of your premises that cells/organisms are programmed.
You are also making recourse to a particularly problematic undefined metric -- what and how do you determine which organism is 'more advanced' than some other? What is the metric of advancement? It is, in fact, a holdover from superstition that saw all life as a glorious unfolding of lower creatures to higher creatures, culminating in mankind. Which is indefensibly stupid not least because it is entirely unsupported by facts of any sort.
Either all creatures are equally advanced, or bacteria are far more advanced than humans because they've been evolving for more generations.
Either drop this 'more advanced' crap or provide facts, evidence, logic, and operational definitions to make it clear and unequivocal for all to see.

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... this does not demonstrate new features. They've performed an equivalent of millions of years of evolution ... where's the more complex life-forms? They're still bacteria!

They are 'more advanced' bacteria in that they demonstrate features strictly absent from the parent population.
How does this not meet your challenge? You're refusing to accept it because it leaves you without a foundation for your creationism.

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Again ... a computer model should be able to at least prove the theory is possible.

See responses from others.

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The problem, in part, is that the random changes are inherently constrained by the laws of physics, chemistry, and thermodynamics

You're grasping at straws ... random mutations are random.

No, they are only random with respect to certain factors, such as future needs of the organism. They are highly constrained. You are handwaving away the hard problem, essentially by ignoring it. The results of that act of ignorance are errors which permeate your argument from the point of deciding these critical factors don't matter. It's as if you were arguing that the SR-71 could not be supersonic because your plastic model would melt at the friction imposed at mach speeds.

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Natural selection is purely the ability for the organism to keep on reproducing. It can fail to do that for many reasons e.g. competition for food, disease etc
But the process is simple

Quote

If it's done in a computer model, measurement will happen, albeit properly the measurement does indeed need to be of survival(reproduction)/failure(to survive and to reproduce). How else do you propose to determine the whether selection occurred at all in a computer model? Randomly?

I completely agree ... but we should be doing as you suggest measuring survival and not measuring for example how fast something goes. If we want to measure speed competition, we need to let the organisms have speed and see which survive, not calculate speeds and set an arbitrary threshold ... does that make sense to what I'm saying now?

And we're back to the critical issue of exactly what do you mean by 'intelligent'. As you use it here, you appear to mean that intelligence is inherently purposive, that it operates with 'purpose aforethought'. That is a peculiarly anthropomorphic, and ultimately too tightly restrictive, a definition of 'intelligence'.
It's clear you throw the word around as a magic wand because you do not, and likely cannot, provide an operational definition that will suit in all cases of your use of the term.
NO ONE is asserting that 'natural selection' is any sort of Grim Reaper going around and thinking about which individuals out of which groups are going to live or die at any given time. Why would anyone assert that when it is so clearly incorrect?
What 'natural selection' is is simply a description of the failure of certain contained-random changes in the genome to persist in a population across time in a given constrained-random environment. It requires no purpose, no planning, no intention or intentionality. It's how the world works. No one has ever shown otherwise.
Nor has anyone shown that changes to the genome do not occur, randomly with respect to their environment and constrained by the laws of physics, chemistry, and thermodynamics.
Nor has anyone shown that information cannot increase due to simply chemical and physical processes, constrained in various natural ways including thermodynamically and by containment.
You've ignored the examples that demonstrate this.
Why is that?
Is 'information' another magic word that you throw around without being able to provide a consistent coherent operational definition for?

qetzal

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Posted: Jan. 16 2015,11:53

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.

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Posted: Jan. 16 2015,12:03

Quote (qetzal @ Jan. 16 2015,12:53)

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.

Heh. ha. haHaHa! Bwahahahahahahaha!
ROFL

I think we're done here.

Except, of course, he's not accepting Lenski's work as having done what it has so clearly done.
What's wrong with Lenski's work, crypto? How are your challenges not already met?

OgreMkV

Posts: 3668
Joined: Oct. 2009

Posted: Jan. 16 2015,12:04

I'd like to add that natural selection is not always a death.

It can be an effective removal of the gene pool. For example, the strongest, fittest, most efficient lion ever born might have a problem reproducing. Which means that he is removed from the gene pool. He can't pass his genes on to the next generation, so he's out of contention.

I'll note that the paper by Lenski (http://myxo.css.msu.edu/papers....lex.pdf specifically mentions that happening in some of their digital organisms.

Quote

However, two mutations reduced fitness by >50%.
One was a point mutation that disrupted replication efficiency. Its
harmful effect was eliminated by the next mutation in the line of
descent, which occurred at a distant site in the genome. The other
very deleterious step was a point mutation, at depth 110, that
knocked out NAND, one of the simplest logic functions. Only two
individuals had this maladapted genotype, yet their descendants
emerged as eventual winners. In fact, in the very next step, this
genotype produced the mutation that gave rise to EQU. Was that
deleterious mutation extremely lucky to hitchhike with such a
beneficial mutation? Or was the deleterious mutation a prerequisite
for producing the EQU function within that genome context? To
distinguish between these hypotheses, we reversed this one-stepprior
mutation in the genotype that first expressed EQU. This
reversal eliminated the EQU function. Therefore, a mutation that
was highly deleterious when it appeared was highly beneficial in
combination with a subsequent mutation. The evolution of a
complex feature, such as EQU, is not always an inexorably upward
climb toward a fitness peak, but instead may involve sideways and
even backward steps, some of which are important.

Note that the "deleterious" mutation, which dropped fitness by greater than 50% was one mutation that resulted in the most fit individuals.

If you program this kind of thing OUT of an evolutionary algorithm, then it is not matching biology (as crypto demands of it).

I will ask a third time, crypto, have you read this paper? It's sort of a massively important paper in the field.

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Posted: Jan. 16 2015,12:13

First, I think Crypto needs to model and replicate in silico, Lenski's result. That would be the bare minimum for a competent model.

If that isn't sufficient, we could discuss the insufficiency later. But first things first. Let's see if we can model microevolution.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

OgreMkV

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Posted: Jan. 16 2015,12:17

BTW: Here's an interesting interpretation of that duon article you linked to.

http://sandwalk.blogspot.ca/2014....ion.htm

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stevestory

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Posted: Jan. 16 2015,12:18

i wonder if he has something not already covered in the Index to Creationist Claims

I doubt it.

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Posted: Jan. 16 2015,12:22

The most important thing that needs to be modeled is the robustness of biochemistry, it's ability to tolerate variation.

Living populations contain multitudes of unique mutations. Individuals are seldom exact copies of other individuals.

So the model operating system and cpu need to have this kind of flexibility built in.

That's why I said early on, that if one is trying to model the origin of life or early evolution, one needs to model chemistry.

Current living things rarely (successfully) change their operating system.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

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Posted: Jan. 16 2015,12:55

Quote (OgreMkV @ Jan. 16 2015,12:17)

BTW: Here's an interesting interpretation of that duon article you linked to.

http://sandwalk.blogspot.ca/2014.......ion.htm

That doesn't work for me. I'll try again.

http://sandwalk.blogspot.com/2014....on.html

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

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Posted: Jan. 16 2015,13:16

I guess he'll be back in a couple of hours with his model.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

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Posted: Jan. 16 2015,18:57

Quote (Doc Bill @ Jan. 16 2015,10:55)

Greetings, NotGuru, we meet again!

Perhaps a full disclosure of your real purpose is in order. I present to you NotGuru's Agenda:

Quote

I paint evolution (non-science) as faith ... because it is.
It's an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who've wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

You still don't address any of the gaping black holes that I've pointed out.

I'm thinking this one is a Gary Gaulin clone, but super tard charged. If you don't mind I'll duck out and get some popcorn.

Is that text an actual quote from cryptoguru, or is it a concise summary of cryptoguru's ideas which doesn't actually use their specific phrasing? I ask because I tried googling that quote, and I couldn't find a source.

cryptoguru

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Posted: Jan. 16 2015,19:14

yeah I thought this would happen ... too many people with different points to address, and not enough time.
(and you guys accuse creationists of Gish Gallop)

Let me address some key ones ....
RE: living cell IS a Turing machine, therefore is computer

Quote

Prove it. Don't assert it, prove it.
You can't because there simply are no significant respects in which it is true.
The entire realms of thermodynamic effects and of self-assembly, with constrained errors, and self-repair, with constrained errors, simply have no equivalent in computers. At all.

Thermodynamic effects, self-assembly and self-repair are all things that a digital computer can do. We use thermodynamic effects in random noise generators, we can build computers using robots that are run by the same computers. Self-repair of the operating system, programs and data is one of the most common things implemented by computer hardware and software.
What do you mean by constrained errors?
So no ... why is it important to you to contradict this simple definition of how DNA in a cell works?

Here is the definition of a turing machine
Turing machine formal definition
The way DNA is processed in a living cell satisfies this definition as agreed with by the evolutionary biologist in the Nature Journal entry I linked to earlier.

Here is the definition of a computer
"A computer is a general purpose device that can be programmed to carry out a set of arithmetic or logical operations automatically. Since a sequence of operations can be readily changed, the computer can solve more than one kind of problem."

DNA as it is transcribed and translated satisfies this definition. We know for example that DNA is functionally non-linear and controls the expression of other parts of the DNA (eg HOX genes and other regulator genes) ... these are complex flow and boolean logic operations. The expression of multiple reading frames (6 we know of ... and potentially others in 3 dimensional space when DNA is folded) in DNA is an example of complex logical operations, which is controlled by boolean logic.

A computer is a Turing machine and vice versa.
DNA is a functional code ... it is processed as a code in the living cell, the functions in the code are used to efficiently describe how to build highly complex structures and to be able to replicate and differentiate its function as it progresses. This is more complicated, robust and versatile than any computer we've ever built or could probably conceive of building.
So my point is DNA is a code that runs in the computer of the living cell, it is more complex than any computer we know .... so how can corruption (mutation) to the operating system code and the program code result in better function? This contradicts our experience, and I claim has still not been demonstrated to happen.

Quote

I'd like to add that natural selection is not always a death.

It can be an effective removal of the gene pool. For example, the strongest, fittest, most efficient lion ever born might have a problem reproducing. Which means that he is removed from the gene pool. He can't pass his genes on to the next generation, so he's out of contention.

Haha amazing ... how did he get removed from the gene pool? A Gene pool isn't actually like a swimming pool you know, genes don't get thrown out for breaking the rules by the life-guard ... He gets removed from the "Gene pool" (population) by dying ... he dies before reproducing (for whatever reason), so his genes aren't passed on. Natural Selection is not looking at his Genes and saying "hey this guy isn't fit enough ... throw him out" ... Natural Selection is just a name given to the fact we have lions that are still reproducing, and that lion isn't because he was less fit so simply dies.
You're picking a fight over something we agree on here. I'm demystifying the explanation of how Natural Selection works, it is death ... it is not just general competition. Yes it IS competition, but only competition that results in something dying and other things not. Remember "Natural Selection is a Blind, Mindless and Unguided Watchmaker" (Dawkins)

Quote

in detail why AVIDA does not do what the writers of the software say it does

No detail needed ... it's simple. AVIDA defines the entity by prescribing a set of 26 functions that can be randomly selected in random combinations. Then evaluation functions are used to test how fit an organism is. Both these things are inaccurate and create a trivial subset of the proposed evolution theory. As I explained before, selected from existing functions is not the same as mutating the code that defines those functions. Biological function is determined on the protein level, proteins are equivalent to AVIDA's 26 functions, and a complex combination of proteins to create higher level function in an organism is equivalent to the combination of functions that AVIDA is "mutating" between. i.e. AVIDA is shuffling protein orders to get different high level functions, and only using 26 proteins. This is NOT the same as mutating the code that defines how the proteins are built .... the equivalence of this in AVIDA would be mutating the code that defines the 26 functions. This is a VERY different problem ... no-one has done that ... mainly because they know it will result in junk.
The problem of trying 26 functions in different combinations to optimise a specific trait is NOT the same as what you are proposing happens in biological evolution.

Quote

Can you say 'begging the question'? You appear to be arguing that cells/organisms are programmed by asserting as one of your premises that cells/organisms are programmed.

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. So far no-one has shown me one.
If you have a biological experiment showing one kind of animal naturally changing into another or developing completely new complex features then show me .... but so far all I've seen from experiments is no different to dog breeding and showing that a Poodle looks wildly different to a Great Dane or a Finch has a bigger beak. This is not evolution, this is artificially breeding out features and standard Mendelian genetics, and certainly isn't anything to do with mutations.

I'm a mathematician and programmer, last time I looked at the laws of logic you can't get information without a sender, matter does not contain the properties of information in itself, as information is outside of matter, it is the arrangement of matter that is information ... so if you're contesting that information can come out of matter by itself simply because of the environment it's in I want you to show me algorithmically how this is possible. Hence the request for a model.

Doc Bill

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Joined: April 2007

Posted: Jan. 16 2015,19:19

Quote (Cubist @ Jan. 16 2015,18:57)

Quote (Doc Bill @ Jan. 16 2015,10:55)

Greetings, NotGuru, we meet again!

Perhaps a full disclosure of your real purpose is in order. I present to you NotGuru's Agenda:

Quote

I paint evolution (non-science) as faith ... because it is.
It's an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who've wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

You still don't address any of the gaping black holes that I've pointed out.

I'm thinking this one is a Gary Gaulin clone, but super tard charged. If you don't mind I'll duck out and get some popcorn.

Is that text an actual quote from cryptoguru, or is it a concise summary of cryptoguru's ideas which doesn't actually use their specific phrasing? I ask because I tried googling that quote, and I couldn't find a source.

It's over at Smilodon's Retreat under the "DNA is not like a computer" thread. Near the bottom of about 4 pages of comments.

Yeah, it's a direct quote. Think Quest/FL/JoeG/a mule/two thick planks/bag of doorknobs - and you'll get the general sense of this guy.

Back to my popcorn!

QED

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Posted: Jan. 16 2015,19:30

In that case, I'm guessing it's not a Gaulin clone at all.

I'm betting on the pidgeon/chess gambit: "wah wah wah - you're being mean to me, so jesus doesn't love you and besides you're wrong - I'm outta here..."

Posts: 4966
Joined: May 2002

Posted: Jan. 16 2015,19:34

Cryptoguru:

Quote

Evolution is:
1) take an organism and let it replicate
2) random mutations should be introduced to the offspring DNA.
3) a selective pressure is applied to the environment the organisms live in
4) less fit organisms will die before replicating due to the pressure
5) most fit organisms will continue to replicate and mutate
6) eventually new functions and traits will emerge

Biological Evolution is presented as a scientific law, it is simple to define, so should be simple to model

My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.

caveats:
- Mutation can't simply combine functions in different arrangements. Mutation must occur on the code that defines the functions themselves, and affect the ability of the organism to build itself, to function and to replicate.
- the selective process can't include measuring properties of the organism to remove them from the population, the selective process must rely on organisms dying off due to the environmental factors. (e.g. energy)

Avida does everything specified there except "model this process", given that Avida's model doesn't include misconceptions.

It is certainly possible to find points of disanalogy between Avida and biological evolution, since Avida's purpose is to establish a "computational chemistry" rather than to be an exact simulation of biological evolution via DNA. However, none of those points of disanalogy appear to have any bearing on the specific "challenge" quoted above. So any dismissals of Avida on grounds other than those stated in the "challenge" above are irrelevant. And, looking back at the discussion on OgreMkV's blog, I'm not seeing any accurate objection made concerning Avida that falls within the parameters of the "challenge".

One such invalid response is the one that equivocates about "functions". In Avida, the functions that can possibly accrue merit are logic operations, none of which are themselves singular codes in an Avidian's genome. Referring to those codes as "functions" in the sense of the quoted "challenge" is a mistake.

It's easy enough to modify "challenges" to be unfulfilled on some point or another. The point isn't to satisfy those with unreasonable doubt; it is to satisfy those who don't have inflexible precommitments.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

cryptoguru

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Posted: Jan. 16 2015,19:45

Quote

Greetings, NotGuru, we meet again!

Perhaps a full disclosure of your real purpose is in order. I present to you NotGuru's Agenda:

Quote

I paint evolution (non-science) as faith ... because it is.
It's an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who've wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

You still don't address any of the gaping black holes that I've pointed out.

I'm thinking this one is a Gary Gaulin clone, but super tard charged. If you don't mind I'll duck out and get some popcorn.

Oh it's that angry Bilbo baggins character who just swears and says I know nothing ... and here he is quoting me out of context.

it was in response to this post from Bilbo, probably one of his least offensive ones

Quote

Typical useless god bot. Argument from incredulity. Has to paint science as a faith because of a narrow, restricted, dogmatic worldview. Forest full of straw men, drenched in tard and burning with the fire of the willfully ignorant. Sucks to be you, NotGuru. Enjoy howling in the darkness.

I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.

OgreMkV

Posts: 3668
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Posted: Jan. 16 2015,20:08

Quote (cryptoguru @ Jan. 16 2015,19:14)

Quote

I'd like to add that natural selection is not always a death.

It can be an effective removal of the gene pool. For example, the strongest, fittest, most efficient lion ever born might have a problem reproducing. Which means that he is removed from the gene pool. He can't pass his genes on to the next generation, so he's out of contention.

Haha amazing ... how did he get removed from the gene pool?

[/QUOTE]Wrong. Because he couldn't reproduce.

This is an example of you having a basic misunderstanding and I'm trying to correct it.

An organism that cannot reproduce, no matter how fit it is in every other particular cannot pass his genes on. He could live for decades longer (some research seems to indicate that being a eunuch means a male could add 25% to his lifespan... at the cost of not passing those genes on).

It doesn't have to be dead. It usually is, but it doesn't have to be. [/QUOTE]

A Gene pool isn't actually like a swimming pool you know, genes don't get thrown out for breaking the rules by the life-guard

[/quote]
Yes, you are correct, I should say, "the breeding population". I'm sorry, I will no longer use analogies in conversation with you.

Quote

... He gets removed from the "Gene pool" (population) by dying ...
he dies before reproducing (for whatever reason), so his genes aren't passed on.

And yet, I just gave you an example of a method, by which an individual could NOT ever contribute their genetics into the population and yet, still be alive.

What you are saying here, is that every woman who has a hysterectomy has died. Every male that has his tubes tied has died. Every cat and dog that's been neutered or spayed has died.

This is trivially wrong.

Quote

Natural Selection is not looking at his Genes and saying "hey this guy isn't fit enough ... throw him out" ... Natural Selection is just a name given to the fact we have lions that are still reproducing, and that lion isn't because he was less fit so simply dies.

No, selection is a process by which the organism is tested against the environment (including other organisms). Those are more fit TEND to reproduce more and those that are less fit TEND to reproduce less.

Again, less fit doesn't imply death. Indeed, you apparently have not read the AVIDA paper (or the part I quoted for you) showing that not only do less fit organisms sometimes reproduce. Those less fit organisms sometimes end up being the most fit.

This has been done with actual biological entities as well. Darwinian Evolution on a Chip by G. Joyce. Same thing as AVIDA. Some mutations resulted in lowered fitness, but they still reproduced and resulted in organisms with much greater fitness.

A simplistic view of life that is wrong.

Quote

You're picking a fight over something we agree on here.

No, because I don't agree with you. Scientists don't agree with you. Reality doesn't agree with you. Lab experiments don't agree with you. Observations of population genetics doesn't agree with you.

Quote

I'm demystifying the explanation of how Natural Selection works, it is death ... it is not just general competition.

No it's not. No matter how many times you say it, doesn't make it true.

Quote

Yes it IS competition, but only competition that results in something dying and other things not.

WHAT is competition? Competition for resources can often result in death. Competition for mates rarely does. But there are numerous cases of less fit organisms that discover a few tricks and reproduce anyway.

Quote

Remember "Natural Selection is a Blind, Mindless and Unguided Watchmaker" (Dawkins)

I love when you guys take Dawkins out of context. It's so telling. Tell me crypto, which book is that from? What page?

What does "unguided" mean to you? That's a critical definition.

For example, to most creationists (well, all that I have met so far), unguided means "random". While "guided" means shaped by an intelligence.

That's a false dichotomy. Guided doesn't mean an intelligence was involved. Fractals are guided by their equations. There are limits to them, but no intelligence has decided and enforced those limits.

When Dawkins speaks of unguided, he means that there is no purpose to life. No guiding hand. The only concern of this generation is to live long enough to reproduce. What happens before or after is not important to them.

The surviving offspring are in the same boat. None of them prepares for the future. None of them think, "Well, it's getting colder, we better let all the long furred ones mate." And yes, this have driven species to extinction... and will again.

I know you creationists don't like this because you feel that God is your guiding hand and things happen because they should. This tends to happen a lot with creationist engineers, programmers, and mathematicians.

I would encourage you to stop that thinking. It's not correct.

Why don't we ask Wesley, he was at a talk given by Dawkins about this? here's a link to his report of the talk. http://pandasthumb.org/archive....-2.html

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OgreMkV

Posts: 3668
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Posted: Jan. 16 2015,20:09

Quote (cryptoguru @ Jan. 16 2015,19:45)

Quote

Greetings, NotGuru, we meet again!

Perhaps a full disclosure of your real purpose is in order. I present to you NotGuru's Agenda:

Quote

I paint evolution (non-science) as faith ... because it is.
It's an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who've wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

You still don't address any of the gaping black holes that I've pointed out.

I'm thinking this one is a Gary Gaulin clone, but super tard charged. If you don't mind I'll duck out and get some popcorn.

Oh it's that angry Bilbo baggins character who just swears and says I know nothing ... and here he is quoting me out of context.

it was in response to this post from Bilbo, probably one of his least offensive ones

Quote

Typical useless god bot. Argument from incredulity. Has to paint science as a faith because of a narrow, restricted, dogmatic worldview. Forest full of straw men, drenched in tard and burning with the fire of the willfully ignorant. Sucks to be you, NotGuru. Enjoy howling in the darkness.

I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.

The problem is that you can't discuss science because your view of it so biased by your religion.

You're so obsessed with the way it should be, that you can't see the way it actually is.

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Posted: Jan. 16 2015,21:14

All the verbiage about information is fascinating, but why not cut to the chase? What specific physical phenomenon described by Darwin or his successors cannot happen? What specific point in the chain of descent is unreachable via the process described by Lenski, Thornton, et al?

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

Acartia_Bogart

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Posted: Jan. 16 2015,23:38

Quote

I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.

If by "so popular" you mean a minority opinion in the US, then I guess it is popular.

What you are referring to is its general acceptance by scientists, the people who have actually conducted research on this. As opposed to religious fanatics who approach the subject with their "minds" already made up.

Posts: 551
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Posted: Jan. 17 2015,01:08

Quote (cryptoguru @ Jan. 16 2015,09:09)

My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome. [emphasis added]

Whether or not you, yourself, are a Creationist, cryptoguru, this challenge of yours is (whether you realize it or not) the hoary old mutations can't create new information argument beloved of Creationists, just dressed up in computer terminology. So please, tell us if you will: What does "new information" look like? Given an arbitrary string of nucleotides, and a mutation which alters that string of nucleotides, how can you tell whether or not the post-mutation version of that string contains any "new" information?

Yes, this is a verbatim re-post. Perhaps cryptoguru will deign to respond to it this time. Perhaps they won't. We shall see.

Posts: 1961
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Posted: Jan. 17 2015,05:14

Maybe I am an oddball; Everywhere I look I observe objects and may extract information from them. The info just sits there ready for detection and observation without any external or supernatural operator having put it there. It sticks to the object like some red dye in a glass of water.

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Rocks have no biology.
Robert Byers.

JonF

Posts: 634
Joined: Feb. 2005

Posted: Jan. 17 2015,07:04

Quote (cryptoguru @ Jan. 16 2015,11:06)

JonF: "adding information" - new and novel functions that didn't exist before that solve a problem that wasn't solved previously.

Such as evolving EQU in Avida or evolving the ability to digest citrate in Lenski's experiments? Why are those not new and novel?

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Joined: Mar. 2013

Posted: Jan. 17 2015,09:50

Quote (cryptoguru @ Jan. 16 2015,20:45)

...
I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.

On the one hand you put it all down to faith versus faith, or faith versus science, and on the other you insist you "didn't want to get into a faith discussion."
You really can't have it both ways.

You are entitled to your opinions, as opinions, even when they are loony [I'm not (yet) saying any particular one(s) of your beliefs is/are loony].
But if you want to argue from a position that evolution is faith, not science, that it is based on a hatred for the idea of God, you have to establish the truth and accuracy of that premise. As a presupposition, it is ludicrous and unsupportable, not least because so very many of the founders and developers of evolutionary theory were and are deeply religious.
To say nothing of how totally insane it is to assert that people hate 'the idea of' God. Generally, ideas as such are neither hated nor adored. But more importantly, the idea of God is one that may or may not be true. The nature of said God is asserted to be all sorts of things, all over the map. We know nothing useful about the nature of any particular deity, and before we can make recourse to the referent of the idea of God, we need to know in some detail and with some considerable precision [can you say 'operational definition'? Do you know what it means?] what the nature and character of the referent actually is.
Otherwise the term is a magic word, swung about to fulfill any current rhetorical needs, which it can do solely because it is an idea unburdened with content.

Evolution is science because it fits all the criteria of science. It is based on demonstrable facts, it makes predictions which can be falsified, it's theoretical structure is logically sound and provides a framework within which a broad variety of objective facts can be placed. It has explanatory and predictive power, it has meaningful operational definitions for its key terms and concepts. It suggests fruitful lines of inquiry and it has withstood the most concerted, and occasionally devious, attacks a host of small-minded ignoramuses, as well as highly intelligent knowledgable individuals have brought to bear.
It is not faith because it is susceptible to revision based on new insights and new facts, it operates in a consistent fashion such that it makes predictions which as a general rule turn out, and is capable of revision in light of those cases where the prediction fails.

I'll get back to your lengthy, but largely pointless and obfuscatory response to portions of my earlier post later in the day or early tomorrow. I actually lack the time to do the fishing it so richly deserves.

The core challenge to you has already been raised, repeatedly: what facts on the table, specifically the known laws of chemistry, physics, and thermodynamics are alleged to be violated by evolution? Where has it been shown that the laws of chemistry, physics, and thermodynamics do not suffice to explain biological phenomena? Which phenomena, and how was it proven that they are not susceptible to natural explanations via chemistry, physics, and thermodynamics?

You find evolutionary theory distasteful, for reasons having nothing at all to do with science, so you attempt to shift out of the realm of science into faith. How is that justified?
Show your work.

qetzal

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Posted: Jan. 17 2015,12:32

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:

Quote

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.

cryptoguru

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Posted: Jan. 17 2015,15:11

Re. faith:

DocBilbo has tried to smuggle in a discussion from another board, which I didn't want to even have there about faith. That is not the point of this subject thread and is an attempt to derail the discussion so it gets into an endless circle of atheists claiming creation-based belief is not science.
Let's leave this subject as it is really a philosophical argument and not something I'm wanting to get sidetracked with here.

Re. experiments:

the point I'm making about experiments (e.g. Lenski's) is that all they have shown is that variation within a kind has occurred ... creationists agree that variation within a kind is happening (e.g. viruses mutate, Finches change beak sizes etc) this is not proof of evolution. This can just as easily be explained as the normal function of the genome to vary. Epigenomic function allows for much variety within an organism on top of variation that already exists in DNA, where entire modules of DNA are regulated and switched on and off by other genes. This is not evolution ... it can happen in one generation, it is not as a result of mutation. So my point here is that these experiments do not demonstrate new features and traits being introduced to the genome, they can be explained as existing information and code being expressed in new ways that is controlled in how the genome responds to input from the environment. This is widely accepted ... hormone responses can switch on silenced genes and vice versa, allowing an organism to adapt to its environment.

Quote

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?

Lenski's experiment has achieved 60,000 generations in April 2014.
You need to understand, the proposed theory of evolution is not about "time" ... it is about how many generations. Lenski's E. Coli has run for the equivalent of 1 million years of human generations. So evolution doesn't need time, it just needs lots of generations, which is what the E. Coli experiment has performed. Forgive me for being sceptical, but I'd expect more from 1 million years' worth of evolution than a change in metabolism, which could be attributed to the regulation of existing genes ... Behe explains this here Lenski article

SO ... this is why I'm asking for proof of the algorithm of evolution. Why is everyone being so sketchy about this? The evolutionary algorithm is simple ... randomly mutate the core code at the resolution of letters (not functions). Enforce selection by allowing organisms to compete for resources and allow them to die under natural conditions. AVIDA does NOT mutate on the nucleotide level, it mutates on the functional level, which is the same as choosing randomly from 26 functions and optimising. It also calculates selection on a feature level, measuring properties ... that is NOT natural selection. This is what their paper says it does. Has anyone read AVIDA's paper here?

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Posted: Jan. 17 2015,15:13

Quote

the point I'm making about experiments (e.g. Lenski's) is that all they have shown is that variation within a kind has occurred

Surely you are not that stupid.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

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Posted: Jan. 17 2015,15:26

Quote (cryptoguru @ Jan. 17 2015,15:11)

the point I'm making about experiments (e.g. Lenski's) is that all they have shown is that variation within a kind has occurred ...

Everyone agrees. It is just that we disagree about where the boundaries between the different kinds lie. For biologists, all evolution occurs within the "Life on Earth" kind.

If you think that Dr. Lenski's experiments show only evolution within the "Eubacteria kind", then we are already in reasonably close agreement. That implies that you also accept evolution within the "Eukaryote kind", since Eubacteria and Eukaryotes are at the same level of classification.

If you want to split things below that level, then you are going to have to list the different kind boundaries, and show how you arrived at those particular boundaries.

rossum

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Posted: Jan. 17 2015,16:04

That's not all the Lenski experiment shows.

The Lenski experiment shows that mutations that reduce reproductive success can survive in a population long enough to enable further mutations that leapfrog function for a given environment.

That is precisely what Behe said couldn't happen. And it is precisely what is necessary to move beyond local maxima.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

cryptoguru

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Posted: Jan. 17 2015,18:28

Quote

Surely you are not that stupid.

Yes, I AM that stupid :-)
I'm making the point that nothing in the Lenski experiment proves evolution, it can just as easily be explained as programmed behaviour. Considering we're discovering more and more deterministic complexity in the genome, it is more than reasonable to assume that all the variation we see is specified complexity that already exists within the genome, and is not the result of random mutation. This has NOT been contradicted by any experiment yet, it is simply being asserted.

Therefore I again ask why there is no workable computer model of the theory of evolution in the form in which it is supposed to occur in the wild?

Quote

If you want to split things below that level, then you are going to have to list the different kind boundaries

Rossum, I'm saying that the variation we see can be explained by deterministic behaviour in the genome and need not be explained by "mutation". A control gene that regulates another gene dependent on an environmental input may make it look like something is evolving, but that function could already exist in the genome.
In fact the more layers of complexity and non-linearity we observe in the genome and how it is processed makes it more difficult to explain how a mutation could ever be understood to be advantageous; with multiple reading frames a mutation to a nucleotide could be imagined to have a positive effect somehow on the expression of a protein, but what about the other types of protein that get expressed from the same code? They're now broken.

This is a multi-layered code, I have previously worked in Cryptography and compression algorithms for many years. The genome implements compression to represent data in an efficient way. Corrupting even one bit of compressed data usually has an effect on multiple parts of the data ... if that data is a program, you can expect the program to crash if enough bits are corrupted.

This makes sense for the genome too (and is observed through genetic diseases) ... that along with the fact that Lenski's experiments fails to show evolution from one kind of an organism (bacteria) to a different, more complex organism despite an equivalent of 1 Million human years of evolution suggests this process doesn't work; except that everyone is the field is saying it works. I'm a sceptic, I want to see actual scientific proof that doesn't just gloss over the facts and pretend that mutation could be the only reason for an increase in cell size or a change in metabolism.

A working and accurate computer model still wouldn't prove evolution is happening in the wild, but it at least would show that it is theoretically viable. Currently I don't see how it is even theoretically possible, from an algorithmic perspective.

Quote

The Lenski experiment shows that mutations that reduce reproductive success can survive in a population long enough to enable further mutations that leapfrog function for a given environment.

Bacteria is also a bad example because it seems to deliberately use fuzzy logic and implement randomness in its genome as part of the programming ... so although a change may look random, it may be deterministic in function.
This is exactly how we program computer viruses. We expect them to evolve in a deliberate way.
So I do think there is some application for evolution as a concept in the modelling of bacteria and viruses, but their function is still deterministic and constrained by the master code, they may reprogram themselves (and transfer/shuffle genes with other bacteria) for versatility, but they can never vary to become a frog. In the case of viruses and bacteria I expect randomness is being used like we use pseudo-random noise generators in computers. We generate random variables and use them in our code ... we are NOT varying the functional part of the code itself randomly.

I think therefore it is misleading to look at what happens in bacteria and extrapolate it to other organisms, when we don't see the same processes happening in them.

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Posted: Jan. 17 2015,18:28

Quote (cryptoguru @ Jan. 16 2015,09:09)

My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome. [emphasis added]

Whether or not you, yourself, are a Creationist, cryptoguru, this challenge of yours is (whether you realize it or not) the hoary old mutations can't create new information argument beloved of Creationists, just dressed up in computer terminology. So please, tell us if you will: What does "new information" look like? Given an arbitrary string of nucleotides, and a mutation which alters that string of nucleotides, how can you tell whether or not the post-mutation version of that string contains any "new" information?

cryptoguru did not respond to this the first two times I posted it; perhaps they merely overlooked it in the rush of responses. Maybe they'll notice it (and respond to it) if the text is larger?

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Posted: Jan. 17 2015,20:13

Will microbes may not be a good example for creationists to use, but microbes account for the entirety of life for 6/7 of the time during which life existed. And microbes are still the dominant life form, by any measure.

Nearly all genes were invented by microbial evolution. So stop posting shit. If you assert that mutation is not random with respect to selection, prove it.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

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Posted: Jan. 17 2015,20:17

Cryptoguru:

Quote

AVIDA does NOT mutate on the nucleotide level, it mutates on the functional level, which is the same as choosing randomly from 26 functions and optimising.

That's still the erroneous equivocation that was already pointed out to be a mistake on Cryptoguru's part. None of the logic functions that obtain merit in Avida are due to singular codes in an Avidian's genome. The functions that accrue merit are built out of multiple codes in the genome, just as specified in Cryptoguru's "challenge" near the start of the thread.

Quote

It also calculates selection on a feature level, measuring properties ... that is NOT natural selection. This is what their paper says it does. Has anyone read AVIDA's paper here?

I'm not sure what the word salad above is supposed to convey other than dismissal. What's a "feature level" and "measuring properties"? If that's supposed to mean that Avida recognizes genomic patterns and rewards those, nothing could be further from the truth. It is the outcome of functional behavior that is the trigger for assigning merit to an Avidian.

But, yes, not only have I read that paper, I've also contributed to the Avida code base.

Lenski et al. 2003:

Quote

As in nature, selection in Avida depends on the phenotypic effects of a mutation in its genetic context and in relation to the organism’s environment; the researcher does not specify a distribution of selection coefficients.

This indicates that what Avida is doing is analogous to what occurs in natural selection. I think Cryptoguru needs more than cryptic dismissal to make his case.

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Posted: Jan. 17 2015,20:35

Not understanding how Avida works is seen in other antievolutionary argumentation, too.

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The whole truth

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Posted: Jan. 17 2015,21:34

Quote (NoName @ Jan. 17 2015,07:50)

Quote (cryptoguru @ Jan. 16 2015,20:45)

...
I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.

On the one hand you put it all down to faith versus faith, or faith versus science, and on the other you insist you "didn't want to get into a faith discussion."
You really can't have it both ways.

You are entitled to your opinions, as opinions, even when they are loony [I'm not (yet) saying any particular one(s) of your beliefs is/are loony].
But if you want to argue from a position that evolution is faith, not science, that it is based on a hatred for the idea of God, you have to establish the truth and accuracy of that premise. As a presupposition, it is ludicrous and unsupportable, not least because so very many of the founders and developers of evolutionary theory were and are deeply religious.
To say nothing of how totally insane it is to assert that people hate 'the idea of' God. Generally, ideas as such are neither hated nor adored. But more importantly, the idea of God is one that may or may not be true. The nature of said God is asserted to be all sorts of things, all over the map. We know nothing useful about the nature of any particular deity, and before we can make recourse to the referent of the idea of God, we need to know in some detail and with some considerable precision [can you say 'operational definition'? Do you know what it means?] what the nature and character of the referent actually is.
Otherwise the term is a magic word, swung about to fulfill any current rhetorical needs, which it can do solely because it is an idea unburdened with content.

Evolution is science because it fits all the criteria of science. It is based on demonstrable facts, it makes predictions which can be falsified, it's theoretical structure is logically sound and provides a framework within which a broad variety of objective facts can be placed. It has explanatory and predictive power, it has meaningful operational definitions for its key terms and concepts. It suggests fruitful lines of inquiry and it has withstood the most concerted, and occasionally devious, attacks a host of small-minded ignoramuses, as well as highly intelligent knowledgable individuals have brought to bear.
It is not faith because it is susceptible to revision based on new insights and new facts, it operates in a consistent fashion such that it makes predictions which as a general rule turn out, and is capable of revision in light of those cases where the prediction fails.

I'll get back to your lengthy, but largely pointless and obfuscatory response to portions of my earlier post later in the day or early tomorrow. I actually lack the time to do the fishing it so richly deserves.

The core challenge to you has already been raised, repeatedly: what facts on the table, specifically the known laws of chemistry, physics, and thermodynamics are alleged to be violated by evolution? Where has it been shown that the laws of chemistry, physics, and thermodynamics do not suffice to explain biological phenomena? Which phenomena, and how was it proven that they are not susceptible to natural explanations via chemistry, physics, and thermodynamics?

You find evolutionary theory distasteful, for reasons having nothing at all to do with science, so you attempt to shift out of the realm of science into faith. How is that justified?
Show your work.

"Evolution is science because it fits all the criteria of science. It is based on demonstrable facts, it makes predictions which can be falsified, it's theoretical structure is logically sound and provides a framework within which a broad variety of objective facts can be placed. It has explanatory and predictive power, it has meaningful operational definitions for its key terms and concepts. It suggests fruitful lines of inquiry and it has withstood the most concerted, and occasionally devious, attacks a host of small-minded ignoramuses, as well as highly intelligent knowledgable individuals have brought to bear.
It is not faith because it is susceptible to revision based on new insights and new facts, it operates in a consistent fashion such that it makes predictions which as a general rule turn out, and is capable of revision in light of those cases where the prediction fails."

No, evolution is none of those things. Evolutionary theory is.

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

The whole truth

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Posted: Jan. 17 2015,22:17

Quote (cryptoguru @ Jan. 17 2015,16:28)

Quote

Surely you are not that stupid.

Yes, I AM that stupid :-)
I'm making the point that nothing in the Lenski experiment proves evolution, it can just as easily be explained as programmed behaviour. Considering we're discovering more and more deterministic complexity in the genome, it is more than reasonable to assume that all the variation we see is specified complexity that already exists within the genome, and is not the result of random mutation. This has NOT been contradicted by any experiment yet, it is simply being asserted.

Therefore I again ask why there is no workable computer model of the theory of evolution in the form in which it is supposed to occur in the wild?

Quote

If you want to split things below that level, then you are going to have to list the different kind boundaries

Rossum, I'm saying that the variation we see can be explained by deterministic behaviour in the genome and need not be explained by "mutation". A control gene that regulates another gene dependent on an environmental input may make it look like something is evolving, but that function could already exist in the genome.
In fact the more layers of complexity and non-linearity we observe in the genome and how it is processed makes it more difficult to explain how a mutation could ever be understood to be advantageous; with multiple reading frames a mutation to a nucleotide could be imagined to have a positive effect somehow on the expression of a protein, but what about the other types of protein that get expressed from the same code? They're now broken.

This is a multi-layered code, I have previously worked in Cryptography and compression algorithms for many years. The genome implements compression to represent data in an efficient way. Corrupting even one bit of compressed data usually has an effect on multiple parts of the data ... if that data is a program, you can expect the program to crash if enough bits are corrupted.

This makes sense for the genome too (and is observed through genetic diseases) ... that along with the fact that Lenski's experiments fails to show evolution from one kind of an organism (bacteria) to a different, more complex organism despite an equivalent of 1 Million human years of evolution suggests this process doesn't work; except that everyone is the field is saying it works. I'm a sceptic, I want to see actual scientific proof that doesn't just gloss over the facts and pretend that mutation could be the only reason for an increase in cell size or a change in metabolism.

A working and accurate computer model still wouldn't prove evolution is happening in the wild, but it at least would show that it is theoretically viable. Currently I don't see how it is even theoretically possible, from an algorithmic perspective.

Quote

The Lenski experiment shows that mutations that reduce reproductive success can survive in a population long enough to enable further mutations that leapfrog function for a given environment.

Bacteria is also a bad example because it seems to deliberately use fuzzy logic and implement randomness in its genome as part of the programming ... so although a change may look random, it may be deterministic in function.
This is exactly how we program computer viruses. We expect them to evolve in a deliberate way.
So I do think there is some application for evolution as a concept in the modelling of bacteria and viruses, but their function is still deterministic and constrained by the master code, they may reprogram themselves (and transfer/shuffle genes with other bacteria) for versatility, but they can never vary to become a frog. In the case of viruses and bacteria I expect randomness is being used like we use pseudo-random noise generators in computers. We generate random variables and use them in our code ... we are NOT varying the functional part of the code itself randomly.

I think therefore it is misleading to look at what happens in bacteria and extrapolate it to other organisms, when we don't see the same processes happening in them.

"I think therefore it is misleading to look at what happens in bacteria and extrapolate it to other organisms, when we don't see the same processes happening in them."

Since that's how you feel, you might want to reconsider making statements like this:

"Lenski's experiment has achieved 60,000 generations in April 2014.
You need to understand, the proposed theory of evolution is not about "time" ... it is about how many generations. Lenski's E. Coli has run for the equivalent of 1 million years of human generations."

Bacteria are not "equivalent" to humans.

I'm looking forward to your response to Cubist.

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

cryptoguru

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Posted: Jan. 18 2015,03:46

Quote

What does "new information" look like?

New information is new and novel genetic material that codes for new function or traits in the organism i.e. not a point mutation in a control gene that switches other pre-existing functionality off/on or a trade/inheriting of genetic material between bacteria ...NEW genetic material that codes for new function; this has never been observed.

Quote

Nearly all genes were invented by microbial evolution.

begging the question! Demonstrate the process ... don't simply assert it happens.

Quote

Bacteria are not "equivalent" to humans.

Straw-man argument ... I never said they were, I was equivocating the process of evolution in both organisms. Bacteria can "evolve" quicker because their generation time is MUCH shorter (hence why Lenski chose E. Coli). So I can compare 26 years of E. Coli to 1 Million years of human evolution ... they are exactly the same amount of the same process. We would expect to see novel traits emerge in humans over 1 million years and be able to identify new genes that didn't exists previously that code for that new trait. We don't see this in Lenski's experiment.

Quote

None of the logic functions that obtain merit in Avida are due to singular codes in an Avidian's genome

You're misunderstanding the point. The original 26 functions (commands) that AVIDA uses are not subject themselves to mutation. So finding new logical functions that are combinations of these elemental functions is trivial using an optimisation algorithm (which is what AVIDA is). You will only get functionality that is described by compounds of those functions.

This is equivalent to having a chemistry set with 26 elements, you combine them randomly and select combinations of chemicals that produce interesting reactions, you optimise over those. You will NEVER create a new chemical element from this process. The elemental level in AVIDA is the function (command), these should therefore be evolved, not prescribed.
AVIDA is a very interesting modelling algorithm, great for solving some real-world competition problems. It does NOT model biological evolution.
I have clarified this point countless times, I don't see how I can simplify it any more for people to understand here.

Explain precisely where, in my description of AVIDA and the biological evolution algorithm I have got any of the details wrong.
AGAIN (to explain this problem one last time)
1) evolution mutates DNA on a nucleotide level affecting function (gene level) and selects on the organism level.
2) AVIDA mutates "DNA" on the gene level affecting compound function and selects on the compound function level.

These are VERY simple concepts to grasp.
Please explain how AVIDA is possibly modelling biological evolution when the core functions (commands) cannot be corrupted under mutation and the selection process is working on the compound functional level (by rewarding compound functions).

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Posted: Jan. 18 2015,04:10

Quote (cryptoguru @ Jan. 18 2015,03:46)

New information is new and novel genetic material that codes for new function or traits in the organism i.e. not a point mutation in a control gene that switches other pre-existing functionality off/on or a trade/inheriting of genetic material between bacteria ...NEW genetic material that codes for new function; this has never been observed.

Yes it has. Lenski's long term experiment showed bacteria developing a new function, the ability to digest citrate. That function was not there previously, and that new function evolved during the experiment.

I can also point to the example of the from Japan, "Nylon digesting bacteria" which happened naturally.

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Soapy Sam

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Posted: Jan. 18 2015,05:09

Quote (cryptoguru @ Jan. 18 2015,09:46)

These are VERY simple concepts to grasp.
Please explain how AVIDA is possibly modelling biological evolution when the core functions (commands) cannot be corrupted under mutation

A model does not have to include everything. It would be a simple matter (in many GAs, at least) to permit 'core function' to be subject to mutation also. If it happened to be fatal when it occurred, the evolving population would remain unperturbed by these occurrences. Mutational change is not 'not evolution' simply because it is not 'core function' change.

Quote

and the selection process is working on the compound functional level (by rewarding compound functions).

The entirety of a genome can be considered a 'compound function'. The survival or otherwise of a genome is assessed at a compound level - whole-genome survival and replication. But there are multiple levels of selection when aggregated over many generations.

Edited by Soapy Sam on Jan. 18 2015,11:12

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Posted: Jan. 18 2015,05:49

Cryptoguru:

Quote

You're misunderstanding the point. The original 26 functions (commands) that AVIDA uses are not subject themselves to mutation. So finding new logical functions that are combinations of these elemental functions is trivial using an optimisation algorithm (which is what AVIDA is). You will only get functionality that is described by compounds of those functions.

This is equivalent to having a chemistry set with 26 elements, you combine them randomly and select combinations of chemicals that produce interesting reactions, you optimise over those. You will NEVER create a new chemical element from this process. The elemental level in AVIDA is the function (command), these should therefore be evolved, not prescribed.

No, I understand "the point" quite well. I've shown the error there before, and I can do it again.

Cryptoguru's analogy would require that he somehow believes biological organisms create new chemical elements. Cryptogurru is wrong. Biological organisms do create novel chemical compounds out of the plain, ordinary elements that are hanging around. Mostly, these are novel proteins, constructed out of a toolkit of 20 amino acids. Cryptoguru's "challenge" conditions are handily met by Avida, which mutates the "code that defines the functions themselves". (That's one leve of indirection, not multiple levels.) Avidian instruction sequences define the functions that accrue merit. Those instruction sequences are mutated, changing the functions. In biology, nucleotide sequences are mutated, resulting in changes in function. And it is not a matter of "optimization" alone: the seed Avidian program is composed of a series of NOP instructions and a section that handles self-replication; the only function performed by the initial Avidian is self-replication. (The self-replication code is also subject to mutation, and Avidians routinely die without progeny due to mutations there that do not preserve self-replication capability.) The logical functions that accrue merit all have to be constructed de novo, they are not performed at some low level and increased, as Cryptoguru erroneously asserts with the "optimising" comments. Cryptoguru wants to endlessly modify his "challenge" to avoid admitting that its conditions have been met. That leads to absurdities in his analogizing, like the one about creating new elements, and in his perversely clinging to error that has clearly been called out.

In biology, you only get codons that are three-tuple combinations of four DNA nucleotides, and you only get proteins that are n-tuple combinations of the fixed set of amino acids that organism uses. (There's a canonical set of twenty amino acids.) The situation in Avida is analogous to one level of indirection, though not two. Fortunately, Cryptoguru's "challenge" only requested one level of indirection. The complaint that functions are built out of combinations is a non-starter, since that is exactly how the biology works, too.

Cryptoguru:

Quote

Explain precisely where, in my description of AVIDA and the biological evolution algorithm I have got any of the details wrong.

There are too many misconceptions in Cryptoguru's discussion of biology to bother with. The notion that biology produces new chemical elements is just the absurd topping on a cake of error.

Quote

AGAIN (to explain this problem one last time)
1) evolution mutates DNA on a nucleotide level affecting function (gene level) and selects on the organism level.
2) AVIDA mutates "DNA" on the gene level affecting compound function and selects on the compound function level.

The first point is pretty sloppy, because most functionality in organisms is at the protein or higher levels.

As for point 2, Cryptoguru apparently has no clue how Avida works, because Avida as in the Lenski et al. 2003 paper doesn''t do anything but select at the Avidian level. There is no process in Avida that permits the propagation of the instruction sequences that define a logic function on its own. This is an own-goal on Cryptoguru's part.

Quote

These are VERY simple concepts to grasp.

Certainly. The problem being that Cryptoguru is completely wrong about point 2.

Quote

Please explain how AVIDA is possibly modelling biological evolution when the core functions (commands) cannot be corrupted under mutation and the selection process is working on the compound functional level (by rewarding compound functions).

I haven't claimed that Avida models "biological evolution". I have claimed that Avida is sufficient to meet the terms of the "challenge" as it was stated early in the thread.

The functions that are awarded merit in Avida can be lost via mutation (the paper Cryptoguru claims to have read discusses this at length), so that is another plain error on his part. And I have noted already the error in claiming that Avida selects at any level lower than that of the Avidian.

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Posted: Jan. 18 2015,05:52

Cryptoguru:

Quote

I never said they were, I was equivocating the process of evolution in both organisms

That word... I do not think it means what you think it means.

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Posted: Jan. 18 2015,06:18

Quote (cryptoguru @ Jan. 18 2015,03:46)

Quote

What does "new information" look like?

New information is new and novel genetic material that codes for new function or traits in the organism i.e. not a point mutation in a control gene that switches other pre-existing functionality off/on or a trade/inheriting of genetic material between bacteria ...NEW genetic material that codes for new function; this has never been observed.

"Never been observed", you say. Well, I say, show me a person who's never heard of a kinkajou, and I'll show you a person who wouldn't recognize a kinkajou if a rabid one was chewing on their face. And in my experience, it's awfully damned common for Creationists who claim that thus-and-such has never been observed, do not actually know what thus-and-such would look like, and therefore those Creationists don't actually have any valid grounds for asserting that thus-and-such "has never been observed". So I want to drill down on your verbiage here, cryptoguru, and see whether you actually do know what you're talking about.

You have a definition of "new information". Groovy. I note that your definition of "new information" is sufficiently imprecise that it doesn't provide any way to tell whether or not a given string of nucleotides qualifies as "new information" under your definition. So let's see if we can dispel the vagueness, shall we?

Your definition of "new information" includes a clause about "new and novel genetic material". Why must the "genetic material" of "new information" be both "new" and "novel"? I ask because "new" and "novel" strike me as basically synonymous, hence, using both words is gratiutous redundancy. But perhaps you weren't being redundant; perhaps you actually are using distinct referents for "new" and "novel", such that the two words are not, in fact, gratuitously redundant. Please explain how "genetic material" which is "new" differs from "genetic material" which is "novel". Is it possible for "genetic material" to be "new" without also being "novel"? Is it possible for "genetic material" to be "novel" without also being "new"?

What does "new and novel genetic material" look like? I'm going to provide some concrete data to work with. Here's an arbitrary nucleotide sequence, with a randomly-picked nucleotide—the thymine in the 4th codon—colored red:
gcc tac agg gat cgt ggg gac ctt acg aat ggc ctt ttt gac tat tct tcg aat cta agc tca gca tca ttc ccg tct acg gga agt ccc ttc cca ata cat atc ctc ggc acc gca ctt gca ggc tca cgc ttc gcg tca ttt agg tca
That sequence of codons yields the following sequence of amino acids, with the 4th amino acid colored red on account of it's the AA that's yielded by the codon with the red-colored nucleotide:
alanine, tyrosine, arginine, aspartic acid, arginine, glycine, aspartic acid, leucine, threonine, asparagine, glycine, leucine, phenylalanine, aspartic acid, tyrosine, serine, serine, asparagine, leucine, serine, serine, alanine, serine, phenylalanine, proline, serine, threonine, glycine, serine, proline, phenylalanine, proline, isoleucine, histidine, isoleucine, leucine, glycine, threonine, alanine, leucine, alanine, glycine, serine, arginine, phenylalanine, alanine, serine, phenylalanine, arginine, serine

One possible mutation of that sequence would be if the thymine in the 4th codon was deleted, like so (and the thereby-altered 4th codon is colored red here):
gcc tac agg gac gtg ggg acc tta cga atg gcc ttt ttg act att ctt cga atc taa gct cag cat cat tcc cgt cta cgg gaa gtc cct tcc caa tac ata tcc tcg gca ccg cac ttg cag gct cac gct tcg cgt cat tta ggt ca
Since a codon is three nucleotides in a row, deleting that one nucleotide from the 4th codon in the original sequence doesn't just change that 4th codon; it also has the effect of changing pretty much every codon after that altered 4th codon. This, in turn, yields a very different sequence of amino acids than the original, unmutated sequence. The red-colored AAs are ones which don't occur at all in the original, unmutated sequence:
alanine, tyrosine, arginine, aspartic acid, valine, glycine, threonine, leucine, arginine, methionine, alanine, phenylalanine, leucine, threonine, isoleucine, leucine, arginine, isoleucine, [end], alanine, glutamine, histidine, histidine, serine, arginine, leucine, arginine, glutamic acid, valine, proline, serine, glutamine, tyrosine, isoleucine, serine, serine, alanine, proline, histidine, leucine, glutamine, alanine, histidine, alanine, serine, arginine, histidine, leucine, glycine, [???]

Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

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Posted: Jan. 18 2015,06:21

And my post here still stands as an accurate summation of things. Avida meets the requirements of Cryptoguru's "challenge" and Cryptoguru's further dismissals have been distributed between the irrelevant and the erroneous.

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"You can't teach an old dogma new tricks." - Dorothy Parker

cryptoguru

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Posted: Jan. 18 2015,06:26

Okay let me explain this in another way ... you seem to keep missing the point.

Let's see if we can agree on this point:-
The genome is a code comprised of symbols (G, A, C, T) stored in nucleotides (the same as computer code characters can be stored in bytes).
This code defines how to build proteins from amino acids arrange them and fold them. Proteins are an elemental functional component. The genome also defines how to assemble the proteins into complex structures, with complex function. The genome is mutated at the nucleotide (symbol) level.

AGREE?

AVIDA is providing 26 elemental functional components (commands) as the building blocks to optimise compound functionality. This is the same as providing 26 proteins and performing stochastic optimisation to find compound functionality. AVIDA only selects BETWEEN these components, it doesn't allow mutation of them at the symbol level (the code that defines these components). Therefore the integrity of those component commands is never affected by the mutation process in AVIDA, and new components commands cannot emerge, there will always be 26 commands.

THIS IS NOT EQUIVALENT!

Pleas explain how any of my assertions here are wrong.

It could be argued that AVIDA is modelling the selection of combination of entire genes to create new functionality and adaptation of an organism to its environment ... I would not dispute that happens in real organisms ... but the elemental functionality never extends, so limits the functionality of the organism.

e.g. a robot that is built to support commands to go forward, backwards, left and right on the ground cannot learn to fly by combining those commands in an optimal order. You cannot select what isn't there to select. This is the level that AVIDA is working on, not the symbol or code level.

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Posted: Jan. 18 2015,06:26

Cubist:

Quote

Your definition of "new information" includes a clause about "new and novel genetic material". Why must the "genetic material" of "new information" be both "new" and "novel"?

In my experience, antievolutionists do this because they think that evolution is supposed to replace de novo creation, so they require that it should look just like de novo creation. They don't want to hear about co-opting function, duplication and divergence, and all the other ways that evolutionary processes actually do things that haven't been done before. Because evolution doesn't do "poof!", they think that they have identified a problem. The fact that nobody else sees this as a problem is very frustrating to them.

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"You can't teach an old dogma new tricks." - Dorothy Parker

cryptoguru

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Posted: Jan. 18 2015,06:28

Quote

That word... I do not think it means what you think it means.

you're right ... it was late when I wrote it ;-)

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Posted: Jan. 18 2015,07:00

I am not "missing the point", I am rebutting erroneous claims.

Cryptoguru:

Quote

Pleas explain how any of my assertions here are wrong.

Already done for a bunch of stuff. Pardon me if I simply review where we are at.

The assertion that biological organisms created new chemical elements was wrong.

The assertion that Avida selected at something lower than the Avidian level was wrong.

The assertion that Avida composing functions out of instruction sequences is not analogous to biological organisms composing proteins out of amino acids is wrong.

The assertion that nobody besides Cryptoguru had read Lenski et al. 2003 was wrong.

Cryptoguru wanted an analogy between critters and computers. He's just unhappy that this exists. Avida provides an instruction set. The sequences of instructions form programs. A computer's instruction set is fixed; changing code sequences does not change the instruction set. Likewise, Avida's instruction set is fixed. Cryptoguru has invoked Turing machines, and the analogous piece there is the tape, and nothing on the tape changes the reader. Biological organisms aren't, in the common course of things, changing either the set of DNA nucleotides or the set of amino acids they use. If Cryptoguru doesn't like the way Avida gets to the functions it rewards, the problem isn't with Avida; the problem is with Cryptoguru's analogy/equivalence between biology and computation. The elements of Cryptoguru's stated "challenge" have been met. He seems intent to change the "challenge" post hoc to exclude things that meet it.

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"You can't teach an old dogma new tricks." - Dorothy Parker

JonF

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Posted: Jan. 18 2015,08:10

Quote (cryptoguru @ Jan. 17 2015,19:28)

I'm making the point that nothing in the Lenski experiment proves evolution, it can just as easily be explained as programmed behaviour. Considering we're discovering more and more deterministic complexity in the genome, it is more than reasonable to assume that all the variation we see is specified complexity that already exists within the genome, and is not the result of random mutation. This has NOT been contradicted by any experiment yet, it is simply being asserted.

Lenski identified the mutations that led to citrate utilization, a new and novel function. Are you alleging that there is some currently unknown information storage and processing mechanism in the cell that pre-programmed those mutations?

If so, interesting theory. Got any evidence for it?

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Posted: Jan. 18 2015,08:14

Quote (cryptoguru @ Jan. 18 2015,07:26)

Okay let me explain this in another way ... you seem to keep missing the point.

Let's see if we can agree on this point:-
The genome is a code comprised of symbols (G, A, C, T) stored in nucleotides (the same as computer code characters can be stored in bytes).
This code defines how to build proteins from amino acids arrange them and fold them.[/quote]
Strictly false. The code is comprised of more than just the symbols. Their specific arrangement and adjacencies matter critically. This is entirely unlike computer code.
Secondly, the code emphatically does not define how proteins fold. Physics and chemistry do, and they do so based on the local environment in which the genetic material and its products exist, as well as the local environment excluding the genetic material and its products.

Quote

Proteins are an elemental functional component. The genome also defines how to assemble the proteins into complex structures, with complex function.

Again, strictly false. There is no one-to-one mapping between genes and the resulting structures of the life-form.

Quote

The genome is mutated at the nucleotide (symbol) level.

AGREE?

With the tiny bit you got correct, yes. With the gross misunderstandings that are sufficient to warrant dismissal of all your claims, of course not.

Quote

...
Pleas explain how any of my assertions here are wrong.

Done and done.

I'll also note that you are ignoring the fact that your original challenge, as yet lacking any explicit modification or discussion by you, has been met in multiples ways by multiple posters. That you ignore this suggests strongly that you see a single path of argument that reaches the conclusion you desire, that you are arguing from what amounts to a script that hangs off that particular singular path, and that you are unwilling and/or unable to deviate from that script when others don't play along. It also indicates strongly that you are unwilling and/or unable to acknowledge that your challenge has been met, because that doesn't match the results you get by your singular preferred argument. The rest of the world understands what it means when one 'preferred' argument out of many appears to succeed, but the facts show it to be incorrect, regardless of how appealing or apparently sound it is. You appear not to understand this.
Your challenge has been met.
Revise it into a different challenge and admit defeat on this front. Of course, that means admitting that you have no basis other than faith and a generalized distaste for rejecting evolutionary theory.
I thank 'The whole truth' for pointing out my careless wording that failed to make the distinction between evolution the fact and 'evolutionary theory'. He's absolutely correct, and my post needs that correction.

I'll also note that it is strictly false to assert that the cell is a Turing machine. The cell does not operate on a strictly clocked mechanism, does not have infinite storage, does not operate by singular read/write operations on singular 'memory cells', etc. That the cell can be modeled by a Turing machine does not make the cell a Turing machine.
That the entirety of the living processes, all essential to the existence of a cell, can be modeled by a single Turing machine is a laughable claim. At the very least, it requires proof, and said proof would be notable and prize-worthy.
Whole-cell modeling is still a very difficult enterprise and does not have a general solution. I've worked in the field, I know this to be true.

And I'll note that you conspicuously fail to understand the point of thermodynamics as a problematic for cells that does not apply to computers. The analogous problem for computers is high-energy gamma radiation randomly flipping bits in memory cells. That phenomenon is rare enough that it did not become problematic 'in the field' until the late 90's, when ECC memory began to be required. Do you understand why this is so? Do you understand the analogy, and its limits?

Finally, I see no point in going back and addressing your response to my post from near the top of the previous page. You give every evidence of being one of those "I've got my mind made up, don't confuse me with facts" people. That a computer can use the various things noted, or can demonstrate them, is irrelevant to the argument, and it is tragic that you do not see that.

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Posted: Jan. 18 2015,08:25

Cryptoguru:

Quote

e.g. a robot that is built to support commands to go forward, backwards, left and right on the ground cannot learn to fly by combining those commands in an optimal order. You cannot select what isn't there to select. This is the level that AVIDA is working on, not the symbol or code level.

Avida's instruction set is Turing-complete. Avidian genomes are sequences of instructions. Any computable function is possible to encode with Avida instructions. The notion that Avida is not capable of doing what computers and Turing machines do is wrong. This is not arguable.

It is possible that Cryptoguru has confused himself. Selection is an effect of the organism interacting with its environment, either in biology or Avida. That there are only certain things that are set up for selection in an Avida experimental environment is analogous to the limits of particular natural environments. Cave-dwelling fish, for instance, aren't in a position to evolve flight in air, either. As it turns out, there are some 60+ logic functions that stock Avida can evaluate in its environmental setup, only nine of which were activated in the Lenski et al. 2003 paper. And as I noted, Avida instruction set programs can encode any computable function. Faulting Avida for not having every computable function set up for reward in every experimental environment is quite ludicrous, and also quite beside the point of the original "challenge", which was that new functions arise from the model genome changes, not that every possible function must arise thereby.

If Cryptoguru means by his objections that Avida cannot be an analogy for biology because of the limits of computation, he has also refuted his own insistence that biology is computation.

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"You can't teach an old dogma new tricks." - Dorothy Parker

OgreMkV

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Posted: Jan. 18 2015,08:38

Quote (Wesley R. Elsberry @ Jan. 18 2015,08:25)

Cryptoguru:

Quote

e.g. a robot that is built to support commands to go forward, backwards, left and right on the ground cannot learn to fly by combining those commands in an optimal order. You cannot select what isn't there to select. This is the level that AVIDA is working on, not the symbol or code level.

This is also interesting in that cryptoguru has previously rejected my statements that evolution can only build on previously existing DNA.

In fact, cryptoguru appears to be using evolutionary science as evidence that evolution can't work.

Truly a strawman of epic proportions.

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Ignored by those who can't provide evidence for their claims.

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Texas Teach

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Posted: Jan. 18 2015,09:09

Quote (OgreMkV @ Jan. 18 2015,08:38)

Quote (Wesley R. Elsberry @ Jan. 18 2015,08:25)

Cryptoguru:

Quote

e.g. a robot that is built to support commands to go forward, backwards, left and right on the ground cannot learn to fly by combining those commands in an optimal order. You cannot select what isn't there to select. This is the level that AVIDA is working on, not the symbol or code level.

This is also interesting in that cryptoguru has previously rejected my statements that evolution can only build on previously existing DNA.

In fact, cryptoguru appears to be using evolutionary science as evidence that evolution can't work.

Truly a strawman of epic proportions.

He's also trying the old creationist trick of dividing mutation and selection to claim that each is insufficient for evolution. Here we have the "natural selection can't do anything new since all the DNA sequences are the same" variant. Others prefer the "mutations can't randomly assemble all the DNA pieces, tornado in a junkyard, blah, blah, blah" variant.

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"I suspect that the English grammar books where you live are outdated" --G. Gaulin

The whole truth

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Posted: Jan. 18 2015,10:08

Quote (cryptoguru @ Jan. 18 2015,01:46)

Quote

What does "new information" look like?

New information is new and novel genetic material that codes for new function or traits in the organism i.e. not a point mutation in a control gene that switches other pre-existing functionality off/on or a trade/inheriting of genetic material between bacteria ...NEW genetic material that codes for new function; this has never been observed.

Quote

Nearly all genes were invented by microbial evolution.

begging the question! Demonstrate the process ... don't simply assert it happens.

Quote

Bacteria are not "equivalent" to humans.

Straw-man argument ... I never said they were, I was equivocating the process of evolution in both organisms. Bacteria can "evolve" quicker because their generation time is MUCH shorter (hence why Lenski chose E. Coli). So I can compare 26 years of E. Coli to 1 Million years of human evolution ... they are exactly the same amount of the same process. We would expect to see novel traits emerge in humans over 1 million years and be able to identify new genes that didn't exists previously that code for that new trait. We don't see this in Lenski's experiment.

Quote

None of the logic functions that obtain merit in Avida are due to singular codes in an Avidian's genome

You're misunderstanding the point. The original 26 functions (commands) that AVIDA uses are not subject themselves to mutation. So finding new logical functions that are combinations of these elemental functions is trivial using an optimisation algorithm (which is what AVIDA is). You will only get functionality that is described by compounds of those functions.

This is equivalent to having a chemistry set with 26 elements, you combine them randomly and select combinations of chemicals that produce interesting reactions, you optimise over those. You will NEVER create a new chemical element from this process. The elemental level in AVIDA is the function (command), these should therefore be evolved, not prescribed.
AVIDA is a very interesting modelling algorithm, great for solving some real-world competition problems. It does NOT model biological evolution.
I have clarified this point countless times, I don't see how I can simplify it any more for people to understand here.

Explain precisely where, in my description of AVIDA and the biological evolution algorithm I have got any of the details wrong.
AGAIN (to explain this problem one last time)
1) evolution mutates DNA on a nucleotide level affecting function (gene level) and selects on the organism level.
2) AVIDA mutates "DNA" on the gene level affecting compound function and selects on the compound function level.

These are VERY simple concepts to grasp.
Please explain how AVIDA is possibly modelling biological evolution when the core functions (commands) cannot be corrupted under mutation and the selection process is working on the compound functional level (by rewarding compound functions).

"... I was equivocating the process of evolution in both organisms."

I know.

"Bacteria can "evolve" quicker because their generation time is MUCH shorter (hence why Lenski chose E. Coli). So I can compare 26 years of E. Coli to 1 Million years of human evolution ... they are exactly the same amount of the same process."

Where do you get the idea that every biological entity* evolves by exactly the same amount from one generation to the next?

*I would have said life form instead of biological entity but I'm including viruses, and not everyone thinks that viruses are life forms.

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Jim_Wynne

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Posted: Jan. 18 2015,10:35

Cryptoguru, condensed:

1. All of biology and most of science is wrong.
2. Frontloading.
3. No evidence, no mechanisms.

I'll put the over/under on this thread at six pages.

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Evolution is not about laws but about randomness on happanchance.--Robert Byers, at PT

Texas Teach

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Posted: Jan. 18 2015,10:41

Quote (Jim_Wynne @ Jan. 18 2015,10:35)

Cryptoguru, condensed:

1. All of biology and most of science is wrong.
2. Frontloading.
3. No evidence, no mechanisms.

I'll put the over/under on this thread at six pages.

Gaulin has no more than that, and his thread is at 429 pages. Never underestimate the needs of TARD-addicts.

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"Creationists think everything Genesis says is true. I don't even think Phil Collins is a good drummer." --J. Carr

"I suspect that the English grammar books where you live are outdated" --G. Gaulin

The whole truth

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Posted: Jan. 18 2015,10:46

NoName, thanks for taking what I said so graciously. :)

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Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

N.Wells

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Posted: Jan. 18 2015,11:53

Quote (cryptoguru @ Jan. 16 2015,19:14)

Quote

I'd like to add that natural selection is not always a death.

It can be an effective removal of the gene pool. For example, the strongest, fittest, most efficient lion ever born might have a problem reproducing. Which means that he is removed from the gene pool. He can't pass his genes on to the next generation, so he's out of contention.

Haha amazing ... how did he get removed from the gene pool? A Gene pool isn't actually like a swimming pool you know, genes don't get thrown out for breaking the rules by the life-guard ... He gets removed from the "Gene pool" (population) by dying ... he dies before reproducing (for whatever reason), so his genes aren't passed on. Natural Selection is not looking at his Genes and saying "hey this guy isn't fit enough ... throw him out" ... Natural Selection is just a name given to the fact we have lions that are still reproducing, and that lion isn't because he was less fit so simply dies.
You're picking a fight over something we agree on here. I'm demystifying the explanation of how Natural Selection works, it is death ... it is not just general competition. Yes it IS competition, but only competition that results in something dying and other things not.

My two cents on this earlier comment: Natural selection is not solely and only about death. It's differential reproductive success, which may or may not be attributable to dying early.

A long-term study of reproductive successes of 142 female sparrowhawks from 1971 to 1984 showed that 23 had no fledglings, 70 had only 1 to 4 fledglings, and 3 had more than 20 fledgelings (21, 22, & 23). Obviously, the genes of the last three become much more widely represented in subsequent generations. Some of the mothers died early, but others simply weren't successful at parenting. This can involve a whole host of reasons other than dying.

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Posted: Jan. 18 2015,12:32

Cryptoguru:

Quote

Haha amazing ... how did he get removed from the gene pool? A Gene pool isn't actually like a swimming pool you know, genes don't get thrown out for breaking the rules by the life-guard ... He gets removed from the "Gene pool" (population) by dying ... he dies before reproducing (for whatever reason), so his genes aren't passed on. Natural Selection is not looking at his Genes and saying "hey this guy isn't fit enough ... throw him out" ... Natural Selection is just a name given to the fact we have lions that are still reproducing, and that lion isn't because he was less fit so simply dies.
You're picking a fight over something we agree on here. I'm demystifying the explanation of how Natural Selection works, it is death ... it is not just general competition. Yes it IS competition, but only competition that results in something dying and other things not.

Here's another way Avida differs from Cryptoguru selection. Avidians get CPU time according to merit. It is perfectly possible for an Avidian to replicate while other Avidians have greater merit. The other Avidians, though, replicate themselves more often and thus the population comes to have more Avidians like those with more merit, and fewer Avidians like those with less.

This, by the way, is not a way in which Avida is distinguished from natural selection.

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cryptoguru

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Posted: Jan. 18 2015,14:18

Wesley R. Elsberry:

Again you've missed the point ... I'm not saying AVIDA should model every possible function, I'm saying that it doesn't model the proposed form of evolution. Real evolution is supposed to mutate the base code ... so you should be mutating the under-the-hood program code that defines the NAND, SWAP, DEC, IO, SUB etc. in AVIDA as this is what happens in a real genome.

I'm not doubting that AVIDA is excellent at solving generic optimisation problems, but it is misleading to pretend it is modelling biological evolution, because the core feature of biological evolution is random mutation of nucleotides (point, insertion, deletion). The variability of that problem is orders of magnitude greater than the simple optimisation problems you're solving with AVIDA.

In DNA, mutations occur at the symbol level of the code that is used to build and assemble proteins, direct their sub-assembly (amino acids ... translational pausing etc) and further controls the protein assembly into complex functional parts. These themselves are part of the whole organism, where cells are differentiated in function and perform many complementary roles with other cells.

AVIDA is basically 26 assembly code instructions, which are mutated randomly under competition until something useful happens. This is not analogous to DNA mutation and selection.

I say it again, THIS is like mutating 26 proteins in DNA to make different complex structures and rewarding certain combinations that give known favourable complex structures. AVIDA is applying mutations on a much higher level than occurs in the Genome, so doesn't allow the possibility of code corruption, base functionality regression and crash, which a real genome does.

This effect is amplified by the fact that the instruction set is Turing-complete ... AVIDA is MOST likely to find useful combinations of the 26 functions ... this is a cumulative SEARCH (similar to WEASEL it has targets), and not like biological evolution. The human genome has billions of base pairs, even mutating 3 neighbouring nucleotides to any codon anywhere in the genome is less likely than winning the lottery twice in a row. Being able to mutate an AVIDA command to another functioning command is 100% likely. DO YOU GET IT YET??? (I doubt it)

Most of the responses I've had so far are so off-the-wall and lacking in fundamental logic that it's impossible to even address their stupidity.

If you guys can't see the difference between a process which mutates nucleotides in a huge code that has MANY layers of complexity, inter-dependency and non-linear function and a process which randomly mutates 26 assembly instructions in different ways, scores combinations that perform a simple function and allows them to compete ... then you're more wilfully ignorant than I had initially assumed.

It's wishful thinking of the highest degree to expect useful behaviour to come out corrupting a computer program. Comparing that to shuffling assembler instructions until you get a useful function is absolutely laughable. I suppose you have to come up with something like this though to keep the funding rolling in and slap the word "evolution" all over the papers so the similarly confused peer reviewers get all excited and happy that evolution is a FACT and we can all sleep soundly.

Also the minion-like responses I've had concerning Lenski's experiment on here are equally hilarious. Trying to deny that after he's performed 60,000 generational steps seeing a small metabolic change is not something to get excited about is utterly self-deceptive.

This is a dying theory indeed when models can't model it ... and experiments don't demonstrate it.
The power behind this theory is you guys ... your zeal at flocking around any assailant and trying to neutralise any attacks on the precious, by employing as much ridicule, incredulity, slander and mock as you can muster whilst still attempting to sound scientific.

I'm going to go and do some actual work that isn't based on fairy tales now ...
... and leave you all to your mutual backslapping and peddling the nonsense postulation that random mutations plus a sprinkling of magic selection (which is the secret ingredient that we should never really define properly lest it became understandably deficient) will eventually mutate a Banana into Barack Obama. I do hope some of you get to use your brains for things that actually benefit people and this is just a hobby thing that you do in your sparetime.

Have fun folks.

Oh ... please DO let me know when Lenski suddenly finds a fish in his E. Coli. That will be a monumental day for all of us.

cryptoguru

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Posted: Jan. 18 2015,14:39

final point to N. Wells

Natural Selection is about death. It doesn't matter what the reasons are for advantage, whether it's because some are stronger, or shorter, or bluer, or have better ovaries, or avoid nightclubs .. whatever. The selective agent is death. If an organism dies before it can reproduce it will be removed from the gene pool. Things that haven't died yet compete for resources, eventually a hereditary line will die off removing it from the competition (death again).

The whole premise of natural selection can be simplified to be death. Differential reproduction is a misleading concept, because the preservation of an advantageous trait can only occur when eventually all other competing hereditary lines are extinct. (death). Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that, so all other lines must become extinct to allow the favoured line to become the parent to the next stage. (I obviously think this is crackers ... I'm just explaining that the evolutionary concept of natural selection is very simple)

My point is that the evolutionary concept of natural selection is easy to model, you just set natural conditions and environments for the organisms to live and compete in and see which survive, you shouldn't be measuring the advantages and rewarding them ... nature does not do that, it just provides conditions for death, those who survive it are considered "selected".

I don't see what all the fuss is about ... just trying to demystify the Natural Selection deity.

Bye for now

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Posted: Jan. 18 2015,15:00

Quote (cryptoguru @ Jan. 18 2015,14:39)

Natural Selection is about death.

No, natural selection is about reproductive success, not death. Death may be important, but only because of its impact on reproductive success. Dying at 20, leaving two children is better than dying at 80, with no children.

The process of natural selection is a bit like compound interest. As an example, take a stable population of 100 organisms; on average each organism has one descendant in the next generation. Now let a beneficial mutation appear with a 1% advantage, so the mutated organism will have on average 1.01 descendants in the next generation. For comparison I include a second mutated organism with a 1% disadvantage. Start with a population of 1 deleterious, 98 neutral and 1 beneficial mutations. See what happens if we let the population reproduce for one thousand generations:

Code Sample

Generation Deleterious Normal Beneficial
---------- ----------- ------ ----------
0 1.00 98.00 1.00
1 0.99 98.00 1.01
10 0.90 98.00 1.10
100 0.37 98.00 2.70
500 0.01 98.00 144.77
700 0.00 98.00 1059.16
1000 0.00 98.00 20959.16

(That should be monospaced, but I can't get it to work well. Sorry.)

You can see how the small 1% advantage is amplified over the generations as the beneficial variant spreads through the population. The deleterious mutation disappears.

This is a very simple model, but it is enough to show the advantage a beneficial mutation has and how it can spread through a population.

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The ultimate truth is that there is no ultimate truth.

N.Wells

Posts: 1836
Joined: Oct. 2005

Posted: Jan. 18 2015,15:06

Quote (cryptoguru @ Jan. 18 2015,14:39)

final point to N. Wells

Natural Selection is about death. It doesn't matter what the reasons are for advantage, whether it's because some are stronger, or shorter, or bluer, or have better ovaries, or avoid nightclubs .. whatever. The selective agent is death. If an organism dies before it can reproduce it will be removed from the gene pool. Things that haven't died yet compete for resources, eventually a hereditary line will die off removing it from the competition (death again).

The whole premise of natural selection can be simplified to be death. Differential reproduction is a misleading concept, because the preservation of an advantageous trait can only occur when eventually all other competing hereditary lines are extinct. (death). Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that, so all other lines must become extinct to allow the favoured line to become the parent to the next stage. (I obviously think this is crackers ... I'm just explaining that the evolutionary concept of natural selection is very simple)

My point is that the evolutionary concept of natural selection is easy to model, you just set natural conditions and environments for the organisms to live and compete in and see which survive, you shouldn't be measuring the advantages and rewarding them ... nature does not do that, it just provides conditions for death, those who survive it are considered "selected".

I don't see what all the fuss is about ... just trying to demystify the Natural Selection deity.

Bye for now

You are pervasively wrong here, because you are simplifying natural selection incorrectly.

Death, although important, is just one of many "selective agents", so differential reproductive success can be extremely different from "life versus death", and simplifying natural selection to "life versus death" has led to many misunderstandings about evolution, such as your misunderstandings. Natural selection is usually much more subtle than just differential mortality rates.

An organism that fails to reproduce as successfully as the neighbors will have a smaller proportion of genes in the next generation. That (with recombination and many generations) can indeed cause the genes to become very rare and eventually be lost from the population. Because of recombination and multiple generations, lineages do not have to go extinct for genes to be lost.

Quote

Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that....

"Millions" is an overstatement, but polymorphic alleles are indeed very common, as are races, sister species, and overlapping ranges between competitors, all of which indicate that the world does not function as simply as you imply.

From http://www.biologyreference.com/Mo-Nu......on.html

Quote

A persistent misconception is that natural selection occurs mainly through differences between organisms in death rates, or differential mortality. Differential mortality can be selective but only to the degree that it creates differences between individuals in the number of reproductive offspring they produce. Reproductive rate, rather than death rate, drives natural selection. A cautious tomcat that seldom crosses busy streets might live to a ripe old age without leaving behind as many descendent kittens as another less staid tomcat killed on a highway at a much younger age. If the short-lived cat leaves more descendants, its genes will spread faster than those of the long-lived cat, and natural selection will favor a short life span. Unless living longer allows or results in higher reproductive success, long life is not favored by natural selection.

See also http://www.zo.utexas.edu/courses....on.html

Edited to add: Thanks for a more specific response, Rossum - you posted while I was writing offline, or I'd have mentioned it.

Posts: 551
Joined: Oct. 2007

Posted: Jan. 18 2015,16:25

Verbatim re-post. I fully realize that cryptoguru's schedule is full up with telling evolutionists how wrong they are, but perhaps they will find the time to explain what they mean when they say "new and novel genetic material", or even determine whether or not one specific concrete example of a mutated nucleotide sequence qualifies as "new or novel genetic material". Or perhaps they will continue to make noise about how wrong evolutionists are. I dunno.

Quote (cryptoguru @ Jan. 18 2015,03:46)

Quote

What does "new information" look like?

New information is new and novel genetic material that codes for new function or traits in the organism i.e. not a point mutation in a control gene that switches other pre-existing functionality off/on or a trade/inheriting of genetic material between bacteria ...NEW genetic material that codes for new function; this has never been observed.

"Never been observed", you say. Well, I say, show me a person who's never heard of a kinkajou, and I'll show you a person who wouldn't recognize a kinkajou if a rabid one was chewing on their face. And in my experience, it's awfully damned common for Creationists who claim that thus-and-such has never been observed, do not actually know what thus-and-such would look like, and therefore those Creationists don't actually have any valid grounds for asserting that thus-and-such "has never been observed". So I want to drill down on your verbiage here, cryptoguru, and see whether you actually do know what you're talking about.

You have a definition of "new information". Groovy. I note that your definition of "new information" is sufficiently imprecise that it doesn't provide any way to tell whether or not a given string of nucleotides qualifies as "new information" under your definition. So let's see if we can dispel the vagueness, shall we?

Your definition of "new information" includes a clause about "new and novel genetic material". Why must the "genetic material" of "new information" be both "new" and "novel"? I ask because "new" and "novel" strike me as basically synonymous, hence, using both words is gratiutous redundancy. But perhaps you weren't being redundant; perhaps you actually are using distinct referents for "new" and "novel", such that the two words are not, in fact, gratuitously redundant. Please explain how "genetic material" which is "new" differs from "genetic material" which is "novel". Is it possible for "genetic material" to be "new" without also being "novel"? Is it possible for "genetic material" to be "novel" without also being "new"?

What does "new and novel genetic material" look like? I'm going to provide some concrete data to work with. Here's an arbitrary nucleotide sequence, with a randomly-picked nucleotide—the thymine in the 4th codon—colored red:
gcc tac agg gat cgt ggg gac ctt acg aat ggc ctt ttt gac tat tct tcg aat cta agc tca gca tca ttc ccg tct acg gga agt ccc ttc cca ata cat atc ctc ggc acc gca ctt gca ggc tca cgc ttc gcg tca ttt agg tca
That sequence of codons yields the following sequence of amino acids, with the 4th amino acid colored red on account of it's the AA that's yielded by the codon with the red-colored nucleotide:
alanine, tyrosine, arginine, aspartic acid, arginine, glycine, aspartic acid, leucine, threonine, asparagine, glycine, leucine, phenylalanine, aspartic acid, tyrosine, serine, serine, asparagine, leucine, serine, serine, alanine, serine, phenylalanine, proline, serine, threonine, glycine, serine, proline, phenylalanine, proline, isoleucine, histidine, isoleucine, leucine, glycine, threonine, alanine, leucine, alanine, glycine, serine, arginine, phenylalanine, alanine, serine, phenylalanine, arginine, serine

One possible mutation of that sequence would be if the thymine in the 4th codon was deleted, like so (and the thereby-altered 4th codon is colored red here):
gcc tac agg gac gtg ggg acc tta cga atg gcc ttt ttg act att ctt cga atc taa gct cag cat cat tcc cgt cta cgg gaa gtc cct tcc caa tac ata tcc tcg gca ccg cac ttg cag gct cac gct tcg cgt cat tta ggt ca
Since a codon is three nucleotides in a row, deleting that one nucleotide from the 4th codon in the original sequence doesn't just change that 4th codon; it also has the effect of changing pretty much every codon after that altered 4th codon. This, in turn, yields a very different sequence of amino acids than the original, unmutated sequence. The red-colored AAs are ones which don't occur at all in the original, unmutated sequence:
alanine, tyrosine, arginine, aspartic acid, valine, glycine, threonine, leucine, arginine, methionine, alanine, phenylalanine, leucine, threonine, isoleucine, leucine, arginine, isoleucine, [end], alanine, glutamine, histidine, histidine, serine, arginine, leucine, arginine, glutamic acid, valine, proline, serine, glutamine, tyrosine, isoleucine, serine, serine, alanine, proline, histidine, leucine, glutamine, alanine, histidine, alanine, serine, arginine, histidine, leucine, glycine, [???]

Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

Doc Bill

Posts: 1039
Joined: April 2007

Posted: Jan. 18 2015,16:49

That was quick! I don't think I've ever seen someone go through the Stages of a Creationist as quickly as CreeptoGuru.

1. Disingenuous Introduction (Hi, everybody! I've got some questions. Hope you can help. Feel free to correct any misconceptions I have!)

2. Creationist boilerplate.

3. Patient explanations by Saint Wes and others. (Doc Bill heavily sedated with DramaTARD to prevent chronic mockery.)

4. There is no evilution! Lenski benski! Whaaaaaa, you're mean to me! Jesus!

5. Flounce.

Thank you, Creepto, for providing us with this hilarious brick of TARD, although it probably won't make it into the Hall of Flame:

Quote

Also the minion-like responses I've had concerning Lenski's experiment on here are equally hilarious. Trying to deny that after he's performed 60,000 generational steps seeing a small metabolic change is not something to get excited about is utterly self-deceptive.

This is a dying theory indeed when models can't model it ... and experiments don't demonstrate it.
The power behind this theory is you guys ... your zeal at flocking around any assailant and trying to neutralise any attacks on the precious, by employing as much ridicule, incredulity, slander and mock as you can muster whilst still attempting to sound scientific.

In the future, Creepto, try to work in some flourish like "altar of Darwin" or "high priests of science." That's a crowd pleaser!

Posts: 4966
Joined: May 2002

Posted: Jan. 18 2015,18:06

Cryptoguru:

Quote

The power behind this theory is you guys ... your zeal at flocking around any assailant and trying to neutralise any attacks on the precious, by employing as much ridicule, incredulity, slander and mock as you can muster whilst still attempting to sound scientific.

Anyone whose analogies require living organisms to create new chemical elements is eminently mockable on their own demerits.

And, by the way, what I engaged in was disagreeing with Cryptoguru, not "missing the point". Given the many exceedingly basic errors I pointed out in his commentary, one would think he'd be a bit less full of himself. Anybody reviewing the thread is likely to see what I see, that Cryptoguru made a bunch of erroneous claims, got told they were erroneous and why they were erroneous, and made his exit with exceedingly bad grace.

Unless, of course, he's one of those people who makes endless farewell tours, and he's just given his first farewell concert.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

OgreMkV

Posts: 3668
Joined: Oct. 2009

Posted: Jan. 18 2015,18:16

Quote (cryptoguru @ Jan. 18 2015,14:39)

final point to N. Wells

Natural Selection is about death. It doesn't matter what the reasons are for advantage, whether it's because some are stronger, or shorter, or bluer, or have better ovaries, or avoid nightclubs .. whatever. The selective agent is death. If an organism dies before it can reproduce it will be removed from the gene pool. Things that haven't died yet compete for resources, eventually a hereditary line will die off removing it from the competition (death again).

The whole premise of natural selection can be simplified to be death. Differential reproduction is a misleading concept, because the preservation of an advantageous trait can only occur when eventually all other competing hereditary lines are extinct. (death). Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that, so all other lines must become extinct to allow the favoured line to become the parent to the next stage. (I obviously think this is crackers ... I'm just explaining that the evolutionary concept of natural selection is very simple)

My point is that the evolutionary concept of natural selection is easy to model, you just set natural conditions and environments for the organisms to live and compete in and see which survive, you shouldn't be measuring the advantages and rewarding them ... nature does not do that, it just provides conditions for death, those who survive it are considered "selected".

I don't see what all the fuss is about ... just trying to demystify the Natural Selection deity.

Bye for now

The selective agent doesn't have to be death. Again, this is trivially untrue... unless you think that neutering a dog kills it.

The animal is alive, but totally unable to pass it's genes on to the next generation. This is an extreme example, but there are plenty in the real world. Especially among herd animals with a single dominant male. Either you are the dominant male or you don't contribute to the genetic population of the group.

"The whole premise of natural selection can be simplified to be death."

No. The whole premise of natural selection is what Darwin said. You might read what the people who came up with the idea actually said instead of attacking a strawman.

Quote

Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that,

I think that this is especially funny. Because biologists think that every single organism is transitional. You are transitional between your parents and your kids. You are transitional between your uncle's kids and your aunt's kids.

There are millions of intermediate evolutionary stages. We don't see all of them because a vast majority are dead and not everything fossilizes. But still, we see them.

We even see transitionals in the genes. In fact, that is one of the reasons that multi-species whole genome studies can work. I've provided you with a paper that shows the transitional nature of genes among closely related species.

So, again, you are attacking a strawman. You say that we believe one thing... which we don't. And then you attack it (incorrectly).

Natural selection is fairly simple. When will you ever understand what it actually is?

To model it, you have to understand it correctly... and you don't.

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Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

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Posted: Jan. 18 2015,18:22

He does write better than GG.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

Doc Bill

Posts: 1039
Joined: April 2007

Posted: Jan. 18 2015,18:29

Quote (Wesley R. Elsberry @ Jan. 18 2015,18:06)

Cryptoguru:

Quote

The power behind this theory is you guys ... your zeal at flocking around any assailant and trying to neutralise any attacks on the precious, by employing as much ridicule, incredulity, slander and mock as you can muster whilst still attempting to sound scientific.

Anyone whose analogies require living organisms to create new chemical elements is eminently mockable on their own demerits.

And, by the way, what I engaged in was disagreeing with Cryptoguru, not "missing the point". Given the many exceedingly basic errors I pointed out in his commentary, one would think he'd be a bit less full of himself. Anybody reviewing the thread is likely to see what I see, that Cryptoguru made a bunch of erroneous claims, got told they were erroneous and why they were erroneous, and made his exit with exceedingly bad grace.

Unless, of course, he's one of those people who makes endless farewell tours, and he's just given his first farewell concert.

Saint Wes, an eternal fan of the Ungrateful Dead.

Woodbine

Posts: 1218
Joined: June 2007

Posted: Jan. 18 2015,19:07

Quote (midwifetoad @ Jan. 19 2015,00:22)

He does write better than GG.

The fish drowning in Lenski's e-coli writes better than Gary.

Doc Bill

Posts: 1039
Joined: April 2007

Posted: Jan. 18 2015,19:34

Quote (Woodbine @ Jan. 18 2015,19:07)

Quote (midwifetoad @ Jan. 19 2015,00:22)

He does write better than GG.

The fish drowning in Lenski's e-coli writes better than Gary.

Well, this is the typical creationist's view of evolution, isn't it?

CreeptoGuru demanded "new" and "novel" thingies and what he was demanding was a New Ford Chromosome 2015 with triple exhausts and a 13 cylinder engine, or some such.

Going back to Pandas, the hedge was "fish with fins and birds with feathers" with no ancestors.

That's what CreeptoGuru is demanding. Ironically, that's the definition of creationism. The fact that CreeptoGuru claims it's never been observed means that creationism has never been observed and that is totally correct. It hasn't!

Well done, CreeptoGuru, you just disproved creationism! Drinks on me.

QED

Posts: 41
Joined: July 2008

Posted: Jan. 18 2015,21:25

Told ya'...fly pigeon, fly!

cryptoguru

Posts: 53
Joined: Jan. 2015

Posted: Jan. 19 2015,07:45

wow ... OK, to avoid being labelled as running from a fight ... I'm going to try once more to see where we can get with a more structured approach
(I'm an amateur MMA fighter so not used to that sort of accusation)

I'm not expecting agreement, but at least it should help clarify where the sticking points are. If discussing a point, instead of posting an essay and saying it covers EVERYTHING, please refer to section and subsection so we all know which point you're contesting. Then we can get to a list of agreed principles, which should allow us to concentrate on the important controversial bits. (What was happening before was a full-scale assault on anything I said or the way I said it irrespective of whether there was agreement on the underlying principles or not.) Please also mark which points you agree on, otherwise I don't know where the common ground is.

Section A: How does the cell work (very very basic version)
1) living cells process a program called DNA
2) DNA is a code (a sequence of 3 symbols codes for amino acid)
3) DNA is processed in a non-linear fashion through regulatory mechanisms with multiple reading frames.
4) The cell eventually produces folded proteins, which are determined by which genes are being read, the reading frame, the regulatory process ... tonnes of stuff ... but it's deterministic (ignoring mutations) and the whole process is defined by the code. (this includes regulation in response to external stimuli ... i.e. input)
5) folded proteins are assembled into complex structures, again this process is controlled by mechanisms which are defined in the code.
6) the cells replicate and differentiate their function in a continuous morphological (yet continually compositionally functional) fashion based on their position in the organism, this process is also controlled by the code.

Section B:
What is Biological Evolution
1) given a population of self-replicating entities (a living cell)
2) random mutation of symbols in the raw code (usually point mutations ... about 50-100 de novo germline mutations per generation in humans)
3) advantages are introduced via the mutations by chance, the advantages are preserved and propagate through the population by "natural selection"
4) Natural selection is the name given to the process whereby environmental conditions apply a pressure for survival on the entities.
5) Entities therefore compete for resources and the ultimately surviving hereditary line is preserved, presumably carrying the genetic advantage that allowed it to overcome its competition.
6) Differential reproduction is a fancy way of saying that the hereditary line of some organisms, due to their inferiority in how they are suited to the environment, eventually (at some level of descent) produce no offspring before dying and therefore leave the competition.
7) Death is the only agent in natural selection, regardless of whether some organisms are only slightly better adapted than others, there will eventually be a point where an entire inferior hereditary line is removed (ultimately by death) from the population (i.e. a discrete process, not a continuous one). It is now as though that line had never existed. This is why death is the only important selector, comparisons between organisms do not come into the selection process ... it is simply a case of whether an organism is sufficiently fit to survive long enough in the environment to reproduce.

(I imagine point 7 will draw the most controversy ... TBH it's not important that you agree on that point for the sake of my argument, so happy to leave Natural Selection as an ambiguous and mysterious force if people would prefer so we can move on to where the actual disagreement should occur)

Section C:
What does AVIDA model
(I'm going to change my analogy here to focus the disagreement away from mutation)
1) 26 logical commands are provided and randomly selected and combined by "mutating" an original arrangement of them.
2) the commands are a list of functional operators (building blocks) that a computer code can be built from. They are Turing complete, so we should expect to be able to build any computer code from them in the correct combination
3) self-replicating digital entities, which have their own virtual processor run and mutate these programs
4) any entities are rewarded when a sequence of commands forms a logical function by increasing their resources

Section D:
comparison of AVIDA to biological evolution
1) an analogy must be drawn between AVIDA commands and the genome
2) it possibly makes most sense (I concede) to assume that AVIDA commands are analogous to codons (and not proteins), so that any mutation will always create a set of valid codons.
3) the level AVIDA is selecting at is therefore analogous to a folded functional protein.

Section E:
problems with model
1) the multi-dimensionality of the genome due to multiple reading frames means that a point mutation in the genome will likely affect the expression of multiple proteins (19K coding genes code for at least 100K different proteins in the human genome). Mutations in AVIDA are mutually exclusive and therefore don't have a regressive effect on the expression of other COMMANDS. This is not a trivial difference, it is analogous to the difference between a bisection method (AVIDA mutation) and a bisection method where the root can change at each iteration (Genome mutation).
2) It is not just multiple reading frames that introduce polymorphism into the genome, but regulatory genes can effect the expression of an entire coding gene. This non-linearity is not modelled in AVIDA, which is a linear sequential code (like assembler). That is, the Genome executes a higher-level language than a sequential instruction set.
3) AVIDA enforces selection by rewarding at the functional level ... it identifies a function as a logical operation and rewards the organism that is presenting it. This is equivalent to natural selection providing feedback scores to the organism on a per-protein level. e.g. protein 1 7/10, protein 2 3/10, protein 3 9/10. This kind of micro-management can't happen in real-life as natural selection is blind and is applied not even to an organism but an entire population. This feature artificially boosts the productivity of hopeful combinations of commands, which otherwise wouldn't be encouraged.
4) The level of variability in AVIDA compared to the genome is like comparing solving a Rubik's cube with cracking 2048-bit RSA encryption. The logical functions which AVIDA selects and guide the optimisation process are trivial ... and also non-distinct. There are infinitely many ways to implement the EQU function using the AVIDA instruction set. Proteins are specific in their form, not just in an abstract functional way. The likelihood of randomly selecting a combination of AVIDA commands that performs a logical function is extremely high, I don't know if it's even possible to work this out considering there are infinitely many combinations that could represent each logical function. (e.g. inc dec inc dec inc dec is equivalent to leaving a register unchanged). In the genome the possibility of just mutating 3 neighbouring nucleotides anywhere in the genome to produce a different codon is less than the chances of winning the national lottery twice in a row, and two proteins with different amino acid chains can likely never be equivalent in function. (unless randomness of function is the required function for the protein)

DISCUSS!

JonF

Posts: 634
Joined: Feb. 2005

Posted: Jan. 19 2015,08:16

You need to supply some serious support for E.4. Particularly, two proteins with different amino acid chains are often equivalent in function. Nobody has any idea how many proteins there are that perform some specified function, but the evidence suggest there's loads of 'em. Plus there are proteins that perform multiple functions.

Zachriel

Posts: 2722
Joined: Sep. 2006

Posted: Jan. 19 2015,08:21

cryptoguru: evolution mutates DNA on a nucleotide level affecting function (gene level) and selects on the organism level.

Evolution also involves recombination and the splicing of new structures from subcomponents.

cryptoguru: The whole premise of natural selection can be simplified to be death.

That is also false. The whole premise of natural selection is reproductive success.

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You never step on the same tard twice—for it's not the same tard and you're not the same person.

Posts: 287
Joined: Dec. 2008

Posted: Jan. 19 2015,08:33

Quote (JonF @ Jan. 19 2015,08:16)

You need to supply some serious support for E.4. Particularly, two proteins with different amino acid chains are often equivalent in function. Nobody has any idea how many proteins there are that perform some specified function, but the evidence suggest there's loads of 'em. Plus there are proteins that perform multiple functions.

The calculation has been done for Cytochrome C: Yockey (1992) calculated that there are 2.3 x 10^93 different amino acid sequences that could make a working Cytochrome C.

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The ultimate truth is that there is no ultimate truth.

cryptoguru

Posts: 53
Joined: Jan. 2015

Posted: Jan. 19 2015,08:39

Cubism: (this is not directly about my last post but answering an earlier clarification from Cubism)

Quote

Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

The issue here is one of scale ... changing a single nucleotide and getting new functionality is more adequately describing a side-effect of switching a control gene rather than amazingly arriving at a new functional sequence through mutation and selection.

So evolution claims that all the differences between a chimp's DNA and ours are caused by random mutation on 2 hereditary lines from a common ancestor. Find a sequence of unique DNA in the human genome (yup you can use the "junk DNA" now too, now we know it's not junk). Now that string you're holding has arrived by random mutation ... selection has preserved it, but mutation created it. That's what I mean by new/novel/unique information. You may be able to handwave that the switching of a few control genes could happen randomly .... we can all accept that.
But ALL that new (unique) code you're holding had to be created by random mutation and it all had to be preserved through natural selection. The mathematician in me is screaming IMPOSSIBLE! The sheer amount of new and structured information that works not in a sequential code way but in an interdependent, non-linear, overlapping code manner that has been randomly mutated piecewise and each intermediate stage is functionally advantageous is off-the-scale probabilistically impossible (in my opinion ... because those stats couldn't even be quantified).

So my point is ... it's easy to show in a small amount of variability that something magic can happen once in a blue moon (that's just normal probability) ... but for magic to be preserved and extended to the level that evolutionists assert is an obvious extrapolation (molecules-to-man), we need to be seeing a LOT of magic and all the time, everywhere. Nobody gets that much luck ... never-mind claiming that every currently existing organism has had this kind of luck. The computer models (like AVIDA) oversimplify the proposed process by hugely simplifying the organism and only modelling tiny problems, this does not demonstrate the kind of variability and specified complexity we observe ... you should be able to model it to these levels if evolution works.

So to summarise my answer ... when I'm talking about new information ... I'm talking about a unique DNA sequence in an organism. I can't see how it would ever be possible for random mutation to create that much dumb luck even given billions of years. That's not an argument from incredulity ... that's me saying from my knowledge of statistics I can't see how it could ever be possible, so the extraordinary claim of evolutionists needs to be demonstrated in a model that addresses the difficult-to-believe parts of the claim, not just that we can randomly arrive at something useful sometimes

N.Wells

Posts: 1836
Joined: Oct. 2005

Posted: Jan. 19 2015,09:14

Quote

1) living cells process a program called DNA
2) DNA is a code (a sequence of 3 symbols codes for amino acid)

Analogies between DNA and either codes or blueprints are convenient, but they can derail very easily. DNA is a very complex organic molecule that interacts with a very large number of other complex molecules in exceedingly complicated ways. It is more like a catalyst than a set of instructions.
http://www.huffingtonpost.com/agustin....36.html
http://www.science20.com/chatter....ot_code
http://livinglifewithoutanet.com/2009.......-a-code

Quote

5) folded proteins are assembled into complex structures, again this process is controlled by mechanisms which are defined in the code.

The process is affected chemically by both the environment and by other proteins formed from other bits of DNA: No "mechanisms" are "defined" by a "code".

Quote

1) given a population of self-replicating entities (a living cell)
2) random mutation of symbols in the raw code (usually point mutations ... about 50-100 de novo germline mutations per generation in humans)
3) advantages are introduced via the mutations by chance, the advantages are preserved and propagate through the population by "natural selection"

1) or multicellular organisms
2) They aren't symbols: if so, what does adenine symbolize?
You are talking about point mutations. These can be dramatic (cf. myostatin blocker mutations). However, even more interesting are larger mutations lilke duplications (read up on polyploidy in ornamental and agricultural plants) and translocations. (You are clear that the advantages are by chance, and not necessarily the mutations, correct?)
3) Also by genetic drift. Differential advantages are also introduced by recombination, far more than by new mutations (cf. dogs, pet hamsters, pet guppies, the genus Brassica, ornamental pigeons, varieties of chickens, etc., etc.).

Quote

4) Natural selection is the name given to the process whereby environmental conditions apply a pressure for survival on the entities.

Genetic drift can also be environmental. If an ice storm wipes out 100% of the birds of one particular species overwintering in a large area, that will have huge effects via genetic drift and none via selection, at least in the area of 100% mortality.

Quote

5) Entities therefore compete for resources and the ultimately surviving hereditary line is preserved, presumably carrying the genetic advantage that allowed it to overcome its competition.
6) Differential reproduction is a fancy way of saying that the hereditary line of some organisms, due to their inferiority in how they are suited to the environment, eventually (at some level of descent) produce no offspring before dying and therefore leave the competition.
7) Death is the only agent in natural selection, regardless of whether some organisms are only slightly better adapted than others, there will eventually be a point where an entire inferior hereditary line is removed (ultimately by death) from the population (i.e. a discrete process, not a continuous one). It is now as though that line had never existed. This is why death is the only important selector, comparisons between organisms do not come into the selection process ... it is simply a case of whether an organism is sufficiently fit to survive long enough in the environment to reproduce.

Because of recombination, two genes in you are not forever linked in your progeny. Even if they occur close together on the same chromosome, translocations etc. can separate them.

It is far easier to understand natural selection in terms of differential reproductive success than differential mortality: for example, think of male praying mantises and similar species where reproductive success means getting eaten by their mates, or cecidomyiian gall midges, where reproductive success means the children eating their way out of the mother and killing her. Yes, sometimes a mutation is very bad, and as a result its owner gets eaten or otherwise dies very quickly, or doesn't even get born in the first place. However, most variations are not that dramatic, and result in slightly more or slightly fewer offspring, and the genes' fortunes rise and fall on that slight difference. The less timid mouse may well get eaten sooner by a cat or an owl, but may well have found more food, mated with more females, and fathered more offspring than its neighbor who rarely ventured out of its burrow and died in its bed at a ripe old age (http://www.jstor.org/discover/10.2307/2462815?sid=21105655083353&uid=4&uid=2).

Mortality rates are important, but if you don't do evolutionary accounting in terms of reproductive success, you will severely misunderstand whole areas such as average age of first reproduction, age-specific expectation of future offspring, r & k strategies, kin selection, and so on and so forth
http://www.zo.utexas.edu/courses....ry.html
http://www.zo.utexas.edu/courses....th.html

cryptoguru

Posts: 53
Joined: Jan. 2015

Posted: Jan. 19 2015,09:14

JonF:
you're right ... I can't quantify it. But are you asserting that the variability in the human genome to build a fully functional human, with a functioning brain (and preprogrammed reflexes) and nervous system is equivalent to a sequentially processed assembler code that just has to make some logic functions?
These are galaxies apart in complexity. And you certainly can't extrapolate the simple case.

Zachriel:

Quote

Evolution also involves recombination and the splicing of new structures from subcomponents.

Sure, but that wouldn't account for significantly long unique sequences that haven't appeared before in the history of that genome. They could only be explained by random mutation coming in somewhere along the way.

Quote

The whole premise of natural selection can be simplified to be death.

People kept saying this ... but it didn't make sense to me to see anything else as the reason for a winner to emerge. Actually you guys may be right about this, now I've thought about it a bit more. If an organism can be removed from the competition through another means other than death (e.g. location) that would work too. So yes, let me retract my statements about Natural Selection only being able to be possibly enforced by death ... ooh I've learned something.

Quote

there are 2.3 x 10^93 different amino acid sequences that could make a working Cytochrome C.

This may be true for a few proteins but certainly isn't the case for all proteins, which require a specific form to be functional. We need to be able to account for the origin of all of them.

Zachriel

Posts: 2722
Joined: Sep. 2006

Posted: Jan. 19 2015,09:32

Quote (cryptoguru @ Jan. 19 2015,09:14)

Zachriel:

Quote

Evolution also involves recombination and the splicing of new structures from subcomponents.

Sure, but that wouldn't account for significantly long unique sequences that haven't appeared before in the history of that genome. They could only be explained by random mutation coming in somewhere along the way.

The process of splicing subcomponents can create new functional structures.

Quote (cryptoguru @ Jan. 19 2015,09:14)

Zachriel:

Quote

The whole premise of natural selection can be simplified to be death.

People kept saying this ... but it didn't make sense to me to see anything else as the reason for a winner to emerge.

An example was provided, of pacific salmon. They all die. Some die before reproducing. Some die immediately after reproducing. Some produce more or healthier eggs. But they all die.

Quote (cryptoguru @ Jan. 19 2015,09:14)

Actually you guys may be right about this, now I've thought about it a bit more. If an organism can be removed from the competition through another means other than death (e.g. location) that would work too. So yes, let me retract my statements about Natural Selection only being able to be possibly enforced by death ... ooh I've learned something.

Good. It's an important point.

--------------

You never step on the same tard twice—for it's not the same tard and you're not the same person.

QED

Posts: 41
Joined: July 2008

Posted: Jan. 19 2015,09:35

"plus a sprinkling of magic selection (which is the secret ingredient that we should never really define properly lest it became understandably deficient) will eventually mutate a Banana into Barack Obama."

Yep- it was inevitable - your "fight" isn't about science at all - it's a socio-political one, crypto. But thanks for letting everyone know.

Next up - why ID should be taught in schools, in
3...2...1...

cryptoguru

Posts: 53
Joined: Jan. 2015

Posted: Jan. 19 2015,09:37

Quote

Analogies between DNA and either codes or blueprints are convenient, but they can derail very easily

I've said this before and I'll assert this again ... DNA is not like a code ... it IS a code and the cell is a Turing-complete computer (not an analogy ... a definition).
It is NOT like a blueprint, a blueprint is a diagram that shows how to build something, it doesn't contain the ability to build the object and necessary materials for the object in itself.

Quote

No "mechanisms" are "defined" by a "code".

That isn't true. DNA code is functionally non-linear ... it is processed by the cell, the expression of proteins is a deterministic process, which is explicitly defined by the DNA code. It uses chemical processes to respond to the environment and toggle control genes and expression of genes, but this functionality is prescribed in the DNA ... if it wasn't deterministic, the DNA could accidentally make a coconut instead of a baby ... my wife would be livid, if she went through all that pain just for a coconut. DNA only does something different if it's responding (according to its own programming) to external events or if it is mutated. Chemistry only describes the physical processes, they do not describe the functionality, which is abstract. That is akin to trying to analyse the functionality of Mac OSX by looking at the flow of electricity through your motherboard, that does not explain the functionality in the program that it is running; just the medium it is using to execute it.

Quote

They aren't symbols: if so, what does adenine symbolize?

They ARE symbols in the representation of the functional code. 3 Symbols constitute a codeword (codon) ... this is what AVIDA works with as its commands. Adenine doesn't "symbolize" anything atomically anymore than the letter 'F' symbolizes anything on your keyboard ... but it is a symbol that is used to build words which are understood in the context of the language they are intended for.

Quote

Genetic drift can also be environmental

True ... I don't see how that affects the scope of what we are considering though.

cryptoguru

Posts: 53
Joined: Jan. 2015

Posted: Jan. 19 2015,09:54

QED'oh:

Quote

Yep- it was inevitable - your "fight" isn't about science at all - it's a socio-political one, crypto. But thanks for letting everyone know.

Your fight with me isn't about science either, it's because I dare to disagree with your paradigm ... who's being socio-political? Science is meant to challenge paradigms, that's how it was started (by creationists).

Quote

wah wah wah

(from earlier)
Come along to an MMA sparring session with me and we'll see who cries first! This pigeon eats off-topic evolutionist evangelists for breakfast. (in a differential fitness sort of way)

So you can shut up now until the conversation ends and you can make your closing speech about how you scared me off good 'n' proper.

At least the other guys on here are having a civil conversation and explaining their view of how it all works.
I'm actually learning something new for once.

N.Wells

Posts: 1836
Joined: Oct. 2005

Posted: Jan. 19 2015,09:59

You are wrong about DNA and codes, but you are far more wrong about

Quote

Genetic drift can also be environmental

True ... I don't see how that affects the scope of what we are considering though.

If you look at a bird book for North America, you will see a very large number of eastern and western pairs of forest-dwelling species or subspecies, consisting of distinctive differences in coloration and calls, which have varying degrees of interfertility. The reason for all these pairs of species appear to be far less a matter of adaptive evolution and natural selection than isolation and genetic drift* following removal of forests across the great plains: e.g., red- and yellow-shafted flickers, lazuli and indigo buntings, black-headed and rose-breasted grosbeaks, Baltimore and Bullock's orioles, etc. Or look at genetic-distance maps of various groups of chimpanzees or gorillas, mollusk sister-species across the Panamanian Isthmus, and so forth. (*Yes, bird coloration and songs are reinforced by sexual selection, which is a form of natural selection, but the initial changes would logically have been drift, and mating preferences are not relevant in organisms like sessile clams.)

QED

Posts: 41
Joined: July 2008

Posted: Jan. 19 2015,10:00

I'm not fighting with you, crypto. I'm just making observations that you're not producing any "new information". But have at it. I can wait.

cryptoguru

Posts: 53
Joined: Jan. 2015

Posted: Jan. 19 2015,10:03

N. Wells:

Quote

You are wrong about DNA and codes, but you are far more wrong about

Oh OK ... sure I'll just take your word for it, you being the expert and all that.

Quote

If you look at a bird book for North America, you will see a very large number of eastern and western ... blah blah blah

This is irrelevant to the point we're discussing, which is about how well AVIDA models biological evolution and how a non-linear functional code that is randomly mutated can expect to gain new function over time.

N.Wells

Posts: 1836
Joined: Oct. 2005

Posted: Jan. 19 2015,10:07

Quote (cryptoguru @ Jan. 19 2015,10:03)

N. Wells:

Quote

You are wrong about DNA and codes, but you are far more wrong about

Oh OK ... sure I'll just take your word for it, you being the expert and all that.

Quote

If you look at a bird book for North America, you will see a very large number of eastern and western ... blah blah blah

This is irrelevant to the point we're discussing, which is about how well AVIDA models biological evolution and how a non-linear functional code that is randomly mutated can expect to gain new function over time.

Don't take my word: I gave you three links, and many more can be found to discuss the same issue.

No, at that point you were generalizing about evolution, not discussing Avida.

cryptoguru

Posts: 53
Joined: Jan. 2015

Posted: Jan. 19 2015,10:16

QED:
I explained what "new information" is:-

Quote

when I'm talking about new information ... I'm talking about a unique DNA sequence in an organism.

Not a point-mutated nucleotide or a spliced copy, look at unique continuous sequences of nucleotides in human DNA that are unrepresented in our purported genetic relatives and perform necessary function. You need to explain how those huge amounts of information originated. You guys claim we get those by successive random mutation, I want to see the possibility of that modelled; because to me when you're dealing with that amount of variability, it's completely impossible.
I worked in cryptography for years ... so I am used to evaluating the likelihood of difficult problems being solved by stochastic processes ... I've got a reasonable handle on the statistics and the process (as well as specialising in biological mathematical & computer modelling - PhD) ... to me this is impossible; so show me a working model that represents even some of the complexity of "real" evolution.

N.Wells

Posts: 1836
Joined: Oct. 2005

Posted: Jan. 19 2015,10:19

DNA is not symbolic. It is a chemical, not a code (or if it is a code, so is water.) Strictly speaking it is not coded, nor is it decoded or interpreted. It is a chemical that interacts chemically, which is not true of any other known codes. (Unless you want to make an issue of smoke signallers coughing.......? :) )

From http://www.antievolution.org/cgi-bin....;t=9614

Quote

The way a computer code works is that the exact sequence of the code - the precise order of the binary 1s and 0s - spells out exactly what operations the computer must perform. But in genetics, the sequence is only part of the picture. Just as important are genetic regulatory networks - which genes are turned on at what times and in combination with which other genes. Phenotypes are not simply the result of particular gene sequences but the result of specific gene-gene (or gene network-gene network) interactions.

But DNA bears little relation to a "code" in a more fundamental way. Consider exactly what a "code" is. A code is a system of arbitrary symbols used to represent ideas and objects. In a sense, language itself is a "code"; the symbol "dog" represents that furry tetrapod with a waggly tail, for example. In a code, the symbols themselves have no inherent meaning. The letter "d" is meaningless by itself, as are the letters "o" and "g". It is only in combination that they derive meaning, and their meaning is derived from the idea that they represent. Furthermore, they only have meaning because we give them meaning. "Dog" is merely the label we apply to Fido; in a universe without sentient beings, "dog" would be meaningless. DNA does not fit this description at all. DNA is not arbitrary in any way; each letter of the genetic "code" is an actual biological compound. ACCGTCGA might be the gene for determining how long your toe hair is, but unlike a code, A, C, T and G each have their own non-arbitrary meaning. And this meaning exists independently of human sentience - the sequence of nucleotides does not have meaning only because we give it meaning. It would have meaning even if humans didn't exist at all.

What DNA is, is a polymeric chemical that follows a dynamic chemical process, governed by universal physical rules. It is only a "code" in the same sense that nuclear fusion is a "code" for how stars produce light

From http://www.talkorigins.org/indexcc....80.html

Quote

The genetic code is not a true code; it is more of a cypher. DNA is a sequence of four different bases (denoted A, C, G, and T) along a backbone. When DNA gets translated to protein, triplets of bases (codons) get converted sequentially to the amino acids that make up the protein, with some codons acting as a "stop" marker. The mapping from codon to amino acid is arbitrary (not completely arbitrary, but close enough for purposes of argument). However, that one mapping step -- from 64 possible codons to 20 amino acids and a stop signal -- is the only arbitrariness in the genetic code. The protein itself is a physical object whose function is determined by its physical properties.

Furthermore, DNA gets used for more than making proteins. Much DNA is transcribed directly to functional RNA. Other DNA acts to regulate genetic processes. The physical properties of the DNA and RNA, not any arbitrary meanings, determine how they act.

An essential property of language is that any word can refer to any object. That is not true in genetics. The genetic code which maps codons to proteins could be changed, but doing so would change the meaning of all sequences that code for proteins, and it could not create arbitrary new meanings for all DNA sequences. Genetics is not true language.

The word frequencies of all natural languages follow a power law (Zipf's Law). DNA does not follow this pattern (Tsonis et al. 1997).

Language, although symbolic, is still material. For a word to have meaning, the link between the word and its meaning has to be recorded somewhere, usually in people's brains, books, and/or computer memories. Without this material manifestation, language cannot work.

DNA is understandable as a specialized alternative to RNA, and RNA is simultaneously the information, the tools to make stuff, and the material out of which both the tools and the structures are made. DNA simply holds the information and hands the rest of the capabilities off to proteins.

I mentioned "DNA as blueprints" not because you said it but because it is another common and partially useful analogy for DNA that can similarly derail horrendously when one extends the analogy to areas where it does not apply.

Quote

You need to explain how those huge amounts of information originated. You guys claim we get those by successive random mutation, I want to see the possibility of that modelled; because to me when you're dealing with that amount of variability, it's completely impossible.

Duplication and mutation create new "information", and so does recombination (because so many developmental outcomes result from chemical interactions between gene products rather than just the presence or absence of individual genes - yet another reason why DNA is not just a code). Also, there is no single "target", but rather a selection of what works well enough or better than the alternatives in terms of resultant numbers of offspring, so simplistic probability calculations don't apply, and neither do simplistic life-or-death dichotomies.

JonF

Posts: 634
Joined: Feb. 2005

Posted: Jan. 19 2015,10:31

Quote (cryptoguru @ Jan. 19 2015,09:39)

Cubism: (this is not directly about my last post but answering an earlier clarification from Cubism)

Quote

Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

The issue here is one of scale ... changing a single nucleotide and getting new functionality is more adequately describing a side-effect of switching a control gene rather than amazingly arriving at a new functional sequence through mutation and selection.

Why?

Quote

The mathematician in me is screaming IMPOSSIBLE!

The mathematician in me is screaming SHOW ME THE NUMBERS! So far all you've shown is personal incredulity.

JonF

Posts: 634
Joined: Feb. 2005

Posted: Jan. 19 2015,10:34

Quote (cryptoguru @ Jan. 19 2015,10:14)

JonF:
you're right ... I can't quantify it. But are you asserting that the variability in the human genome to build a fully functional human, with a functioning brain (and preprogrammed reflexes) and nervous system is equivalent to a sequentially processed assembler code that just has to make some logic functions?
These are galaxies apart in complexity. And you certainly can't extrapolate the simple case.

You are asserting a qualitative difference between Avida and biological evolution. Quantifiable or not, yes, the human body is a lot more complex that what Avida can produce. Partly due to the lack of time and lots of trials. But I see no reason why the process that produced EQU in Avida can't produce a human being in real life.

JonF

Posts: 634
Joined: Feb. 2005

Posted: Jan. 19 2015,10:35

Quote (cryptoguru @ Jan. 19 2015,10:37)

Quote

Analogies between DNA and either codes or blueprints are convenient, but they can derail very easily

I've said this before and I'll assert this again ... DNA is not like a code ... it IS a code and the cell is a Turing-complete computer (not an analogy ... a definition).

You don't get to just define a cell as a Turing-complete computer. You need to demonstrate that the cell meets the requirements of a Turing-complete computer. Which you supposedly know.

I could define a pair of scissors as a Turing-complete computer. But I would be objectively wrong. Calling a tail a leg doesn't make it one.

cryptoguru

Posts: 53
Joined: Jan. 2015

Posted: Jan. 19 2015,10:40

N.Wells:
who wrote that nonsense??
This point isn't even worth arguing ... it's called "Genetic code" and they're called "codons" for a reason.
It fulfils all the criterion for being a code ... in fact, a computer code; as it is processed by the cell in a Turing-complete manner.
I don't think many people on here would agree with your point ... and interestingly AVIDA itself models the cell as a computer with a processed instruction set.

Information is the arrangement of matter, the DNA code is in the arrangement of the chemicals (not in the chemicals themselves). Information is abstract. DNA is not just a chemical zipper! It is addressable and uses boolean logic to regulate parts of the code, so is functional.
The information in a book is not described by the chemical constituents of the ink and the pages, it is the arrangement of these molecules that contains the information.

N.Wells

Posts: 1836
Joined: Oct. 2005

Posted: Jan. 19 2015,10:48

Quote (cryptoguru @ Jan. 19 2015,10:40)

N.Wells:
who wrote that nonsense??
This point isn't even worth arguing ... it's called "Genetic code" and they're called "codons" for a reason.
It fulfils all the criterion for being a code ... in fact, a computer code; as it is processed by the cell in a Turing-complete manner.
I don't think many people on here would agree with your point ... and interestingly AVIDA itself models the cell as a computer with a processed instruction set.

DNA is extremely complicated, so we do not have language to do it justice, so we use analogies and metaphors. That's fine, until we mistake the analogy or the metaphor for reality and drive the analogy into areas where it does not pertain. That's what you are doing.

Quote

Information is the arrangement of matter, the DNA code is in the arrangement of the chemicals (not in the chemicals themselves). Information is abstract. DNA is not just a chemical zipper! It is addressable and uses boolean logic to regulate parts of the code, so is functional. The information in a book is not described by the chemical constituents of the ink and the pages, it is the arrangement of these molecules that contains the information.

I'm not sure what you are getting at. The sequence of nucleotides in a gene determine what protein is produced and how it folds, but a) a lot of variation is tolerated and some makes no difference at all, and b) information in DNA is most specifically not in its arrangement in terms of the physical arrangement of the genes, but merely in the timing of production of proteins and the chemistry of how those proteins interacts. (Proximity on a chromosome affects the likely of two genes getting separated, but does not mean that they will be expressed at the same time: as you said, not a zipper.)

JonF

Posts: 634
Joined: Feb. 2005

Posted: Jan. 19 2015,10:49

Quote (cryptoguru @ Jan. 19 2015,11:16)

QED:
I explained what "new information" is:-

Quote

when I'm talking about new information ... I'm talking about a unique DNA sequence in an organism.

Not a point-mutated nucleotide or a spliced copy, look at unique continuous sequences of nucleotides in human DNA that are unrepresented in our purported genetic relatives and perform necessary function.

That explanation is incompatible with the previous definition. A point mutation produces a unique DNA sequence. You are trying to be as vague as possible. Some mathematician.

Do you know what an operational definition is? Your first try was one, your second try isn't.

Quote

You need to explain how those huge amounts of information originated. You guys claim we get those by successive random mutation, I want to see the possibility of that modelled; because to me when you're dealing with that amount of variability, it's completely impossible.

Yeah, good ol' personal incredulity. Much better than evidence.

Quote

I worked in cryptography for years ... so I am used to evaluating the likelihood of difficult problems being solved by stochastic processes ... I've got a reasonable handle on the statistics and the process (as well as specialising in biological mathematical & computer modelling - PhD) ... to me this is impossible; so show me a working model that represents even some of the complexity of "real" evolution.

You need to define exactly want you mean by representing some of the complexity of "real" evolution. You need to have an operational definition of the product of such a model, and you need to demonstrate that such a model is practical.

Meanwhile we've got lots of examples of real and modeled complex evolution, not as complex as human evolution, but nobody's found any reason why the results we have cannot be extrapolated to "real " evolution. And there have been lots of studies of what rates of various processes are required to produce what we see. Are you familiar with those studies? Would you care to guess what their results are?

cryptoguru

Posts: 53
Joined: Jan. 2015

Posted: Jan. 19 2015,11:06

JonF:
Yes I am personally incredulous ... I am not asserting that proves anything ... I'm saying that the burden of proof is on you to show that this (relatively new) proposed mechanism which seems to defy laws of logic could even theoretically do what is suggested

Quote

But I see no reason why the process that produced EQU in Avida can't produce a human being in real life.

That's because you want to believe that ... it hasn't been demonstrated that it's even possible. People are claiming that AVIDA proves biological evolution ... it doesn't! We just showed that ... It proves you can find a logical function using stochastic process on a Turing-complete set of instructions.

Quote

You don't get to just define a cell as a Turing-complete computer.

It's actually probably even Turing-universal
Efficient Turing-universal computation with DNA polymers

cryptoguru

Posts: 53
Joined: Jan. 2015

Posted: Jan. 19 2015,11:19

Quote

That explanation is incompatible with the previous definition. A point mutation produces a unique DNA sequence. You are trying to be as vague as possible. Some mathematician.

You misunderstood what I said there. I said "point mutation" singular ... not sequence of point mutations.

EXAMPLE

GCATTUCAGUUGATUCCATATGGCTU
GCATTUCAGTUGATUCCATATGGCTU

The U has been point-mutated to a T ... I don't consider the whole sequence new information. I'm not even going to consider it "new information" until there is a reasonably sized sequence of unique information. Let's set it to be bigger than you could create by chance.

For example, a sequence of 200 nucleotides that is unique to that organism requires 1 in 4^200 chance of arriving at randomly in the traditional way of monkeys typing randomly on a base-4 keyboard. So I want to see how the process of evolution could theoretically produce something of that complexity ... i.e. too difficult to get using monkeys, yet functional.

Posts: 4003
Joined: Mar. 2008

Posted: Jan. 19 2015,11:48

Quote

The U has been point-mutated to a T ... I don't consider the whole sequence new information. I'm not even going to consider it "new information" until there is a reasonably sized sequence of unique information. Let's set it to be bigger than you could create by chance.

What's the minimal size sequence change necessary to make a difference in viability or relative reproductive success?

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

JonF

Posts: 634
Joined: Feb. 2005

Posted: Jan. 19 2015,11:51

Quote (cryptoguru @ Jan. 19 2015,12:06)

JonF:
Yes I am personally incredulous ... I am not asserting that proves anything ... I'm saying that the burden of proof is on you to show that this (relatively new) proposed mechanism which seems to defy laws of logic could even theoretically do what is suggested

I don't see it as defying the laws of logic. Eaxactly what laws nd how do they defy them?

It is nice that you admitted all you have is armchair philosophizing.

Quote

But I see no reason why the process that produced EQU in Avida can't produce a human being in real life.

That's because you want to believe that ... it hasn't been demonstrated that it's even possible.

Indeed we have not directly observed biological evolution on the scale of hundreds of thousands of years and widely varying environments. There's good reasons for that; it's totally impractical. I haven't seen any objective reasons why the extrapolation isn't reasonable. From you or anyone.

Quote

People are claiming that AVIDA proves biological evolution ... it doesn't! We just showed that ... It proves you can find a logical function using stochastic process on a Turing-complete set of instructions.

The stochastic process of descent with modification and selection. I.e. evolution.

Quote

You don't get to just define a cell as a Turing-complete computer.

It's actually probably even Turing-universal
Efficient Turing-universal computation with DNA polymers

DNA can be used as a computer in a test tube. That's not what it does in the cell. Try again.
xxx

Doc Bill

Posts: 1039
Joined: April 2007

Posted: Jan. 19 2015,12:01

It appears that CreeptoGuru suffered a concussion to have written this creationist boilerplate tripe:

Quote

You misunderstood what I said there. I said "point mutation" singular ... not sequence of point mutations.

EXAMPLE

GCATTUCAGUUGATUCCATATGGCTU
GCATTUCAGTUGATUCCATATGGCTU

The U has been point-mutated to a T ... I don't consider the whole sequence new information. I'm not even going to consider it "new information" until there is a reasonably sized sequence of unique information. Let's set it to be bigger than you could create by chance.

Now Creepto is defining his own terms again in fine creationist style. You'll have to better than this to impress us, boy-o!

Creepto ate the dog.
Creepto ate the hog.

In Creepto-speak there is no new information. I guess you'd need something like this:

Creepto ate the dog.
Creepto prepared the mongoose in a rich butter sauce.

Oh, now I get it. The mongoose recipe is definitely bigger than I could get by chance, although instead of butter I would have fried that puppy in tard.

JonF

Posts: 634
Joined: Feb. 2005

Posted: Jan. 19 2015,12:02

Quote (cryptoguru @ Jan. 19 2015,12:19)

Quote

That explanation is incompatible with the previous definition. A point mutation produces a unique DNA sequence. You are trying to be as vague as possible. Some mathematician.

You misunderstood what I said there. I said "point mutation" singular ... not sequence of point mutations.

EXAMPLE

GCATTUCAGUUGATUCCATATGGCTU
GCATTUCAGTUGATUCCATATGGCTU

The U has been point-mutated to a T ... I don't consider the whole sequence new information. I'm not even going to consider it "new information" until there is a reasonably sized sequence of unique information. Let's set it to be bigger than you could create by chance.

For example, a sequence of 200 nucleotides that is unique to that organism requires 1 in 4^200 chance of arriving at randomly in the traditional way of monkeys typing randomly on a base-4 keyboard. So I want to see how the process of evolution could theoretically produce something of that complexity ... i.e. too difficult to get using monkeys, yet functional.

Then you need a new operational definition of information, since by your original definition a point mutation adds information.

Gene duplication followed by point mutation. Much longer than 200 nucleotides. and observed over and over again.

{ABE}Gene Genesis: Scientists Observe New Genes Evolving from Mutated Copies
Evolution by gene duplication: an update

N.Wells

Posts: 1836
Joined: Oct. 2005

Posted: Jan. 19 2015,12:03

Point mutations change the information in a sequence and can have major consequences. The best known are deleterious, because we examine diseases for genetic components, but this doesn't have to be the case. Duplications of DNA plus a point mutation in one of the pair are indisputably new information.

Some of the myostatin blocker mutations are quite simple: http://en.wikipedia.org/wiki.......ostatin
and show how you could get more body mass and muscle for the same Shannon information (if you "broke" the myostatin blocker gene without deleting anything) or even from less of the vague information that IDists like to talk about (cases that result from deletion of a gene or portion of a gene).

See regular cows and http://mhpstrong.com/wp-cont....cow.jpg
regular and "bully" whippets
http://articles.elitefts.com/wp-cont....cs1.jpg
regular mice and "supermice"
http://www.havokjournal.com/wp-cont....g11.png
and google to learn about Liam Hoekstra.

OgreMkV

Posts: 3668
Joined: Oct. 2009

Posted: Jan. 19 2015,12:06

Quote (cryptoguru @ Jan. 19 2015,11:19)

Quote

That explanation is incompatible with the previous definition. A point mutation produces a unique DNA sequence. You are trying to be as vague as possible. Some mathematician.

You misunderstood what I said there. I said "point mutation" singular ... not sequence of point mutations.

So you agree that point mutations can happen. So, what law (biological, chemical, physical, or logical) prevents multiple point mutations from happening over time?

Quote

EXAMPLE

GCATTUCAGUUGATUCCATATGGCTU
GCATTUCAGTUGATUCCATATGGCTU

The U has been point-mutated to a T ... I don't consider the whole sequence new information. I'm not even going to consider it "new information" until there is a reasonably sized sequence of unique information.

What is the "reasonably sized sequence"?

What units?

Why?

Quote

Let's set it to be bigger than you could create by chance.

Why?

Show that something other than chance AND known biochemical processes control mutations.

Quote

For example, a sequence of 200 nucleotides that is unique to that organism requires 1 in 4^200 chance of arriving at randomly in the traditional way of monkeys typing randomly on a base-4 keyboard. So I want to see how the process of evolution could theoretically produce something of that complexity ... i.e. too difficult to get using monkeys, yet functional.

This is an EXTREMELY common misconception among creationists.

Somehow, they all have this notion, that like computer program... DNA springs into existence, fully formed, with the exact sequence that needs to exist for the organism now.

1) This is false. Each gene, allele, ERV, SNP, etc has a long history of existence. This long history shows the many changes each one of these genes (et. al.) has gone through to reach the point it is now.

You are actually saying that biologists must defend the creationist point of view... that is that all genes (et. al.) must have appeared exactly as they are now.

2) Your value of 1 in 4^200 does not include any of the other thousands of values that can directly or indirectly affect the sequence. You need a bit for methylation. You need bits for histone complexes. You need bits that include regulatory sequences. etc. etc. etc.

You can't even accurately calculate the probability for these events.

3) Even if you could, you are not considering the number of attempts. AND the value of successful, but not complete attempts. Genes are not computer programs that must be formed exactly correct or they will not work. There are plenty of genes that work pretty well. The literature is full of examples of this... I've given you papers that show this. It also exists in evolutionary algorithms.

Further, as has been shown to you both in biochemical examples and genetic algorithms examples, mutations that would cause deleterious effects can be propagated through the population and eventually result in a net benefit.

For example, Joyce's Darwinian Evolution on a Chip paper shows that in less than 72 hours, there were four complexes of mutations that resulted in a 92 fold increase in substrate attachment efficiency.

Of course, you have also ignored (apparently) both living examples in humans of mutations that confer large advantages. That of the HIV immunity of a small group of Northern Scandinavians and the heart disease immunity of a small group of Italians.

Finally, I think it important to point out that your sequence specificity requirement doesn't actually match reality. There are several genes in the human population with several thousand alleles. You do know that alleles are variations in a gene, yes? That is, the variation of a DNA sequence.

For example, HBB-A has some 2000+ alleles and HBB-B (IIRC) has over 3000 alleles.

Another point is that THIS is what Dawkin's WEASEL program was trying to show. That, while it would take very, very long time for monkeys to randomly produce the phrase, any form of selection reduces that time significantly.

Talking about mutations and genes is meaningless without including selection, drift, and the multiple other methods of winnowing.

Edited by OgreMkV on Jan. 19 2015,12:06

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Posted: Jan. 19 2015,14:48

The allele thing is the creationism killer. Any simulation of evolution has to include the possibility of neutral and nearly neutral variations.

And the ability of neutral and slightly detrimental variations to give rise to beneficial inventions.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

cryptoguru

Posts: 53
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Posted: Jan. 19 2015,15:43

Quote

Creepto ate the dog.
Creepto ate the hog.

In Creepto-speak there is no new information. I guess you'd need something like this:

Creepto ate the dog.
Creepto prepared the mongoose in a rich butter sauce.

You should definitely be proud of yourself Bilbo, those English lessons are starting to pay off.

Of course I was being arbitrary ... my definition of "new information" is substantial unique sequences in a genome (i.e. not shared with assumed relative species) that wouldn't be expected by a series of random events.

So if you showed me

BILBO PAID OVER THE ODDS FOR SHOES
and
BILBO PAID OVER THE ODDS FOR HOES

Although both those sentences make sense to me, I can quite easily explain that the first one arose by chance rather than any optimisation process requiring natural selection.

So I'm asking for a unique sequence that couldn't just arrive fully formed by accident ... i.e. I want proof of the evolution process producing something hard that Bilbo couldn't just cook up by throwing a die.

Saying ... "well here we are ... tada, the human!" is just begging the question, so I'm after proof of the theory

Quote

So, what law (biological, chemical, physical, or logical) prevents multiple point mutations from happening over time?

None ... never said it couldn't

Quote

Somehow, they all have this notion, that like computer program... DNA springs into existence, fully formed

You're straw-manning again Mr Ogre McCarthy ... I never said that's what I think evolutionists believe ... and I obviously don't believe that. My point was that if you compare a chimp to a human there are unique sequences of DNA in humans, evolution needs to explain how a sequence that big can appear over time (yes kazillions of years if you like) ... but it still has to be functional and there right? So whether it was caused by thousands of point mutations, or a whole bunch of splicing and point mutations and stuff until you got that unique functional sequence that comprises compressed instruction sets for building proteins. You need to demonstrate that.

AVIDA is not demonstrating that level of magic, it just optimises the combination of some functions to create logical functions. We're not talking a few logical operands on the genome that have been created, we're talking MULTI-DIMENSIONAL SUPERCODES ... Supercodes ... supercodes ... super... (echoes into distance)

and Lenski has some E. Coli on his farm E-I-E-I-O
But on that farm there's not a chicken E-I-E-I-O
(join with me Bilbo)

So Lenski hasn't observed anything unbacteria-like going on yet after 60,000 generations, and AVIDA is unable to model anything more complicated than joining a few assembler instructions in sequence and rewarding the organism every time a logical function is found. METHINKS IT IS NOT A WEASEL YET

More proof please

BTW Kevin, please don't write the word Allele again ... you're banned from using it from now on from overuse.

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Posted: Jan. 19 2015,16:02

Quote

So Lenski hasn't observed anything unbacteria-like going on yet after 60,000 generations

And this is supposed to be a surprise?

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

Texas Teach

Posts: 2082
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Posted: Jan. 19 2015,16:15

Quote (midwifetoad @ Jan. 19 2015,16:02)

Quote

So Lenski hasn't observed anything unbacteria-like going on yet after 60,000 generations

And this is supposed to be a surprise?

Only because creationists think that we should see bacteria giving birth to a crocoduck if evolution were true.

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"I suspect that the English grammar books where you live are outdated" --G. Gaulin

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Posted: Jan. 19 2015,16:18

Your straw man reeks of oil of ad hominem.

It's fairly ready to disprove evolution if you define evolution as creationism minus a deity.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

Doc Bill

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Posted: Jan. 19 2015,16:31

This is why it's impossible to have a discussion with a creationist. They just don't possess human brains.

Creepto's argument from incredulity expressed thusly:

Quote

So to summarise my answer ... when I'm talking about new information ... I'm talking about a unique DNA sequence in an organism. I can't see how it would ever be possible (argument from incredulity) for random mutation to create that much dumb luck (argument from incredulity)even given billions of years. That's not an argument from incredulity (OH, YES IT IS!!)... that's me saying from my knowledge of statistics (No, you haz not!!) I can't see how it could ever be possible (argument from incredulity), so the extraordinary claim of evolutionists (argument from incredulity) needs to be demonstrated in a model that addresses the difficult-to-believe parts (argument from incredulity) of the claim, not just that we can randomly arrive (argument from incredulity) at something useful sometimes

That argument of Creepto's is quite incredible! Really, this is better than GG? Perhaps, but only on the Loony Tunes scale.

OgreMkV

Posts: 3668
Joined: Oct. 2009

Posted: Jan. 19 2015,16:37

Quote (cryptoguru @ Jan. 19 2015,15:43)

Quote

Creepto ate the dog.
Creepto ate the hog.

In Creepto-speak there is no new information. I guess you'd need something like this:

Creepto ate the dog.
Creepto prepared the mongoose in a rich butter sauce.

You should definitely be proud of yourself Bilbo, those English lessons are starting to pay off.

Of course I was being arbitrary ... my definition of "new information" is substantial unique sequences in a genome (i.e. not shared with assumed relative species) that wouldn't be expected by a series of random events.

So if you showed me

BILBO PAID OVER THE ODDS FOR SHOES
and
BILBO PAID OVER THE ODDS FOR HOES

Although both those sentences make sense to me, I can quite easily explain that the first one arose by chance rather than any optimisation process requiring natural selection.

I'd like to point out that this is ANALOGY and therefore, not really good for talking about evolution or even genetics.

What's interesting though, is that it actually proves the point that evolution works by incremental steps that actually work.

Of course, unlike words, DNA/proteins can have variations that make small changes to efficiency. As, the aforementioned papers I mentioned to you show.

Quote

So I'm asking for a unique sequence that couldn't just arrive fully formed by accident ... i.e. I want proof of the evolution process producing something hard that Bilbo couldn't just cook up by throwing a die.

So, you're asking for proof that evolution doesn't work?

Man, you are all over the place.

You do understand that selection is involved... and multiple other factors. right?

Whatever, it's been shown to happen. Already. You don't accept the evidence, but the models and the experiments and the observations and the whole genome studies and the partial genome studies all show that this happens.

Quote

Saying ... "well here we are ... tada, the human!" is just begging the question, so I'm after proof of the theory

Which shows you know nothing about science.

Quote

So, what law (biological, chemical, physical, or logical) prevents multiple point mutations from happening over time?

None ... never said it couldn't

That's not true. You have stated multiple times that it contradicts that laws of nature and logic.

What laws were you referring to?

Quote

Somehow, they all have this notion, that like computer program... DNA springs into existence, fully formed

You're straw-manning again Mr Ogre McCarthy ... I never said that's what I think evolutionists believe ... and I obviously don't believe that.

It's not obvious at all that don't believe that. You have stated it multiple times.

You want to know what the odds are that a modern gene sequence can appear by random processes. That's what you asked for.

You don't understand that modern genes (and their various alleles) came from the previous generation's genes (and their various alleles) and those came from the previous generation's genes (and their various alleles), etc, etc, etc.

Quote

My point was that if you compare a chimp to a human there are unique sequences of DNA in humans,

Not as many as you seem to think.

Quote

evolution needs to explain how a sequence that big can appear over time (yes kazillions of years if you like) ... but it still has to be functional and there right?

There was an entire issue of Nature devoted to this, several years ago. Surely you have read all those articles right? Those whole genome studies of Pan and Homo and Gorilla shows this.

Oh, I'm sorry, do you require a step-by-step, mutation-by-mutation change.

I'm sure we can do that, right after you provide a step-by-step ancestral tree for yourself, from present, to the first human. Can't do that? It's unreasonable? Yeah, we know.

Quote

So whether it was caused by thousands of point mutations, or a whole bunch of splicing and point mutations and stuff until you got that unique functional sequence that comprises compressed instruction sets for building proteins. You need to demonstrate that.

Again, it's been done. You don't accept it. Fortunately no one who does the work cares what you think.

Quote

AVIDA is not demonstrating that level of magic, it just optimises the combination of some functions to create logical functions. We're not talking a few logical operands on the genome that have been created, we're talking MULTI-DIMENSIONAL SUPERCODES ... Supercodes ... supercodes ... super... (echoes into distance)

Because we all know that EQU is just an optimization of NAND, right?

Quote

and Lenski has some E. Coli on his farm E-I-E-I-O
But on that farm there's not a chicken E-I-E-I-O
(join with me Bilbo)

I find it funny that whenever creationists are given the information that they desire, they immediately transition to "It's still a bacteria".

You obviously only read one article in my blog.

http://www.skepticink.com/smilodo....l-a-dog

Quote

So Lenski hasn't observed anything unbacteria-like going on yet after 60,000 generations, and AVIDA is unable to model anything more complicated than joining a few assembler instructions in sequence and rewarding the organism every time a logical function is found. METHINKS IT IS NOT A WEASEL YET

More proof please

And no one, except creationists, expect him to. He's discovered, for all intents and purposes, a new species. It's happened before.

Perhaps you need to learn a little more about biology and why no one expects to find a crocoduck.

As far as AVIDA, I think it's clear to everyone that the organisms created the coding structure for logic functions without any input from humans.

That's pretty impressive, except to someone who must, for whatever reason, deny that such a thing happened.
[/quote]

BTW Kevin, please don't write the word Allele again ... you're banned from using it from now on from overuse.[/quote]
Wow, you've been on this forum for almost 3 whole days and already have the power of banning.

You are either supremely arrogant or an utter ass, with a significant fraction voting for both.

Unlike you, I use terminology as is appropriate.

Finally, I note that while you responded to a minor point I made, you ignored some significant questions. I'm sure that this was a minor oversight on your part, for your reference, I've included those questions below.

What is the "reasonably sized sequence"?

What units?

Why?

edit: because I keep forgetting about the preview bug.

Edited by OgreMkV on Jan. 19 2015,16:37

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Posted: Jan. 19 2015,16:37

The writing is better. The ideas are pretty standard straw man boilerplate.

The basic argument is that you can never get from there to here by walking. No calculations presented.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

OgreMkV

Posts: 3668
Joined: Oct. 2009

Posted: Jan. 19 2015,16:47

Quote (Doc Bill @ Jan. 19 2015,16:31)

This is why it's impossible to have a discussion with a creationist. They just don't possess human brains.

Creepto's argument from incredulity expressed thusly:

Quote

So to summarise my answer ... when I'm talking about new information ... I'm talking about a unique DNA sequence in an organism. I can't see how it would ever be possible (argument from incredulity) for random mutation to create that much dumb luck (argument from incredulity)even given billions of years. That's not an argument from incredulity (OH, YES IT IS!!)... that's me saying from my knowledge of statistics (No, you haz not!!) I can't see how it could ever be possible (argument from incredulity), so the extraordinary claim of evolutionists (argument from incredulity) needs to be demonstrated in a model that addresses the difficult-to-believe parts (argument from incredulity) of the claim, not just that we can randomly arrive (argument from incredulity) at something useful sometimes

That argument of Creepto's is quite incredible! Really, this is better than GG? Perhaps, but only on the Loony Tunes scale.

It's funny because this is the exact same line of thinking that tripped of Behe in the Kitzmiller trial.

Behe: The maths say it's a really big number.
Rothschild: But there's 7 orders of magnitude more bacteria in one ton of soil... 16 orders of magnitude more bacteria on Earth... and that's in any one year... of which we have to consider the multi-billion year history of the planet.
Behe: Well, yeah... but...

There is no "but". There's only the really big, scary number and the creationist demand that we produce a modern protein by totally random processes... and crypto has stated multiple times.

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Posted: Jan. 19 2015,16:56

That, plus the minor detail that a modern bacterium is adapted to it's current ecosystem and isn't bloody likely to evolve into a squirrel.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

cryptoguru

Posts: 53
Joined: Jan. 2015

Posted: Jan. 19 2015,17:41

Quote

That, plus the minor detail that a modern bacterium is adapted to it's current ecosystem and isn't bloody likely to evolve into a squirrel.

Not even a squirrel was likely to evolve into a squirrel.

It's just amazing what variety a little bit of random mutation, a fight for survival and an overactive imagination can do. (don't forget 3D graphics and bold statements of fact in narration over the top)

Well this HAS been fun gentlemen ... I think we've done a full circle, which probably means you're right and I'm wrong, just because you say so. And because it makes complete sense, right!

Also remember to say that I don't know anything about biology, or evolution ... or mathematics ... or the mystical natural selection angel after I'm gone.

It's time for QED to give his closing statement ... and for Bilbo to do his Sesame Street ending ... "and today we learned the number 6 and the letter Z and learned all about how evolution is a fact ... and that's a fact children ... see you all next week"

And probably time for Kevin to get the wrong end of a stick again and gnaw on it.

It's been an absolute pleasurable pleasure

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Posted: Jan. 19 2015,18:06

Flounce II.

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Doc Bill

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Posted: Jan. 19 2015,18:09

Flounce Deux for the amateur MMA "expert."

That's what I call cut-and-run.

Too bad. I was working on a post showing how a point bit mutation or a frame shift didn't necessarily cause a program to crash. It would do something different quite likely, but it would do something!

In the early days of using microprocessors we were so tight on RAM that tight code and very clever programming was not only the rage but often necessary. I recall writing an algorithm that changed a couple of lines of command code depending on what was going on. It might be "shift left" in one iteration and "shift right" in another.

So, Creepto summary:

Knows jack about the theory of evolution.
Knows jack about statistics.
Knows jack about probability.
Knows jack about chemistry.
Knows jack about the English language.
Knows jack about computers.

The perfect creationist!

He's probably asking himself, "Who's Jack?"

JonF

Posts: 634
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Posted: Jan. 19 2015,18:09

Yeah, standard creationist refusal to learn.

Tell you MMA pals you're too much of a pussy to learn about what you're criticizing. Plus no mathematician would make claims about such a complex process based on intuitionp plus ignorance of the system.

What a poseur.

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Posted: Jan. 19 2015,18:18

Congrats to Cryptoguru for reading some of the responses and making some changes to his argumentation. This is not commonly observed in these sorts of exchanges. Plus, welcome back to the beginning of the second farewell tour. (I wrote that last sentence before the second flounce.) I'm still not inclined to accept changes in the original challenge, though, so I will be specifically noting those.

Quote (cryptoguru @ Jan. 19 2015,07:45)

[...]

Section D:
comparison of AVIDA to biological evolution
1) an analogy must be drawn between AVIDA commands and the genome
2) it possibly makes most sense (I concede) to assume that AVIDA commands are analogous to codons (and not proteins), so that any mutation will always create a set of valid codons.
3) the level AVIDA is selecting at is therefore analogous to a folded functional protein.

A problem with (3) is that I've already pointed out the level of selection is the Avidian, not any sub-sequence of its genomic instruction sequence.

Quote (cryptoguru @ Jan. 19 2015,07:45)

Section E:
problems with model
1) the multi-dimensionality of the genome due to multiple reading frames means that a point mutation in the genome will likely affect the expression of multiple proteins (19K coding genes code for at least 100K different proteins in the human genome). Mutations in AVIDA are mutually exclusive and therefore don't have a regressive effect on the expression of other COMMANDS. This is not a trivial difference, it is analogous to the difference between a bisection method (AVIDA mutation) and a bisection method where the root can change at each iteration (Genome mutation).

This is not in the original challenge, and is thus irrelevant to answering the original challenge. The Avida instruction set includes "mov-head", "jump-head", and "set-flow", which can and do change expression dramatically. Avida itself has been used to perform in silico experimentation on overlapping genes:

Quote

One consequence of overlapping genes is to reduce the tolerance for mutation. Virtual experiments conducted within the past several years using a software system called Avida have indicated that overlapping reduces the probability of accumulating so-called neutral mutations in a gene (mutations that have no effect). Neutral mutations are unlikely with overlapping genes, because the mutation must have no effect on two genes with different reading frames.

But like I said, that's all irrelevant to the original challenge.

Quote (cryptoguru @ Jan. 19 2015,07:45)

2) It is not just multiple reading frames that introduce polymorphism into the genome, but regulatory genes can effect the expression of an entire coding gene. This non-linearity is not modelled in AVIDA, which is a linear sequential code (like assembler). That is, the Genome executes a higher-level language than a sequential instruction set.

Again, this concern is nowhere to be seen in the original challenge, and is thus irrelevant to the original challenge. Plus, the Avida documentation notes:

Quote

One major concept that differentiates this virtual assembly language from its real-world counterparts is in the additional uses of nop instructions (no-operation commands). These have no direct effect on the virtual CPU when executed, but often modify the effect of any instruction that precedes them. In a sense, you can think of them as purely regulatory genes. The default instruction set has three such nop instructions: nop-A, nop-B, and nop-C.

But like I said, that's all irrelevant to the original challenge.

Quote (cryptoguru @ Jan. 19 2015,07:45)

3) AVIDA enforces selection by rewarding at the functional level ... it identifies a function as a logical operation and rewards the organism that is presenting it. This is equivalent to natural selection providing feedback scores to the organism on a per-protein level. e.g. protein 1 7/10, protein 2 3/10, protein 3 9/10. This kind of micro-management can't happen in real-life as natural selection is blind and is applied not even to an organism but an entire population. This feature artificially boosts the productivity of hopeful combinations of commands, which otherwise wouldn't be encouraged.

Bogus in many particulars. Group selection is about as dead a concept as it is possible to get in biology. Not so long ago, Cryptoguru asserted this:

Quote

1) evolution mutates DNA on a nucleotide level affecting function (gene level) and selects on the organism level.

which appears to be that rarity in logical fallacies, a contradiction. It also indicates that Cryptoguru's conceptual movement on this particular is in a bad direction.

Avida does not examine the genomic instruction sequence to recognize something. It examines the output from the IO instruction of the Avidian that indicates that it correctly performed a behavior, in the Lenski et al. 2003 paper the rewarded behaviors comprised a set of nine logic operations. An Avidian can internally compute every logic function around and receive exactly zero extra CPU cycles of merit if it fails to output the results to the environment via the IO instruction. I've already mentioned this before. The assertion that things are otherwise is a persistent misunderstanding on Cryptoguru's part.

Avida's award of merit for Avidian behaviors is analogous to biological organisms getting better/more nutrition, or greater movement efficiency, or better artifact construction (nest, hive, or tools) due to a favorable trait. There is really nothing to object to on this point, and this is no problem for the model.

As far as the final quoted sentence goes, some traits have to have relative benefits in order to simulate natural selection. This has to happen in the model since it happens in biology. This is not a problem for the model.

Quote (cryptoguru @ Jan. 19 2015,07:45)

4) The level of variability in AVIDA compared to the genome is like comparing solving a Rubik's cube with cracking 2048-bit RSA encryption. The logical functions which AVIDA selects and guide the optimisation process are trivial ... and also non-distinct. There are infinitely many ways to implement the EQU function using the AVIDA instruction set. Proteins are specific in their form, not just in an abstract functional way. The likelihood of randomly selecting a combination of AVIDA commands that performs a logical function is extremely high, I don't know if it's even possible to work this out considering there are infinitely many combinations that could represent each logical function. (e.g. inc dec inc dec inc dec is equivalent to leaving a register unchanged). In the genome the possibility of just mutating 3 neighbouring nucleotides anywhere in the genome to produce a different codon is less than the chances of winning the national lottery twice in a row, and two proteins with different amino acid chains can likely never be equivalent in function. (unless randomness of function is the required function for the protein)

Again, this concern is nowhere to be seen in the original challenge, and is thus irrelevant to the original challenge. The original challenge made no restrictions on the size of a novel function.

Proteins are not absolute, on-off switches of function for a given amino acid sequence/fold configuration. Proteins often exhibit partial functionality. Physiologists also know that proteins work better and worse for a given function at different temperatures. Proteins also often tolerate substitutions of amino acids without drastic changes in function. Even Douglas Axe's work shows that he had to go to swapping out large swaths of amino acids in order to almost entirely eradicate barnase function. So perhaps the two proteins are not equivalent; that does not mean that they are significantly different, which is what Cryptoguru's argument requires. See also Dayhoff's Atlas of Protein Sequence and Structure, which shows the differences in the proteins used for the same purpose across a variety of organisms. Those often show multiple amino acid differences in even a relatively short protein like cytochrome-c. That's been around since the 50's, so there's not much excuse for not knowing that before spewing.

About "In the genome the possibility of just mutating 3 neighbouring nucleotides anywhere in the genome to produce a different codon is less than the chances of winning the national lottery twice in a row"...

That is really unclear. Does Cryptoguru mean the odds of getting a different codon given three neighboring nucleotides mutate? Three nucleotides specify a codon, given four nucleotides, that's a total of sixty-four possible codons. Randomly picking new values for each of the three nucleotides will only yield the same codon in 1/4*1/4*1/4 = 1/12 of the time, or about 8%. The complement of that is about 92%. Does he mean instead, as I suspect, that single nucleotide mutations are rare, and that getting three adjacent ones are even rarer? True, but it doesn't work out as he seems to wish. Changing a single nucleotide would give a different codon by definition, and given a uniform sampling of codons, that yields about an 80% chance of a different codon that yields a different amino acid as a result. Yeah, the SNP event is ~1e-9, but a change in amino acid resulting is pretty common as a result of an SNP. One does not need to change all three nucleotides to get a different codon, nor to get a different amino acid as a result.

Nor do I buy the "probability is extremely high" gambit based on arm-waving. Cryptoguru should either show his work or give it up. Towards that work...Sure, there are infinite ways to get EQU function. And for each one of those, Cryptoguru needs to estimate the number of Avida programs of the same length that do not provide EQU function. For his claim, he needs to show that number is far from L^26-1, where L is the program length. A probability will incorporate that other number, and not just count the "hits". A sample of program lengths from the minimal EQU length to, say, 50, should suffice. My own assessment of probability of EQU, based on actually having used Avida, programmed Avida, and programming and testing Avida-ED changes, is that hitting on EQU randomly is a tiny, tiny probability. That's arm-waving, too, but with some experience to back it. Then there is the result in the Lenski et al. 2003 paper that directly addresses this concern experimentally:

Quote

At the other extreme, 50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection would not preserve the simpler functions that provide foundations to build more complex features. Indeed, none of these populations evolved EQU, a highly significant difference from the fraction that did so in the reward-all environment (P ~ 4.3 x 10^-9, Fisher's exact test). However, these populations tested more genotypes, on average, than did those in the reward-all environment (2.15 x 10^7 versus 1.22 x 10^7; P < 0.0001, Mann-Whitney test), because they tended to have smaller genomes, faster generations, and thus turn over more quickly. However, all populations explored only a tiny fraction of the total genotypic space. Given the ancestral genome of length 50 and 26 possible instructions at each site, there are ~5.6 x 10^70 genotypes; and even this number underestimates the genotype space because length evolves.

The only real numbers in this particular aspect of the discussion indicate that for Cryptoguru "extremely high likelihood" can refer to a probability smaller than 1 in 2.15 x 10^7. Your mileage may vary.

But like I said, that's all irrelevant to the original challenge.

Quote (cryptoguru @ Jan. 19 2015,07:45)

DISCUSS!

Cryptoguru's original challenge has been met. If Cryptoguru wants to move on to a different challenge as his objections seem to indicate, he should at least acknowledge that his prior one was met before stating a new challenge.

Much of the discussion that ensued after Cryptoguru's original challenge was due to Cryptoguru's inability to focus on the terms of the challenge he himself wrote. There seems to be a curious vagueness about whether Cryptoguru wants a model of natural selection, a model of genetic inheritance, a model of codon replacement, or a model of abiogenesis itself. Certainly the objections raised afterwards have touched upon all of those. There is a concept called salience that Cryptoguru ought to get familiar with. A model aimed at determining whether new information can arise in computer code via an evolutionary process doesn't need to be freighted with most of the irrelevancies that he has discussed. In the extreme, it appears that Cryptoguru wants the equivalent for biology of the "theory of everything".

The other significant fraction of Cryptoguru's output concerned things that he believed were true, but weren't. For instance, the majority of Cryptoguru's claims concerning the Avida system were and are, charitably speaking, bunk. This didn't prevent Cryptoguru spouting falsehoods with fervor and vehemence, and ironically insisting that others had gotten their facts wrong on that score.

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The whole truth

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Joined: Jan. 2012

Posted: Jan. 19 2015,18:29

Quote (cryptoguru @ Jan. 19 2015,13:43)

Quote

Creepto ate the dog.
Creepto ate the hog.

In Creepto-speak there is no new information. I guess you'd need something like this:

Creepto ate the dog.
Creepto prepared the mongoose in a rich butter sauce.

You should definitely be proud of yourself Bilbo, those English lessons are starting to pay off.

Of course I was being arbitrary ... my definition of "new information" is substantial unique sequences in a genome (i.e. not shared with assumed relative species) that wouldn't be expected by a series of random events.

So if you showed me

BILBO PAID OVER THE ODDS FOR SHOES
and
BILBO PAID OVER THE ODDS FOR HOES

Although both those sentences make sense to me, I can quite easily explain that the first one arose by chance rather than any optimisation process requiring natural selection.

So I'm asking for a unique sequence that couldn't just arrive fully formed by accident ... i.e. I want proof of the evolution process producing something hard that Bilbo couldn't just cook up by throwing a die.

Saying ... "well here we are ... tada, the human!" is just begging the question, so I'm after proof of the theory

Quote

So, what law (biological, chemical, physical, or logical) prevents multiple point mutations from happening over time?

None ... never said it couldn't

Quote

Somehow, they all have this notion, that like computer program... DNA springs into existence, fully formed

You're straw-manning again Mr Ogre McCarthy ... I never said that's what I think evolutionists believe ... and I obviously don't believe that. My point was that if you compare a chimp to a human there are unique sequences of DNA in humans, evolution needs to explain how a sequence that big can appear over time (yes kazillions of years if you like) ... but it still has to be functional and there right? So whether it was caused by thousands of point mutations, or a whole bunch of splicing and point mutations and stuff until you got that unique functional sequence that comprises compressed instruction sets for building proteins. You need to demonstrate that.

AVIDA is not demonstrating that level of magic, it just optimises the combination of some functions to create logical functions. We're not talking a few logical operands on the genome that have been created, we're talking MULTI-DIMENSIONAL SUPERCODES ... Supercodes ... supercodes ... super... (echoes into distance)

and Lenski has some E. Coli on his farm E-I-E-I-O
But on that farm there's not a chicken E-I-E-I-O
(join with me Bilbo)

So Lenski hasn't observed anything unbacteria-like going on yet after 60,000 generations, and AVIDA is unable to model anything more complicated than joining a few assembler instructions in sequence and rewarding the organism every time a logical function is found. METHINKS IT IS NOT A WEASEL YET

More proof please

BTW Kevin, please don't write the word Allele again ... you're banned from using it from now on from overuse.

cryptoguru, I'm trying to understand your arguments and I have some questions. First, will you please answer this one that I asked earlier:

Where do you get the idea that every biological entity evolves by exactly the same amount from one generation to the next? I would have said life form instead of biological entity but I'm including viruses, and not everyone thinks that viruses are life forms.

In regard to this:

"Of course I was being arbitrary ... my definition of "new information" is substantial unique sequences in a genome (i.e. not shared with assumed relative species) that wouldn't be expected by a series of random events."

I don't understand what you're asking for. Will you explain more fully and provide some examples of what would satisfy your definition of new information?

Also:

What is your stance in regard to CSI, FSCI, dFSCI, FSCO/I, and IC?

From an intelligent design perspective, how would you explain diseases, parasites, deformities/aberrations, and extinctions?

Do you believe that humans are not descended from earlier life forms?

Do you believe that all humans have identical genomes?

Do you believe that all butterflies have identical genomes?

Do you believe that all butterflies that can mate and have viable offspring with each other (the same 'biological species') have identical genomes?

Do you accept that evolution occurs, including evolution in/of humans? If so, do you believe that evolution has a goal? If so, what is the goal, especially in regard to humans? And do you believe that the goal was/is designed/created/directed by a supernatural 'God'?

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Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

OgreMkV

Posts: 3668
Joined: Oct. 2009

Posted: Jan. 19 2015,18:49

Yep, it's been fun. Cryptoguru has been utterly crushed. Shown to have limited knowledge of biology... and computing for that matter (which is odd because he claims to be an expert).

He does seem to be an expert in using creationist arguments, without understanding the implications. He is definitely an expert in not answer questions asked of him and demanding that we answer all his questions (even though they make no sense) perfectly.

In other words, he will go on and claim that he won.

I will definitely link back to this thread in any further replies to crypto elseswhere. And remind him that he ignored several questions by myself and others and he might want to get on those...

Thanks everyone!

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

Posts: 4966
Joined: May 2002

Posted: Jan. 19 2015,19:30

Cryptoguru:

Quote

So Lenski hasn't observed anything unbacteria-like going on yet after 60,000 generations, and AVIDA is unable to model anything more complicated than joining a few assembler instructions in sequence and rewarding the organism every time a logical function is found. METHINKS IT IS NOT A WEASEL YET

Strike whatever-number-of-clueless-claims-he's-made-about-Avida.

Avida has been used to generate and evaluate UML models and for the generation of firmware for wireless sensors to be deployed in wireless sensor networks, and those are a couple of applications that I knew about before I left MSU back in 2009. MSU got the BEACON grant shortly thereafter, and things have been hot in the lab since then.

Question: how much research did Cryptoguru do about the topic of his claim before vomiting it forth? My guess is zero, zip, zilch, and nada.

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"You can't teach an old dogma new tricks." - Dorothy Parker

Doc Bill

Posts: 1039
Joined: April 2007

Posted: Jan. 19 2015,19:51

Surprisingly, one interesting thing came out of the Creepto exchange over on Smiledon's Retreat and that was an update to the Paley argument.

Paley imagined a pocket watch being found on the heath because the pocket watch was the most sophisticated instrument of his time. Likewise, Creepto imagines the cell as a computer because it is the most sophisticated instrument of his time (although I might vote for the non-stick pan - I digress.)

So, over on Ogre's site I imagined Paley finding a fully charged iPhone on the heath. He would pick it up and after a bit of fiddling let's say he turns it on. Magic, he would think! Sure, there's no ATT and no WiFi but he could run a few stand-alone apps and the camera.

Imagine his joy and wonder at this incredible thing!

But, by the next day when he gathered his scientific pals at his house, alas, the iPhone is discharged and sits there, mute and a black screen. Nothing Paley does can revive it.

Subsequently, he and his friends take it apart and what do they see? Nothing recognizable. Not a single part. It's just all black squares and strings of copper and a substance they can't recognize as plastic. It's a total mystery.

I thought about this given Creepto's fascination with his computer analogy. Why a computer? Because that's all he knows. He doesn't have the imagination to think beyond that analogy.

And, clearly, he doesn't have the faintest inkling about chemistry.

So, my question to my fellow Mornington Crescent travelers is this: what would you find on the heath?

N.Wells

Posts: 1836
Joined: Oct. 2005

Posted: Jan. 19 2015,19:59

Quote (cryptoguru @ Jan. 19 2015,17:41)

Not even a squirrel was likely to evolve into a squirrel.

http://www.newscientist.com/article....ng.html
Doesn't count because this is change in age of first reproduction and not DEATH.

http://web.mit.edu/~jfc.......dae.pdf
Doesn't count because it's a pain to deal with all that data, and it's only two genes and more than one point mutation.

http://www.washingtonpost.com/wp-dyn....._2.html
Doesn't count because it's just one population replacing another and I don't want to hear about alleles

Quote

From http://squirrelmapper.org/faq_evo....olution
What is the genetic difference between black and gray squirrels?

Black and gray squirrels are only different based on one gene. Alleles are variations on DNA sequences at a specific location on a chromosome (usually different forms of the same gene). The allele for squirrel fur color has two different possible sequences – one that codes for gray fur and one that codes for black fur. Each squirrel has two copies of this allele. If a squirrel has two copies of the gray allele, then it will be gray, but if it has either one copy of the gray and one of the black or if it has two copies of the black allele, then it will be black. The gray type is actually genetically recessive, which is somewhat counterintuitive since it is the more common genotype these days!

Most dark pigmentation in mammals is associated with the MC1R gene. The MC1R gene regulates how much brown/black pigment (eumelanin) versus pale red/yellow pigment (phaeomelanin) is added to hairs as they grow. When the alpha melanocyte-stimulating stimulating hormone (αMSH) binds to the MC1R gene, eumelanin (dark pigment) is produced; otherwise phaeomelanin (light pigment) is produced. In black squirrels, the MC1R gene has undergone a small deletion (24 base pairs of DNA) that corresponds to just 8 amino acids. This deletion hastens binding of the αMSH to the MC1R gene increasing production of eumelanin (the mechanism is not yet known). This is known as the EB allele. In the gray squirrel a complete MC1R gene (lacking the deletion) blocks binding of αMSH increasing production of phaeomelanin. This is known as the E+ allele. The EB allele is incompletely dominant to the E+ allele. So E+/E+ is the genotype of the gray squirrel, EB/EB is the genotype of the black squirrel, and EB/E+ (or E+/EB) is the genotype of the brown-black squirrel. In the field it’s hard to distinguish a black EB/EB from a black EB/E+ squirrel but look carefully: the EB/EB is jet black all over but and EB/E+ squirrel have mostly brown-black backs but a distinctly lighter-colored (often orange-colored) belly. It’s quite likely that there are other genes and alleles at work but at present this is our best understanding of the genetic mechanism at work.

Still just a damn squirrel. What did I tell you?

Kaibab squirrels from Albert squirrels: http://www.sbs.utexas.edu/levin/bio213/evolution/speciation.html
Doesn't count because I can't imagine a black belly and forelimbs leading to DEATH. Plus no one saw it happen.

http://link.springer.com/article....6065.f0
Doesn't count because I was talking about TREE squirrels.

http://link.springer.com/article....-9250-7
Once again, not TREE squirrels, plus it talks about global warming, so it's clearly biased.

http://www.scielo.sa.cr/scielo.....0100020
Doesn't count because most of them have "sciurus" in their name, so of course they're all going to be similar.

http://evolution.berkeley.edu/evolibr....br....4
Heck, that's birds and pine cones and they're still birds and pine cones, and besides which not one single squirrel died preferentially. Also, if you are going to talk about co-evolution, you have to prove evolution first.

http://today.duke.edu/2003.......02.html
They left out one of the 51 genera of squirrels, so get back to me when they do a real study.

https://pure.york.ac.uk/portal.....29.html
Cranial characters support findings from studies of mandibles, which support molecular results ( http://goodnight.corral.tacc.utexas.edu/UAF........ses.pdf ), which confirm biogeographic patterns, which show that a high degree of sociality must have evolved twice. Well, I've been antisocial my entire life, so I can't believe that would have happened.

http://www.ncbi.nlm.nih.gov/pubmed.....7921359
http://evolution.berkeley.edu/evolibr....ipmunks
Lots of death, and all we get is bottlenecks. I want evolution!!!

http://link.springer.com/article....ss=true
Oh for god's sake, I asked for squirrels, those are frigging chipmunks.

Well, that was fun. Get back to me when you have someone who saw it happen.

Driver

Posts: 649
Joined: June 2011

Posted: Jan. 19 2015,20:39

Quote (Doc Bill @ Jan. 20 2015,00:51)

So, my question to my fellow Mornington Crescent travelers is this: what would you find on the heath?

Which part of the Heath?

Lots of condoms on West Heath.

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Why would I concern myself with evidence, when IMO "evidence" is only the mind arranging thought and matter to support what one already wishes to believe? - William J Murray

[A]t this time a forum like this one is nothing less than a national security risk. - Gary Gaulin

Doc Bill

Posts: 1039
Joined: April 2007

Posted: Jan. 19 2015,21:03

Quote (Driver @ Jan. 19 2015,20:39)

Quote (Doc Bill @ Jan. 20 2015,00:51)

So, my question to my fellow Mornington Crescent travelers is this: what would you find on the heath?

Which part of the Heath?

Lots of condoms on West Heath.

I was thinking Heath Robinson who shot a condom from the Albert Memorial to Kensington Palace, that bounced into Pan's ... well, best not said where it bounced.

Enough said that Creepto couldn't find his way from South Kensington to Green Park on a Sunday, much less to Mornington Crescent on any day.

You will find me at King's Cross, platform 9 3/4.

Posts: 4003
Joined: Mar. 2008

Posted: Jan. 19 2015,21:16

On the moor, one might find a hound from hell.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

Doc Bill

Posts: 1039
Joined: April 2007

Posted: Jan. 19 2015,21:19

Only in Kate's bush.

Posts: 1961
Joined: May 2007

Posted: Jan. 20 2015,00:59

Quote (Zachriel @ Jan. 19 2015,08:21)

cryptoguru: evolution mutates DNA on a nucleotide level affecting function (gene level) and selects on the organism level.

Evolution also involves recombination and the splicing of new structures from subcomponents.

cryptoguru: The whole premise of natural selection can be simplified to be death.

That is also false. The whole premise of natural selection is reproductive success.

How true. Ratio of death is fixed at 100%. Ratio of reproduction most likely never reach that figure.

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Rocks have no biology.
Robert Byers.

Posts: 551
Joined: Oct. 2007

Posted: Jan. 20 2015,04:40

Quote (cryptoguru @ Jan. 19 2015,08:39)

Cubism: (this is not directly about my last post but answering an earlier clarification from Cubism)

Bad start. For the record, cryptoguru: The 'handle' I use online does not, in fact, have an "m" in it. Said handle is Cubist, not Cubism. I don't find your (repeated!) Cubism-not-Cubist error to be offensive or anything, but I gotta admit it strikes me as indicative of… hmm… a certain level of attentiveness and/or general intellectual ability, let's say.

Quote

Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

The issue here is one of scale…

…and a bad continuation following on from a bad start, in that it ignores my query re: how come you (cryptoguru) said that the "new information" of "genetic material" has to be both "novel" and "new".

Re-posting the paragraph about how come it's gotta be both "new" and "novel" which you ignored: Why must the "genetic material" of "new information" be both "new" and "novel"? I ask because "new" and "novel" strike me as basically synonymous, hence, using both words is gratuitous redundancy. But perhaps you weren't being redundant; perhaps you actually are using distinct referents for "new" and "novel", such that the two words are not, in fact, gratuitously redundant. Please explain how "genetic material" which is "new" differs from "genetic material" which is "novel". Is it possible for "genetic material" to be "new" without also being "novel"? Is it possible for "genetic material" to be "novel" without also being "new"?

Perhaps you'll deign to honor the questions in that paragraph with answers, cryptoguru. Or not. [shrug]

Onward.

Quote

Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

The issue here is one of scale ... changing a single nucleotide and getting new functionality is more adequately describing a side-effect of switching a control gene rather than amazingly arriving at a new functional sequence through mutation and selection.

You may be right that "scale" is, indeed, the "issue". But regardless of whether or not "scale" is any kind of "issue" anywhere, I note that you didn't answer either of the questions in the text you quoted. That's okay, I can ask those questions again.

[clears throat]

Let's say that Sequence X is the arbitrary 150-nucleotide sequence "gcc tac agg gat cgt ggg gac ctt acg aat ggc ctt ttt gac tat tct tcg aat cta agc tca gca tca ttc ccg tct acg gga agt ccc ttc cca ata cat atc ctc ggc acc gca ctt gca ggc tca cgc ttc gcg tca ttt agg tca". Let's also say that Sequence X1 is the 149-nucleotide sequence "gcc tac agg gac gtg ggg acc tta cga atg gcc ttt ttg act att ctt cga atc taa gct cag cat cat tcc cgt cta cgg gaa gtc cct tcc caa tac ata tcc tcg gca ccg cac ttg cag gct cac gct tcg cgt cat tta ggt ca" that results when one removes the "t" from the fourth codon in Sequence X.

One: Does Sequence X1 qualify as "new and novel genetic material"? It's a yes-or-no question, cryptoguru; either yes, Sequence X1 does, in fact, qualify as "new and novel genetic material", or no, Sequence X1 does not, in fact, qualify as "new or novel genetic material". It's all well and good to go on about "probability" and "scale" and yada yada, but I really would like to see a yes or a no, and thus far, I ain't seen a yes or a no.

Two: Does Sequence X1 contain any "new and novel genetic material"? Again, it's a yes-or-no question, to which either yes, it does or no, it doesn't would both be relevant responses. Going on about "scale" and "probability" and yada yada, contrariwise, is not a particularly relevant response, as best I can tell.

Quote

So evolution claims that all the differences between a chimp's DNA and ours are caused by random mutation on 2 hereditary lines from a common ancestor. Find a sequence of unique DNA in the human genome (yup you can use the "junk DNA" now too, now we know it's not junk). Now that string you're holding has arrived by random mutation ... selection has preserved it, but mutation created it. That's what I mean by new/novel/unique information.

That's nice. You didn't mention "unique" before. Please explain how "genetic material" which is "unique" differs from "genetic material" which is either "new" or "novel". Is it possible for "genetic material" to be "unique" without also being either "new" or "novel"? Is it possible for "genetic material" to be "novel" without also being "new" or "novel"?

Does Sequence X1 qualify as "unique"?

Quote

You may be able to handwave that the switching of a few control genes could happen randomly…

I'm not handwaving a thing, cryptoguru. I'm attempting to get you to explain the meaning of your statement that "New information is new and novel genetic material…".

Quote

So to summarise my answer ... when I'm talking about new information ... I'm talking about a unique DNA sequence in an organism.

Groovy. Is Sequence X1 a "unique" DNA sequence?

Posts: 4966
Joined: May 2002

Posted: Jan. 20 2015,07:22

Quote (OgreMkV @ Jan. 19 2015,18:49)

Yep, it's been fun. Cryptoguru has been utterly crushed. Shown to have limited knowledge of biology... and computing for that matter (which is odd because he claims to be an expert).

He does seem to be an expert in using creationist arguments, without understanding the implications. He is definitely an expert in not answer questions asked of him and demanding that we answer all his questions (even though they make no sense) perfectly.

In other words, he will go on and claim that he won.

I will definitely link back to this thread in any further replies to crypto elseswhere. And remind him that he ignored several questions by myself and others and he might want to get on those...

Thanks everyone!

I've found claims of expertise on the part of antievolutionists to be routinely exaggerated. The examples of old-school "creation scientists" claiming doctoral degrees who either didn't have them or were based on things tantamount to diploma mill paper were legendary. In discussions online, it is a commonplace that an antievolutionist will attempt to bolster a bogus claim with an appeal to personal authority. The late Bob Schadewald had a wonderful phrase about the general social phenomena in creationist circles about claiming that they themselves comprised a group of "top scientists": "the elevation of mediocrities". It does work out to another way to say "a big fish in a small pond", but it was so elegantly stated.

Cryptoguru's various complaints about computer models did seem to indicate that he didn't have much of a grounding in computational theory. There are many ways to get to a paycheck in computer technology that do not require that, so I don't really have an issue with the claim that someone is paying him for computer work, but I have deep suspicions about the relevance of his experience to what he is trying to discuss. (Cryptography itself seems to have a closer-than-usual relation to computational theory, so that aspect is pretty puzzling.) He certainly didn't let his deep specific ignorance of Avida stop him from making baldly ridiculous claims about it.

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"You can't teach an old dogma new tricks." - Dorothy Parker

Posts: 2729
Joined: Mar. 2013

Posted: Jan. 20 2015,08:55

Just in case he pops back in, didn't want him to miss this.

Quote (cryptoguru @ Jan. 18 2015,14:39)

final point to N. Wells

Natural Selection is about death. It doesn't matter what the reasons are for advantage, whether it's because some are stronger, or shorter, or bluer, or have better ovaries, or avoid nightclubs .. whatever. The selective agent is death. If an organism dies before it can reproduce it will be removed from the gene pool. Things that haven't died yet compete for resources, eventually a hereditary line will die off removing it from the competition (death again).

The whole premise of natural selection can be simplified to be death. Differential reproduction is a misleading concept, because the preservation of an advantageous trait can only occur when eventually all other competing hereditary lines are extinct. (death). Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that, so all other lines must become extinct to allow the favoured line to become the parent to the next stage. (I obviously think this is crackers ... I'm just explaining that the evolutionary concept of natural selection is very simple)

My point is that the evolutionary concept of natural selection is easy to model, you just set natural conditions and environments for the organisms to live and compete in and see which survive, you shouldn't be measuring the advantages and rewarding them ... nature does not do that, it just provides conditions for death, those who survive it are considered "selected".

I don't see what all the fuss is about ... just trying to demystify the Natural Selection deity.

Bye for now

Crypto, no one but you treats 'Natural Selection' as a deity, or a putative deity. Not least because there's nothing magic about it. You almost get it, but your prejudices prevent you from seeing how badly you beg the question and distort the facts, all to reach a pre-determined answer that fits your biases rather than the facts. If that means the facts have to be changed, too bad for the facts, right?
I've bolded and italicized one of the significant parts where you goe completely wrong.
I've underlined the next significant bit where you go completely wrong. Note in particular the error where you assert that there is, or evolutionists somehow thing there is or must be an a priori 'favored one'. Ludicrous and a fantasy of your own imagination and biases.
We do, in fact, see exactly what you assert we do not but should expect. It's (slightly) obscured in the present because we do not yet have the next stages with respect to which everything now alive is an 'intermediate'. But more to the point, within any species (an artificial distinction, entirely conceptual) we see a wide variety of traits -- cats, cows, rats, rutabagas, dogs, dolphins, none are cookie-cutter identical to all other members of the species. Your conception is that a 'species' is a set of identical clones, which is ludicrous. No one but creationists make this claim or try so hard to mask the underlying reality of variation within constraints.
Your argument hasn't a leg to stand on. It has all the conceptual rigor of a fever dream. It's content has all the grounding in facts and evidence that the DT's do.

Amadan

Posts: 1337
Joined: Jan. 2007

Posted: Jan. 20 2015,15:36

Quote (Wesley R. Elsberry @ Jan. 20 2015,13:22)

Quote (OgreMkV @ Jan. 19 2015,18:49)

Yep, it's been fun. Cryptoguru has been utterly crushed. Shown to have limited knowledge of biology... and computing for that matter (which is odd because he claims to be an expert).

He does seem to be an expert in using creationist arguments, without understanding the implications. He is definitely an expert in not answer questions asked of him and demanding that we answer all his questions (even though they make no sense) perfectly.

In other words, he will go on and claim that he won.

I will definitely link back to this thread in any further replies to crypto elseswhere. And remind him that he ignored several questions by myself and others and he might want to get on those...

Thanks everyone!

I've found claims of expertise on the part of antievolutionists to be routinely exaggerated. The examples of old-school "creation scientists" claiming doctoral degrees who either didn't have them or were based on things tantamount to diploma mill paper were legendary. In discussions online, it is a commonplace that an antievolutionist will attempt to bolster a bogus claim with an appeal to personal authority. The late Bob Schadewald had a wonderful phrase about the general social phenomena in creationist circles about claiming that they themselves comprised a group of "top scientists": "the elevation of mediocrities". It does work out to another way to say "a big fish in a small pond", but it was so elegantly stated.

Cryptoguru's various complaints about computer models did seem to indicate that he didn't have much of a grounding in computational theory. There are many ways to get to a paycheck in computer technology that do not require that, so I don't really have an issue with the claim that someone is paying him for computer work, but I have deep suspicions about the relevance of his experience to what he is trying to discuss. (Cryptography itself seems to have a closer-than-usual relation to computational theory, so that aspect is pretty puzzling.) He certainly didn't let his deep specific ignorance of Avida stop him from making baldly ridiculous claims about it.

On a related note: approach with Extreme Caution any book whose author perceives a need to place "Ph.D" after their name on the cover.

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"People are always looking for natural selection to generate random mutations" - Densye 4-4-2011
JoeG BTW dumbass- some variations help ensure reproductive fitness so they cannot be random wrt it.

KevinB

Posts: 524
Joined: April 2013

Posted: Jan. 20 2015,16:57

Quote (Doc Bill @ Jan. 19 2015,19:51)

So, my question to my fellow Mornington Crescent travelers is this: what would you find on the heath?

I'd play Heathrow Terminal 4, and expect to find a Boeing 747, though not necessarily in conjunction with either a tornado or a junkyard.

Amadan

Posts: 1337
Joined: Jan. 2007

Posted: Jan. 21 2015,13:25

Quote (KevinB @ Jan. 20 2015,22:57)

Quote (Doc Bill @ Jan. 19 2015,19:51)

So, my question to my fellow Mornington Crescent travelers is this: what would you find on the heath?

I'd play Heathrow Terminal 4, and expect to find a Boeing 747, though not necessarily in conjunction with either a tornado or a junkyard.

You've obviously never experienced Terminal 1 on Christmas Eve, which bears an uncanny resemblance to both.

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"People are always looking for natural selection to generate random mutations" - Densye 4-4-2011
JoeG BTW dumbass- some variations help ensure reproductive fitness so they cannot be random wrt it.

OgreMkV

Posts: 3668
Joined: Oct. 2009

Posted: Jan. 21 2015,16:27

I find it especially amusing when an article comes out the same week (or day) we're discussing something.

http://www.nature.com/ng....96.html

Quote

We describe a new computational method for estimating the probability that a point mutation at each position in a genome will influence fitness. These 'fitness consequence' (fitCons) scores serve as evolution-based measures of potential genomic function. Our approach is to cluster genomic positions into groups exhibiting distinct 'fingerprints' on the basis of high-throughput functional genomic data, then to estimate a probability of fitness consequences for each group from associated patterns of genetic polymorphism and divergence. We have generated fitCons scores for three human cell types on the basis of public data from ENCODE. In comparison with conventional conservation scores, fitCons scores show considerably improved prediction power for cis regulatory elements. In addition, fitCons scores indicate that 4.2–7.5% of nucleotides in the human genome have influenced fitness since the human-chimpanzee divergence, and they suggest that recent evolutionary turnover has had limited impact on the functional content of the genome.

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Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

Posts: 1961
Joined: May 2007

Posted: Jan. 22 2015,00:21

Quote (Amadan @ Jan. 20 2015,15:36)

Quote (Wesley R. Elsberry @ Jan. 20 2015,13:22)

Quote (OgreMkV @ Jan. 19 2015,18:49)

Yep, it's been fun. Cryptoguru has been utterly crushed. Shown to have limited knowledge of biology... and computing for that matter (which is odd because he claims to be an expert).

He does seem to be an expert in using creationist arguments, without understanding the implications. He is definitely an expert in not answer questions asked of him and demanding that we answer all his questions (even though they make no sense) perfectly.

In other words, he will go on and claim that he won.

I will definitely link back to this thread in any further replies to crypto elseswhere. And remind him that he ignored several questions by myself and others and he might want to get on those...

Thanks everyone!

I've found claims of expertise on the part of antievolutionists to be routinely exaggerated. The examples of old-school "creation scientists" claiming doctoral degrees who either didn't have them or were based on things tantamount to diploma mill paper were legendary. In discussions online, it is a commonplace that an antievolutionist will attempt to bolster a bogus claim with an appeal to personal authority. The late Bob Schadewald had a wonderful phrase about the general social phenomena in creationist circles about claiming that they themselves comprised a group of "top scientists": "the elevation of mediocrities". It does work out to another way to say "a big fish in a small pond", but it was so elegantly stated.

Cryptoguru's various complaints about computer models did seem to indicate that he didn't have much of a grounding in computational theory. There are many ways to get to a paycheck in computer technology that do not require that, so I don't really have an issue with the claim that someone is paying him for computer work, but I have deep suspicions about the relevance of his experience to what he is trying to discuss. (Cryptography itself seems to have a closer-than-usual relation to computational theory, so that aspect is pretty puzzling.) He certainly didn't let his deep specific ignorance of Avida stop him from making baldly ridiculous claims about it.

On a related note: approach with Extreme Caution any book whose author perceives a need to place "Ph.D" after their name on the cover.

From Norway, “The Mystery of Life – Intelligent Causation in Nature”

https://d3oh18gu5j3rjh.cloudfront.net/9788271....71....0

ETA Sure looks designed, but intelligent?

Edited by Quack on Jan. 22 2015,14:17

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Rocks have no biology.
Robert Byers.

Posts: 1961
Joined: May 2007

Posted: Jan. 22 2015,00:26

Deleted.

Edited by Quack on Jan. 22 2015,00:34

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Rocks have no biology.
Robert Byers.

Posts: 2729
Joined: Mar. 2013

Posted: Jan. 22 2015,07:54

The 'crypt-keeper' may be beyond the reach of reason, lost deep in his confusions and errors, but this would repay his attention:
Winning vs. Not Losing

Evolution never requires 'the best', it only ever "requires" the adequate, the 'good enough'. It is pitiless and remorseless in that there is no point at which it can be guaranteed that there will be 'good enough'. The universe, far from being 'fine tuned' for life, is incredibly hostile to it.

Posts: 4003
Joined: Mar. 2008

Posted: Jan. 22 2015,09:24

There's a thread at UD where they are arguing that unexpected permissiveness or robustness in the genome -- allowing mutations that have little or no effect on viability -- is a certain sign of Jebus.

They are citing the book, "Arrival of the Fittest" as evidence against evolution.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

stevestory

Posts: 13407
Joined: Oct. 2005

Posted: Jan. 22 2015,13:08

the islands of functions are incredibly isolated. That proves ~~Baby Jesus~~ Intelligent Designer! You know what's even more proof? The exact opposite!

Socrates's grandkids these are not...

Posts: 4003
Joined: Mar. 2008

Posted: Jan. 22 2015,15:29

Quote (stevestory @ Jan. 22 2015,13:08)

the islands of functions are incredibly isolated. That proves ~~Baby Jesus~~ Intelligent Designer! You know what's even more proof? The exact opposite!

Socrates's grandkids these are not...

Makes sense. The best evidence for design would be evidence that evolution works.

If evolution works, it is designed. Therefore Jebus.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

Posts: 4966
Joined: May 2002

Posted: Jan. 22 2015,17:25

Quote (midwifetoad @ Jan. 22 2015,15:29)

Quote (stevestory @ Jan. 22 2015,13:08)

the islands of functions are incredibly isolated. That proves ~~Baby Jesus~~ Intelligent Designer! You know what's even more proof? The exact opposite!

Socrates's grandkids these are not...

Makes sense. The best evidence for design would be evidence that evolution works.

If evolution works, it is designed. Therefore Jebus.

Dembski didn't like it when I pointed out that his triad of properties for a designer were shared by natural selection.

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"You can't teach an old dogma new tricks." - Dorothy Parker

OgreMkV

Posts: 3668
Joined: Oct. 2009

Posted: Jan. 22 2015,20:00

Quote (Wesley R. Elsberry @ Jan. 22 2015,17:25)

Quote (midwifetoad @ Jan. 22 2015,15:29)

Quote (stevestory @ Jan. 22 2015,13:08)

the islands of functions are incredibly isolated. That proves ~~Baby Jesus~~ Intelligent Designer! You know what's even more proof? The exact opposite!

Socrates's grandkids these are not...

Makes sense. The best evidence for design would be evidence that evolution works.

If evolution works, it is designed. Therefore Jebus.

Dembski didn't like it when I pointed out that his triad of properties for a designer were shared by natural selection.

So far, in the years since Darwin's Black Box... no ID proponent has even tried to talk about the "I". They just talk about the "D"...

O.o

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Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

Posts: 551
Joined: Oct. 2007

Posted: Jan. 22 2015,21:51

Quote (OgreMkV @ Jan. 22 2015,20:00)

Quote (Wesley R. Elsberry @ Jan. 22 2015,17:25)

Quote (midwifetoad @ Jan. 22 2015,15:29)

Quote (stevestory @ Jan. 22 2015,13:08)

the islands of functions are incredibly isolated. That proves ~~Baby Jesus~~ Intelligent Designer! You know what's even more proof? The exact opposite!

Socrates's grandkids these are not...

Makes sense. The best evidence for design would be evidence that evolution works.

If evolution works, it is designed. Therefore Jebus.

Dembski didn't like it when I pointed out that his triad of properties for a designer were shared by natural selection.

So far, in the years since Darwin's Black Box... no ID proponent has even tried to talk about the "I". They just talk about the "D"...

O.o

ID-pushers also don't talk about the Manufacturer. Which is rather a curious omission, if ID really is the dispassionate search for truth that ID-pushers like to claim ID is. After all, people have come up with any number of Designs for thingies that don't actually exist, on account of nobody manufactured any physical instances of those Designs. And leave us not forget that real scientists actually do have a protocol for detecting Design, a protocol which is based on forming a testable hypothesis of Manufacture. Because, like, if whatever-it-is wasn't Manufactured, there wouldn't be any whatever-it-is to declare Designed or otherwise, you know?

The whole truth

Posts: 1554
Joined: Jan. 2012

Posted: Jan. 23 2015,00:08

Quote (Cubist @ Jan. 22 2015,19:51)

Quote (OgreMkV @ Jan. 22 2015,20:00)

Quote (Wesley R. Elsberry @ Jan. 22 2015,17:25)

Quote (midwifetoad @ Jan. 22 2015,15:29)

Quote (stevestory @ Jan. 22 2015,13:08)

the islands of functions are incredibly isolated. That proves ~~Baby Jesus~~ Intelligent Designer! You know what's even more proof? The exact opposite!

Socrates's grandkids these are not...

Makes sense. The best evidence for design would be evidence that evolution works.

If evolution works, it is designed. Therefore Jebus.

Dembski didn't like it when I pointed out that his triad of properties for a designer were shared by natural selection.

So far, in the years since Darwin's Black Box... no ID proponent has even tried to talk about the "I". They just talk about the "D"...

O.o

ID-pushers also don't talk about the Manufacturer. Which is rather a curious omission, if ID really is the dispassionate search for truth that ID-pushers like to claim ID is. After all, people have come up with any number of Designs for thingies that don't actually exist, on account of nobody manufactured any physical instances of those Designs. And leave us not forget that real scientists actually do have a protocol for detecting Design, a protocol which is based on forming a testable hypothesis of Manufacture. Because, like, if whatever-it-is wasn't Manufactured, there wouldn't be any whatever-it-is to declare Designed or otherwise, you know?

Good points.

IMO the IDiots (cdesignproponentists) omit the manufacture part because it's the 'creation' part and using the 'c' word is a no-no in their agenda to dishonestly shove their religious dogma into schools, etc., and call it science.

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Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

Posts: 1961
Joined: May 2007

Posted: Jan. 23 2015,01:50

Quote (Cubist @ Jan. 22 2015,21:51)

Quote (OgreMkV @ Jan. 22 2015,20:00)

Quote (Wesley R. Elsberry @ Jan. 22 2015,17:25)

Quote (midwifetoad @ Jan. 22 2015,15:29)

Quote (stevestory @ Jan. 22 2015,13:08)

the islands of functions are incredibly isolated. That proves ~~Baby Jesus~~ Intelligent Designer! You know what's even more proof? The exact opposite!

Socrates's grandkids these are not...

Makes sense. The best evidence for design would be evidence that evolution works.

If evolution works, it is designed. Therefore Jebus.

Dembski didn't like it when I pointed out that his triad of properties for a designer were shared by natural selection.

So far, in the years since Darwin's Black Box... no ID proponent has even tried to talk about the "I". They just talk about the "D"...

O.o

ID-pushers also don't talk about the Manufacturer. Which is rather a curious omission, if ID really is the dispassionate search for truth that ID-pushers like to claim ID is. After all, people have come up with any number of Designs for thingies that don't actually exist, on account of nobody manufactured any physical instances of those Designs. And leave us not forget that real scientists actually do have a protocol for detecting Design, a protocol which is based on forming a testable hypothesis of Manufacture. Because, like, if whatever-it-is wasn't Manufactured, there wouldn't be any whatever-it-is to declare Designed or otherwise, you know?

ID is best explained as the concept of magic in action. And that kind of magic is best explained by the existence of an Intelligent Magician. But what is the best explanation of His fondness of beetles?

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Rocks have no biology.
Robert Byers.

KevinB

Posts: 524
Joined: April 2013

Posted: Jan. 23 2015,14:14

Quote (Quack @ Jan. 23 2015,01:50)

But what is the best explanation of His fondness of beetles?

Perhaps He just got caught out by the order multiple in the Creation Supplies catalogue. (Like ordering 1000 boxes of paperclips, instead of 1 box of 1000 paperclips.)

JohnW

Posts: 3217
Joined: Aug. 2006

Posted: Jan. 23 2015,14:54

Quote (KevinB @ Jan. 23 2015,12:14)

Quote (Quack @ Jan. 23 2015,01:50)

But what is the best explanation of His fondness of beetles?

Perhaps He just got caught out by the order multiple in the Creation Supplies catalogue. (Like ordering 1000 boxes of paperclips, instead of 1 box of 1000 paperclips.)

"Customers who ordered tiger beetles also ordered:
Rove beetles
Stag beetles
Scarab beetles
Weevils
..."

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Math is just a language of reality. Its a waste of time to know it. - Robert Byers

There isn't any probability that the letter d is in the word "mathematics"... The correct answer would be "not even 0" - JoeG

Posts: 4003
Joined: Mar. 2008

Posted: Jan. 23 2015,15:01

He couldn't resist free shipping.

ETA:

No doubt she subscribed to Mover Prime.

Edited by midwifetoad on Jan. 23 2015,15:02

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

Henry J

Posts: 5760
Joined: Mar. 2005

Posted: Jan. 23 2015,15:22

Quote (JohnW @ Jan. 23 2015,13:54)

Quote (KevinB @ Jan. 23 2015,12:14)

Quote (Quack @ Jan. 23 2015,01:50)

But what is the best explanation of His fondness of beetles?

Perhaps He just got caught out by the order multiple in the Creation Supplies catalogue. (Like ordering 1000 boxes of paperclips, instead of 1 box of 1000 paperclips.)

"Customers who ordered tiger beetles also ordered:
Rove beetles
Stag beetles
Scarab beetles
Weevils
..."

VW Beetle...
Beetle Bailey...

KevinB

Posts: 524
Joined: April 2013

Posted: Jan. 23 2015,16:24

Quote (Henry J @ Jan. 23 2015,15:22)

Quote (JohnW @ Jan. 23 2015,13:54)

Quote (KevinB @ Jan. 23 2015,12:14)

Quote (Quack @ Jan. 23 2015,01:50)

But what is the best explanation of His fondness of beetles?

Perhaps He just got caught out by the order multiple in the Creation Supplies catalogue. (Like ordering 1000 boxes of paperclips, instead of 1 box of 1000 paperclips.)

"Customers who ordered tiger beetles also ordered:
Rove beetles
Stag beetles
Scarab beetles
Weevils
..."

VW Beetle...
Beetle Bailey...

Yeah, yeah, yeah.

ie. => Rock Ferry (Birkenhead), which forces the next move to be Pier Head, due to the Gerry Marsden codacil.

Jim_Wynne

Posts: 1208
Joined: June 2006

Posted: Feb. 07 2015,11:01

Quote (Jim_Wynne @ Jan. 18 2015,10:35)

Cryptoguru, condensed:

1. All of biology and most of science is wrong.
2. Frontloading.
3. No evidence, no mechanisms.

I'll put the over/under on this thread at six pages.

The house wins.

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Evolution is not about laws but about randomness on happanchance.--Robert Byers, at PT

OgreMkV

Posts: 3668
Joined: Oct. 2009

Posted: Feb. 12 2015,19:31

AND he's back... on Smilodon's Retreat. He refuses to come here.

Although, he hasn't said word one about information or DNA is a computer.

Now, he's on about how radiometric dating is flawed and can't work. I think he's using that dino bone "paper" with the black "tissue" as evidence. We won't say though.

He's also got this thing about birds... though I think I shut him up about that one too.

Cthulhu he's dumb.

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Ignored by those who can't provide evidence for their claims.

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Posts: 287
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Posted: Feb. 13 2015,03:50

Quote (KevinB @ Jan. 23 2015,16:24)

ie. => Rock Ferry (Birkenhead), which forces the next move to be Pier Head, due to the Gerry Marsden codacil.

"Why did Jesus not appear in Liverpool?"

"Because his miracle of walking on the water is nothing special in Liverpool."

"How come?"

"The quality of Mersey is unstrained."

Ba-dum, tish.

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The ultimate truth is that there is no ultimate truth.

KevinB

Posts: 524
Joined: April 2013

Posted: Feb. 13 2015,05:17

Quote (rossum @ Feb. 13 2015,03:50)

Quote (KevinB @ Jan. 23 2015,16:24)

ie. => Rock Ferry (Birkenhead), which forces the next move to be Pier Head, due to the Gerry Marsden codacil.

"Why did Jesus not appear in Liverpool?"

"Because his miracle of walking on the water is nothing special in Liverpool."

"How come?"

"The quality of Mersey is unstrained."

Ba-dum, tish.

Given the atrociously Bard pun, are you playing Stratford Upon Avon, Stratford International or Fenny Stratford?

cryptoguru

Posts: 53
Joined: Jan. 2015

Posted: Feb. 17 2015,09:39

I'm back through popular demand ... can't be bothered to read through all the replies since I last visited. But happy to debate on one topic at a time.
Yeah I never answered all the questions, because some I didn't read as there were so many, and some I didn't have time to answer as the conversation kept changing direction or different angles were being approached by different people at the same time, plus the entropy of contributors who think discussion is simply calling your opponent stupid and rejecting everything they say without basis. So let's take this at a more reasonable pace ... because I do have a life.

So McOgre (Kevin),
When you say I lost the debate about dinos->birds ... is that the one where you said that dinos evolved into birds and I showed that hundreds of birds in their modern form appear in the fossil record alongside dinos in the Cretaceous layer without transitional form? And you got upset because I said that therefore Velociraptor and T-Rex couldn't have been bird ancestors as they have been widely depicted in the media and literature and museums. And you just wanted to talk about Archaeopteryx? (which looks remarkably like a Hoatzin) And they've found another "earlier" Jurassic feathered bird fossil in China (Xiaotingia). Anyway the birds from dinos thing is quite funny, but even assuming evolution is true there's no proof for dino-bird evo at all, it's simply assumed. Arguing from similar morphology is stupid, as we could simply assert that sharks (fish) and dolphins (mammals) are closely related.

Anyway back to the original problem. (we can discuss the other issues once the allegations that I'm avoiding answering questions stops)

Let me rephrase my original question again, because it seemed to keep getting lost in piles of straw men.
Show me a mechanism that can generate the equivalent information of an ORFan gene (i.e. significant amount of new genetic material, not just a couple of point mutations in regulatory genes that switch other code off/on) using only random mutations and an environmentally driven competition model (i.e. doesn't cheat by rewarding micro-feature improvements that wouldn't be selectable in a natural environment.)
Avida cheats on 2 accounts, it rewards micro-feature improvements by testing if a logic function (target) has been achieved on mutation and not simply on the performance of the resultant organism ... and it only requires a small amount of new information to generate new features (e.g. 9 commands can perform EQU). ORFan genes represent thousands of unique sequences of base-pairs that must be demonstrated can arrive through simple mutation and natural selection.

For those who may be tempted to argue that you don't need to prove anything algorithmically, I've previously shown that the physical evidence is open to interpretation .... but even if it wasn't, you should be able to demonstrate that the general theory of evolution applied to biology can work in principle. (random mutation plus competition can create significantly quantifiable, more complex and apparently designed solutions to problems). We can't use known targets for this, or it is simply a stochastic search and not evolution. Mutation should also allow degeneration of functionality, in the genome, all the organism's functionality can be affected by mutation; even it's most basic operations are defined and built by the code itself. Therefore mutations should be able to break replication and all other basic survival processes of the organism, not only shuffle some existing functionality.

BTW: I'm not an ID person ... I'm a pure-pedigree young earth, bible-thumping creationist. (like Newton & Keppler & Boyle and loads of other religious wingnut scientists before me) But hold back on the abuse .. and the radio-dating arguments (which we can have a bit later if you like) ... let's stay on topic

Posts: 4003
Joined: Mar. 2008

Posted: Feb. 17 2015,10:06

Pick up a copy of Wagner's "Arrival of the Fittest" and get back. Your point mutations can accumulate indefinitely (as per the title of Wallace's original paper).

In lieu of that, please present an argument based on actual research, why mutations can't accumulate indefinitely.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

cryptoguru

Posts: 53
Joined: Jan. 2015

Posted: Feb. 17 2015,10:18

Quote

please present an argument based on actual research, why mutations can't accumulate indefinitely

Of course mutations can accumulate indefinitely ... they do.
I'm asking you to prove that random accumulative mutations can create new functional code and not break the original code.
What we observe in biology is mutations accumulating in the genome and causing more degenerative disease every generation. Show me how THAT is not the case and that there is new information arising somewhere, somehow. Show me algorithmically how information could possibly arise randomly (without sneaking it in using target-based search algorithms) and without calling a point mutation on a regulatory gene "new information".
I want to see from an informatics perspective how useful, functional and non-linear information that solves a problem can arise automatically.

N.Wells

Posts: 1836
Joined: Oct. 2005

Posted: Feb. 17 2015,10:32

Quote (cryptoguru @ Feb. 17 2015,09:39)

I'm back through popular demand ... can't be bothered to read through all the replies since I last visited. But happy to debate on one topic at a time.
Yeah I never answered all the questions, because some I didn't read as there were so many, and some I didn't have time to answer as the conversation kept changing direction or different angles were being approached by different people at the same time, plus the entropy of contributors who think discussion is simply calling your opponent stupid and rejecting everything they say without basis. So let's take this at a more reasonable pace ... because I do have a life.

So McOgre (Kevin),
When you say I lost the debate about dinos->birds ... is that the one where you said that dinos evolved into birds and I showed that hundreds of birds in their modern form appear in the fossil record alongside dinos in the Cretaceous layer without transitional form? And you got upset because I said that therefore Velociraptor and T-Rex couldn't have been bird ancestors as they have been widely depicted in the media and literature and museums. And you just wanted to talk about Archaeopteryx? (which looks remarkably like a Hoatzin) And they've found another "earlier" Jurassic feathered bird fossil in China (Xiaotingia). Anyway the birds from dinos thing is quite funny, but even assuming evolution is true there's no proof for dino-bird evo at all, it's simply assumed. Arguing from similar morphology is stupid, as we could simply assert that sharks (fish) and dolphins (mammals) are closely related.

Cretaceous birds are often "modern" (used very loosely) in some aspects while not in others. Xiaotingia is one of a growing number of fossils somewhere in the base of archaeopterygids, dromaeosaurs, and troodontids, and how it gets classified depends on how the groups are defined. However, it isn't a bird in most senses of the word. The most detailed analysis (Senter et al., 2012) found Archaeopteryx to be a avialian, Anchiornis to be a troodontid, and Xiaotingia to be a basal deinonychosaurian, but this is likely to change as new fossils are found of other critters and as definitions shift to accomodate the new information. This complexity happens because all these guys are extremely similar in a great many details. Modern classification of fossils without DNA depends on statistical analysis of similarity using many dozens of characters, because similarity overall matches relatedness in living forms. Classification no longer rests on single characters picked by an expert (the "it has feathers, so it's a bird" school of classification), and absolutely never relied on gross similarities unsupported by similarities in fine details (your "Archaeopteryx looks like a hoatzin" idea). Archaeopteryx does not look very like a hoatzin at all when one looks at its fine details. However, it does match Velociraptor in quite a lot of details.

Descent of birds from theropods is not an "assumption", but a comclusion, based on cladistic analysis of data from comparative anatomy. No dinosaur experts claim that Tyrannosaurus and Velociraptor were direct ancestors of birds: they are close relatives (Tyrannosaurus a bit less so), but T & V are Cretaceous, whereas birds apparently date back to the Jurassic.

Bear in mind that the Cretaceous lasted about 80 million years (longer than the time since the non-avian dinosaurs went extinct), so the presence of primitive members of comparatively modern Neornithine bird groups by the end of the Cretaceous should not be confused with the abundance of Enantiornithine birds without any neornithines earlier in the Cretaceous.

OgreMkV

Posts: 3668
Joined: Oct. 2009

Posted: Feb. 17 2015,10:40

Quote (cryptoguru @ Feb. 17 2015,10:18)

Of course mutations can accumulate indefinitely ... they do.
I'm asking you to prove that random accumulative mutations can create new functional code and not break the original code.

Sure. Here.

Zhao, L., Saelao, P., Jones, C. D. & Begun, D. J. Origin and Spread of de Novo Genes in Drosophila melanogaster Populations. Science (2014). doi:10.1126/science.1248286

and

Wu, D.-D. D., Irwin, D. M. & Zhang, Y.-P. P. De novo origin of human protein-coding genes. PLoS Genet. 7, e1002379 (2011).

Done.
Next.

We don't have to show it mathematically (although, that's trivial). Because it happens in the real world.

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Ignored by those who can't provide evidence for their claims.

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