Exploring the protein universe: a response to Doug Axe

Ah yes, Axe playing the weary game of "I can't demonstrate that I am right in practice, but I can prove that you are wrong in theory." Let the handwaving begin.

What Axe and Gauger did was study a "transition" that has never been proposed to have happened. They examined a transition from one currently-existing protein to another currently-existing protein. It's as though they analyzed the "transition" from a cat to a dog, when they should have analyzed the transition from ancestral mammals to dogs and/or cats. Their conclusions tell us something about protein structure and function but, crucially, not about the evolution of those proteins.

I agree that the work seems to advance a strawman, and that this is seriously problematic. My intent was to credit Gauger and Axe with performing well-controlled and technically effective experiments, and to separate the irrelevance of their results from their scientific competence.

If Axe wishes to show that proteins (or presumably, ultimately, genes for proteins) need to be magically designed, why doesn't he take the obvious logical approach?

1) Understand and acknowledge how the theory of evolution proposes that changes in proteins across lineage, individuals, and/or time come about.

2) Based on either a new experiment (ideal) or historical data, propose a scenario under which "design" makes a prediction that is clearly different from anything predicted by the theory of evolution, with respect to say, a single protein. This will require explaining how things that are designed can be differentiated from things that are not, which will implicitly require him to be able to give an example of something that isn't designed.

3) Carry out the experiment. If the results support "design", in a way that objective biologists agree upon, then we can conclude that "design" has at least once been detected.

4) We still have the issue that the theory of evolution presents an adequate explanation for the diversity and relatedness of the biosphere. If Axe can't detect design using fair, unbiased testing, that's not an issue. If he can show unequivocal evidence of a protein (or, presumably, gene for a protein) being magically designed, then he is still left with the question of whether "design" is a relevant component of the history of life on earth. However, detecting design at all would be a necessary first step here.

5) Instead of this, he sets up straw man scenarios, and then disproves his own creation. Why would an honest man behave that way?

I also find it puzzling, given Axe's obvious scientific competence. I'm aware that within the creationist model, evolution MEANS the morphing of one CURRENT organism into another CURRENT organism. This is the only thing evolution can possibly mean, given the dictum that there has never been an entirely new organism since the day of creation and never can be.

If Axe is following this model, then he is implicitly assuming that proteins also have never evolved, and that "evolution" of proteins can only refer to one current functional protein changing into another current functional protein. And yes, this might require design.

But failure to find any indications in support of a false model really doesn't contribute much to our knowledge.

By the way, Steve Mattheson, thanks for the posting and the response.

I am on my way out the door but have a couple of other quick points to make.

1) For those who seek to find evidence against a given hypothesis, let alone a strong theory, surely the first step is to be absolutely sure of a fair representation of the position one argues against.

2) A good example of a set of experiments which could have detected supernatural intervention, even though that was not the point of it, is Lenski's E. coli experiments

Even a non-creationist like me can agree that certain results would have severely challenged the theory of evolution.

The theory of evolution predicts that citrate + alleles will arise only at something reasonably related to known mutation rates in E. coli, but will then be selected for.

Any massively more rapid than expected adaptation to citrate would have been extremely challenging to contemporary evolutionary theory.

While this would not have proven divine intervention, and while Lenski's team undoubtedly would have sought natural explanations, a result like this might have given design advocates something to work from. Perhaps they could have ordered their own citrate - E. coli from the supply house, set up their own experiments, and, if armed a priori with that all so important ability to distinguish between that which is designed and that which isn't, in a way that objective observers could agree on before the experiment, attempted to reproduce such a result and show how design best explains it.

However, Lenski did not get that result.

Oddly, many creationists expressed hope, not that an undeniable miraculous intervention by design would occur (as one would logically expect them to), but rather, hope that the bacteria simply wouldn't evolve at all. Indeed, Schafly of Conservapedia when so far as to vehemently deny even the highly predictable evolution of the citrate + trait, outrageously demand that the bacteria be sent to him, and so on. However, even this ambivalent result, which would not have supported ID/creationism, but merely failed to show a simple example of evolution, is not what was seen.

Still, although these experiments failed to support design, surely one would expect that they would provide a model for experiments by sincere ID advocates. I cannot understand why this has not been the case.

Here are some more biologically relevant questions for Axe to consider in his next paper:

1) Can duplicated genes increase the number of functional copies of a gene by a process involving random mutation and natural selection

2) Can duplicated genes give rise to gene families consisting of genes with related functions by a process involving birth and death of duplicated genes

3) Can duplicated genes give rise to genes with new functions by a process involving random mutation and natural selection and what could possibly prevent this from happening

These are some of the major mechanisms by which new genes and new functions are actually hypothesized to arise. There is a great deal of evidence that these events do occur naturally, so proving that they cannot happen will be a really tall order. Or maybe he should just stick to straw man arguments, they are so much easier.

Now why would anyone publish meaningless nonsense dealing only with misrepresentations of evolutionary theory? Maybe the journal isn't really

unbiased.

I think what Steve Matheson is saying is that Axe's work is "good" in the sense that he is good at formulating a testable hypothesis and also good at performing experiments that test the hypothesis. This puts him streets ahead of the usual theistic evolutionist/ID proponent. But where Axe falls down is in applying his hypothesis to evolutionary theory, where he seems to think he has demonstrated a major flaw in evolution when in fact all he has shown is a major flaw in evolution as it is commonly misunderstood by theistic evo/ID proponents. Is that a fair summary, Steve?

Chris Lawson said: I think what Steve Matheson is saying is that Axe's work is "good" in the sense that he is good at formulating a testable hypothesis and also good at performing experiments that test the hypothesis. This puts him streets ahead of the usual theistic evolutionist/ID proponent. But where Axe falls down is in applying his hypothesis to evolutionary theory, where he seems to think he has demonstrated a major flaw in evolution when in fact all he has shown is a major flaw in evolution as it is commonly misunderstood by theistic evo/ID proponents. Is that a fair summary, Steve?

Chris Lawson said: I think what Steve Matheson is saying is that Axe's work is "good" in the sense that he is good at formulating a testable hypothesis and also good at performing experiments that test the hypothesis. This puts him streets ahead of the usual theistic evolutionist/ID proponent. But where Axe falls down is in applying his hypothesis to evolutionary theory, where he seems to think he has demonstrated a major flaw in evolution when in fact all he has shown is a major flaw in evolution as it is commonly misunderstood by theistic evo/ID proponents. Is that a fair summary, Steve?

Steve,

I meant theistic evolutionist in the sense that I have never seen Axe described as a full-blown ID proponent. That may well be due to my lack of reading about Axe, so I was trying to be inclusive in case he doesn't self-identify as an IDist.

While we're on the subject, though, do you consider your belief in theistic evolution to be a scientific position or a philosophical/religious position? And if scientific, what do you consider the most compelling evidence?

Chris Lawson said: Steve, I meant theistic evolutionist in the sense that I have never seen Axe described as a full-blown ID proponent. That may well be due to my lack of reading about Axe, so I was trying to be inclusive in case he doesn't self-identify as an IDist. While we're on the subject, though, do you consider your belief in theistic evolution to be a scientific position or a philosophical/religious position? And if scientific, what do you consider the most compelling evidence?

The pig-headed response of the science establishment to the emergent principles potentially present in life is, of course, a glaring symptom of its addiction to reductionist beliefs - happily abetted by the pharmaceutical industry, which greatly appreciates having minutiae relevant to its business worked out at taxpayer expense. The rejection of emergence is justified as defending science from mysticism. The ostensible scientific view is that life is chemical reactions, and that the bold, manful thing to do is identify and manipulate them with stupendous amounts of money and supercomputers. The corresponding mystical view is that life is a beautifully unknowable thing that can only be screwed up by humans with all their money and computer cycles. Between these extremes we have the profoundly important, but poorly understood, idea that the unknowability of living things may actually be a physical phenomenon. This does not make life any less wonderful, but simply identifies how its inaccessibility could be fully compatible with reductionist law. Unknowability is something we see all the time in the inanimate world, and it is actually not mysterious at all. Other, more primitive, systems exhibiting it have evaded computer solution up until now, and some of us are confident that they always will. Whether similar effects occur in biology remains to be seen. What is certainly true, however, is that arrogantly dismissing the possibility will lead to an endless and unimaginably expensive quagmire of bad experiments.

Chris Lawson said: I think what Steve Matheson is saying is that Axe's work is "good" in the sense that he is good at formulating a testable hypothesis and also good at performing experiments that test the hypothesis. This puts him streets ahead of the usual theistic evolutionist/ID proponent. But where Axe falls down is in applying his hypothesis to evolutionary theory, where he seems to think he has demonstrated a major flaw in evolution when in fact all he has shown is a major flaw in evolution as it is commonly misunderstood by theistic evo/ID proponents. Is that a fair summary, Steve?

Chris Lawson said: Steve, I meant theistic evolutionist in the sense that I have never seen Axe described as a full-blown ID proponent. That may well be due to my lack of reading about Axe, so I was trying to be inclusive in case he doesn't self-identify as an IDist. While we're on the subject, though, do you consider your belief in theistic evolution to be a scientific position or a philosophical/religious position? And if scientific, what do you consider the most compelling evidence?

harold said: By definition, a straw man claim set up to be demolished is not a "good" hypothesis, and an "experiment" designed to have a pre-determined outcome, and performed to go through the motions of "doing an experiment", does not "test" anything. To me, doing this is the quintessence of being VERY, VERY BAD at "formulating a testable hypothesis and also good at performing experiments that test the hypothesis".

One might credit Axe with at least performing a skillful fraud. Inept con games are so annoying.

Great stuff by Axe and co. I really think he is close to finding the silver bullet to kill the beast of Darwinism.

I have submitted a new paper to the journals on the subject of how the massive difference in efficacy between the directed evolution of proteins under artificial selection compared with that of natural selection and random drift.

The Darwinists will rue ever having used directed evolution as a means of explaining how natural evolution works.

Or maybe we can give Axe credit for fairly meticulously demonstrating that evolution does in fact not follow paths nobody ever said it followed, or alternatively that the creationist notion of evolution as a morphing from one current form to another current form simply does not happen.

Kind of like assuming that flight MEANS flapping your arms and flying to the moon. So Axe has done excellent science in establishing through good methodology that this does not and can not happen. This leaves two possible problems: 1) Why would anyone try to disprove a definition of "flight" that bears no resemblance to the common scientific understanding, and 2) it's possible that Axe or those in his camp will use his study as "scientific proof" that "flight" is not possible.

Oh, how tiresome.

No, Flint, I didn't mean you. But ... do you want to argue with this guy? He is barking mad.

Steve M, I would suggest you put a stop to these postings ASAP since otherwise it's just going to be an endless stream of ranting, abuse, and petulance.

None of you seem to realize that proteins are highly specialized molecular entities that are marginally stable. They are made up of distinct domains that bear no relationship with one another. You can't claim that the T-box and the forkhead box share a common ancestor protein domain. Evolutionary theory has no explanation for the origin of protein domains and functions other than trial and error over deep time. But you can keep hitting your head against a brick wall ad infinitum and it will only give you a headache.

Great stuff by Axe and co. I really think he is close to finding the silver bullet to kill the beast of Darwinism.

Atheistoclast is right about the brick wall+headache thing, the tried it... that's why he's here now proselytizing for ID-creationism.

Atheistoclast said: Great stuff by Axe and co. I really think he is close to finding the silver bullet to kill the beast of Darwinism. I have submitted a new paper to the journals on the subject of how the massive difference in efficacy between the directed evolution of proteins under artificial selection compared with that of natural selection and random drift. The Darwinists will rue ever having used directed evolution as a means of explaining how natural evolution works. None of you seem to realize that proteins are highly specialized molecular entities that are marginally stable. They are made up of distinct domains that bear no relationship with one another. You can’t claim that the T-box and the forkhead box share a common ancestor protein domain. Evolutionary theory has no explanation for the origin of protein domains and functions other than trial and error over deep time. But you can keep hitting your head against a brick wall ad infinitum and it will only give you a headache.

Hey folks ... last time this guy showed up here to rant he was given his very own thread over at ATBC as a ranting platform. He didn't show. If you must pick up the gauntlet, you might do it over on ATBC ... it's likely he won't show this time, either, but it's not like that's a bad thing, is it?

Naw, Dale, he's just an attention whore and a troll. He must be feeling neglected over at TalkRational so brought his travelling circus here.

Dale Husband said: Oh wow, yet another Creationist lunatic who has absolutely no idea what an idiot he is. Everything he said above is nonsense.

ATHEISTOCLAST said:

Dale Husband said: Oh wow, yet another Creationist lunatic who has absolutely no idea what an idiot he is. Everything he said above is nonsense.

Yet another Evolutionist who has nothing to offer other than ad hominem insults in sheer desperation at his own ignorance.

Yet another Evolutionist who has nothing to offer other than ad hominem insults in sheer desperation at his own ignorance.

harold said: Atheistoclast - I would greatly appreciate it if you would answer any of the following questions.

1) What is an example of something that is not intelligently designed?

2) Who is the designer?

3) What did the designer do?

4) When did the designer do it?

5) How did the designer do it?

6) Specifically how does Axe's work present any challenges to the theory of evolution?

Dale Husband's comment consists of some insults, followed by what appears to be a correct observation. There is no ad hominem.

DS said: 1) Can duplicated genes increase the number of functional copies of a gene by a process involving random mutation and natural selection?

2) Can duplicated genes give rise to gene families consisting of genes with related functions by a process involving birth and death of duplicated genes?

3) Can duplicated genes give rise to genes with new functions by a process involving random mutation and natural selection and what could possibly prevent this from happening?

These are some of the major mechanisms by which new genes and new functions are actually hypothesized to arise. There is a great deal of evidence that these events do occur naturally, so proving that they cannot happen will be a really tall order. Or maybe he should just stick to straw man arguments, they are so much easier.

The Face on Mars. The Giant’s Causeway.

The Elohim.

He designed things.

Throughout the course of Earth’s history.

We don’t know yet. We are working on it.

I have proposed directed evolution by artificial selection as a way in which Darwinists can save face and make a climbdown.

He’s basically showing how enzymes are too complex to have been fashioned by blind laws and imperfect reproduction

No. They can only give rise to genes that are slightly different in relation to each other. A new paper has come out by a leading researcher in the field that examined how evolution in gene duplicates leads to nothing in the end. http://www.sciencedirect.com/scienc[…]searchtype=a

harold said:

No. They can only give rise to genes that are slightly different in relation to each other. A new paper has come out by a leading researcher in the field that examined how evolution in gene duplicates leads to nothing in the end. http://www.sciencedirect.com/scienc[…]searchtype=a

Remarkably, although you seem to have written that paper yourself, it still doesn't actually support your contention here. You seem to be arguing against a straw man. No-one has ever argued that all gene duplications always result in novel functional proteins. Just that it is one of the ways in which they can arise. Don't waste your time arguing against that, as it's already very well established. So in fact, your answer should be "yes".

I am surprised that so many of you can't understand the difference between artificial selection(intelligent design) and natural selection (Darwinism).

The former selects on the basis of his telos. That is, his aim or purpose and not that of greater reproduction. This is why AS is teleological. It is not restricted by the need to offer gains in viability and fertility or else we wouldn't have seedless fruit.

We are able to do things in the lab (directed evolution) and in agriculture (artificial selection) that Nature cannot. We are applying our knowledge of genetic engineering whereas Nature is blind and dumb.

ATHEISTOCLAST said:

DS said: 1) Can duplicated genes increase the number of functional copies of a gene by a process involving random mutation and natural selection?

Absolutely.

2) Can duplicated genes give rise to gene families consisting of genes with related functions by a process involving birth and death of duplicated genes?

Absolutely.

3) Can duplicated genes give rise to genes with new functions by a process involving random mutation and natural selection and what could possibly prevent this from happening?

No. They can only give rise to genes that are slightly different in relation to each other. A new paper has come out by a leading researcher in the field that examined how evolution in gene duplicates leads to nothing in the end. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2K-52R9DM0-1&_user=10&_coverDate=04%2F28%2F2011&_rdoc=1&_fmt=high&_orig=gateway&_origin=gateway&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=3db3102abfa9ba6dce092d641895e9db&searchtype=a

These are some of the major mechanisms by which new genes and new functions are actually hypothesized to arise. There is a great deal of evidence that these events do occur naturally, so proving that they cannot happen will be a really tall order. Or maybe he should just stick to straw man arguments, they are so much easier.

I think you will find that copying one thing is not the same thing as creating something else.

ATHEISTOCLAST said: I am surprised that so many of you can't understand the difference between artificial selection(intelligent design) and natural selection (Darwinism). The former selects on the basis of his telos. That is, his aim or purpose and not that of greater reproduction. This is why AS is teleological. It is not restricted by the need to offer gains in viability and fertility or else we wouldn't have seedless fruit. We are able to do things in the lab (directed evolution) and in agriculture (artificial selection) that Nature cannot. We are applying our knowledge of genetic engineering whereas Nature is blind and dumb.

I think you misread the abstract. There is a belief among evolutionists that a duplicate will either find a new function or lose its preexisting function.

Actually, what happens is that duplicates just stay as they are - they may degenerate somewhat and lose some of their functionality and expression but they will remain intact.

Also, natural selection tends to compensate (for prior degeneration) rather than to innovate.

ATHEISTOCLAST said:

DS said: 3) Can duplicated genes give rise to genes with new functions by a process involving random mutation and natural selection and what could possibly prevent this from happening?

No. They can only give rise to genes that are slightly different in relation to each other. A new paper has come out by a leading researcher in the field that examined how evolution in gene duplicates leads to nothing in the end.

harold said: The obvious first step in arguing against a scientific idea, is to make sure that you fully understand that idea and represent it fairly. Instead, you are arguing against a straw man.

Of course, it is often the case that duplicates do eventually lose their function, and it is sometimes the case that gene duplicates are the source of new function. Those are facts. But no-one has ever said that this happens instantly or absolutely invariably.

This is factually false. There is no force which prevents duplicated gene segments from experiencing mutations.

It's conceivable that a situation could exist in which having serial copies of the same gene is selected for, but there is certainly no reason to think that this happens in every case.

If you disagree, then please explain in detail why duplicated genes are less subject to normal biochemical mutation events than other types of DNA.

Another statement that indicates that you don't understand the theory of evolution.

Offspring are genetically different from parents. Some genetic variability is expressed as phenotypic variability. If some phenotypes have a relative reproductive advantage, they are likely to be selected for, and if so, the alleles associated with those phenotypes will increase in frequency in the population.

It has nothing to do with "degeneration" or conscious innovation.

atheist:

If you actually bothered to read the reference I presented, you would find that at least four different fates are described for duplicate genes. You are incorrect in your characterizations. It would appear that you have not bothered to read the relevant literature. Please do so and then come back if you want to argue when you are better informed.

Now, why do you claim that duplicate genes "suffer from degenerative mutations more than do singletons"? Exactly what do you mean by this? Do you mean that they can evolve through non functional intermediates? Do you mean that they are under less selective pressure that single copy genes? Do you mean the mutations themselves or the results of selection? What mechanism do you propose for this? If it involves intelligence, whose intelligence? What are the motives behind this? What is the purpose of this? In short, what are you talking about? Do you even know? Can you provide a reference that isn't form Biocomplexity?

Creating straw man arguments is a worthless pursuit, especially when you have no idea what evidence already exists. Seems that Axe uses the same bag of tricks. Otherwise, how can you explain the fact that he completely ignored mechanisms involving duplicate genes, even though you claim that "evolutionists" all believe certain things?

DS said: If you actually bothered to read the reference I presented, you would find that at least four different fates are described for duplicate genes. You are incorrect in your characterizations. It would appear that you have not bothered to read the relevant literature. Please do so and then come back if you want to argue when you are better informed.

Now, why do you claim that duplicate genes "suffer from degenerative mutations more than do singletons"?

Exactly what do you mean by this?

Do you mean that they can evolve through non functional intermediates?

Do you mean that they are under less selective pressure that single copy genes?

Do you mean the mutations themselves or the results of selection?

What mechanism do you propose for this?

If it involves intelligence, whose intelligence?

What are the motives behind this? What is the purpose of this? In short, what are you talking about? Do you even know? Can you provide a reference that isn't form Biocomplexity?

Your comments in this thread show a propensity for blatant falsehood.

atheist:

The fourth fate was a new metabolic function.

The whole point is that, since selection is re;axed in duplicates genes, one copy is free to mutate in any way whatsoever and that can lead to a new function.

Of course they are liable to degenerate, with respect to the original function. So they are now free to take on new functions. What could possibly stop this? I don't think that relaxed selection means what you think it means.

You are the one who is misrepresenting an entire field of science. You are the one who needs to start from the beginning. You are ignoring basic genetic mechanisms.

ATHEISTOCLAST said: ??? No intelligence is required for mutational degeneration!

Of course, it is often the case that duplicates do eventually lose their function, and it is sometimes the case that gene duplicates are the source of new function. Those are facts. But no-one has ever said that this happens instantly or absolutely invariably.

They have. The consensus among biologists is that: 1) Duplicates can gain function: neofunctionalization. 2) Duplicates can lose function: nonfunctionalization. 3) Duplicates can divide functions between them: subfunctionalization

I think you are playing with words.

Y'know ... I'm not above arguing with trolls on occasion. But I just don't understand how some folks cannot resist it under any circumstances. For me, it gets painfully boring very quickly.

DS said: The whole point is that, since selection is relaxed in duplicates genes, one copy is free to mutate in any way whatsoever and that can lead to a new function.

Of course they are liable to degenerate, with respect to the original function. So they are now free to take on new functions. What could possibly stop this? I don't think that relaxed selection means what you think it means.

You are the one who is misrepresenting an entire field of science. You are the one who needs to start from the beginning. You are ignoring basic genetic mechanisms.

mrg said: Y'know ... I'm not above arguing with trolls on occasion. But I just don't understand how some folks cannot resist it under any circumstances. For me, it gets painfully boring very quickly.

I wish the ATHEISTOCLAST (a phony name if there ever was one), would explain exactly how evolution via natural selection including random mutations violates any known laws of chemistry or physics. Sure, some molecular forms are highly improbable, but improbability does not imply impossibility and the whole issue of natural selection is to apply a directional force to the genes of organisms to make them change over time.

Natural selection indeed cannot account for the incredible complexity of the molecules. You know what does? The ability of carbon atoms to link to four other atoms at once, including other carbon atoms. As a result, the complexity of organic molecules is INFINITE!

So his arguments are entirely useless.

ATHEISTOCLAST said:

DS said: The whole point is that, since selection is relaxed in duplicates genes, one copy is free to mutate in any way whatsoever and that can lead to a new function.

No. The copy is not free to mutate in any direction - that is ridiculous- relaxed selection does not mean no purifying selection exists. At most a gene duplicate will evolve a variant function that is slightly different from the original - as with RNASE1B.

Of course they are liable to degenerate, with respect to the original function. So they are now free to take on new functions. What could possibly stop this? I don't think that relaxed selection means what you think it means.

Relaxed selection means that duplicates are liable to succumb to deleterious mutations more than singletons. If you look at any gene family you will see this.

You are the one who is misrepresenting an entire field of science. You are the one who needs to start from the beginning. You are ignoring basic genetic mechanisms.

The whole field of science? I suggest you read the paper I cited. Then come back to me.

harold said: However, there are lurkers here, some of whom are less informed about biomedical science than the regulars.

Genetics (1999) 151:1531-45

Science (2000) 290:1151-55

P R S L B (1994) 256(1346):119-124

Bioessays (1998) 20(10):758-8

PLOS Genetics (2010) 6(12):e1001255

Nature Review Genetics (2008) 9:938-950

Journal of Functional and Structural Genomics (2003) 3:35-44

All of these references and thousands more, have reached the conclusion that duplicated genes can take on new functions. It may be a rare event, but it can and does happen. Relaxed selection or subfunctionalization can serve as intermediate stages, but new functions can and do arise. How odd that you would think that we do not understand this in the age of genomics.

Once you have addressed all of this evidence, someone might be willing to discuss it further with you. Until then, there really is no point in any further discussion.

DS said: Genetics (1999) 151:1531-45 Science (2000) 290:1151-55 P R S L B (1994) 256(1346):119-124 Bioessays (1998) 20(10):758-8 PLOS Genetics (2010) 6(12):e1001255 Nature Review Genetics (2008) 9:938-950 Journal of Functional and Structural Genomics (2003) 3:35-44 All of these references and thousands more, have reached the conclusion that duplicated genes can take on new functions. It may be a rare event, but it can and does happen. Relaxed selection or subfunctionalization can serve as intermediate stages, but new functions can and do arise. How odd that you would think that we do not understand this in the age of genomics. Once you have addressed all of this evidence, someone might be willing to discuss it further with you. Until then, there really is no point in any further discussion.

LOL, Steve. I am sure you read all those papers!

Give us specific examples of "new" functions arising. "Variant" functions, that are only slightly different, don't count.

Anyway, I am pleased that the NCSE's polemic against ID has backfired. I had threatened Synthese with legal action.

http://www.nytimes.com/2011/05/14/us/14beliefs.html?pagewanted=1&_r=1

It is a victory for all decent Americans.

ATHEISTOCLAST said: LOL, Steve. I am sure you read all those papers! Give us specific examples of "new" functions arising. "Variant" functions, that are only slightly different, don't count. Anyway, I am pleased that the NCSE's polemic against ID has backfired. I had threatened Synthese with legal action. http://www.nytimes.com/2011/05/14/us/14beliefs.html?pagewanted=1&_r=1 It is a victory for all decent Americans.

And someone should mention that the link provided fails to support what it is said to support, and to a certain degree even refutes it. But who ever heard of a creationist providing a reference citation to something either irrelevant or the opposite of what it is alleged to have said? Why, the very idea!

So now we start with the arbitrary exclusion of any and all examples due to obvious fact that the atheist is an undeniable authority on the subject. After all, he has submitted a paper on the topic somewhere, it might even be accepted. That certainly makes him an expert.

Oh well. There are literally thousands of examples. But then again, an expert in the field would already know this. Let's try this one:

PNAS (1998) 95(7):2508-13

From the abstract:

The genes for eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN) in primates belong to the ribonuclease gene family, and the ECP gene, whose product has an anti-pathogen function not displayed by EDN, was generated by duplication of the EDN gene about 31 million years ago.

Notice that we have know about this particular example for over thirteen years now and the atheist guy still doesn't seem to have a clue.

Now of course the "expert" will; no doubt find some reason why this example just isn't good enough. Who cares. He obviously doesn't have a clue what he is talking about. The only field he has any competence in seems to be ignorance. If he wants to discuss the Axe paper, this is the place. If he wants to continue to display his ignorance, the bathroom wall is the place he belongs.

... the atheist is an undeniable authority on the subject.

Atheistoclast said: None of you seem to realize that proteins are highly specialized molecular entities that are marginally stable. They are made up of distinct domains that bear no relationship with one another. You can't claim that the T-box and the forkhead box share a common ancestor protein domain. Evolutionary theory has no explanation for the origin of protein domains and functions other than trial and error over deep time. But you can keep hitting your head against a brick wall ad infinitum and it will only give you a headache.

Matt Young said:

... the atheist is an undeniable authority on the subject.

He is not an atheist; he is an atheistoclast (as in iconoclast), a breaker of atheists.

He is not an atheist; he is an atheistoclast (as in iconoclast), a breaker of atheists.

Atheistoclast said: None of you seem to realize that proteins are highly specialized molecular entities that are marginally stable. They are made up of distinct domains that bear no relationship with one another. You can't claim that the T-box and the forkhead box share a common ancestor protein domain. Evolutionary theory has no explanation for the origin of protein domains and functions other than trial and error over deep time. But you can keep hitting your head against a brick wall ad infinitum and it will only give you a headache.

Matt Young said:

... the atheist is an undeniable authority on the subject.

He is not an atheist; he is an atheistoclast (as in iconoclast), a breaker of atheists.

It is obvious Steve and DS don't know what they are talking about. They cited this paper as an example of gene duplicates acquiring new functions:

Genetics. 1999 Apr;151(4):1531-45.

Now what is the actual title?

Preservation of duplicate genes by complementary, degenerative mutations.

It basically states that duplicate genes degenerate in such a way as they differentiate their functionality among them - this is called "subfunctionalization." No new functionality is created in this process. It is a division of labor.

What Darwinists want is evidence of neofunctionalization. They claim it is widespread but a really great paper by two evolutionists reports that neofucntionalization is not common at all:

Questioning the ubiquity of neofunctionalization.
Gibson TA, Goldberg DS.

http://www.ncbi.nlm.nih.gov/pubmed/19119408

They conclude: "In light of these findings, we believe that protein interaction evolution is more persuasively characterized by subfunctionalization and self-interactions."

It reminds me of what Susumu Ohno, the man who proposed evolution by gene duplication said in his now discredited research on "nylonase" (which tuned out to be a bogus example of a frameshift)

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC345072/

The mechanism of gene duplication as the means to acquire new genes with previously nonexistent functions is inherently self limiting in that the function possessed by a new protein, in reality, is but a mere variation of the preexisted theme.

Game, set and match.

ATHEISTOCLAST said: It is obvious Steve and DS don't know what they are talking about. They cited this paper as an example of gene duplicates acquiring new functions: Genetics. 1999 Apr;151(4):1531-45. Now what is the actual title? Preservation of duplicate genes by complementary, degenerative mutations. It basically states that duplicate genes degenerate in such a way as they differentiate their functionality among them - this is called "subfunctionalization." No new functionality is created in this process. It is a division of labor. What Darwinists want is evidence of neofunctionalization. They claim it is widespread but a really great paper by two evolutionists reports that neofucntionalization is not common at all: Questioning the ubiquity of neofunctionalization. Gibson TA, Goldberg DS. http://www.ncbi.nlm.nih.gov/pubmed/19119408 They conclude: "In light of these findings, we believe that protein interaction evolution is more persuasively characterized by subfunctionalization and self-interactions." It reminds me of what Susumu Ohno, the man who proposed evolution by gene duplication said in his now discredited research on "nylonase" (which tuned out to be a bogus example of a frameshift) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC345072/ The mechanism of gene duplication as the means to acquire new genes with previously nonexistent functions is inherently self limiting in that the function possessed by a new protein, in reality, is but a mere variation of the preexisted theme. Game, set and match.

ATHEISTOCLAST said: It is obvious Steve and DS don't know what they are talking about. They cited this paper as an example of gene duplicates acquiring new functions: Genetics. 1999 Apr;151(4):1531-45. Now what is the actual title? Preservation of duplicate genes by complementary, degenerative mutations. It basically states that duplicate genes degenerate in such a way as they differentiate their functionality among them - this is called "subfunctionalization." No new functionality is created in this process. It is a division of labor. What Darwinists want is evidence of neofunctionalization. They claim it is widespread but a really great paper by two evolutionists reports that neofucntionalization is not common at all: Questioning the ubiquity of neofunctionalization. Gibson TA, Goldberg DS. http://www.ncbi.nlm.nih.gov/pubmed/19119408 They conclude: "In light of these findings, we believe that protein interaction evolution is more persuasively characterized by subfunctionalization and self-interactions." It reminds me of what Susumu Ohno, the man who proposed evolution by gene duplication said in his now discredited research on "nylonase" (which tuned out to be a bogus example of a frameshift) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC345072/ The mechanism of gene duplication as the means to acquire new genes with previously nonexistent functions is inherently self limiting in that the function possessed by a new protein, in reality, is but a mere variation of the preexisted theme. Game, set and match.

Here is another PT favorite:

Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict

PNAS 2010 107 (50) 21593-21598

Oh example that doesn't count because is happened in a fish.

For a good review of the evolution of duplicated genes, along with a discussion of neofunctionalization complete with examples:

TRENDS Eco Evo (2003) 18(6):292-298

Game, set and match. (6-0, 6-0, 6-0)

It seems to me that part of the problem is that creationists usually think that thinks like major transitions in evolution require vast amounts of new biochemistry to be invented.

People like Atheistoclast will argue a "fish can't evolve into a reptile" or "monkey into a man" because the sequence space needed to be traversed to find new function, is too large for a "random search". Something like that.

But it seems to me this is exactly where a study like this one comes in : http://pandasthumb.org/archives/2011/04/the-true-story.html
Where it becomes pretty obvious that most of the biochemistry of life has already evolved, and what has been going on ever since is changes in regulatory networks, duplications and shufflings. In other words, to go from "monkey to man" doesn't require the re-inventions of vast stretches of novel protein-coding sequence, all of it is already there. We are simply taling minor changes in expressions and timings.

DS said: Here is another PT favorite: Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict PNAS 2010 107 (50) 21593-21598 Oh example that doesn't count because is happened in a fish.

Sorry about the lack of spellchecking in that one -.-

ATHEISTOCLAST said: Is this an example of "neofunctionalization"? No. Because it represents only an improvement on what was already there. It is, as Ohno would claim, a variation on the preexisting theme. And this is the best that the Darwinists have to offer.

ATHEISTOCLAST said:

DS said: Here is another PT favorite: Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict PNAS 2010 107 (50) 21593-21598 Oh example that doesn't count because is happened in a fish.

Again, you haven't read the paper. That is the problem with you - you read the headline and the spin and buy into it. I suspect you believe everything you read in the newspapers. Had you even bothered to read the abstract the authors actually write that: "In one duplicate, the N-terminal SAS domain was deleted and replaced with a nascent signal peptide, removing pleiotropic structural conflict between SAS and ice-binding functions and allowing rapid optimization of the C-terminal domain to become a secreted protein capable of noncolligative freezingpoint depression." So, they infer that the N-terminus of the duplicate was deleted and part of the UTR, containing a signal peptide sequence, was then exonized (similar to what happened in the Sdic gene). They then claim that a pre-existing ice-binding function at the C-terminus was subsequently optimized. Natural selection can do this sort of thing. It can optimize and it can compensate. If you read the KPNA gene family paper I cited, you will see that the same processes there were observed in Cheng's paper. Is this an example of "neofunctionalization"? No. Because it represents only an improvement on what was already there. It is, as Ohno would claim, a variation on the preexisting theme. And this is the best that the Darwinists have to offer.

Sorry, I meant Steve.

And by the way, the authors obviously think it is an example of neofunctionalization, that's why they included the word in the title. Man, those whacky creationists are always trying to redefine inconvenient words.

But you gotta love the Behe Argument in practice. Just claim something never happens, and dismiss all examples of it actually happening as "not good enough". Heads I win, tails you lose.

Anyway, I am pleased that the NCSE’s polemic against ID has backfired. I had threatened Synthese with legal action. http://www.nytimes.com/2011/05/14/u[…]d=1&_r=1

Atheistoclast makes a testable prediction that can be evaluated and proven right or wrong

The knife now serves as an antifreeze. YOu lose.

DS said: You lose.

And the spoon also serves as an antibacterial agent:

Zhang, J. et al. (1998) Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci.U. S. A. 95, 3708–3713

This is from the paper you claimed I did not read, once again without any evidence. You can try to deny it all you want, but these are NEW functions.

You have asserted that natural selection has no capacity to innovate, without giving any reason why. I have proven that gene duplications followed by random mutations, (frameshifts, deletions and substitutions), followed by natural selection can actually accomplish this. So now you are reduced to arguing that nylonase, antifreeze, and antibacterial functions are not new. Good luck with that.

Clown.

ATHEISTOCLAST said:

DS said: I have already told you twice, you cannot exclude examples because of the types of mutations that caused the neofunctionalization. That is not the issue. The only issue is if a new function evolved. It did. Deal with it.

No. The issue is whether a "new" function evolved. If I sharpen a knife, and thus improve its potency, does the knife now have a "new" function?

ATHEISTOCLAST said: Now let me guess: you think "nylonase" is an enzyme that allows bacteria to "eat" nylon. You are one of those people, aren't you?

Read it for yourself:

For instance, the eosinophil-derived neurotoxin (EDN) and eosinophil cat- ionic protein (ECP) genes of humans were generated in the lineage of hominoids and Old World monkeys via gene duplication [42]. Both genes belong to the RNase A gene superfamily. After duplication, a novel antibacterial activity emerged in ECP. This activity is absent in human EDN and the EDN of New World monkeys, which represents the progenitor gene before duplication. More surprisingly, the antibacterial activity of ECP does not depend on the ribonuclease activity [43].

Arguing that certain types of mutations don't count is like arguing that your straight isn't any good because you threw away a pair to get it.

Arguing that a knife can't take on a new function as a screw driver with only a minor modification isn't going to convince someone who is using the screwdriver.

Look dude, you can disagree with the authors all you want, but they used the term neofunctionalization. If you disagree, write a rebuttal paper. Until you do, there is absolutely no reason for anyone to accept your interpretation of their work. Why do creationists always do that?

harold said:

Anyway, I am pleased that the NCSE’s polemic against ID has backfired. I had threatened Synthese with legal action. http://www.nytimes.com/2011/05/14/u[…]d=1&_r=1

So this is why Synthese put up that humiliating disclaimer, because this random nut who lives in the UK threatened to sue them. That's incredibly embarrassing. We have established that Atheistoclast... 1) Cannot or will not accurately express what evolutionary biologists might think about topics in general. 2) Cannot or will not understand the literature on gene duplication and/or protein function. 3) Denies reality when it is pointed out to him. 4) Keeps insisting that others have advanced illogical straw man positions even when they tell him that no-one has ever advanced such position. It is hard to imagine a more profound failure. The first step for anyone who wants to discuss evolution of new protein function via an initial step of gene duplication is to become very familiar with the existing literature. That's basic. That's what an undergraduate writing a paper would have to do; in fact, that's what I always did as an undergraduate writing papers. Atheistoclast would receive a grade of zero if I were teaching a class. If you can't read, understand, and fairly critique and summarize what has already been established, well, that's that. Game over. Having said that, I rank Atheistoclast well above Axe or any other DI weasels. 1) Atheistoclast makes a testable prediction that can be evaluated and proven right or wrong. Of course, it has been proven wrong and he won't admit it. But at least he made a testable prediction. 2) Atheistoclast comes right out and admits that his designer is a specific sectarian deity.

And yes I would say that the ability to hydrolyze a new type of linkage in a new type of molecule that never existed before in nature is definitely a NEW function. It's not only NEW it's NOVEL. So much for the no innovation routine.

Don't get your jockeys all in a twist, He'll be gone after next Saturday ;-)

ATHEISTOCLAST said:

Stanton said:

ATHEISTOCLAST said: Now let me guess: you think "nylonase" is an enzyme that allows bacteria to "eat" nylon. You are one of those people, aren't you?

So why is nylonase not two examples of the evolution of a novel protein with a novel function? As far as I can tell, it's solely because you say it isn't so.

Ask Negoro et al. They determined that

ATHEISTOCLAST said:

DS said: And yes I would say that the ability to hydrolyze a new type of linkage in a new type of molecule that never existed before in nature is definitely a NEW function. It's not only NEW it's NOVEL. So much for the no innovation routine.

That's because you don't understand biochemistry and the fact that many enzymes are promiscuous. Read Negoro's paper on the subject http://www.isnature.org/events/2008/Summer/Readings/Negoro2005_Nylonase_Molecular_Basis.pdf and learn something for a change.

That’s because you don’t understand biochemistry

and the fact that many enzymes are promiscuous.

One last try.

Are feathers new enough for you? Are they different enough from scales for you? You do know where the genes for feathers came from don't you:

"Phylogenetic analyses demonstrate that evolution of archosaurian epidermal appendages in the lineage leading to birds was accompanied by duplication and divergence of an ancestral β-keratin gene cluster. As morphological diversification of epidermal appendages occurred and the β-keratin multigene family expanded, novel β-keratin genes were selected for novel functions within appendages such as feathers."

BMC Evo Bio (2010) 10:148-158

And crystallin genes come from gene duplication and divergence of heat shock proteins and they have been duplicated and taken on many different metabolic functions as well. I told you there were thousands of examples. You have to disprove all of them. You have't adequately addressed a single one yet.

Look, claiming that anything not designed and manufactured by god directly cannot be defined as new isn't going to work. Incredulity and word games aren't going to work. Saying that enzymes are promiscuous doesn't help. It's a novel function, it evolved, deal with it.

Are feathers new enough for you? Are they different enough from scales for you? You do know where the genes for feathers came from don’t you:

ATHEISTOCLAST said:

harold said: I can assure you that everyone you are talking to, even if some of them are physical or information scientists by formal training, does understand biochemistry, and that you do not. However, the second half of your sentence is correct.

Trouble is that the editors and reviewers of the journals think differently about me or else they wouldn't have published 3 papers of mine - all with references to biochemistry.

Typical of a creationist, you like poorly specific words. However, yes, many enzymes do have a range of varying catalytic functions that they can perform with varying efficiencies.

Typical of a Darwinist. You start out being polite and civil and then resort to name-calling and generalizations.

This instantly proves that Axe is completely full of shit, doesn't it? Now get back to answering DS and Stanton.

How so? Why does multifunctionality "disprove" Axe?

So that would be no. You don't have any answer whatsoever for any of the examples I have presented. You don't have any alternative and you don't have any reason why anyone should accept your interpretation over that of the actual authors.

Thanks for playing.

ATHEISTOCLAST said:

DS said: So that would be no. You don't have any answer whatsoever for any of the examples I have presented. You don't have any alternative and you don't have any reason why anyone should accept your interpretation over that of the actual authors. Thanks for playing.

Stop being so childish and annoying. You keep throwing papers at me without even having read them yourself. I tend to read the smallprint and details rather than the big headlines and abstracts. You have nothing whatsoever to contribute and have no presence in the scientific literature whereas I do.

ATHEISTOCLAST said:

Stanton said: "Promiscuous enzymes"? Why are you so extremely hesitant to summarize what Negoro et al said to disqualify nylonase from being novel proteins with novel functions, even though that's what they are?

Because I expect people to read the paper and not have me spoonfeed them as always happens on this forum. Negoro's experiments found that nylonase evolved from an esterase (and not as a result of the frameshifting event Ohno claimed) which already had Ald-hydrolytic as well as esterolytic capability. In this respect, it was a "promiscuous" enzyme. A couple of amino acid changes in the catalytic cleft of the enzyme greatly enhanced the former which meant it could break down some of the oligomers associated with nylon production - but also very inefficiently (2%). Thus, it was an amplification of a preexisting function.

I find it amusing that Joe Bozo comes over here to Panda's Thumb and pretends to be Mr. Serious Scientist, yet the trail of excreta he has left at Talk Rational shows his true colors as a particularly outrageous troll.

Why should we assume that these 3 published papers make you a god of science with unimpeachable authority?

typical of a Darwinist. You start out being polite and civil and then resort to name-calling and generalizations.

Negoro’s experiments found that nylonase evolved from an esterase (and not as a result of the frameshifting event Ohno claimed) which already had Ald-hydrolytic as well as esterolytic capability. In this respect, it was a “promiscuous” enzyme. A couple of amino acid changes in the catalytic cleft of the enzyme greatly enhanced the former which meant it could break down some of the oligomers associated with nylon production - but also very inefficiently (2%). Thus, it was an amplification of a preexisting function.

ATHEISTOCLAST said: A variation of a variation of a variation of a variation of an integrase will still remain as an integrase. It cannot evolve into a cyclin or a keratin for that matter. No Darwinist would even claim such a thing. And yet there exists no common ancestry for all genes in the genome. It is as if the basic types have all been separately created as must have been the case with the primal organism.

Take transadolase. It has been mutating and evolving for 1.5 billion years within the eukaryotic lineage and yet its functionality is the same in a human as in a yeast cell.

Natural selection is a conserving force in biology. It explains why the genome hasn't completely degenerated due to mutational pressures. It is not some substitute for the creative and intelligent agency that is to be inferred from the complexity and organization of living beings.

Sorry, but this the truth, the whole truth and nothing but the truth.

A variation of a variation of a variation of a variation of an integrase will still remain as an integrase.

ATHEISTOCLAST said:

Stanton said: Furthermore, it's hypocritical of you to express distaste in having to "spoonfeed us," and complain about DS "throwing papers at (you) without reading them," when you, yourself, kept throwing papers at us without explaining why they (allegedly) support your claims until repeatedly asked.

The difference is that DS doesn't understand the papers he glances at. I have fully read and understood them. I don't take my cue from some science magazine like SA or NS.

And the simple fact is that scientists and their interpretations can be wrong. Ohno was wrong about claiming that nyylonase had been created by a frameshift. But this didn't stop the Darwinists for 20 years from claiming it was proof of how novelty can arise from a freak accident.

I am skeptical about the claims made by evolutionary biologists because they receive funding . and lots of it, to find evidence in support of Darwinism.

Folks, "ATHEISTOCLAST" is the author of the unimportant paper that he has repeatedly referenced, having described himself as "a leading researcher in the field." (That unimportant paper is his only publication referenced at PubMed.)

Besides dishonestly referring to himself as "a leading researcher in the field," he advances a false definition of neofunctionalization in order to trivialize what he calls "Darwinism."

All future comments by him on this thread will be moved to the Bathroom Wall, as will all responses to him from this point on.

How many times does it have to be explained to you? That is sufficient. That is how evolution works. Deal with it already.

Or do you think that feathers are just a minor modification of promiscuous scales?

Thanks Steve.

I suppose you believe there are no known natural limits to evolutionary change?

Sorry, Steve, simultaneous posts. No more replies to him here.

Wolfhound said: I find it amusing that Joe Bozo comes over here to Panda's Thumb and pretends to be Mr. Serious Scientist, yet the trail of excreta he has left at Talk Rational shows his true colors as a particularly outrageous troll.

I find the most visible feature of a crank is the belief that everyone else is obligated to take him seriously.

"No, it is your obligation to sell your idea -- and even if your idea is good, acting like a clown isn't a good sales tactic."

Why does Atheistoasshole keep insisting others who reject his work haven't read his paper? Maybe they have and know he is lying? Just because an idea is acceptable to your mind doesn't mean it should be acceptable to EVERYONE'S minds. You may be suffering from delusions. You may be engaging in fraud. From what I've seen of him so far, he no only has made no credible case, he acts like someone who mistook this blog for a comedy club.

As a lurker here, I'd like to respond to the suggestion much earlier in the thread that we lurkers may benefit from what must be tired and circular arguments to many of you.

I'm a scientist in a non-related field (polymer chemistry) who became interested in the manufactured controversy over sound biological science when creatonists in Kansas, then Florida threatened my son's secondary science education. While I understand most of the core arguments here, I don't keep up with biology journals.

I'd just like to say how much we lurkers appreciate answers and rebuttals by actual working scientists. Several of my colleagues now lurk as well, and have come to rely on this site as a resource for our vigilant monitoring of our kids' education. I'm not sure how you have the patience to do what you do when "challenged" by the same baseless arguments again and again, but many of us are grateful that you present evidence that we haven't yet seen. The humor is icing on the cake. (Yeah, I'm talkin' to you, Louis).

Your efforts are heard and appreciated. We thank you.

QED_99 said: As a lurker here, I'd like to respond to the suggestion much earlier in the thread that we lurkers may benefit from what must be tired and circular arguments to many of you. I'm a scientist in a non-related field (polymer chemistry) who became interested in the manufactured controversy over sound biological science when creatonists in Kansas, then Florida threatened my son's secondary science education. While I understand most of the core arguments here, I don't keep up with biology journals. I'd just like to say how much we lurkers appreciate answers and rebuttals by actual working scientists. Several of my colleagues now lurk as well, and have come to rely on this site as a resource for our vigilant monitoring of our kids' education. I'm not sure how you have the patience to do what you do when "challenged" by the same baseless arguments again and again, but many of us are grateful that you present evidence that we haven't yet seen. The humor is icing on the cake. (Yeah, I'm talkin' to you, Louis). Your efforts are heard and appreciated. We thank you.

I, too, want to thank QED_99 for his or her encouragement. It is good to know that, besides the handful of regular commenters, there are actually lurkers who read the material and profit from it. Because, yes, it is frustrating to read (or write) the same old refutations of the same old fallacies posed by people who cannot or will not learn. I always excuse that practice by reasoning that we are writing for people who will learn - are eager to learn - but do not contribute. Often, as a nonbiologist, I am in that "learner" category myself. I hope others will chime in occasionally, whether with questions, comments, or simply encouragement.

ATHEISTOCLAST said: LOL, Steve. I am sure you read all those papers! Give us specific examples of "new" functions arising. "Variant" functions, that are only slightly different, don't count. Anyway, I am pleased that the NCSE's polemic against ID has backfired. I had threatened Synthese with legal action. http://www.nytimes.com/2011/05/14/us/14beliefs.html?pagewanted=1&_r=1 It is a victory for all decent Americans.

DavidK said:

ATHEISTOCLAST said: LOL, Steve. I am sure you read all those papers! Give us specific examples of "new" functions arising. "Variant" functions, that are only slightly different, don't count. Anyway, I am pleased that the NCSE's polemic against ID has backfired. I had threatened Synthese with legal action. http://www.nytimes.com/2011/05/14/us/14beliefs.html?pagewanted=1&_r=1 It is a victory for all decent Americans.

Threatened legal action? Sounds like a Casey Luskin wanna-be with his blathering.

Pages 1 and 5 load instantly, 2 - 5 won't load

QED_99,

It's nice to know that our circular arguments with creationists aren't entirely wasted. Having said that, there is an excellent resource where all these creationist pseudo-arguments and their scientific refutations have been collected in an eminently navigable site called talk.origins. Google it and I doubt you'll be disappointed.

This is OT, but anyone who can get to Cincinnati: Neil Shubin is giving the Insights lecture at the Cincinnati Museum center on Thus May 19 , 7:30 p.m. http://www.cincymuseum.org/information_center/programs_events/InsightsLectureSeries.asp

dpr

QED_99 said: As a lurker here, I'd like to respond to the suggestion much earlier in the thread that we lurkers may benefit from what must be tired and circular arguments to many of you. ... Your efforts are heard and appreciated. We thank you.

I heartily endorse the comments of QED_99. I'm a longtime lurker who is politically active and is very concerned about the fate of science education in this country and around the world. I read this blog every day and though I have no expertise to contribute, I view it as one of the most educational and enjoyable science blogs on the net. I also enjoy seeing the creo's have their hats handed to them. Many thanks to the professionals who give their time to educate those of us who listen.
Many thanks,
Bill

OK, that's sincerely interesting. Now are there any creationist lurkers out there? Is there any more than the usual handful of trolls?

Show of hands? Inquiring minds want to know.

I'm just like Bill above and QED_99 and also read this blog everyday with no significant science expertise to contribute. However, I do on ocassion "steal" many of the great refute's of our creationist's silly science I find here to use elsewhere. Hope no one minds to much. Keep up the good science. Thanks.

mrg said: OK, that's sincerely interesting. Now are there any creationist lurkers out there? Is there any more than the usual handful of trolls? Show of hands? Inquiring minds want to know.

Frank J said: First, it just hit me why I have been scarce here, and less scarce at Talk.Origins lately. Even with an outlet like the BW, too many threads here invariably get hijacked, not just by the trolls, but by those who can't keep the "feeding" to a minimum. At TO I speculated recently that "creationists" (evolution deniers ranging from geocentrist Biblical literalists to "progressive" OECs to "pseudoskeptics" - BTW thanks again for one of my favorite terms) who do not have an urge to post probably prefer the comfort of sites that mostly ban comments from supporters of mainstream science. So my guess is that most lurkers already accept evolution. I hope at least that there are some fence-sitters who see how vacuous and mutually-contradictory the so-called "alternatives" to evolution are, and how evasive their advocates are about their "theories." I'll say it again. Whenever I persist in asking "creationists" questions about their "theories," invariably they troll elsewhere.

On the other hand, the trolls never learn.

— Mike Elzinga

Frank J said: ...So my guess is that most lurkers already accept evolution. I hope at least that there are some fence-sitters who see how vacuous and mutually-contradictory the so-called "alternatives" to evolution are, and how evasive their advocates are about their "theories." I'll say it again. Whenever I persist in asking "creationists" questions about their "theories," invariably they troll elsewhere.

This blog was created largely in response to the promotion of "Intelligent Design" by the Discovery Institute.

A feature of this blog is that it is a forum in which evolution-denying ID/creationists can, indeed, present their ideas to the best of their ability -and have them refuted.

An alternate approach, an approach I vehemently disagree with, is to ignore ID/creationists.

Yet a third approach is to not only ignore ID/creationists, but to also insist that everyone else do the same thing.

I believe that ID/creationists are relentless. Their goals are social and political. They need to be countered constantly. Fortunately, it is relatively easy to counter those who are objectively wrong.

Both Axe and Bozorgmehr are examples of a certain type of ID/creationist. They do a small amount of lab work that is technically adequate enough for publication, albeit not in a real journal in the case of Axe, but in both cases, sufficient to possibly fool the ignorant.

But they are not really doing research. Research seeks answers. They seek to support pre-determined dogma by claiming to have disproven straw man claims. Their ID/creationist presuppositions are in no way supported by their research.

They deserve to be rebutted.

I want to add my thanks to those of QED_99, Bill and Bobsie. Long time lurker here who reads this site everyday when time allows. Coming from a fundamentalist Scottish Presbyterian background I absolutely believed in creationism and went to the web to shore up my beliefs, only to stumble across TalkOrigins! I am not a scientist but did a reasonable science degree at university, now work in the software industry.
PT is very useful in communicating REAL science, but also exposing the liars in the creationist movement (ID=creationism in my view). My daily read includes ScienceBlogs, PT, Richard Dawkins, SciBlogsNZ… My very fundamentalist family are painfully, and wilfully ignorant, preferring magic over nature – it pains me to listen to their ignorance.
I get many a chuckle out of the way you take down the idiots who try to appear friendly then gradually expose themselves when prodded. Your efforts are much appreciated so please keep rebutting the pseudoscience!

Noble_Rotter said: I want to add my thanks to those of QED_99, Bill and Bobsie. Long time lurker here who reads this site everyday when time allows. Coming from a fundamentalist Scottish Presbyterian background I absolutely believed in creationism and went to the web to shore up my beliefs, only to stumble across TalkOrigins! I am not a scientist but did a reasonable science degree at university, now work in the software industry. PT is very useful in communicating REAL science, but also exposing the liars in the creationist movement (ID=creationism in my view). My daily read includes ScienceBlogs, PT, Richard Dawkins, SciBlogsNZ… My very fundamentalist family are painfully, and wilfully ignorant, preferring magic over nature – it pains me to listen to their ignorance. I get many a chuckle out of the way you take down the idiots who try to appear friendly then gradually expose themselves when prodded. Your efforts are much appreciated so please keep rebutting the pseudoscience!

They deserve to be rebutted.

— harold

Pertinent article over on PHYSORG:

http://www.physorg.com/news/2011-05-errors-protein-evolution-biological-complexity.html

No comments there yet. The comment level on PHYSORG is lower than it is here, if not quite as low as that on YouTube. From what I've seen, YouTube is the absolute zero reference for commentary.

mrg said: Pertinent article over on PHYSORG: http://www.physorg.com/news/2011-05-errors-protein-evolution-biological-complexity.html No comments there yet. The comment level on PHYSORG is lower than it is here, if not quite as low as that on YouTube. From what I've seen, YouTube is the absolute zero reference for commentary.

There might be some other fussing about it, one researcher making a comment about the superiority of Nature's "designs" and playing the "neutral evolution versus adaptation" game -- which I personally thing is a "glass half-empty / glass half-full" argument, mostly useful to creationists trying to leverage it to discredit evo science.

Frank J said:

They deserve to be rebutted.

— harold

(3rd try, having trouble posting) People like Axe need to be not only rebutted at every opportunity, but forced at every opportunity to state exactly what they think happens, when instead of “evolution.” Without even checking I would bet that Axe is, like Behe, an old-lifer (not just old-earther) who accepts common descent, but at the same time refuses to criticize YEC or traditional OEC. Sure, they will do anything to weasel out of questions about their “theory,” but that only reinforces to lurkers how they play games, and at best lack confidence in any alternate “theory” that they are trying to peddle. If they truly had confidence in some alternate explanation, they’d be eager to elaborate on it, and defend it on its own merits, not on the same long-refuted “weaknesses” of “Darwinism.” And they’d have the guts to challenge other evolution-deniers. Not just the occasional polite criticism that YECs and OECs have for each other and IDers (who won’t dare return the favor), but something approaching “equal time.” That they refuse to do that shouts “it ain’t about the science” louder than the best rebuttal we can provide. The thread-hijacking trolls here are another story. IMO, FL deserves 1 or 2 polite replies, but those like Byers and Steve P. can be safely ignored without worrying about them misleading any lurkers. Besides, my point is that if you keep asking them questions about their “theories,” they eventually become the ones doing the ignoring.

Thanks John - FWIW people who base their world view on belief systems are not for turning by books or argument. The best way is through a voyage of self discovery that I have been through. Curiosity lead me to do check facts and facts led to the, then horrifying, conclusion that I had been lied to for 20+ years! How do you tell your family that little gem? Anyway many thanks for the pointers to the books I will add them to my reading list.

As regards the argument over design if you believe in any kind of "designer" how can there be anything in the universe that is NOT designed? You are admitting your designer is less than perfect (not biblical) if you admit there is ANYTHING that can be identified as "undesigned" (or is that indesigned?)

No self respecting theist will ever admit any imperfections in their version of god - ergo ID is just word games to avoid using Genesis chap1 and getting laughed at.

I am a non-biologist person with a love of science, a good deal of formal training in theology, and (alas) extensive experience in the care and feeding of Internet communities.

I note that there are good trolls (i.e. the ones who sabotage their own objectives by provoking discussion that provides lurkers with well-founded ammunition against their specious assertions) and bad trolls (i.e. those whose objectives are simply to terminate all discussion by changing the topic of the thread to a discussion of themselves).

Feed the Type I trolls, but discuss the issues rather than the trolls. Starve the Type II trolls by not noting their presence at all.

- ergo ID is just word games to avoid using Genesis chap1 and getting laughed at.

— Noble_Rotter

Noble_Rotter said: Thanks John - FWIW people who base their world view on belief systems are not for turning by books or argument. The best way is through a voyage of self discovery that I have been through. Curiosity lead me to do check facts and facts led to the, then horrifying, conclusion that I had been lied to for 20+ years! How do you tell your family that little gem? Anyway many thanks for the pointers to the books I will add them to my reading list. As regards the argument over design if you believe in any kind of "designer" how can there be anything in the universe that is NOT designed? You are admitting your designer is less than perfect (not biblical) if you admit there is ANYTHING that can be identified as "undesigned" (or is that indesigned?) No self respecting theist will ever admit any imperfections in their version of god - ergo ID is just word games to avoid using Genesis chap1 and getting laughed at.

ESTES EVOLUCIONISTA TEM MUITA FÉ PARA ACREDITAR QUE UMA EXPLOSÃO ORGANIZA AS COISAS, SÃO MUITO BOBINHOS!

DS said:

asics gel said: are made up of distinct domains that bear no relationship with one another. You can’t claim that the T-box and the forkhead box share a common ancestor protein domain. Evolutionary theory has no explanation for the origin of protein domains and functions other than trial and error over deep time. But you ca

Google exon shuffling, then go away. And FYI, not finishing your sentences is rude. You shouldn't just leave

Dale Husband said: Maybe he got raptured?

I find it interesting on this thread how so called scientist "smart guys" name call ("Trolls") I find it to be bad form. For the record. While interviewing the scientists engaged in the controversies under investigation, when asked, "Do you think that science is provisional, that scientists have to be willing to reexamine any view that they hold if necessary?" All the scientists whom are interviewed will respond affirmatively. Later, when asked, "Could evolutionary theory be false?" To this question you will receive three different answers. Most will responded quite promptly that, no, it could not be false (in fact contradicting themselves). A few opponents of the consensus will responded that not only could it be false but also it was false. A very few will respond "Yes, any scientific theory could be false in the abstract, but given the current state of knowledge, the basic axioms of evolutionary theory are likely to continue to stand up to investigation."

Philosophers tend to object to such conceptual plasticity. So do scientists but only when this plasticity works against them. Otherwise, they do not mind it at all. In fact, they get irritated when some pedant points it out.

You ALL (on both side of the argument) look like fools to me. In a waste of time that neither side will listen. Simply because it can never be proven with out any doubt on either side and both beliefs (and they are belief systems) take some faith to believe.

azjones said: I find it interesting on this thread how so called scientist "smart guys" name call ("Trolls") I find it to be bad form.

You ALL (on both side of the argument) look like fools to me.

Simply because it can never be proven with out any doubt on either side and both beliefs (and they are belief systems) take some faith to believe.

azjones said: I find it interesting on this thread how so called scientist "smart guys" name call ("Trolls") I find it to be bad form. For the record. While interviewing the scientists engaged in the controversies under investigation, when asked, "Do you think that science is provisional, that scientists have to be willing to reexamine any view that they hold if necessary?" All the scientists whom are interviewed will respond affirmatively. Later, when asked, "Could evolutionary theory be false?" To this question you will receive three different answers. Most will responded quite promptly that, no, it could not be false (in fact contradicting themselves). A few opponents of the consensus will responded that not only could it be false but also it was false. A very few will respond "Yes, any scientific theory could be false in the abstract, but given the current state of knowledge, the basic axioms of evolutionary theory are likely to continue to stand up to investigation." Philosophers tend to object to such conceptual plasticity. So do scientists but only when this plasticity works against them. Otherwise, they do not mind it at all. In fact, they get irritated when some pedant points it out. You ALL (on both side of the argument) look like fools to me. In a waste of time that neither side will listen. Simply because it can never be proven with out any doubt on either side and both beliefs (and they are belief systems) take some faith to believe.

Ah. You two are perfect examples. And you take the bait so quickly. MGR, you are the only puffed up one who expects others to "kiss your ass". I'm just pointing it out. Like I said "they get irritated when someone points it out".
And to Mr. DS. I never said which belief system I choose to believe if either. Just the lunacy of your unbending debate. A true intellectual will have to admit that we can never go back in time to prove our belief and our conjecture on how life as we now know it came to be from life as it was and even when there was no life at all. Only the prideful will continue to say they know. And in fact usually the ones who feel insecure by not having all the answers. From what I see both camps are full of these.

Oh yes, and to MGR your E-mail "lesson" for all us stupid ones is no better constructed than the poor example of science that you are here to attack. So you really can't have it both ways. yes the guy trying to prove fault in evolution is probably not doing a great job. But bding the same is hardly making your case any stronger

Oh yes, and to MGR your E-mail "lesson" for all us stupid ones is no better constructed than the poor example of science that you are here to attack. So you really can't have it both ways. yes the guy trying to prove fault in evolution is probably not doing a great job. But doing the same is hardly making your case any stronger

Look at me the fool who posts twice. Yes I am no "smart guy" but willing to see the imperfection in myself.

azjones said: MGR, you are the only puffed up one who expects others to "kiss your ass". I'm just pointing it out.

Like I said “they get irritated when someone points it out”.

azjones said: Look at me the fool who posts twice. Yes I am no "smart guy" but willing to see the imperfection in myself.

azjones said: I find it interesting on this thread how so called scientist "smart guys" name call ("Trolls") I find it to be bad form. For the record. While interviewing the scientists engaged in the controversies under investigation, when asked, "Do you think that science is provisional, that scientists have to be willing to reexamine any view that they hold if necessary?" All the scientists whom are interviewed will respond affirmatively. Later, when asked, "Could evolutionary theory be false?" To this question you will receive three different answers.

Most will responded quite promptly that, no, it could not be false (in fact contradicting themselves). A few opponents of the consensus will responded that not only could it be false but also it was false. A very few will respond “Yes, any scientific theory could be false in the abstract, but given the current state of knowledge, the basic axioms of evolutionary theory are likely to continue to stand up to investigation.”

Philosophers tend to object to such conceptual plasticity. So do scientists but only when this plasticity works against them. Otherwise, they do not mind it at all. In fact, they get irritated when some pedant points it out.

There is one consideration, however, which goes well beyond the implications of the above difficulties. Not only is there no evidence that evolution ever has taken place, but there is also firm evidence that evolution never could take place. The law of increasing entropy is an impenetrable barrier which no evolutionary mechanism yet suggested has ever been able to overcome. Evolution and entropy are opposing and mutually exclusive concepts. If the entropy principle is really a universal law, then evolution must be impossible. The very terms themselves express contradictory concepts. The word "evolution" is of course derived from a Latin word meaning "out-rolling". The picture is of an outward-progressing spiral, an unrolling from an infinitesimal beginning through ever broadening circles, until finally all reality is embraced within. "Entropy," on the other hand, means literally "in-turning." It is derived from the two Greek words en (meaning "in") and trope (meaning "turning"). The concept is of something spiraling inward upon itself, exactly the opposite concept to "evolution." Evolution is change outward and upward, entropy is change inward and downward.

Simply because it can never be proven with out any doubt on either side and both beliefs (and they are belief systems) take some faith to believe.

Amazing that in less than an hour two of you respond to little old me. If you were so smart I would think you would have better things to do like something "Applicable" in the science world that has a use. Instead of trying to defend your sacred evolution and atheism that you bow to. Getting along with others requires some tolerance for belief that is not like yours. Both sides want to push out anyone who has a different belief instead of making room for it.

Ah. Mike did his homework. And now uses the claims of a washed up old Henery Morris, to prove I am wrong. But I never claimed the many claims of henry morris were true. I just used his words on the subject of debate, not science. You see you still can't "Prove". And you still can't admit it. I certainly think many of the fools who try to disprove evolution use faulty science. But it does go both ways. I'm just trying to point out the arrogance and prideful positions taken by both sides that really are counter productive to the true seeker.

mrg said:

azjones said: MGR, you are the only puffed up one who expects others to "kiss your ass". I'm just pointing it out.

Well, having pointed it out ... what are we supposed to do now?

Like I said “they get irritated when someone points it out”.

Oh heavens man, I'm only here for the laughs, and all the regulars know it.

azjones said: Amazing that in less than an hour two of you respond to little old me. If you were so smart I would think you would have better things to do like something "Applicable" in the science world that has a use.

azjones said: because that was not funny to me.

Does any of this have anything to do with the Ivory Billed Woodpecker by any chance?

I won't be back. I will now leave you regulars alone to fight it out. Just drop some of the all knowing pride. Neither of you can really say you know for certain. just admit it

azjones said: You see you still can't "Prove". And you still can't admit it.

The tedious tone trolls seem to be reproducing.

Mike Elzinga said: Does any of this have anything to do with the Ivory Billed Woodpecker by any chance?

One last thing to mike. You said. "However, uncritical acceptance of sectarian beliefs is the norm within those sects that object to the findings of science. To uncritically accept sectarian dogma while demanding that science “prove with out any doubt” is hypocritical."

Yes it is hypocritical. But it also is the other way, to expect proof with out doubt of creation. And that side is the one who claims to be in the business of proving theory by peer review. The other side is in the business of believing on faith. Both side appear to be hyporitical in this debate.

azjones said: Yes it is hypocritical. But it also is the other way, to expect proof with out doubt of creation. And that side is the one who claims to be in the business of proving theory by peer review. The other side is in the business of believing on faith. Both side appear to be hyporitical in this debate.

Mike Elzinga said:

azjones said: Yes it is hypocritical. But it also is the other way, to expect proof with out doubt of creation. And that side is the one who claims to be in the business of proving theory by peer review. The other side is in the business of believing on faith. Both side appear to be hyporitical in this debate.

This continues to misrepresent. I have been a part of the scientific community for over 50 years. I know scientists from all over the world, from different ethnic, religious, and political backgrounds. Most simply don’t care about what thousands of sects believe or don’t believe. It never enters into their work or thinking. It has been primarily the antievolution sectarians who have generated all the problems. They are the ones using a wide range of socio/political tactics to inject ID/creationism into the schools. There has never been a corresponding socio/political movement to inject science into churches.

ME, just ignore him, he'll leave.

azjones said: You just fail to see that what you teach in schools is a belief and a theologhy and it does not allow for others.

mrg said: ME, just ignore him, he'll leave.

Mike Elzinga said: Yup. It looks like Kris or maybe Steve P.

azjones said: I won't be back. I will now leave you regulars alone to fight it out. Just drop some of the all knowing pride. Neither of you can really say you know for certain. just admit it

azjones said:

Mike Elzinga said:

azjones said: Yes it is hypocritical. But it also is the other way, to expect proof with out doubt of creation. And that side is the one who claims to be in the business of proving theory by peer review. The other side is in the business of believing on faith. Both side appear to be hyporitical in this debate.

This continues to misrepresent. I have been a part of the scientific community for over 50 years. I know scientists from all over the world, from different ethnic, religious, and political backgrounds. Most simply don’t care about what thousands of sects believe or don’t believe. It never enters into their work or thinking. It has been primarily the antievolution sectarians who have generated all the problems. They are the ones using a wide range of socio/political tactics to inject ID/creationism into the schools. There has never been a corresponding socio/political movement to inject science into churches.

Gee Mike I could not tell you have been in the Science community for 50 years. Hear the sarcasim? You just fail to see that what you teach in schools is a belief and a theologhy and it does not allow for others. But being in your group of smart guys for so long you can't see it. In fact it is that side that has pushed the other out of the schools in every way and only allows it only in the Churches. And how is pushing science in a church a private entity relateable to pushing belief in a public arena such as a school? And really I did not misrepresent anything in fact, I am seeing it right now in you. Thanks for proving my point so well. You want to only allow your belief in the public schools, to the point that a teached can't even pray without fear of litigation. The intolerance comes both ways and you are part of it instead of the solution.