Exploring the protein universe: a response to Doug Axe

| 184 Comments

One of the goals of the intelligent design (ID) movement is to show that evolution cannot be random and/or unguided, and one way to demonstrate this is to show that an evolutionary transition is impossibly unlikely without guidance or intervention. Michael Behe has attempted to do this, without success. And Doug Axe, the director of Biologic Institute, is working on a similar problem. Axe’s work (most recently with a colleague, Ann Gauger) aims (in part, at least) to show that evolutionary transitions at the level of protein structure and function are so fantastically improbable that they could not have occurred "randomly."

Recently, Axe has been writing on this issue. First, he and Gauger just published some experimental results in the ID journal BIO-Complexity. Second, Axe wrote a blog post at the Biologic site in which he defends his approach against critics like Art Hunt and me. Here are some comments on both.

Read the rest at Quintessence of Dust.

184 Comments

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.

In other words, driven by uncontrollable biases, they set up a straw man and demolished it.

Given this, in what sense does Mattheson mean that their work is “good”?

Technically good work is not good by definition. Adequate technical performance is necessary, but by no means sufficient, for “good” work.

Work which attributes straw man hypotheses to others, and then “refutes” that which no-one has ever suggested, is at best worthless, and at worst outright deceptive.

How can such work be “good”?

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?

While I can’t speak for Steve, that too was my impression. In this case Axe is light years ahead of his fellow Dishonesty Institute “savants” like Behe, Dembski, Meyer and Wells who seem incapable of designing credible hypotheses and tests of them. But, unfortunately, just like his “peers” he looks at individual trees without considering the entire “forest”.

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?

Yes, that’s what I mean, although I don’t get why you think “theistic evolutionist” ideas should be lumped with ID. I’m a theistic evolutionist, as commonly understood.

The comparison in the BIO-Complexity paper is a strawman, and a blatant one. It’s disappointing and it’s unnecessary. But the experiments are rigorously done and they do point to approaches that could be used to address some questions that are relevant. And I insist on hoping that the scientists at Biologic can connect with the real scientific community and make some meaningful contributions. If nothing else, I thought a couple of hard-working scientists generating real data were worthy of some respect.

Thanks for the comment.

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?

Okay, got it.

Try my blog for answers to the TE thing.

I am an absolute outsider wrt this subject but I feel like quoting R. B. Laughlin again:

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?

I don’t get it. I just don’t get it.

How can someone who sets up straw man “hypotheses” that are so absurd that they don’t need to be tested in the first place, and that no-one has ever proposed anyway, and then demolishes them, be considered “good at formulating a testable hypothesis and also good at performing experiments that test the hypothesis”?

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”.

Suppose I’m a crank who denies that hothouses can be useful in tomato agriculture. I could do something like grow some tomatoes (of a variety used by hothouse advocates) in a legitimate hothouse, and grow genetically identical tomatoes, in conditions that are controlled as well as possible for everything else, in the same place, with the same soil, fertilizer, and light exposure, but without a hothouse, and then test whether or not the actual claims of hothouse advocates, fairly understood and described, are supported. That would be a “good” way to test the hypothesis that a hothouse can have some defined impact on growing tomatoes.

Alternately, I could lie and attribute some straw man claim to hothouse advocates, perhaps implying that they claim that hothouse-grown tomatoes will grow legs and invade Tokyo, for example. I could then set up a biased “experiment” which anyone would agree in advance would rule out my straw man. I could then make the non sequitur claim that it is theoretically impossible for hothouses to have any effect in tomato agriculture.

Now, in either case, I might be a good technician. But in the latter case, how anyone could conceivably suggest that I was “good at formulating a testable hypothesis and also good at performing experiments that test the hypothesis” is beyond me.

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?

Actually Chris, Axe is a Dishonesty Institute mendacious intellectual pornographer. His Biologic Institute has been established as the “scientific laboratory” associated with the Dishonesty Institute.

With apologies to Steve, I wrote my earlier reply to yours without noting your snarky comment on “theistic evolutionism”. Judging from what I have read from Steve, I think he does as fine a job in separating his theological and scientific interests as does his fellow Evangelical Protestant Christian, invertebrate paleontologist Keith Miller (no relation to Ken Miller) and, I might, add Ken Miller too (Though I am skeptical of Ken’s embrace of a weak form of the anthropic principle. However, Ken, has said too that those who embrace faiths hostile to science should discard them. Finally, as an aside, in light his decades-long work on behalf of promoting the teaching of biological evolution and being such an eloquent defender of it before school boards and in court, he is this year’s recipient of the Society for the Study of Evolution’s Stephen Jay Gould Prize, which has been awarded previously to Genie Scott (2009) and Sean B. Carroll (2010).).

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”.

I can’t believe Axe doesn’t know that his so-called experiment doesn’t test any aspect of the current theory of evolution. In fact, I can’t think of any theory of evolution, even going back to Lamarck and Erasmus Darwin, that Axe could be testing. This is just one more dishonest publicity stunt to give a gloss of “scientism” to the Christian Reconstructionists at the Disco Institute.

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.

You be sure to let us know when your “directed evolution” evolves a dog into a cat. OK?

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.

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

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.

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

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.

All future contributions to this particular conversation will be moved to the Bathroom Wall.

Atheistoclast: you are welcome to provide arguments in favor of your claims, but further comments like that one will be moved to the Bathroom Wall, which is still more attention than is merited.

mrg said:

ME, just ignore him, he’ll leave.

Yup. It looks like Kris or maybe Steve P.

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

Maybe Kris, but he’s into kicking-his-heels tantrums and this hasn’t gone that far.

Steve P is smarmy.

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

Already did asshat. Testing a theory for over one hundred and fifty years and never once falsifying it is good enough for a start. On the other hand, you have revealed yourself as someone who apparently doesn’t trust science but nevertheless uses it for his own convenience. Now that is the definition of a hypocrite.

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.

Typical Liar for Jesus says he’s going away but then doesn’t. I am SO surprised.

About this Entry

This page contains a single entry by Steve Matheson published on May 13, 2011 12:42 PM.

Still think you have free will? was the previous entry in this blog.

Raindrop impressions Trace fossil – raindrops is the next entry in this blog.

Find recent content on the main index or look in the archives to find all content.

Categories

Archives

Author Archives

Powered by Movable Type 4.381

Site Meter