The Final Adventures of the Blind Locksmith

By Carl Zimmer | April 10, 2006 1:10 am

lockandkey200.jpgOn Thursday I wrote about a new paper reporting the reconstruction of a 450-million year old hormone receptor, and experiments indicating how it evolved into two receptors found in living vertebrates such as ourselves.

On Friday I took a look at the initial response to the paper from intelligent design advocates at the Discovery Insitute. They claim that there exist biological systems that show “irreducible complexity,” which could not possibly have evolved. In response to the new research, intelligent design advocates claimed that hormones and their receptors do not actually make the cut as irreducibly complex systems. But to do so, they had to ignore their own published definition of irreducible complexity.

As I mentioned on Friday, the Discovery Institute promised more, and more they have delivered. Not scientific papers published in peer reviewed scientific journals, of course, but a lot of press releases and such. There’s a lot to wade through as of Sunday evening, and no doubt even more to come. But none of it amounts to much. They spend a lot of time rehashing their claim that irreducible complexity is not touched by this research. And they also use another standard strategy: raising doubts about whether a particular evolutionary scenario could take place, or whether biologists have done enough work to make their case.

It’s odd in a way, that they should go to these lengths. For one thing, they repeatedly claim that the whole experiment has nothing to do with irreducible complexity. For another, they dismiss this evolutionary change as minor stuff that they have no trouble with.

“There is nothing in the paper that an ID proponent would think was beyond random mutation and natural selection,” Michael Behe writes “…Intelligent design proponents happily agree that such tiny changes can be accomplished by random mutation and natural selection.”

Not happily enough, it seems.

Before I get into the objections, let me recap what the scientists found. They compared two kinds of hormone receptors, MR and GR for short. MR binds tightly to a hormone called aldosterone, and plays a role in keeping electrolytes in balance. GR binds to a hormone called cortisol and plays a role in stress, immunity, and other responses. The scientists found that MR and GR evolved from a common ancestral receptor, which was accidentally duplicated in the common ancestor of all fishes and land vertebrates.

When they reconstructed the ancestral receptor, they found that it bound to aldosterone, cortisol, and a third hormone called DOC.

This was surprising, since aldosterone evolved long after this receptor did. The result indicates that the tight link between MR and aldosterone was not there when MR first evolved. Instead, it must have bound DOC, which has a similar structure to aldosterone. Only tens of millions of years later did aldosterone evolve and become associated with MR in land vertebrates.

The reconstructed ancestral receptor revealed an equally suprising story for GR. The main feature of its evolution must have been that it lost its aldosterone sensitivity and retained its sensitivity to cortisol. The scientists found that it changed by two amino acids. They tested out mutant proteins carrying each one of these changed amino acids (known as S106P and L111Q). L111Q on its own reduced the sensitivity of the receptor to all three hormones. S106P did not have the same effect as L111Q. It reduced sensitivity to aldosterone and cortisol, but left DOC response strong. Once the GR receptor had the S106P mutation, the L111Q mutation reduced the aldosterone response even more but then raised cortisol to the sort of sensitivity found in our own cells today. So the scientists suggested that this was the most likely path by which the ancestral receptor could have evolved into the GR receptor.

Behe describes these mutations this way:

“In the ‘most promising’ intermediate protein (the one that has just the S106P alteration) the protein has lost about 99% of its ability to bind DOC and cortisol, and lost about 99.9% of its ability to bind aldosterone.”

You get the notion that the receptor has been crippled in some devastating way. Indeed, Behe suggests, “One would think that the hundred-fold decrease in the ability to bind a steroid would at least initially be a very detrimental change that would be weeded out by natural selection.”

There’s really no reason to think that. The response of receptors to hormones is not some simple one-to-one relationship that you can summarize with a single number. Here’s the graph. Aldosterone is green, DOC is blue, and cortisol is red.

thornton%20graph%20300.jpg

You can see how L111Q just pushes the response curve flat. Flood it with all the aldosterone, cortisol, or DOC you want, and you won’t get any significant response. But S106P receptors still respond to the hormones. They just need a higher concentration. In fact, DOC responds much more strongly in S106P than in the ancestral form at high concentrations. But these concentrations are not abnormally high. Indeed, they’re typically of many receptors in living animals.

This graph offers no indication then that natural selection must have weeded out S106P mutants. Even if the shift in the DOC response did affect ancient fish, we can’t forget that these fish also had the other kinds of receptors, MR, which are very responsive to DOC.

In fact, the S106P might have even been able to survive even if it had been moderately harmful. Moderately harmful mutations can withstand natural selection if they are linked to beneficial genes, for example, if they exist in a small population where natural selection is weak. So nothing in what scientists know about how natural selection works says that the S106P pathway is prohibited by natural selection.

But that’s still not enough for intelligent design folks, of course. Behe writes,

“The authors do not test for that [that S106P would be weeded out by natural selection]; they simply assume it wouldn’t be a problem, or that the problem could somehow be easily overcome. Nor do they test their speculation that DOC could somehow act as an intermediate ligand. In other words, in typical Darwinian fashion the authors pass over with their imaginations what in reality would very likely be serious biological difficulties.”

Is it me, or is it strange that intelligent design advocates are telling biologists that they aren’t working hard enough, that they are not getting enough results from their lab work? Remember, this is the same Michael Behe whose sole peer-reviewed paper in the past eight years was a computer model (and a pretty poor one, it turned out). Compare that to the work of Joe Thornton, the principal investigator on the new paper. In the past eight years he’s published twenty papers on hormones and their evolution: he’s been sequencing hormone receptor genes, working out how they respond to different hormones, determining how they’re related to one another, and even resurrecting them after 450 million years of oblivion. All Behe is doing is complaining that Thornton hasn’t done enough, without even bothering to explain how a scientist could even set up the sort of test he demands. The fact of evolution, which Discovery Institute folks like to ignore, is that natural selection is tough to measure precisely even in living populations. The challenge gets far greater after millions of years have passed. Scientists can detect the fingerprint of natural selection on various genes, but they may never be able to recover the precise chain of events that drove the evolution of a new kind of gene.

Yet that doesn’t mean that scientists can know nothing about evolutionary history. Here we have tightly integrated systems (MR, GR, and their hormones) which appear to have evolved stepwise from a common ancestor. Even though the receptors and their hormones are tightly integrated today, that doesn’t mean that they couldn’t have functioned without their partners. MR evolved long before its aldosterone partner did, and it just happened to have a structure that would allow it to latch on. As for GR, Thornton and co. have even showed which parts of the ancestral gene mutated, and offered a sequence of events by which those mutations may have taken place.

And guess what? Thornton is now back in his lab right now, working with his colleagues to test their own hypothesis. The folks at the Discovery Institute folks might want to take a break from their empty complaints and give it a try.

Update 4/10 3 pm: Ian Musgrave at Panda’s Thumb explores yet another way in which Behe contradicts himself (even under oath!).

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Comments (36)

  1. Intelligent Design, as defined by Michael Behe is nothing more than a convenient “straw man” for you and other neo-darwinian evolutionists.
    You seem to think that if you defeat Behe’s premises and the thinking of the Discovery Institute that all of your problems will go away.
    I do not represent the Discovery Institute, I am not a religious creationist and I do not defend Michael Behe, Bill Dembski or the “Intelligent Design Movement”
    And you have been unable to address my criticisms, choosing instead to ignore them.
    But they will not go away. Neither the Thornton paper or the Tiktaalik fossil provides any support for the view that a neo-darwinian mechanism of random mutation and natural selection is the mechanism that was responsible for the emergence of the highly organized structures, processes and systems that are found in living organisms.
    At best, they demonstrate that changes have occurred over time, that living organisms are related to each other and they suggest the possibility of a common origin.
    But there is not one shred of empirical evidence that a neo-darwinian mechanism was responsible or that this evolution was not simply the unfolding of an algorithm, a set of instructions, that were programmed into the genome when it first arrived on earth.
    Since development of the adult organism from its first few cells into a functional entity with countless structures, processes and systems is known to be controlled by a set of instructions embedded in the DNA of the genome, why is it so difficult to envision that the evolution of life on earth is not similarly controlled by a pre-existing set of instructions?
    I may pass on to my reward before this issue is resolved, but resolved it will be, unfortunately, not in your favor. My suggestion to you is to think ahead of the curve. Denounce neo-darwinism and learn to live with the fact that at the present time, we just do not know the answer.

  2. Monte Davis

    Still going strong after fifty years:

    “There is no ‘God of the gaps’ to take over at those strategic places where science fails; and the reason is that gaps of this sort have the unpreventable habit of shrinking.”

    C.A. Coulson, Science And Christian Belief (1955)

  3. The other thing that Behe doesn’t consider is that many ligand/receptor systems have two receptors: high and low affinity. This makes it easier to fine tune responses to differences between the levels of ligand around; you can get a set of responses when there’s a little ligand, and a superset of that when there’s lots. As a result, there could have been a selective pressure to keep the lower affinity receptor around for long enough for the second ligand to develop.

  4. It’s hard for the people at the Discovery Institute to do lab work because it is hard to fit labs into a post office box. Seriously, whether they have a building or not, they are an advocacy group for creationism pretending to be a scientific “institute.”

  5. Jason Malloy

    But there is not one shred of empirical evidence that a neo-darwinian mechanism was responsible or that this evolution was not simply the unfolding of an algorithm, a set of instructions, that were programmed into the genome when it first arrived on earth.

    You think that if you can remember your childhood that your dogmas about being an adult who has lived on this earth for decades will be “proved” and that all your problems will just magically go away. But there is not one *shred* of evidence that the universe wasn’t created 3 seconds ago, along with all your memories and the physical illusions of age.

    Why is everyone just ignoring my substantive and totally noncrazy comment box rantings?? Clearly you’re all afraid.

  6. Why is everyone just ignoring my substantive and totally noncrazy comment box rantings??

    It’s also worth noting those of us who have been around for a while somewhat realise that he never has anything based on ‘facts’ to offer. Hence, we just ignore him.

    Carl, I particularly liked your analysis and in particular I liked how you’ve pointed out the ‘research’ output of Behe against these researchers. There is a distinct irony in Behe attacking the ‘work’ of other scientists when he has published a single paper in eight years. The irony will be lost on ID supporters however, but then again, the meaning of most research being conducted will also.

  7. UndergradChemist

    The different levels of concentrations needed could be easily dealt with via a feedback loop, making the system quite stable towards perturbations caused by minor mutations. Does such a loop exist, I wonder?

  8. Jim A.

    Charlie Wagner wrote:

    But there is not one shred of empirical evidence that a neo-darwinian mechanism was responsible or that this evolution was not simply the unfolding of an algorithm, a set of instructions, that were programmed into the genome when it first arrived on earth.

    1. Do you have any physical evidence for such an “algorithm”?

    2. To create such a program at the beginning of life, it seems you would need to know the entire history of the earth beforehand, i.e. all future chemical changes in the atmosphere and oceans (on an hour-by-hour basis) and all future configurations of the continents and climate changes. If the Designer is that skilled, why couldn’t he/she/it just manufacture a planet compatible with the planned end-product of evolution? Why waste time with those thousands of intermediate beings?

    3. The fossil record appears to be inconsistent such a perfect planner. We see many life experiments that didn’t lead to anything, and even some successful species that got caught in disasters and went extinct.

    4. If you don’t know the complete history of the earth, then an up-front plan is worthless. You need a trial-and-error method, where life tests different options as it goes along, based on the unpredictable, constantly changing circumstances. This seems consistent with what we know about life history.

  9. Owlmirror

    (Charlie Wagner’s rant)

    I’ve seen these comments before, and I don’t quite understand them. I am not a scientist, but I think I have a reasonably close simple approximation of understanding to be able to grasp how science works in general, and what I understand strongly suggests a huge problem with this reasoning.

    The biggest problem is one of theoretical simplicity, or parsimony.

    As I understand the process, scientific theorizing strongly prefers the simplest explanation. This isn’t just because simplicity is good for its own sake, but because the simplest theory is the one which can be most simply tested. If there’s a more complicated aspect of that theory which cannot be tested – and the more complicated aspects of what is being observed can be explained by a simpler theory that can be tested – then that more complicated aspect isn’t necessary as part of the theory, and can be discarded.

    Hm. That paragraph was pretty complicated. Maybe an example would help.

    Here’s a simple one – it’s an old joke:

    A naive person is asked what the greatest invention of the modern era is. The person responds, not with “airplanes” or “television”, but with “the thermos”.

    The thermos?

    “The thermos. It keeps hot stuff hot, and cold stuff cold. How does it know?”

    That’s a good example of creating a more complicated theory than is necessary. That is, the naive person is theorizing that the thermos has some particular mechanism that can determine the temperature of what is inside of it, and furthermore, has devices to maintain that temperature, all in a simple, smooth, cylindrical container that needs no electricity. Presumably the person thinks that there is some sort of thermostat, heating element, and cooling element, all inside the thermos.

    The simpler explanation (that the thermos is a double-walled container, with a vacuum between the two walls, and that one of the known physical properties of a vacuum is to minimize thermodynamic change, and therefore minimize temperature change) may seem more complicated at first, but it’s something that can be tested and demonstrated. The naive person’s theory of temperature detection mechanisms and maintainers can be shown to be unnecessary and unsupported by the data, and can therefore be rejected.

    Intelligent Design, like the naive thermos theory, is something that looks “simpler” at first, but is actually far more complicated than evolutionary theory – and that complexity isn’t supported by the data, and it isn’t internally consistent.

    All Intelligent Design theories require the existence of a designer who is intelligent. The problem with this is that our best understanding of our intelligence is that it is an emergent process of our brains, and our brains have in turn evolved along with the rest of our bodies over the course of billions of years.

    But if evolution is not a sufficient theory to explain how intelligence can arise, then by what mechanism did the intelligent designer arise? Who designed the intelligence of the designer? Doesn’t it follow that an intelligence that great had to have been designed by an intelligence that was even greater? Surely an intelligence like that couldn’t have just… evolved, right?

    Charlie’s idea of “the unfolding of an algorithm, a set of instructions, that were programmed into the genome when it first arrived on earth” is actually even more complicated than the DI’s idea of a designer who occasionally intervenes to create “irreducibly complex” biological structures and systems. It posits a designer who is so incredibly intelligent that they would not just intervene when necessary, but actually programmed exactly what changes would occur with a genetic program that would run for billions of years, spawning billions of different kinds of organisms.

    What’s the mechanism by which this program is implemented? It should be easy to find, since it is within every single organism on Earth. And how exactly would the effects of this program differ from natural variation and selection?

  10. owlmeter wrote:

    “As I understand the process, scientific theorizing strongly prefers the simplest explanation.”

    Not true.

    When multiple competing theories have equal predictive powers, the principle recommends selecting those that introduce the fewest assumptions and postulate the fewest hypothetical entities or scenarios.

    The only reason for having theories and hypotheses is to guide experiment. They have no value on their own as truth.
    The very idea of “selecting” between competing theories is ridiculous. It brings us no closer to the truth. The way to decide among competing theories is to test them, not decide which is probably true based on some theoretical calculations or by using some trick, like Occam’s Razor.
    After you collect all of the data, then you can draw conclusions as to what is or is not likely. And one theory will usually emerge as superior. Truth does not flow from the human imagination, it flows from experiment and observation. That’s the only thing that has value. Speculation is interesting and keeps the mind amused and helps us to design experiment, but it serves no purpose in it’s own right.
    In that regard, neo-darwinism is heavily laden with unproven assumptions and hypothetical scenarios, more than I’m willing to abide.
    But in the really crucial test of the theory’s validity, the empirical data that supports it, neo-darwinism comes up severely wanting. There simply is no evidence at all that establishes a link, a nexus, a bridge between the trivial effects of mutation and natural selection and the emergence of highly organized structures, processes and systems, such as those found in living organisms.
    That variation can accumulate to the point where new structures, processes and systems can be generated is nothing more than a colossal leap of faith, unbefitting our regard for the scientific method.
    My goal is not so much to promote intelligent input as it is to debunk neo-darwinism. I offer intelligent input as an alternative hypothesis, to be tested and evaluated like any other hypothesis. I will be the first to admit that while the belief that intelligence was involved is compelling, empirical data to support that hypothesis is lacking at present.

  11. Owlmirror,
    Sorry about getting your name wrong. I just woke up and I’m a little bleary :-)

  12. Evolution of IC: Evolution of Hormone-Receptor Complexity

    Michael Behe is known as the author of the concept of Irreducible Complexity (IC, but see [note 1]). However, he has given several different, not entirely consistent, definitions of IC. Everyone is familiar with the “multiple parts” defini…

  13. Thanks for the trackback Carl, I should have checked The Loom first of course, but I claim distraction by small children. I’ve added a trackback now though.

    Now to pull this discussion on track from Charlies’ opining.
    Carl wrote (in response to Behe suggesting that the S106P mutation was deleterious):

    But S106P receptors still respond to the hormones. They just need a higher concentration. In fact, DOC responds much more strongly in S106P than in the ancestral form at high concentrations. But these concentrations are not abnormally high. Indeed, they’re typically of many receptors in living animals.

    Indeed, for DOC typical plasma concentrations range from 5 nM to 10 nM (and of course these are higher, sometimes much higher under stimulation), which would be more than adequate to stimulate the S106P receptors to the levels seen in the ancestral receptor. Typical plasma cortisol levels (around 165 nM) would provide only half the stimulation in the ancestral receptors, but stress-induced levels would activate the S106P receptor to the same extent as in the wild type receptors. Indeed, the Telost GR has effectively the same cortisol sensitivity as the S106P receptor (actually, its a bit less sensitive, and a fair bit less effective, than the S106P receptor), and fish seem to be doing just fine. So for all intents and purposes, the S106P mutation is neutral.

    Now, Thornton at least, being a steroid receptor specialist (and most of his receptor soecialist readers) would be aware of plasma steroid hormone levels and hence know he was talking about effectively neutral mutations. Behe is very unlikley to know what these levels are (and failed to look closely at figure 2B, showing the very low Telost sensitivity to cortisol), and assumed BCT pulled neutrality out of a hat.

  14. To create such a program at the beginning of life, it seems you would need to know the entire history of the earth beforehand, i.e. all future chemical changes in the atmosphere and oceans (on an hour-by-hour basis) and all future configurations of the continents and climate changes.

    Jim A, I think that a sufficiently advanced coder could prepare his life forms to look for optimal local solutions to these sorts of problems over generations, even without the knowledge you insist he/she/it would need.

    I would probably try to use some sort of genetic algorithm, myself.

    I’m sorry, I just couldn’t resist.

  15. Triskele

    Mr O’Donnell would do well to remember that sometimes an unproven idea leads to a theory, which can lead to an experiment, the outcome of which sometimes leads to proof which can substantiate an idea as a fact.

    Some such ideas have even changed how we see the world and our perception of reality.

    Have a double serving of humour, with a little imagination on the side…

  16. B. Spitzer

    from Charlie Wagner:
    Neither the Thornton paper or the Tiktaalik fossil provides any support for the view that a neo-darwinian mechanism of random mutation and natural selection is the mechanism that was responsible for the emergence of the highly organized structures, processes and systems that are found in living organisms.

    My hunch is that most of the folks reading these comments are already familiar with this constant insistence that the glass is half empty. So this is for the lurkers:

    Mr. Wagner, you’re right about one important thing– neither the Thornton paper nor the Tiktaalik fossil prove that evolution took place by random mutation and natural selection. At the same time, however, you are very wrong to expect either one of them to prove everything about the theory of evolution. I’m afraid it’s you who is building straw men.

    The Thornton paper does not claim to prove the entire ToE. What it does claim is that it is possible for systems with interdependent parts to evolve without any intelligent input, including front-loading. What the discovery of the Tiktaalik fossil demonstrates is yet another transitional form, at a particularly interesting moment in evolutionary history. The claims are quite modest.

    Because it is such an enormous theory, different lines of evidence must be used to evaluate different aspects of the ToE. If you’re trying to determine whether random mutation and selection are sufficient for the job, here are a couple of more relevant lines of evidence:

    1) Only one kind of function can be favored by natural selection. Natural selection only favors genes that are good at generating more copies of themselves. If all of the complex systems and structures in biology evolved by RM and NS, then they must function to generate more copies of themselves. No matter where we look in nature, that is the “function” that all complex biological entities have– they help their bearer survive and reproduce.

    Are you saying that a front-loading intelligence just happened to build into his designs the exact same function that is favored by NS? That is not a parsimonious answer.

    2) Population genetics makes some very powerful predictions about what amount of diversity we should see in nature if all of these structures evolved due to RM and NS. If you’re not up on your population genetics, you should try looking into it– there’s some fascinating stuff on that subject.

    3) Perhaps you didn’t realize this, but the Thornton paper, unless I’m mistaken, reconstructed the ancestral enzyme based on our understanding of how mutation and selection should operate. In other words, their (accurate!) prediction relied on evolutionary theory about RM and NS. If we’re totally wrong about RM and NS, how is it that scientists can use these ideas to make predictions that turn out to be correct?

    There are a number of other lines of evidence which strongly support the idea that RM and NS are two of the most important forces which shaped today’s organisms– the use of the ratio of synonymous: nonsynonymous mutations to find important functional sites on a protein is an excellent example.

    Charlie Wagner:
    And you have been unable to address my criticisms, choosing instead to ignore them.

    No, Charlie, you are mistaken. Your questions have been asked over and over again, and I’ve seen them answered over and over again. I suspect that you just don’t like the answers. And that is not our fault.

  17. B Spitzer wrote:

    “Mr. Wagner, you’re right about one important thing– neither the Thornton paper nor the Tiktaalik fossil prove that evolution took place by random mutation and natural selection.”

    Thank you. I rest my case.

    “What it does claim is that it is possible for systems with interdependent parts to evolve without any intelligent input, including front-loading.”

    It shows that evolution has occurred, but it does not rule out intelligent input or front-loading.

    “What the discovery of the Tiktaalik fossil demonstrates is yet another transitional form, at a particularly interesting moment in evolutionary history.”

    Transitional fossils are a red herring. The only problem with transitional foossils that I have is that there are not enough of them to account for the large number of transitional forms required by neo-darwinism. But transitional forms, in and of themselves are perfectly compatible with intelligent design. They don’t help us to determine the mechanism of evolution.

    “If we’re totally wrong about RM and NS, how is it that scientists can use these ideas to make predictions that turn out to be correct?”

    The value of prediction is overrated. A theory may make perfectly correct predictions and still be completely wrong. There are numerous examples in the history of science. Phlogiston theory and Ptolemy’s geocentric theory come to mind. There are numerous other examples of theories that made correct predictions but were totally wrong.

  18. Middle Professor

    1. An “evolutionary” algorithm programmed into the DNA need not know all future states of the earth as long as the algorithm incorporated if..then statements to direct the mutations in the correct direction. This would be analagous to phenotypic plasticity during ontogeny. But this sort of directed mutation mechanism would require a Lamarckian mechanism and would certainly be difficult in those of us whose germ and somatic cells are separated early in development. Regardless, as OwlMirror noted, this is certainly not a very parsimonious explanation.

    2. A more fundamental flaw in the argument (as picked up in a more humerous way by Jason Malloy), and one that is frustratingly common among all these folks loosely linked by their aversion to modern evolutionary theory, is that we have no shred of evidence that a neo-darwinian mechanism was responsible [for any historical event like the duplication and subsequent evolution of the steroid receptor]. Good historical science is not about proving the explanation of an historical event – this cannot be done. Its about discovering general principles that allow the development of a model that can explain, in theory, a historical event. Different aspects of the model make predictions which can be tested, but a proof that this is the way it worked is neither given nor sought.

    Of course, your unfolding model of evolution is not immune to this pseudocriticism either.

    3. So its not that I don’t believe that there could not be an algorithm encoded in the DNA that could account for the entire history of evolutionary changes, its that I’ve yet to see any explicit model of this, with predictions and experiments testing the predictions and how the the experiments might support this unfolding model and reject aspects of neo-Darwinian theory. Of course I’m not looking for this either, so if you have examples of experimental work testing predictions of the unfolding model, I’m all eyes.

  19. Charlie should really stop repeating the same things over and over again in one forum, and then leave in disgust for another forum when no one accepts his position. My first step when encountering a troll is to google some of their sentences to see where they have either: 1) wrote it before, or 2) plagiarized someone else. Linky.
    http://scienceblogs.com/pharyngula/2006/01/elsberry_on_dkos.php#comment-5218
    If you’ll take a look, Charlie’s first paragraphs are identical in both cases. My advice to everyone is to take into account the fact that Charlie simultaneously says that experiments can’t really prove anything, but that somehow a couple recent studies not proving everything single-handedly is supposed to be a weakness of thojse studies. If he would make a choice between embracing science and being anti-science, then we could at least address his arguments in one form or another. But seeing as how he can’t decide whether empirical evidence could in principle change his mind on anything or that the current state of evidence just isn’t enough (and could tell us what would be) then he will continue to change his arguments to suit either approach.
    And my advice to Charlie is to attract some visitors to your site with some good content. Your first entry on hoaxes/myths is already partly false – sugar DOES cause cavities, because it feeds bacteria that produce acid, causing tooth decay.

    Carl – nice job with all three locksmith posts, I’m preparing an article on Behe for the following Tangled Bank (April 26) and I’ll hook up some links to your stuff.

  20. Owlmirror

    The value of prediction is overrated. A theory may make perfectly correct predictions and still be completely wrong.

    Oy.

    No, Charlie. This is a basic misstatement of science. A theory is proven to be wrong by showing that a specific prediction that it makes fails.

    For example, Phlogiston theory made certain predictions about how combustion works. These predictions worked in some cases, and failed in others.

    Geocentrism makes certain predictions about the motion of the planets, at least one of which failed when tested by Galilei using his telescope.

    Incidentally, even before Galilei, the difference between Copernican heliocentrism and geocentrism was that geocentrism was far more complicated as a theory, what with epicycles and subepicycles and equants and so on. Heliocentrism was far simpler – and did not have to deal with answering what the mechanism of the epicycles was (crystal spheres and subspheres, forsooth). That’s an example of science demonstrating that Occam’s Razor is indeed the preferable method of choosing between two theories.

  21. Owlmirror

    Truth does not flow from the human imagination, it flows from experiment and observation. That’s the only thing that has value. Speculation is interesting and keeps the mind amused and helps us to design experiment, but it serves no purpose in it’s own right.

    Well, sure. And that’s why Intelligent Design is not accepted. It’s certainly something that has been imagined by humans, but there have been no experiments to prove it.

    But I’m not sure that I made myself clear, when I was talking about parsimony. Let me try again.

    Current evolutionary theory states that variation and selection over thousands of generations (and billions of years of time, allowing many thousands of thousands of generations) are both necessary and sufficient to explain the variation of life as we know it. There are certain other factors involved, of course, such as interaction with other organisms, and the effects of various climatological changes, and astrophysical and geological disasters.

    Evolutionary theory is inherently self-contained. There may be additional interactions that I left out or haven’t been found yet, but the point is that everything that affects life on this planet is a result of natural interactions that occur on this planet. Evolution only assumes existing natural laws.

    Intelligent design, as a theory, lacks that self-containedness. It tries to explain life by way of a pre-existing intelligence – but it gives no explanation of where that intelligence came from or how it arose.

    So rather than solving the problem of how life develops (by assuming that some intelligent entity did it), ID raises important new problems to be solved: Who is this intelligent entity? Where did this intelligent entity come from?

    Perhaps this intelligent entity arose naturally? This demonstrates that intelligence can arise on its own, which in turn demonstrates that evolution is sufficient to create intelligence, which raises the question of why you need to posit in the first place that an intelligent entity modified life here on Earth – especially when there’s no evidence of such interference.

    Perhaps the intelligent entity was itself created by a previous intelligent entity? Well, then what created that entity?

    That’s what I meant by parsimony: The simple, self-contained idea that life exists because of physical rules interacting in complex ways over a long period of time.

    Intelligent Design, taken to its logical conclusion, requires an infinite regress of intelligent designers, since no designer could have evolved intelligence on its own.

    “I offer intelligent input as an alternative hypothesis, to be tested and evaluated like any other hypothesis.”

    How can a hypothesis which requires an infinite regress as one of its base assumptions be tested?

  22. Unsympathetic reader

    Spitzer writes: “What it does claim is that it is possible for systems with interdependent parts to evolve without any intelligent input, including front-loading.”

    Mr. Wagner responds: “It shows that evolution has occurred, but it does not rule out intelligent input or front-loading.

    It doesn’t rule out the possibility that the universe was created last Tuesday, either, or that open-faced peanut butter sandwiches most often fall face down. It also doesn’t rule out the possibility that the Red Sox will win the World Series in 2012, or that sun will rise tomorrow, or that the biological systems were created deep in the past by Invisible Pink Unicorns (my pet hypothesis).

    I’d say that there are a staggering number of terribly interesting possibilities that the data doesn’t rule out.

    Thanks for the useful insight!

  23. Middle Professor wrote:

    “An “evolutionary” algorithm programmed into the DNA need not know all future states of the earth as long as…”

    Just as the “developmental” algorithm programmed into the DNA at fertilization does not need to know all of the future states that the organism will encounter. Most biologists have accepted the fact that both “nature” and “nurture” contribute to development, probably in a ratio of 2/3 nature to 1/3 nurture.
    I suspect that the “evolutionary” algorithm would function in a similar way with the evolutionary potential encoded in the genome accounting for most of the evolution but able to be modified by environmental constraints.
    There is good reason to suspect that the genome may be environmentally adaptive and responsive to different conditions. I view the genome as a dynamic rather than static entity.
    There are many different ways that new information can become encoded in the genome as well as new algorithms. New DNA can be inserted by viruses, by horizontal gene transfer and new epigenetic routines can be established to modify the activation and expression of already existing genes.
    Besides, we study the genome as it looks today, after most evolution has already taken place. What did it look like 600 million years ago when evolution was just beginning?

    “Its about discovering general principles that allow the development of a model that can explain, in theory, a historical event. Different aspects of the model make predictions which can be tested, but a proof that this is the way it worked is neither given nor sought.”

    But the model can be falsified. The model may make predictions that can be tested but a thousand correct predictions are of little value if ONE prediction doesn’t hold up. As Feynman said: “”If it disagrees with experiment, it’s WRONG!”
    Unfortunately this advice is not heeded by those who are so heavily invested in a theory that they forget that they are scientists. They attempt to “patch up” the theory and save it from the dustbin of history. Neo-darwinism has so many patches that one wonders how it can still be believed.
    For example, punctuated Equilibrium which was an attempt to explain away the fact that the fossil record does not support neo-darwinian gradualism and the ludicrous attempts to explain the hierarchal structure of living organisms, a structure that does not support neo-darwinian gradualism, as being supportive.

  24. Inoculated Mind wrote:

    “If you’ll take a look, Charlie’s first paragraphs are identical in both cases.”

    I freely admit that I recycle a lot of my own material. How many different ways are there to say the same thing? Having been a teacher for 33 years, I learned early on that you can’t just say something once and expect people to get it. By repeating the same ideas over and over, there is a better chance that some of it will sink in. Unfortunately in my teaching, as well as in my posting over the past 10+ years, my experience has been that many people are just plain unreceptive.

    “Charlie simultaneously says that experiments can’t really prove anything, but that somehow a couple recent studies not proving everything single-handedly is supposed to be a weakness of thojse studies. ”

    In science nothing is ever “proven”. Science attempts to inform us what is “most likely”. So experiments can determine what is most likely.
    It is also incumbent that empirical evidence be presented to support any scientific claims. This evidence can take the form of observation or experiment. Absent empirical support, as in the case of neo-darwinism, the claims are “just-so” stories.

    “If he would make a choice between embracing science and being anti-science, then we could at least address his arguments in one form or another.”

    I am firmly pro-science. But I am not averse to criticizing science when it is sullied and cheapened by ideologues who try to promote bogus theories in the name of science. Neo-darwinism claims to be “scientific” but it is not. It is as far away from the science I believe in as religious creationism.

  25. Owlmirror wrote:

    “Current evolutionary theory states that variation and selection over thousands of generations (and billions of years of time, allowing many thousands of thousands of generations) are both necessary and sufficient to explain the variation of life as we know it.”

    And where is the empirical evidence to support this claim? Where is the evidence that establishes a nexus between variation and selection and the emergence of highly organized structures, processes and systems? It simply does not exist.
    This is not a competition between two theories, although it seems that the debate has been so framed. It is a search for the most likely explanation as to how life arose on earth. There may be other explanations that have not been considered or tested. To restrict yourself to neo-darwinism or intelligent design is not being scientific. Science demands empirical evidence. There is little or no empirical evidence for either of these two scenarios. That leaves us with only one choice: look for other alternatives. The creationists are locked into “god did it” and the evolutionists are locked into neo-darwinism. It’s time to think outside the box and examine other alternatives.

    “Intelligent Design, taken to its logical conclusion, requires an infinite regress of intelligent designers, since no designer could have evolved intelligence on its own.”

    Neo-darwinism also requires an infinite regress of pre-existing forms on which variation can act. It no more answers the question of where it all began than intelligent design or cosmic ancestry does.

    “Life comes from space because life comes from life”

  26. Owlmirror

    Neo-darwinism also requires an infinite regress of pre-existing forms on which variation can act.

    Not in the least.

    Evolutionary theory does not require “an infinite regress of preexisting forms”; it only requires the laws of physical organic chemistry. It is completely compatible with abiogenesis.

    While abiogenesis is still a hypothesis, it has some experimental evidence in its favor, and in addition, it has the benefit of parsimony, since it too only requires the laws of physical organic chemistry.

    It no more answers the question of where it all began than intelligent design or cosmic ancestry does.

    Intelligent design, as I pointed out, requires an infinite regress. Cosmic ancestry just pushes out abiogenesis (and evolution, perhaps) to space, which is hardly a huge problem.

    “Life comes from space because life comes from life”

    I don’t understand that statement.

  27. David B. Benson

    Charlie Wagner might care to look at actual Genetic Algorithm results. Probably the most impressive is the little X-band antenna evolved for NASA (JPL) as the communication device on certain satellites or deep-space probes. The thing looks wierd, sort of like a spider drawn by Dr. Seuss. Antenna designers state they never would have come up with it.

    Another use of Genetic Algorithm evolution is electronic circuits: Several of these novel designs are patentable. See J.R. Koza et al., Evolving Inventions, “Scientific American”, v. 288 #2 (2003 Feb), pp 52–59.

    While not biological genetic evolution, the Genetic Algorithm is written to duplicate the major features of neo-Darwinian evolution. Thus these examples, and many more, provide a controlled, replicable setting for understanding certain aspects of biology.

  28. Owlmirror

    Where is the evidence that establishes a nexus between variation and selection and the emergence of highly organized structures, processes and systems?

    What sort of evidence do you think would be sufficient?

    What alternatives are there to “highly organized structures, processes and systems are emergent properties of cumulative variations in the reproduction of living beings and the effects of natural selection”?

    Are these alternatives internally consistent and complete (that is, without the infinite regress required by intelligent design theory)?

    Is there any evidence – any at all – that these alternatives are absolutely necessary to resolve the problems you have with evolution?

  29. Jason Malloy

    By repeating the same ideas over and over, there is a better chance that some of it will sink in.

    Agreed, by copy-and-pasting the same four comments over and over in the comments sections of every other entry on well-trafficked, high-profile blogs, you can piggy-back on the hard-won, well-deserved audiences of others’ to draw attention to yourself that otherwise could not be earned by the rightful merits of your thinking.

    You, sir, are a troll and a pathetic crank of the highest order. Your exploitation of Carl’s real estate to divert his readers to your own embarrassing idee fixe is nothing less than spamming.

    Sadly, your distasteful comment spamming also works to dissuade more serious discussions that might otherwise blossom in response to Mr. Zimmer’s outstanding science writing. The question is, why is it even tolerated?

  30. el nico

    David B. Benson, do you have a link to this xband antenna? the device sounds cool and i haven’t been able to find a picture on the net.

  31. David B. Benson

    Re #29: el nico, I am afraid I don’t have a link. I saw the picture in a book about evolutionary computing. Maybe a better analogy is the form of coral which grows sort of like a tree. Anyway, it would make a great prop for a ‘space aliens’ sf movie…

  32. Owlmirror

    Re: 29 (el nico), & 30 (David B. Benson)

    The “Evolutionary Antenna Design” press release, photographs, and videos are here:

    http://www.nasa.gov/centers/ames/news/releases/2004/04_55AR.html

    “The AI software examined millions of potential antenna designs before settling on a final one,” said project lead Jason Lohn, a scientist at NASA’s Ames Research Center, located in California’s Silicon Valley. “Through a process patterned after Darwin’s ‘survival of the fittest,’ the strongest designs survive and the less capable do not.”

    The software started with random antenna designs and through the evolutionary process, refined them. The computer system took about 10 hours to complete the initial antenna design process. “We told the computer program what performance the antenna should have, and the computer simulated evolution, keeping the best antenna designs that approached what we asked for. Eventually, it zeroed in on something that met the desired specifications for the mission,” Lohn said.

  33. Owlmirror

    A few more words responding to Charlie Wagner’s assertions. Hopefully, this will be the last.

    Returning to phlogiston, I just wanted to point out the predictions where it “worked” were actually illusionary. Phlogiston was based on a naive observation: most common things that burn become lighter; some things seem to vanish entirely. The theory went that their phlogiston was being used up by burning.

    The Wikipedia article points out that when metals burn, they become heavier. If all things that burn contain phlogiston that becomes used up, how could that be?

    However, the experiments that falsified phlogiston completely were the extremely thorough ones which invovled weighing the material, and the air that it was burning in, and comparing it afterwards to all of the resulting gasses and ash of the burned materials – and finding that the masses were actually the same. This led to the correct chemical explanation that burning is a reaction which involves the combination of oxygen with something in a material, and that some compounds with oxygen were gases (thus explaining the apparant “disappearance” of the burned material), and some were solids (the metal oxides that were actually heavier than the original metal before it was burned).

    In addition, it also led to the parsimonious theory of conservation of matter (and later, conservation of energy as well); an extremely important scientific development.

    The model may make predictions that can be tested but a thousand correct predictions are of little value if ONE prediction doesn’t hold up. As Feynman said: “If it disagrees with experiment, it’s WRONG!”

    Well, yes and no. Sometimes the problem is that the theory is failing to predict, rather than having a prediction fail.

    For example, once chemistry was better understood, there was still a problem that did not make sense: The question of how the sun managed to keep on burning. This involved using the then-current best possible measurements of the sun’s mass and material, and making the calculations using that information of how long such a chemical reaction could be sustained – and coming up far short of anything that made sense given other observations which demonstrated the age of the earth. Yet other predictions made by chemistry theory did still work. Rather than throwing out chemistry, scientists figured that some other reaction was going on; that some additional information was necessary.

    They also tried to show that perhaps the sun’s energy was derived from then-current Newtonian mechanical effects; the result of some sort of gravitational effect. Yet that too didn’t seem to be able to last long enough to yield a result that was consistent with other data.

    It wasn’t until the twentieth century that enough additional information was known about the subatomic physical structure of matter, and the reactions that could take place between subatomic particles, that an explanation of the sun’s energy that was consistent with all known data was able to be made.

    They attempt to “patch up” the theory and save it from the dustbin of history. Neo-darwinism has so many patches that one wonders how it can still be believed.

    As I tried to show above, science is all about patching existing theories.

    While some theories have indeed been relegated to the dustbin (such as phlogiston), that was because they were always wrong when examined closely. But many other theories only needed to be modified, not rejected entirely. Chemistry still exists, despite the existence of fusion; indeed, with an understanding of subatomic theory, chemistry was enhanced to include the existence of isotopes. Newton’s mechanics are “wrong”, since Einstein’s relativity is a better description of reality, but since in most instances that humans work with, they are good, close approximations, Newton’s “Laws” are still taught to young schoolchildren, and are enhanced with Einsteinian relativity for more advanced students.

    Ultimately, if you truly want to “debunk” neo-darwinism, just as chemists and physicists quantified the problem with chemical and mechanical explanations for solar energy, you’re going to have to quantify your objections in such a way that it is irrefutably clear that it is physically impossible for variation and selection to account for “highly organized structures, processes and systems”, as you put it.

    Your statements that the analysis of the hormone receptor and the Tiktaalik fossil don’t support evolution are meaningless without that quantified argument.

  34. Owlmirror wrote:

    “A few more words responding to Charlie Wagner’s assertions. Hopefully, this will be the last.”

    Ok, I’ll let you have the last word. Thanks for the replies. Perhaps you might be interested in my blog:
    enigma dot charliewagner dot com
    or my website:
    www dot charliewagner dot com

  35. David B. Benson

    Owlmirror, thanks for the link!

  36. Danniel Soares

    charlie wagner wrote:

    “But there is not one shred of empirical evidence that a neo-darwinian mechanism was responsible or that this evolution was not simply the unfolding of an algorithm, a set of instructions, that were programmed into the genome when it first arrived on earth.”

    The thing work the other way. People are not supposed to prove that something someone vaguely imagines and gives no clue about, is not the case.

    Those who propose a hypothesis of orthogenic evolution that are supposed to give evidence for that, and preferably, describing a hypothesis that could be refutable.

    I think, however, that the possibility of natural selection and the many contingencies that turned upside down the history of evolution, to say the least, are already enough to dismiss the idea of orthogenic evolution. Unless, of course, the breeds created by humans were programed in this first organism, and just coincidentally, someone “discovered” it, rather than creating through breeding.

    Also, all the contingencies that are usually supposed to had effected drastically the evolution (such as massive extinctions and other big environmental changes), which, I think, were not expected to affect a pre-programed evolution, had again, coincidentally, occurred in a way that seems that they caused changes on the course of on evolution.

    With all that in mind, ateleological evolution seems to be much more likely. And also do not requires a totally unkwnown processo fo creationg a “orthogenetic code” in the first cell that arose. That would require something highly speculative such as directed panspermia or a sort of mix between Gaia hypothesis and panspermia, it requires way too much than the present evidence.

    And by the way, I think that no one is a “neo-darwinist” since Weissman´s times

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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.

About Carl Zimmer

Carl Zimmer writes about science regularly for The New York Times and magazines such as DISCOVER, which also hosts his blog, The LoomHe is the author of 12 books, the most recent of which is Science Ink: Tattoos of the Science Obsessed.

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