Archive for October 2008

Logan Gage (DI) analogizes DNA with our evolved, undesigned, natural languages

October 31, 2008

On the DI’s weblog, Logan Gage quotes a Dr. Story (from Christianity Today), then proceeds to rapidly get matters quite wrong:

Rana, like Behe before him, may be commended for providing a layman’s description of a number of astonishingly intricate cellular processes. But his portraits of cellular workings will fail to convince most mainstream scientists for the same reason that Behe’s book has been roundly dismissed: The analogy between manmade machines and cells is a poor one at best. Cellular components, although machine-like in some respects, do not behave like manmade machines. They self-assemble and self-manufacture, and they are able to transform available energy sources such as light to fuel metabolic activity.

Now what’s wrong with this reply? Didn’t we all learn from Hume that arguments from analogy are inherently weak? 

….  How anyone who has seen a bacterial flagellum could think there is not a strong resemblance to an outboard motor in both appearance and function is, I admit, beyond me. Behe’s Critics Fail to Understand Analogies and Design Detection

Actually, while Dr. Story is right enough in what he does mention, there are much better reasons not to accept Behe’s “arguments,” such as the fact that Behe manages to explain nothing about the lack of “common authorship,” after lines have diverged, of the various vertebrate wings, and of the two adaptive immune systems.  But the poor analogy of life’s machinery with designed machinery is certainly not a negligible argument, particularly because of the self-assembly that does not exist in human-made productions (one could argue that we now have harnessed self-assembly somewhat.  That it is nothing like life’s self-assembly is certain, however).

Moving to Gage’s response, I have never once understood the claim that there is a strong resemblance of the bacterial flagellum to an outboard motor.  The latter is made of metal, and is a heat engine (except for electrics, which also fail to work like a flagellum does).  The former’s materials are constrained by evolution, as is its chemical fuel.  And the parts do not look much the same at all, except in the rather misleading very mechanistic-looking illustrations that IDists are fond of using (there is nothing misleading about the figure to which he linked in normal science instruction, but it is misleading where one is claiming a strong resemblance between outboard motors and flagella).  Aside from rotary motion, I know of nothing closely or moderately analogous between an outboard motor and a flagellum, and that rotary motion is produced in a very different manner, while also propelling a very different sort of rotor.

Here, at figure 2, is an actual photomicrograph of a bacterial flagellum. It is somewhat machine-looking, all right (it is considered to be a machine, by today’s definition), but it looks far less like one of our mechanisms than the illustration to which Gage linked.

Gage moves on to the fact that self-assembly is disanalogous, but claims analogy all the same, because reproduction of bacteria means that their machinery is “MORE complex” than our own. Which suggests that he is playing fast and loose with words and definitions.  See for yourself:

According to Story, “Cellular components, although machine-like in some respects, do not behave like manmade machines. They self-assemble and self-manufacture, and they are able to transform available energy sources such as light to fuel metabolic activity. The cell can also replicate itself and copies of its parts, given energy and simple raw materials.”

But what does this show? Only that while cellular components are similar in many ways, they are also different in that…cells are actually much MORE complex than human-made machines! And therefore, it is likely that the process by which the cells originated is at least as complex as the process by which human-made machines appear (which we know involves intelligent design). What, after all, would we conclude if we stumbled upon a factory where machines not only worked with amazing efficiency but, before wearing out, actually reproduced themselves with astounding accuracy and converted energy from their environment into usable fuel so that they never needed electricity or gas?

In sum, if Rana is indeed making an argument from analogy, I think he escapes Story’s criticism unscathed.  Behe’s Critics Fail to Understand Analogies and Design Detection

Gage is apparently confused by Behe’s “complexity argument,” thereby being unable to notice that reproduction is hardly analogous with our non-reproductive machines, and indeed, reproducing robots and factories of our design are expected to have to reproduce very differently from how bacteria do.

Paley also made this argument, that reproduction of his example, the watch, would imply even greater intelligence behind it.  Which might be reasonable for Paley, because he did not recognize the reproduction is exactly what evolution needs, and, one might argue, even “predicts.”  Moreover, the reproductive methods of both eukaryotes (often with eukaryotic flagella getting the sperm to the egg) and of prokaryotes only make sense in evolutionary context, for IDists have never come up with a “design explanation” for the existence of sex and of bacterial conjugation.  The fact is that clades distribute according to clonal (with conjugation) patterns, and to sexual patterns, quite as one would expect from evolutionary predictions, and do not exhibit intervention by any “designer.”

Gage failed to support the analogy, and to show that reproduction is anything but a source of evidence that evolution occurred without any reason to suppose that any intelligence intervened.

Gage again:

What is worse for Dr. Story is that Behe does NOT make an argument from analogy, anyway. The arguments proffered by both Behe and other design theorists like Dembski and Meyer focus on the properties humanly designed objects and biological objects actually share, not properties that have some analogous resemblance.  Ibid.

Actually, Behe rests almost all of his “arguments” on faulty analogies, although he does base his “irreducibly complex argument” on faulty assumptions–these assumptions being both the “purpose” for which he never provides evidence, and the silly notion that complexity sans the design characteristic of rationality is evidence of intelligent intervention.

I wrote the post linked here before the present one, so that I could refer back to it.  Behe’s acceptance of the molecular clock as a viable possibility, and the evidence of common descent–which likewise depends upon non-intervention by a designer–demonstrate that Behe is not resting his “argument” upon similarities with human designs, he is trying to claim that non-teleological evolutionary expectations are the result of a designer.  It was Paley who argued that life really was made like an architect or artificer would produce, while Behe refuses all tests of design, mainly because he has no evidence for design.

Those who worry about “interference” should relax.  The purposeful design of life to any degree is easily compatible with the idea that, after its initiation, the universe unfolded exclusively by the intended playing out of laws.  Michael Behe  The Edge of Evolution, 232

This is Behe with his get-out-of-jail-free card.  In the end, his ID predicts absolutely nothing (though in other places he claims otherwise), including intervention (which contrasts with his interventionist view of the “Cambrian Explosion” in DBB).  This is completely contrary to what Gage said above, although it is also completely contrary to most of what Behe wrote in his books as well.  Yet in this place, he is (if he understands the implications of this statement) pointedly denying the “shared properties” of human and biological entities, for clearly, shared properties would require intervention by a designer that made objects akin to our own.

This was Gage’s supporting “argument” for the idea that Behe is discussing “shared properties” of human-made and biological entities:

For instance, these theorists often point to what is at the heart of all biological life, namely DNA. They then point out that this biological information has the SAME semantic properties that human written or spoken language has. They are not making an analogy at all.  Behe’s Critics Fail to Understand Analogies and Design Detection

I do not recall Behe making such an argument, although I would not be surprised if he has done so.  But there are two large problems for such an argument:  The first is that human languages also were not “designed,” with semantic structure apparently evolving at least part of the way prior to language, and evolving since humans began to truly speak.  It is begging the question to assume that human language was somehow “designed” apart from evolution, when all of the evidence indicates that, like nucleic codes, human language evolved.  The second problem pales by comparison, but of course the semantic structure of DNA is not that of a “natural language” at all.

I suppose that Gage is trying to claim that because human language (which he assumes, against the evidence, was “designed” or some such thing) has semantics, and the genetic code can be understood to have semantics, that the two have the same properties.  Since the DNA code, and what is encoded by it, is not like a “natural language” used by humanity, it is the same old argument by “analogy” that is presented by Gage–at least as weak as all of the other “analogies.” 

And, as I stated above, if we actually follow the analogy we’ll end by recognizing that human language semantics evolved without guidance (save our own evolving guidance), and so did DNA with its “semantics”.  So they can have that analogy, if they want to have it, and we will understand that DNA must have evolved, instead of being intelligently designed.

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How could the molecular clock work with design happening?

October 30, 2008

The molecular clock has been vigorously debated since it was proposed, and many issues surrounding it are still contended.  Overall, however, it remains a viable possibility.  Michael Behe, DBB, 174

He is right both about questions remaining, and that it is a viable possibility.

But how could it be, if ID were correct?  From Aristotle, down to Paley and the creationists, τεχνη or design has always been marked off from “nature” (nature in the exclusive sense) or “physis”.  Indeed, Behe and most of the other prominent IDists like to suggest that the “Cambrian Explosion” is an obvious time when “design” was effected (DBB 27-28).  And yet the molecular clocks (mostly DNA, now) tick through the “Cambrian Explosion” without marking any break from the usual processes, even though it is possible that more refined methods could yet capture an uptick in change (not the break that most would expect from a designer intervening, however).

For so long the various sorts of creationists have tried to argue that intervention by God would be obvious.  Since it never has been, however, Behe increasingly writes as though no intervention can ever be observed, from any sort of mark of design, to any break in the molecular clocks.

This criticism has nothing to do with the accuracy of molecular clocks, which may in fact not be as reliable as some have claimed.  It is that Behe never expects any of the effects of intervention to be visible in life (if these were found, you can be sure that most IDists, probably including Behe, would quickly adopt them, though).  This, perhaps, is the most important change that ID has produced, since the older IDist Paley, and traditional creationists, always expected design to be observable–and generally not by christening complexity as “evidence for design,” like Behe illegitimately does.

As it happens, we could easily apply Paley’s criticisms of the evolutionary concepts of his day (before Darwin came up with a scientific theory) to Behe’s evidence-free designer/evolution-tweaking God, because a major argument of Paley’s book was precisely that design has positive evidence in its favor (arguable then, but not now), while evolutionary ideas were lacking in evidence (not entirely true, since common ancestry did comport well with evolution).  Really, anyone who wanted to show conclusively how ID avoids all legitimate tests (falsification being the best rule-of-thumb) would do so by comparing Paley’s attempts to show that design is falsifiable, with Behe’s never-ending attempts to avoid all reasonable tests of ID.

This is part of a series of posts that I am combining into one long post, which may be found at Darwin’s Black Box.

What is ID’s efficient cause?

October 29, 2008

IDists are keen to return Aristotle’s “final cause” to the sciences, or at least to biology (see Dembski, for example).  Which is rather sad, because they can give us no evidence for the purpose of organisms, instead they wish to insist that life “had to be designed” and thus has purpose.  One has to wonder what good that would be to know, since we would still need to be able to discover purpose for it to impact us, and ID has never been able to demonstrate any purpose (to be sure, nearly all IDists have sacred writings in mind to provide specific purpose, but will not admit it in their supposed science).

So OK, they want final causes (aside from those of animals such as humans), and perhaps formal and material causes as well, but where is their “efficient cause”?  That is the closest that Aristotle’s “causes” (aitia, which probably would translate better as “reasons” than “causes”) come to fitting with scientific causation in the classical realm, they do not deny the importance of efficient causes, and yet they have none whatsoever.

It should be noted that Aristotle was not one who simply called “intelligence” or “design” the cause or the reason (not of a manufactured item, that is), the aition, because intelligence is just a faculty, and design is merely a category of actions or “causes”.  Thought using intelligence might be a cause, and design may be part of a specific process, but simply invoking intelligence, thought, or design would explain nothing by themselves.  There is an apparent exception to Aristotle’s “efficient cause” as a specific cause or set of causes, which is God the unmoved mover–a very indefinite “cause”–but even IDists don’t appeal to such ancient fictions, partly because it would too readily reveal the religious motivation behind ID.

Aristotle has these things to say of the “efficient cause”:

Again (3) the primary source of the change or coming to rest; e.g. the man who gave advice is a cause, the father is cause of the child, and generally what makes of what is made and what causes change of what is changed.

e.g. both the art of the sculptor and the bronze are causes of the statue. These are causes of the statue qua statue, not in virtue of anything else that it may be-only not in the same way, the one being the material cause, the other the cause whence the motion comes.

All causes, both proper and incidental, may be spoken of either as potential or as actual; e.g. the cause of a house being built is either ‘house-builder’ or ‘house-builder building’.

In investigating the cause of each thing it is always necessary to seek what is most precise (as also in other things): thus man builds because he is a builder, and a builder builds in virtue of his art of building. This last cause then is prior: and so generally.

Further, generic effects should be assigned to generic causes, particular effects to particular causes, e.g. statue to sculptor, this statue to this sculptor; and powers are relative to possible effects, actually operating causes to things which are actually being effected.  Aristotle’s Physics

In a scientific sense, this is all rather imprecise.  But even Aristotle’s generic causes, such as “the art of building,” is far more precise and meaningful than anything we have gotten out of ID as an efficient cause.  Dembski even makes “efficient cause” more precise than Aristotle does:

The efficient cause is the immediate activity that produced the statue–Michelangelo’s actual chipping away at a marble slab with hammer and chisel.  Dembski

Dembski’s example of an efficient cause moves us closer to scientific causation, and is a typical example used by those who are explaining Aristotle’s “four causes”.  Despite the fact that he waffles on mechanism in that article–and attacks the strawman of design being “barred from the content of science” (has any archaeologist tried to explain pottery without intelligent agents involved somehow?)–he is still hardly consistent when he makes statements such as this one:

You’re asking me to play a game: “Provide as much detail in terms of possible causal mechanisms for your ID position as I do for my Darwinian position.” ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories. Notorious Dembski comment

Ah yes, Dembski has neither evidence for a final cause, nor for an efficient cause.  Likewise with Behe, who pretends to take a more scientific approach than Dembski, he will not even commit to the specificity that an ancient thinker like Aristotle would:

Another problem with the argument from imperfection is that it critically depends on a psychoanalysis of the unidentified designer.  Yet the reasons that a designer would or would not do anything are virtually impossible to know unless the designer tells you specifically what those reasons are.  One only has to go into a modern art gallery to come across designed objects for which the purposes are completely obscure (to me at least).  Features that strike us as odd in a design might have been placed there by the designer for a reason–for artistic reasons, for variety, to show off, for some as-yet-undetected practical purpose, or for some unguessable reason–or they might not.  DBB, 223

What, people refuse to call something like that science?  Notice how desperate he is to claim no distinguishing marks of design (since he knows that these are lacking from life that we have not engineered) that he goes to deliberately obscure art as his “example.” 

Yet in the first and second Dembski links (to the same source), it is argued, against a strawman, that design is readily detectable.  To be sure, he misunderstands his own sci-fi analogy as the search for “complex specified information,” when in fact it was rationality behind the signal that indicated intelligence.  Dembski explaining what was detected in the movie Contact:

In this sequence of 1126 bits, 1’s correspond to beats and 0’s to pauses. This sequence represents the prime numbers from 2 to 101, where a given prime number is represented by the corresponding number of beats (i.e., 1’s), and the individual prime numbers are separated by pauses i.e., 0’s).  Dembski

Yes, that’s right, it isn’t complexity that is discovered (Dembski calls unlikely simplicity by the name “complexity,” a distortion even of the meaning of the term), it is rationality.  Even Behe gets it slightly, and ludicrously brings up rational agents:

Rational agents can coordinate pieces into a larger system (like the ship) to accomplish a purpose.  Edge of Evolution, 168

Yes, and the context from which that comes has any number of rationally-devised artifacts being discovered.  Nevertheless, note how carefully he words it, to avoid the implication that life ought to appear rationally designed if it was intelligently designed.  He’s still relying on evident “purpose,” which he deliberately tried to avoid as a test of “design” in the previous quote.  There, too, he wrote of “reasons” for design, as he denied their visibility, suggesting that he knew very well that he was denying that purpose is evident in life, while in this later quote he is trying to suggest that rationality is found exactly through evident purpose (as he had also done in DBB, prior to denying it in order to avoid predicting evident purpose in life–in response to those who noted exactly the lack of purpose in so many aspects of life).

The fact of the matter is that both Dembski and Behe do not wish “design” to be tested by evidence of purpose, for they know that, for instance, malaria pathogens do not seem to fit any kind of evident purpose.  They bring up purpose in order to ignore efficient causation and the rationality typically evident behind such causation (even if some art is hard to figure out, the rationality of the frames betrays intelligence via rational efficient causation).  Likewise, they totally avoid efficient causation, for as I previously argued, they have no causes at all, only unconstrained accident (or whim).

Evolution is also fraught with accident (see link above), but these are “lawful accidents,” of the kind that are permitted and even (probabilistically) predicted.  We have “efficient causation,” or more exactly, scientific causation.  And what is interesting to note is that while Dembski and Behe contradict themselves and each other with their “arguments,” primarily because they can show no “intelligent design” causation whatsoever, earlier ID really did mean to find the marks of intelligence and rationality in life:

…We allege, that the same principle of intelligence, design, and mechanical contrivance, was exerted in the formation of natural bodies, as we employ in making of the various instruments by which our purposes are served […]. William Paley

Paley was looking for efficient cause (see also pp. 8 & 233 of the above link for his criticisms of explanations lacking in efficient causes), and for observable purpose.  Behe and Dembski contradict themselves on these matters, while generally trying to smuggle “purpose” in via “complexity.” 

Paley’s ID was tolerably close to a scientific hypothesis–which Darwin took seriously.  By avoiding all causes (even the ones they bring up, like “purpose”–Aristotle’s “final cause”), the current crop of IDists cannot even match Paley’s now-failed “science,” nor even keep from contradicting themselves as they both claim that purpose and rationality are evident, and that they are not.

This is part of a series of posts that I am combining into one long post, which may be found at Darwin’s Black Box.

Evolutionary history of tuberculosis deciphered

October 28, 2008

Or more exactly, the evolutionary history of Mycobacterium tuberculosis complex has been deciphered, indicating that there are two clades:

ScienceDaily (Oct. 22, 2008) — The evolutionary timing and spread of the Mycobacterium tuberculosis complex (MTBC), one of the most successful groups of bacterial pathogens, remains largely unknown. Here, using mycobacterial tandem repeat sequences as genetic markers, we show that the MTBC consists of two independent clades, one composed exclusively of M. tuberculosis lineages from humans and the other composed of both animal and human isolates.

The latter also likely derived from a human pathogenic lineage, supporting the hypothesis of an original human host. Using Bayesian statistics and experimental data on the variability of the mycobacterial markers in infected patients, we estimated the age of the MTBC at 40,000 years, coinciding with the expansion of “modern” human populations out of Africa. Moreover, the diversification of the oldest EAI and LAM populations took place during plant and animal domestication. Science Daily

It’s a somewhat interesting story, particularly due to its relevance to understanding tuberculosis as a disease.

One just has to wonder, in addition, how IDists propose to decide that this branch indicates normal processes of evolution (as at least most self-identified “IDists” would), while another branching happens to be due to design, despite the fact that it reveals no substantially different patterns.  Of course I have brought this up several times already, however it’s worth bringing up yet again, because it is important to understanding diseases like malaria (how adaptable are pathogens?), and because this aspect puts IDists squarely in the camp of creationists and their inability to tell “design” apart from “Darwinism.”

To put it more starkly than I have previously–the methods used for determining clades do not differ substantially across the taxa.  Some of the details change, of course, but the principles, the standards, are the same going back to the Cambrian and beforehand.  Furthermore, they do not differ meaningfully for “suddenly evolving” immunity genes like TCR and BCR (at least parts of which exist in the agnathans–hagfish and lampreys, but are much more diversified and important to jawed vertebrates–the gnathostomes–which use them in their adaptive immune systems, unlike agnathans with their adaptive immune systems), or the apparently far more sedately-changing Toll and Toll-like receptor genes.

Surely it is (in any “design” sense) a mystery of how malaria, tuberculosis, and humans, along with their ancestors, can be phylogenetically analyzed in essentially the same manner no matter whether we study their “designed” parts or their “evolved” parts.  Meaning that there is no obvious difference in causation of evolution across the taxonomic groups (and there is no definite way to assign the taxonomic categories, other than species, although the cladistic branches are not at all arbitrary), and no reason at all to think that design makes any difference to understanding the relationships of pathogens and hosts.  This is important to recognize when analyzing disease and our immune system, as well as when we recognize that Plasmodium spp. are vulnerable to certain drugs precisely because of their very different “lawfully accidental” evolutionary history–which means that drugs targeting the Plasmodium apicoplast have a good chance of being non-toxic to humans.

Then again, in a sense it’s somewhat silly to be discussing the IDist inability to distinguish “design” from “normal evolution” when they have no ability even to show that resistance to chloroquine (which Behe goes on about) actually evolved, rather than be the result of a miracle, or a series of miracles.  The fact is that the IDists attempt to empty science of any and all of the meaning that science gains by matching up cause and effect, and by understanding that similar effects have similar causes (unless, of course, another identifiable cause producing similar effects has been found–IDists only claim that it has, by refusing to differentiate the effects of “design” from those of evolution).

So it’s fail all the way, actually.  Of course they can’t say how “designed clades” differ from “evolved clades,” because they can’t ever rule out “design” with their (lack of) standards.

Malaria has evolved cold tolerance

October 25, 2008

To put matters in perspective, consider a related problem that has stumped malaria.  Although malaria is a ferocious parasite, quite willing to eat anything that gets in its path, P. falciparum needs a warm climate to reproduce.  If the temperature falls below about 65°F, the parasite slows down.  When the temperature gets to 61°F, it can’t reproduce  It’s stymied.  If a mutant parasite appeared that was tolerant to somewhat lower temperatures–not to freezing conditions, just to cool temperatures–it would be able to invade regions that are now closed to it.  Edge of Evolution, 82

Behe seems to think that P. falciparum is the only malarial parasite that infects humans.  P. falciparum is restricted to quite warm regions, but P. vivax has indeed invaded much cooler regions, including London in past centuries.  P. vivax tolerates temperatures of five degrees Celsius cooler, which amounts to nine degrees Fahrenheit cooler:

Compared with the more virulent Plasmodium falciparum, P. vivax tolerates a wide range of temperature environments (minimum: 16°C vs. 21°C for P. falciparum), which may explain its broader distribution. Host Switch Leads to Emergence of Plasmodium vivax Malaria in Humans

Then too, since Behe has no idea of what temperatures P. falciparum endured in the past, he does not know that it has not evolved to tolerate lower temperatures than it could initially.  Regardless of that, it is unsurprising that a Plasmodium species can live in cooler regions than can P. falciparum.

And when one species can survive in a region in which a related species cannot, competition often prevents evolution to fit the competitor’s adaptation.  After all, it may require several changes to endure cooler temperatures, and they may initially come with costs which make the species less fit.  When one species already can endure cooler temperatures it is not particularly likely that another species will, and especially not in the rather short time period in which P. falciparum has been infecting humans.  Nevertheless, P. vivax suggests that it could happen in other species, particularly if somehow P. vivax went extinct.

Behe could always ask why P. vivax can’t endure 6°C, or -6°C, or cryogenic temperatures.  And who knows, maybe he will.   But as I have previously argued, it is not for us who accept the constraints of science and evolution to explain why evolution is not all-powerful, it is for him to try to explain why his omnipotent god fails to reveal omnipotence in “his designs.” 

Evolving to live at lower temperatures has not “stumped malaria,” as he claims.  In fact, with P. vivax living at lower temperatures, P. falciparum‘s lack of evolution to tolerate lower temperatures is in line with evolutionary expectations, considering the relatively short time in which it has has to evolve.  So there you are, malaria seems to fit evolutionary expectations quite well, and Behe fails in this detail as well.

This is part of a series of posts that I am combining into one long post, which may be found at The Edge of Evolution

ID’s problem is not particularly poor design, but the evident cause of “poor design”

October 23, 2008

…The key to intelligent-design theory is not whether a “basic structural plan is the obvious product of design.” Behe, DBB, 223.

Let’s try this idea out on real science:  The key to evolutionary theory is not whether a basic structural form is the obvious product of evolution.

What?  Could anything be less scientific than claiming that finding the “obvious product” of design (or evolution) is not the key to ID (or to evolutionary theory)?

The context indicates that Behe just wants to insist over and over again that “irreducible complexity” is evidence for design, which, if it was, would mean that intelligent people would never have accepted evolutionary theory.  More importantly, if “irreducible complexity” indicated any sort of design, surely it would be accompanied by the obvious products of design–if by “design” we mean anything that is at all within our sphere of observation.  Back when ID was honest, if not especially coherent or cogent, Rev. William Paley wrote something quite the opposite of what Behe wrote:

Ought it then to be said, that though we have little notion of an internal mould, we have not much more of a designing mind?  The very contrary of this assertion is the truth.  when we speak of an artificer or an architect, we talk of what is comprehensible to our understanding, and familiar to our experience.  We use no other terms, than what refer us for their meaning to our consciousness and observation… Natural Theology

But you know, since design is not a comprehensible explanation, Behe et al. have to reverse Paley, and insist that the incomprehensible (as they portray the mere gaps in our knowledge) is the mark of design, thus easily putting ID into the same category as “internal moulds” and Lamarckist conceptions of evolution.

A little later than the quote that begins this post, Behe is complaining that Ken Miller demands perfection from “the designer,” and suddenly finds human design to be analogous (showing how incoherent he is).  That is, humans often make designs which are not optimized, so why not build the retina of the eye backwards in vertebrates (Miller was arguing that the backward retina is contrary to design), even though it is the “right direction” in cephalopods?  Well, apart from the fact that the IDists’ “designer” is God, clearly any entity having the intelligence to design the immune system could surely think well enough to put the retina in properly, instead of backwards.

Nevertheless, I do not especially like the “backward retina” argument against design, mainly because that fact means almost nothing except that the eye was not designed.  While it is well and good to point out that life was not designed, ID has never once had any scientific argument, nor any realistic shot at fooling more than a few biologists into thinking that it was.  Both for public relations, and for maintaining the integrity of science, what we have to do is to show that evolutionary theory explains life.  The “backward retina” is not readily shown to be the result of evolution (evidence from the time when it was fixed is scant, at best), while other “poor designs” are.

 In this linked post I made the point that pterosaur and bat wings are “poorly designed” next to bird wings. Again, though, that is only the minor issue pointing to the greater issue, which is that, for example, bat wings are simply the way that they are because of the constraints imposed by (unguided) evolution upon the modification of mammal forelimbs into wings.  The problem that IDists need to explain is why “design” follows constraints of evolution, not the constraints of any known intelligence, when it produces bat wings.  Any number of factors might cause a designer to produce a less than stellar design, of course, so the important question is why the only identifiable factors behind “poor design” in organisms are the constraints of unintelligent evolution.

Moving beyond that post, however, it is important that “poor design” is found rather more often just where one would expect in evolution, during the transitional periods.  Archaeopteryx has many of the advantages of birds, including the feathers which are sculpted into the wonderful avian aerfoil wing.  Yet it is not at all as efficient or “well designed” as modern birds are, whether because of its heavy teeth and jaw (by comparison to modern birds’ light bills, that is), its bony tail, or the fact that it lacked the “ligament-based force balance system” (Nature) that makes modern bird flight less work than it was for Archaeopteryx.

One could look at any of the major changes in form and lifestyle and see there fulfilled the predictions of evolution that “incomplete optimization” during the transitional period of complex is inevitable, whether it is the transition of fish to tetrapod, tetrapod to whale, or dinosaur to bird (actually, genetic evidence suggests that bats flew prior to evolving sonar, so this too would be an incomplete transition at least for the sonar-using bats.  Without fossils of the transition, though, I only include this likely example parenthetically).  Obviously I could belabor the point and dig up the details of the transitions, however these would not add much to the argument. 

The fact is that while human designs do undergo transitions in which they are not optimized, there is nothing in human design like the millions of years of suboptimal “design” which afflict evolutionary transitions.  Their designer-God certainly would not be expected to be troubled by the trial-and-error methods that humans utilize.  Only evolution is expected to transition between modes of life via often-poor, evolutionarily constrained “body plans,” and only it could predict that bat wings will not show any kind of “common authorship” with bird wings subsequent to bird and bat lines diverging.

It is no wonder that Behe tries so hard to ignore the many practical tests of evolution, and to replace these with impractical tests which require lost evidence in order to work.  What else can he do?  He cannot point to any “obvious product of design” in life (save what we have genetically or otherwise modified), nor can he explain anything via “design” that evolution not only explains, but predicts–from the lack of common authorship of changes after divergence in (primarily) vertical-inheritance organisms, to the enduring “poor design” of bat wings, and on to the “poor designs” of Archaeopteryx which are based on the fact that it was still a dinosaur that was yet evolving its flight abilities.

There does not seem to be any other pseudoscience which tries so hard to bypass all of the reasonable tests of both itself and its “rival.”  Perhaps this is because no idea held by millions of people has been debunked in so many ways, and with so many examples, as ID/creationism has been.

This is part of a series of posts that I am combining into one long post, which may be found at Darwin’s Black Box.

Horizontal transmission of a transposon in animal species

October 22, 2008

Here is the core of the article, in my opinion:

The fact that invasive DNA was seen in a bush baby but not in any other primates, and in a tenrec but not in elephants, hints that something more exotic than standard inheritance is going on.

However, this patchy distribution by itself does not rule out the traditional method, as some of the species could have lost the transposon DNA throughout evolutionary history.

So the team looked at the position of the hAT transposon – if it had been inherited from a common ancestor it would have been found in the same position, with respect to other genes, in each species. But they could not find a single case of this.

Since first entering the genome, the hAT has been able to reproduce dramatically – in the tenrec, 99,000 copies were found, making up a significant chunk of its DNA. Feschotte speculates that this must have had a dramatic effect on its evolutionary development.

“It’s like a bombardment”, he says. “It must have been evolutionarily significant because the transposon generated a huge amount of DNA after the initial transfer.”

Feschotte says he expects many more reports of horizontal gene jumping. “We’re talking about a paradigm shift because, until now, horizontal transfer has been seen as very rare in animal species. It’s actually a lot more common than we think.”  New Scientist

“More” is probably a good bet, all right, but horizontal transmission of genes is still not all that common in animals, so far as we can tell.  Still, 99,000 copies is bound to have made a difference in the evolution of the tenrec.

I thought the story itself was interesting, but it also has elements in its discovery that demonstrate how out-of-the-ordinary animal genetics can be and is discovered.  IDists sometimes like to point to the fact that this or that scientist agrees that design could be detected. 

But that’s their entire problem, it could be detected and it never is.  Meanwhile, science continues to find “non-canonical” changes and evolutionary patterns, such as this gene being laterally transferred into animal genomes.  It is entirely a matter of what has evidence and what does not.  Vertical transmission is by far the dominant form of gene transmission in, say, vertebrate species, as indicated by both conserved genes and by the lack of commonality after taxa diverge.  Horizontal transmission occurs, and is identifiable by its “lawfully accidental” appearance in unrelated species, as well as by the fact that the gene is not found in the same places in the genomes of the animals having a particular gene.

Now if we could ever find the commonality of authorship in any evolutionary development, such as older IDists predicted, ID would at last have some evidence in favor of it.