Thursday, September 09, 2004

Larson's Review

Christianity Today has published this review of the pro-ID book Doubts About Darwin, by Thomas Woodward. The reviewer is Edward Larson, whose 1997 book Summer for the Gods is an excellent account of what really happened during the Scopes trial (personally, I found L. Sprague De Camp's 1968 book The Great Monkey Trial to be even better, but it is much harder to find).

Larson's review is not harsh enough for my taste, but he does point out that the book gives the reader no inkling of the fact that ID has made essentially no progress among scientists, either in terms of respect or in funding. However, I think this paragraph might leave readers with a false impression:


As Woodward illustrates, the writings of other key ID proponents have broadened the critique of Darwinism. Unlike Johnson, Behe does not deny the core evolutionary concept of common descent for all organisms, but in Darwin's Black Box he does assert that some biochemical processes (such as the cascade of multiple proteins required for blood clotting) are too irreducibly complex to have originated in the step-by-step fashion envisioned by modern Darwinists. Recalling the old claim that the eye could not have evolved piecemeal because it only functions as a whole, Behe maintains that something intelligent must have designed certain functional systems into organisms.

For his part, Dembski invokes mathematical probability filters (like those used to sift radio signals from outer space for messages sent by intelligent beings) to suggest that life's complexity is more likely the product of design than chance. In Icons of Evolution, Wells debunks various outdated bits of scientific evidence still invoked by some to support evolution theory, such as long-discredited pictures illustrating similarities in the embryonic development of various species and dubious experiments demonstrating the power of natural selection in transforming the peppered moth.


There are a couple of problems here, the most serious one being the suggestion that Wells successfully debunked anything in Icons. Wells' descriptions of recent experiments on peppered moths were vastly more inaccurate than anything the textbooks were describing. As for the “long-discredited pictures”, the embryological evidence for evolution is as strong as ever. All Wells managed to do was point out that a handful of biology textbooks were using outdated photos to make the correct point. In most of these books the photos have been updated with more accurate pictures. Check out Alan Gishlick's magisterial take-down of Wells, available here, for more on this.

Also, it is not possible for something to be “too irreducibly complex”. You are either irreducibly complex or you are not. Larson might also have pointed out that Behe's use of the blood clotting cascade to make his point was especially weak, considering that biologists have uncovered rather a lot of data regarding the evolution of that system.

Larson's review does not explain why ID has been so unsuccessful among scientists. He merely summarizes some of the ID arguments, and then states that scientists want nothing to do with it. He should have said explicitly that scientists reject ID because they find ID arguments unconvincing, to put it mildly. As it stands, his review can be spun to provide support for the idea that scientists are dogmatically opposed to anything that smacks of God.

Is it a Parody?

It has been pointed out to me that the website for Objective: Chrisitan Ministries, which I linked to in one of yesterday's postings, is probably a parody. Having read some of their articles more carefully, I think this is porbably right. I couldn't find anything to explicitly identify the site as a parody, but the clues are there nonetheless.

Assuming it is a parody, I would say it's a bit too good. The articles they have up there are similar in both tone and substance to genuine conservative Christian websites that I have enocuntered. I suspect that supporters of Answers in Genesis, for example, would find much here they agree with.

Wednesday, September 08, 2004

The Meyer Fiasco, V

Every time I start thinking the The Discovery Institute just can't get any sleazier, they find yet another new low to prove me wrong. They have now weighed in with these comments about Stephen Meyer's article. This essay is dated September 8, meaning they have had time to digest the press release from the BSW that I reported on in part two of this series. Sadly, they don't even mention it.

Instead they are making the preposterous argument that somehow the National Center for Science Education has flip-flopped on the importance of peer-review:


For the past few years the Darwinian lobbyists at the National Center for Science Education (NSCE) have falsely complained that scientists who support the theory of intelligent design don’t publish peer-reviewed articles and don’t make their case at scientific conferences.

“Now an article has appeared in a biology journal that even the NCSE can’t find a way to spin out of existence,” responds Dr. John West, Associate Director of Discovery Institute’s Center for Science and Culture (CSC). “So what does it do? Claim the article shouldn’t have been published despite the fact it was approved by peer-review. Apparently politicians aren’t the only ones who do flip-flops.”


Is it actually possible that there are people who can't see through this? The article shouldn't have been published because all of its major claims are wrong. If it is true that it went through honest peer-review, then what we have is a breakdown in the peer-review process. You will search the NCSE archives in vain for any statement to the effect that peer-review is fool-proof.

Of course, as reported in my previous entries in this series, we now have reason to doubt that the peer-review process was above-board in this case. We know that the editor responsible for handling the paper circumvented the normal procedures of the journal. For now, we have only his word about the three peer-reviewers on the paper.

At the end of the article, Discovery's spin doctors offer this paragraph to rebut the idea that ID folks don't publish in the peer-reviwed literature:


West also points out the spurious nature of the NCSE’s previous claim that supporters of intelligent design have not produced peer-reviewed publications. Mathematician William Dembski published a peer-reviewed monograph with Cambridge University Press, The Design Inference (1998). Biochemist Michael Behe has published his ideas recently in the peer-reviewed science journal Protein Science as well as previously in Philosophy of Science (2000) and And Stephen Meyer edited an entire volume of peer-reviewed articles with Michigan State University Press, Darwinism, Design, and Public Education (2003).


Of course, the NCSE has never claimed that supporters of ID don't publish in the peer-reviewed literature. The claim is that they don't publish their arguments about ID in the peer-reviewed literature, because they know their arguments don't stand up to honest scrutiny.

With that in mind, let's take Mr. West's examples one at a time, shall we? The Design Inference had nothing to do with ID. It was published in a series on probability and decision theory, particularly from a philosophical viewpoint. The Michael Behe paper they are referring to (abstract available here) likewise has nothing to do with ID. It is an amusing piece of mathematical modelling, but provides absolutely nothing that is helpful to the ID cause. The Philosophy of Science article was a reply to critics, it was not a piece of original research. Finally, the Michigan State University Press anthology was published as part of a series on Rhetoric and Public Affairs. The individual chapters were not reviewed for their scientific merits.

People on my side of this issue who still think ID folks should be dealt with courteously need to wake up and pay more attention to this kind of garbage.

The Meyer Fiasco, IV

I suspect that most creationist organizations will simply ignore the highly dubious way in which Meyer's article managed to get into print, and will continue to produce essays like this one from Objective: Christian Ministries. No simple excerpt could do justice to this Zell Miller-esque rant, so I think I'll just reproduce the whole thing:


Evolutionists Forced By Preponderance Of Evidence To Finally Publish Intelligent Design Paper In Peer-Reviewed Journal

(8/25/2004) The origin of biological information and the higher taxonomic categories by Stephen C. Meyer of the Discovery Institute, an important paper in the history of Science on par with Watson and Crick's paper on the structure of DNA which demolishes all the false icons of Evolutionism and breaks open Darwin's black box by showing that only the Intelligent Design of the Lord can account for the origins of the bauplans of the higher taxa, has been published in the highly-respected journal Proceedings of the Biological Society of Washington (Vol. 117, No. 2, pp. 213-239). After years of stonewalling and refusal to acknowledge that the theory of Evolutionism is in crisis, Evolutionists have admitted defeat and allowed their tightly controlled peer-review journal to finally publish the truth. The PBSW's editor, Richard von Sternberg, who is also on the editorial board of the Baraminology Study Group, has long been forced by the hegemony of Evolutionist dogma to keep papers supporting ID out of the journal. But because of Dr. Meyer's devastating critique of Evolutionistic teachings on the Punctuated Equilibrium, and his discovery of high levels of Complex Specified Information (CSI) in animal kinds from the Cambrian Explosion, the forces of Evolutionism had no viable excuse not to allow von Sternberg to publish Dr. Meyer's paper. Now that the flood gates are open, hundreds of other papers supporting Intelligent Design will soon be appearing in all relevant journals, thus marking the end of Evolutionism's strangle hold on academia. We are truly living in wondrous times.

[UPDATE 9-4-2004] Respected news organizations the Washington Times and World Net Daily are both reporting that Evolutionists -- acting through Darwinian activists at a notorious anti-Creation message board called “The Panda's Thumb” -- have gone on the offensive and are responding to this fatal blow to Evolutionist Philosophy with "hysteria, name-calling and personal attack." In particular, Evolutionist thought police are accusing PBSW's editor Sternberg of “being a Creationist” (he is, as mentioned above, on the editorial board of the BSG as well as a signatory to the Discovery Institute's “A Scientific Dissent on Darwinism”) and suggesting that the paper “received some editorial shepherding through the peer review process.” Poppycock! As Sternberg notes, the paper was found by three peer reviewers to be “meritorious, warranting publication.”

It's becoming clear that Darwinists just can't accept that the game's up. Listen guys... you had a good run. You got a large number of people to actually believe they are monkey's uncles while you mingled with Hollywood elite on the set of Jurassic Park and lived it up on tenure at fancy colleges. But it's over. Now just peacefully turn in your lab coats and go join the phrenologists stuffing envelopes from their homes.

By the way, the full paper is now on-line at Discovery Institute: The origin of biological information and the higher taxonomic categories by Stephen C. Meyer. We advise you to make a backup copy before desperate Darwinian hackers try and take the site down.


The Meyer Fiasco, III

Some readers might be wondering how someone with solid creationist credentials managed to become the editor of a reputable journal. The answer is that there is no litmus test for becoming the editor of a journal. I know little about Sternberg's credentials, but I suspect his record of scientific accomplishment is solid enough, if not extraordinary. The fact that he has creationist sympathies is neither nere nor there in assessing his qualifications to serve as editor. It is one more counterexample to the creationist delusion that the scientific establishment is engaged in conspiracies against them.

On the other hand, now that it is clear that Sternberg broke protocol to get an article published that was inappropriate for the journal (a paper that almost certainly would not have survived any honest referreeing process), it will be interesting to see how other creationists react to this. Will they be forthright and criticize Sternberg for abusing his position this way? Will they protest that they want their ideas to compete fairly, no more and no less, in the scientific marketplace? I'm not holding my breath.

The Meyer Fiasco, II

Meanwhile, The National Center for Science Education is reporting that the Biological Society of Washington, the group that publishes the journal in which Meyer's papaer appeared, has weighed in with this statement:


The paper by Stephen C. Meyer in the Proceedings (“The origin of biological information and the higher taxonomic categories,” vol. 117, no. 2, pp. 213-239) represents a significant departure from the nearly purely taxonomic content for which this journal has been known throughout its 124-year history. It was published without the prior knowledge of the Council, which includes officers, elected councilors, and past presidents, or the associate editors. We have met and determined that all of us would have deemed this paper inappropriate for the pages of the Proceedings.

We endorse the spirit of a resolution on Intelligent Design set forth by the American Association for the Advancement of Science, and that topic will not be addressed in future issues of the Proceedings. We are reviewing editorial policies to ensure that the goals of the Society, as reflected in its journal, are clearly understood by all. Through a web presence (www.biolsocwash.org) and contemplated improvements in the journal, the Society hopes not only to continue but to increase its service to the world community of taxonomic biologists.


Based on this statement, it seems clear that the normal editorial process was not followed in this case. I'd still like to know more about those three stellar referrees, however.

Another question is raised by the BSW statement: The Proceedings of the Biological Society of Washington is a fairly obscure journal that primarily publishes articles in the subject of taxonomy. Why, then, did Meyer choose to send his paper to this journal? Was it because he knew the editor, Richard Sternberg, would give the paper preferential treatment? Given that Sternberg did not follow the normal procedures of the journal, that seems all too plausible.

The Meyer Fiasco, I

In last Wednesday's post I reported on the publication of this pro-ID article by Stephen Meyer. It appeared in the journal The Proceedings of the Biological Society of Washington. As reported in this lengthy critique from the Panda's Thumb, the scientific arguments in the paper were so bad that it was a mystery how it ever survived peer-review.

There have been some developments in that regard.

First, The Scientist has weighed in with this article on the subject.

The article sheds some light on the mystery of the peer-review process used for the article:


Richard Sternberg, a staff scientist at the National Center for Biotechnology Information who was an editor of the Proceedings at the time, told The Scientist via E-mail that the three peer reviewers of the paper “all hold faculty positions in biological disciplines at prominent universities and research institutions, one at an Ivy League university, one at a major US public university, and another at a major overseas research institute.”

“The reviewers did not necessarily agree with Dr. Meyer's arguments but all found the paper meritorious, warranting publication,” Sternberg said.


It seems a bit odd that a small journal like PBSW would send a paper out to three different reviewers. Most journals have a paper referreed by one, maybe two reviewers. Occasionally a third will be called in to break a tie between the previous two. Here the description of the reviewers sounds suspiciously stellar. I'd like to know more about who these reviewers were.

On the other hand, it is possible that Sternberg sent it to three referrees precisely because the subject matter was so controversial. I find that unlikely, but I won't dismiss it out of hand. It would be unusual, though not unheard of, to reveal the identity of the referree's. On the other hand, surely the referree's reports could be released.


Tuesday, September 07, 2004

Hunter in Wonderland, Part 2.5

UPDATE: Sept. 8, 4:20 pm: I corrected some typos and made small changes in the phrasing in certain parts of this entry.


When I began to respond to Cornelius Hunter's thoughts from this thread over at ISCID, I said I would not respond to any further posts he made on this topic. I said that because these sorts of internet debates can easily go on forever, and I wanted to cut-off the discussion at a point where failure to respond would not be interpreted as admission of defeat.

However, Hunter has now responded to my second entry in this series (my essay is available here, Hunter's reply is available here (scroll down to the bottom of the page)). I'm afraid that Hunter's reply is so wide of the mark, that I have to weigh in one more time to try to make my argument clear. But I definitely will not be replying directly to any reply he makes to this post. And this time I really mean it!

One of the main points of contention is whether the universality of the genetic code can be considered strong evidence for evolution. I say it is. He says it isn't.

To be precise, I argued that the complete universality of the cellular machinery used to translate the code across all known species speaks well for common descent, since it would be very difficult to defend common descent in the face of multiple, different sets of cellular machinery. I then argued (basing myself on Miller, who was basing himself on Landweber) that the small variations in the code that are known occur in patterns that also are suggestive of common descent.

Finally, I addressed the question of how many changes from the standard code could be tolerated before we would have to discard the idea of universal common descent. I commented that it would require far more knowledge of evolutionary genetics than I possess to answer that question. It would depend on things like how sensitive an organism is to changes in the code, and what sorts of natural mechanisms could be produced to explain how a codon that originally coded for one amino acid (or a stop) later comes to code for something different.

After providing a brief quote of my thoughts on the matter, Hunter writes this:


Rosenhouse is not alone here, as this is a difficult question. What is clear, however, is that it would be difficult, as I earlier pointed out, to place a tight limit on the evolution of the code without presupposing evolution. Amino acids tyically have multiple codons so single codon reassignment does not mean a complete absence of the corresponding amino acid. Furthermore, many amino acids are similar, so conservative code changes are conceivable. And finally, proteins are quite robust to amino acid substitutions. Perhaps someday we'll find evidence for the code's rigidity, but at this point we have only speculation.

So this invalidates Rosenhouse's claim that the near universality of the code is strong evidence for common descent. Greater differences in the code, at this point anyway, could be explained by evolution and common descent.


Hunter does not address my point that the universality of the cellular apparatus speaks well for common descent. Common descent would be out the window without this universality, and there is no rival theory that also accounts for this universality. Chalk it up to common design if you want to, but then you will have to explain why it amused the designer to make trivial changes in the code in a handful of species.

And while it is true that common descent could account for greater changes than we actually find, it is equally true that there are good reasons to believe that there are limits to how far you can change the code before sacrificing the viablility of the organism. For that reason, the fact that the code varies very little across species speaks well for common descent.

To put it another way, the more universal the genetic code the easier it is to accept common descent. To bring variant codes under the tent of common descent, we need to invoke other mechanisms to explain how the divergence happened. As things stand, geneticists have provided a number of possible mechanisms for how one codon could change what it codes for in a given species, and these mechanisms are adequate to explain the variations we actually encounter. These mechanisms have their limits, however.

But where Hunter really starts to go wrong is in his next paragraph. He says I was too uncritical in my acceptance of Miller's claim that the pattern of divergences from the standard code is itself suggestive of common descent. Hunter writes:


Actually, there is no such evidence. Miller's powerful confirmation is, in reality, scattered across various types of organisms. For example, the UAR codon is observed to switch from &lduqo;stop” to “Gln” in green algae, various ciliates, and some diplomonads. Likewise, the UGA codon is observed to switch from “stop” to “Trp” in other various ciliates and two firmicutes. There is no powerful, unexpected confirmation of evolution here. [1]

Unfortunately Rosenhouse accepts Miller's tale unequivocally, concluding that “the pattern of divergences that are known are also consistent with the idea that they are derived from the standard code via descent with modification.”


The citation at the end of the first paragraph is to the paper “Rewiring the Keyboard: Evolvability of the Genetic Code” by Knight, Freeland, and Landweber (though for some reason Hunter only mentions Knight). Landweber was the senior author on the paper. It appeared in Nature Reviews: Genetics in 2001. This is the same paper Miller was citing in his work.

Miller was basing his statement about the pattern of differences from the standard code on a similar statement made by Dr. Landweber herself. So if Miller is confused on this point, then so is the senior author on the paper in question.

Happily, Miller and Landweber are right, and Hunter is wrong. Landweber et al are quite explicit in the paper that in certain cases, the same codon shift occurred in unrelated species. Nothing Miller wrote (or by extension me in quoting him) contradicts that. That was not the issue. The question is whether the patterns of divergences that we find across species is consistent with common descent. For example, once a shift occurs in some lineage, does the change persist in the evolutionary cousins of that species? Or are the variations from the standard code effectively random with respect to the phylogenies we have inferred from other means? The elaborate diagram reproduced by Miller in his essay shows that these patterns are indeed consistent with common descent.

This is another example of Hunter being too enamored of the idea that convergence is some sort of problem for evolution. He seems to think that the mere fact that same codon shift was converged upon in separate lineages condemns common descent. He consistently fails to consider what sorts of natural mechanisms can account for such convergences.

From here Hunter turns back to fossils. Sadly, he also turns back to some of the truly dopey arguments I criticized so strongly in my initial posting in this discussion (avialable here):


Regarding the fossils, Rosenhouse mistakenly thinks that “The fossil record reveals a history of life that is consistent with evolutionary expectations.” Actually, evolution does not expect for phenomenal complexity to appear abruptly. In fact, it does not expect phenomenal complexity at all. Also, if the earth was full of nothing but bacteria that could just as easily be described as being consistent with evolutionary expectations.


Hunter made a similar remark in responding to criticisms of Richard Wein. After describing the complexity of the echolocation system in bats, he writes:


Evolution does not predict this complexity, nor does it have a scientific explanation for how it arose. Therefore, this is not consistent with evolution and is evidence against it.


Alas, this is total nonsense.

Hunter seems to think that “phenomenal complexity” is some sort of precisely defined technical term. Like maybe evolution could explain mere complexity, or perhaps extreme complexity, but not phenomenal complexity.

What could it possibly mean to say that “evolution does not expect phenomenal complexity”? A process in which random variations are sifted through a non-random selection process can lead to outcomes far more complex than what you started with. That's simply a fact about such processes. On the other hand, since there is also an element of chance involved in the process, there is no guarantee that complexity will increase (Hunter is, at least, right on that point). So complexity by itself is not evidence one way or another for evolution.

Curiously, ID proponents like Michael Behe and William Dembski understand this very well. That is why both of them attempted to identify special kinds of complexity (irreducible complexity in Behe's case, complex specified information in Dembski's) that were outside of what natural selection could produce. As it happens, neither was successful, but we won't rehash that debate here.

To determine if a particular system could have been crafted by natural selection it is not enough to diagnose it as being complex. Furthermore, there is no shortage of complex systems whose origins have been largely revealed. No doubt Hunter would sweep this work under the rug as being unscientific, but he would simply be wrong to do so.

Hunter continues to deteriorate with his next paragraph:


Regarding comparative anatomy, a few posts back Rosenhouse agreed that massive convergence would be a problem for evolution, now he finds it to be vindication:


quote:
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But why is convergence a problem for evolution? If the various genetic modifications required to produce saber teeth occur with reasonably high probability, and if there is selection pressure in favor of such teeth, then the convergence of these structures is easy to explain in terms of standard mechanisms. In fact, under such circumstances, a lack of convergence would be puzzling. In this sense, many known convergences can be viewed as vindications for evolutionary theory.
--------------------------------------------------------------------------------

Evolutionists generally do not acknowledge evidential problems. Hence, massive convergence becomes a vindication for evolution. Rosenhouse denies evolution invokes ad hoc explanations, but this is ad hoc.


The interior quote is from me. Hunter begins his reply to this with a slur against the intellectual integrity of evolutionists. He then attributes to me the idea that massive convergence becomes a vindication for evolution, which is not what I said. (And let me also point out that “massive” like “phenomenal” and “striking” is not a technical term). He then says that my brief description of the conditions under which we might expect convergence to happen is ad hoc. It is not. I am simply pointing out that the prolonged action of natural selection can lead to similar solutions to similar problems. Again, that's simply a fact about natural selection. It is not a kluge meant to get around inconvenient data.

Hunter continues:


Although he agreed that massive convergence is a problem for evolution, Rosenhouse now asks why evolution is incapable of explaining convergences. That is a convenient way of framing the problem, but it misses the point. Above, Rosenhouse claimed the pentadactyl pattern strongly suggests common descent. They are obvious similarities right? So they strongly suggest common descent because they must have come from a common ancestor.


Of course, I did not say that massive convergence is a problem for evolution. Here's what I actually said:



Rampant convergent evolution would be a problem if we found several lineages evolving major, complex morphological innovations in parallel.



I thought my point here was obvious, but for Hunter's sake I guess I better spell it out. First, at the risk of being repetitive, we note that “convergent evolution” is not a precisely defined term. Generally we have in mind certain similarities in design that did not arise as a result of common descent. By itself, this is not a problem. The end result of prolonged natural selection is that organisms end up better adapted to their environment than they were at the start. Sometimes that means crafting similar adaptations to solve similar problems. The streamlined shape of fish and dolphins is a good example of this. So there is nothing in the mere fact of convergence that calls evolutionary theory into doubt.

However, though evolution will often craft similar solutions to similar problems, it is asking too much of chance for evolution to produce identical complex systems in unrelated lineages. That's what I was holding out as troubling for common descent.

Hunter's statement that I have framed the problem conveniently is yet another example of his unwillingeness to take seriously just what it is that evolutionists have been saying all these years. The problem isn't that I have framed the problem in some convenient way, it is that Hunter thinks he can make bold assertions about what evolution does and does not predict without fully considering all of the available resources evolution has at its disposal.

The identical forelimb design of humans, cats, whales and bats is an example of having the identical bones in the same relative positions to one another in a situation where there is no functional explanation for the similarity (indeed, the design seems rather ill-suited for many of the purposes it is put to). The level of morphological similarity here is far greater than in any of the examples of convergence Hunter is so fond of. The lack of a functional explanation for the structure makes it hard to view it as the outcome of natural selection crafting similar solutions to similar problems. That all suggests common descent as the most likely explanation. In my opening post of this series, I discussed the various methods scientists use to distinguish homologies from analogies. Hunter asserted that I missed his point (and more on that in part three). But here Hunter plainly needs to give more thought to how homologies and analogies can be distnguished.

Hunter continues:


But now, with similarities that could not conceivably have been inherited from a common ancestor, this too is a vindication because it must have been caused by similar mechanisms responding to similar selective pressures. This is ad hoc. If a similarity can conceivably be ascribed to a common ancestor then it is viewed as a homology and strong evidence. If it cannot be, then it is viewed as an analogy, and again strong evidence.


This is just a repetition of his earlier pargraph, but it does make explicit his refusal to consider the possibility that homologies can be distinguished from analogies. Hunter is plainly descending into cartoon arguments here. As I've already explained, there is nothing ad hoc in explaining convergence as the end result of known evolutionary mechanisms.


The point is that if similar designs are present in distant species, where common descent cannot be used to explain those similarities, then common descent need not be invoked to explain similarities in species that are not so distant. Homologies, such as the pentadactyl pattern, were a key argument for Darwin. He viewed them as a mandate for common descent. But this argument is contradicted by the convergences. It is not scientific to say that the pentadactyl similarity mandates common descent when there are other such similarities that do not mandate common descent. The argument is arbitrary. It is not a question of whether the theory allows for similar adaptations to evolve, it is question of whether or not evolution is supported by the evidence.


But there aren't “other such similarities” that do not mandate common descent. That's the whole point! “Similarity” is not a technical term. The pentadactyl pattern of various mammalian forelimbs shows a fundamentally different sort of similarity from the saber-like teeth of certain marsupial and placental mammals, or the streamlined shape of fish and dolphins. Hunter's failure to recognize this point is fatal is to his argument here.

Hunter concludes his essay with a cartoon discussion of my thoughts about the distinction between origin of life research and evolutionary biology. He writes:


Regarding the question of origin of life (OOL) Rosenhouse continues to maintain that the creation of the DNA code is outside of evolution and an OOL problem. But he avoided answering my question. Does he think the creation of the DNA code is a serious problem for OOL? If not then this is merely a rhetorical dodge since he would believe the code evolved (somehow).


The answer to Hunter's question here will depend on what he means by the phrase “serious problem”. The origin of the DNA code is the central question in OOL research. Currently I agree that there is no really persuasive explanation for how it formed. In that sense, it is a serious problem for OOL research.

There are a lot of possible explanations, however, and that is enough to dismiss any claims that we must resort to the supernatural in explaining its origin. If Hunter means that our failue so far to come up with a fully plausible explanation for the code is good reason to think that the problem is fundamentally insoluble then I would not agree with his description. OOL is an infant science, and it seems to me that progress is being made.

Also, I'm not comfortable with saying that the code evolved. I would say that it formed by some naturalistic process that probably shared certain characteritics with evolution by natural selection.

Hunter continues:


Furthermore, Rosenhouse fails to understand that DNA code evolution falls into the category of Darwinian evolution, even according to his own definition:

quote:
--------------------------------------------------------------------------------
The universal common ancestor possessed a genetic code, and that is the point from which evolution is considered to begin. To even discuss anything like a Darwinian evolutionary process, you need a collection of imperfect replicators competing for resources. The first replicators were likely far simpler than the first thing that was unambiguously alive, but the fact remains that evolutionary theory takes for granted a certain minimal level of complexity. The distinction between the origin of life, and the subsequent development of life once it appeared, is not complicated.
--------------------------------------------------------------------------------

We can agree with all this, and it means the DNA code evolution falls into the Darwinian evolutionary process. The code had to have evolved from simpler codes. How strange that the first cells to appear with the extant code constitute “a collection of imperfect replicators” but in going back just one step in the code's evolution we no longer have “a collection of imperfect replicators.”


Here I thought I was writing in English, but perhaps not. I asserted that anytime you have a collection of imperfect replicators competing for resources, you have something “like a Darwinian evolutionary process”. Indeed. But the fact remains that when we talk about evolutionary biology we are thinking of the development of life from the universal common ancestor onward. Learning what happened before the universal common ancestor is certainly of interest to evolutionary biologists, but studying that question requires different tools and different ideas from those evolutoinary biologists rely on.

Probably the modern code did form through a process that shares certain attributes with natural selection. OOL researchers often use the term “chemical selection” to capture this similarity, while also making it clear that they are talking about something different from natural selection as that term is usually used.

Hunter is eager to lump evolutionary biology together with OOL because the latter is not nearly as well developed a science as the former. He accuses me of resorting to various rhetorical tricks, but here we find him trying to bring down evolution by associating it with a branch of science with some large unresolved questions.

The remaining paragraphs of Hunter's essay contribute nothing new to the discussion. Since I'm sure my regular readers must be getting tired of these very long posts, I will stop here for now. I will write one more long post addressing the third part of Hunter's original essay.

Monday, September 06, 2004

Cordova's Comment

I mentioned Salvador Cordova in this post, in which I replied to some comments he made concerning my dispute with Cornelius Hunter.

In the comments section to this post(comment 7220, to be exact) from the Panda's Thumb about Stephen Meyer's recent pro-ID article in the Proceedings of the Biological Society of Washington, Cordova has offered up this bit of juvenile bravado:


On a side note, Dr. Rosenhouse wrote a rebuttal to one of the student’s “letters to the editor” in the JMU campus newspaper. You see, 3 letters to the editor in 2003-2004 by students were published in the campus newspaper attacking Darwinism. I had nothing to do with that (unfortunately, otherwise they’d have been better written letters). Nonetheless it shows the increasing sympathies towards ID in Dr. R’s own secular college campus. Ain’t it heart warming.

In Dr. R’s own school, more and more students refuse to bow the knee to Darwin. Dang, in his own back yard!!! Oh, I suspect there are some ID sympathizers in the faculty too. YIKES!

I should say, I’m pleased to have helped his JMU kids see the light of ID. Some of the best science students at JMU are (gasp) up-and-coming IDists. Wooohooo!

I would have advised the student in question not to have written the article which Dr. R rebutted. Andrew is young and learning, thus I will teach him better arguments. I’m pleased to say I helped a few JMU students become creationists and intend to help a few more see the light.


Ahem. Cordova means three op-ed pieces, not three letters-to-the-editor. And we should point out that while there were three articles, there were only two authors. Two of them were written by the same person.

The article by “Andrew” is available online here. His main argument, inspired by the Disney animated movie Finding Nemo, was that evolution can not possibly explain the symbiotic relationship between the clown fish and the sea anemone.

My reply is available here (scroll down to the third letter). A professor in the philosophy department here also offered a negative appraisal of the original article, and you can read his thoughts here.

And I appreciate Cordova's implication that my refutation of the arguments from the original article was correct.

Sunday, September 05, 2004

Hunter in Wonderland, Part Two

I will now continue with my response to Cornelius Hunter's response to my earlier essays concerning his work. See my post from this past Tuesday, available here, to find the relevant links to past posts.

The second part of Hunter's essay addresses the universality of the genetic code, and I'm happy to report that his discussion of this topic is far better than his previous writings had led me to believe he was capable of. We pick up the action in the second paragraph:


Taken at face value, Rosenhouse's claim means that common descent is false since the DNA code is not universal. Variations of the code exist in nature. Therefore, will Rosenhouse reject common descent? No, Rosenhouse surely is thinking of more significant variations. How much more significant? We don't know, for Rosenhouse has not defined any criteria. If Rosenhouse wants to claim the universality of the DNA code as a prediction of common descent, he will need to explain why the known variations do not violate this prediction. Specifically, he will need to explain what are the limits of DNA code evolution.


Hunter is referring to this statement I made in my original post:



Actually, the universality of the DNA code, and the universality of the cellular machinery used to translate that code, are evidence for a universal common ancestor. If these universals were not present it would be essentially impossible to argue that any two modern species share a common ancestor somewhere in the past.



And here I will accept a small criticism. I should have been more careful when referring to the universality of the code. It is certainly true that in a very small percentage of species we find that a handful of codons code for proteins different from what the “standard” code predicts. Given that, as Hunter suggests, I should have been more explicit about what the hypothesis of universal common descent leads us to expect about the genetic code.

So let's go about that now. First, to what extent can the code be called universal? Biologist Ken Miller has weighed in three times on this topic here (scroll down to the essay “A Dying Theory Fails Again”). Since I can not improve on his discussion, I will reproduce some choice excerpts below:


All living organisms translate the genetic code using ribosomes, tiny protein building factories, they all translate it with the aid of small molecules called transfer RNA, they all read it in the same direction, and they all read it in the same way, translating the code 3 letters at a time into sequences of amino acids, the building blocks of proteins. It is indeed true that in some organisms, a handful
of these 3-letter “words” have different meanings. Our own cells, for example, contain little structures known as mitochondria in which 4 of the 64 words have different meanings from the “standard” code. In most organisms, these differences are so slight as to be trivial. In common molds, for example, the sequence “UGA” is translated into the amino acid tryptophan. In the standard code, it's a “stop” signal. The other 63 words, however, are identical between humans, elephants, daisies, and molds.

What does all this mean? As evolutionary biologists were quick to realize, slight
differences in the genetic code are similar to differences between the dialects of a single spoken language. The differences in spelling and word meanings between the American, Canadian, and British dialects of English reflect a common origin. Exactly the same is true for the universal language of DNA. 48 of the 64 words are identical in all living organisms, and only 16 are known to vary across the enormous diversity of living things.


Let us consider first the universality of the cellular machinery used to translate the genetic code. It's hard to see how the hypothesis of a universal common ancestor could survive the discovery that living organisms possessed a variety of fundamentally different systems for translating the code. We would then have to hypothesize that some lineage of organisms began with one system for translating the code and later evolved an entirely new system in its place. That may not be strictly impossible, but it seems sufficiently unlikely that the hypothesis of universal common ancestry would be defeated by such a discovery. In light of this, the universality of this cellular machinery is good evidence in favor of common ancestry.

Now, for the code itself. There are a number of known natural mechanisms that can explain how an individual codon comes to code for something other than what the standard code dictates in some species or other. So the mere fact that there are small divergences does not invalidate common descent. The question then becomes just how many divergences the common descent hypothesis can tolerate. It would take someone more knowledgeable about evolutionary genetics than I am to give a good answer to that, but Miller's analogy to dialects of a language is well-taken. People in the Southern United States speak English differently from people in the North, but no one says they speak a different language. On the other hand, English and French are certainly different languages despite having a few words in common. At some point divergences from the standard code could pile up to the point where we would say it is just a different code. I don't know where the line gets drawn, but considering that such variations as are actually known are tiny indeed, I don't think we need to dwell on that point.

Evolution is all about patterns of differences, so we next ask what can be inferred from the catalog of variants from the standard code that have been discovered. Miller addresses this point as well, reproducing a diagram from a paper by Laura Landweber (et al) of Princeton University. The diagram shows that the deviations from the standard code that are known are themselves related by common descent. Here's Miller again:


Dr. Landweber's comments refer to the phylogenetic “tree” shown in Figure 2 of her paper, which is reproduced below. As she noted, rather than falsifying Darwin's idea of descent from a common ancestor, these “subtle derivatives” of the “standard” code actually provide powerful evidence for the common descent of all organisms from a single ancestor.

Look closely at the figure from this paper, and you'll see something remarkable. The
variations from the standard code occur in regular patterns that can be traced directly back to the standard code, which sits at the center of the diagram. What this means is that these slight variations of the code provide powerful — and unexpected — confirmation of the evolution of the code from a single common ancestor.


So the situation seems pretty good for the hypothesis of common descent. The universality of the cellular machinery used to translate the code and the near universality of the code itself speak well for the hypothesis. Furthermore, the pattern of divergences that are known are also consistent with the idea that they are derived from the standard code via descent with modification. I see nothing in this data that speaks against universal common ancestry. Nor do I know of any rival theory that explains these facts.

From here Hunter continues with:


This would be a daunting task given the limited state of our knowledge. Beyond this, it would also be daunting because evolution routinely considers ad hoc and speculative explanations for what we observe in nature. It would be different if we were testing a more straightforward, more easily modeled hypothesis, such as Kirchhoff's Voltage Law. In that case predictions could be computed mathematically using well-defined equations. But evolution and common descent are broad processes, driven by a wide range of causes and influences. Hence, these processes are capable of explaining a wide range of phenomena, especially given the level of speculation that is often permitted. It is not easy to show why an observable, such as variations in the DNA code, would falsify common descent.


I would certainly dispute the claim that evolution routinely considers ad hoc explanations, and evolution certainly does not permit any more speculation than any other scientific theory, but Hunter's broader point is spot on. It is certainly true that the predictions of evolutionary theory are not as sharp as those of the more mathematical theories we find in physics. That's not a defect in evolutionary theory, it is simply a reflection of the fact that there are many factors that affect the evolutionary trajectories taken by living populations, and the whole process contains an element of chance.

Sadly, Hunter seems to forget this obvious point in framing many of his arguments against evolution. Later in the thread I linked to above, Hunter writes the following:


Complexity is also obvious in the fossils. What do we know? We know that fossil species remain essentially unchanged for long, geological, periods of time. And we do know that complexity appears early and often. For example, the trilobite eye of 400 Myr was said to be “an all-time feat of function optimization.”


The fossil record reveals a history of life that is consistent with evolutionary expectations, and that documents numerous sequences of transitional forms that find no explanation outside of evolutionary theory. Against this Hunter presents the fact that the fossil record also documents long periods of stasis in fossil species. But why is that a problem for evolution? If Gould and Eldredge are right, then the pattern of stasis and relatively rapid change should be viewed as a vindication for modern theories of speciation, not as a problem for evolution. After acknowledging that known evolutionary process can explain a wide range of phenomena, Hunter fails to consider possible explanations for the data he cites.

As for the complexity of the trilobite eye, I'm sure Hunter realizes that the 400 mya date he cites is about 200 million years after multicelleular creatures appear in the fossil record. That's plenty of time for a decent eye to evolve.

He goes on to say:


I cannot prove the independent evolution of features is impossible. But what we do know is that these same designs would have had to have evolved on different continents, over geological time periods. This happens over and over, but evolution is a contingent process. There many ways to solve design problems in biology. The design space is large and multi dimensional in biology, with many different potential solutions. This is why evolutionists maintain that if we were to replay natural history, we would get a different world with different species and designs. There are no pre determined solutions. But these convergences contradict this and call into question Darwin's argument that similarities are strong evidence for evolution.


Comparative anatomy reveals many patterns of similarities that strongly suggest common descent (the identical bone structure of the forelimb in humans, whales and cats is a famous example). Against this, Hunter presents the fact of convergent evolution. He is fond of citing things like the converged upon saber teeth of certain marsupial and placental mammals. But why is convergence a problem for evolution? If the various genetic modifications required to produce saber teeth occur with reasonably high probability, and if there is selection pressure in favor of such teeth, then the convergence of these structures is easy to explain in terms of standard mechanisms. In fact, under such circumstances, a lack of convergence would be puzzling. In this sense, many known convergences can be viewed as vindications for evolutionary theory. Hunter routinely gives examples of convergences and asserts that they bode ill for evolution. But he never explains why known mechanisms are incapable of explaining the examples he cites.

Now, back to his main essay. Hunter changes gears in his next paragraph:


This is, however, not the main problem presented by the DNA code. I pointed out in the essay that the DNA code and associated machinery are highly complex. Evolution lacks a detailed explanation of how it evolved. Rosenhouse complains that this is a topic for the origin of life, not evolution: “Evolutionary theory has nothing to say one way or the other about the origin of the code. The code is simply taken as a given.”


Hunter writes that evolution lacks a detailed explanation for the evolution of the genetic code. Well, so does Einstein's theory of relativity, a fact that is about as relevant as Hunter's statement. It is a simple fact, not a complaint, that evolution is a separate subject from the origin of life. Darwin was explicit about this in The Origin of Species, as have most scientists since then.

Our entire understanding of how evolution happens is based on understanding the mechanisms that lead to changes in gene frequencies from one generation to the next. The universal common ancestor possessed a genetic code, and that is the point from which evolution is considered to begin. To even discuss anything like a Darwinian evolutionary process, you need a collection of imperfect replicators competing for resources. The first replicators were likely far simpler than the first thing that was unambiguously alive, but the fact remains that evolutionary theory takes for granted a certain minimal level of complexity. The distinction between the origin of life, and the subsequent development of life once it appeared, is not complicated.

Hunter continues:


Actually, evolutionary theory has plenty to say about the origin of the code, it just isn't very specific. The problem is not that the origin of the code has nothing to do with evolution, the problem is that evolution is unable to explain, beyond handwaving, how protein synthesis arose. Nonetheless, my point does not hinge on categorical definitions. Rosenhouse can draw the line between evolution and the origin of life problem however he likes. Evolutionists such as Mark Ridley still rely on the argument that homologies such as the DNA code would not exist "if the species had independent origins." [Ridley, 49]


At the risk of repeating myself, I'm sorry, but evolutionary theory has nothing to say about the origin of the code. Certainly there has been a lot of research into the origin of protein synthesis, and many theories have been proposed as a result of this research. But those ideas should be regarded as separate from evolutionary theory. Hunter discusses some of these theories in a later post. Without passing judgment on the worth of these theories, I would simply point out that none of them were proposed by evolutionary biologists. And to the extent that evolutionary biologists do write about the origin of life, the ideas their writings are based on come from other branches of science.

Of course, I did not say that the origin of the code has nothing to do with evolution. If we had a good understanding of how the code evolved we would also gain a better understanding of the earliest stages of evolution. But the fact remains that the origin of the code will almost certainly not be discovered by evolutionary biologists.

Findings in one branch of science often have relevance for people in other branches, but the lines between the branches are no less real for that.

And, sorry again, but Hunter's point does hinge on categorical definitions. If the origin of life is a discipline separate from evolutionary biology, then it is hardly proper to use difficulties in origin of life research to indict evolutionary biology. The quote from Ridley does nothing to alter that assessment. He is assuming only that it is asking too much of chance to argue that precisely the same genetic code and translation apparatus evolved more than once. You don't need a detailed theory of how the code originated to justify that assumption.

After writing this essay, Hunter posted some further thoughts on this subject later in the same thread. Since this later addition mostly just repeats his claims about the difficulty of explaining the origin of the code, I don't think it merits a separate response.