THEORIES OF SPECIATION

In my exchange with Vox, I've used the gloss TENS to stand for the 'Theory of Evolution by Natural Selection.' But it would be a mistake to think that evolutionary theory as a whole is defined exclusively this way.

John Wilkins, as is his habit, says much that it thought-provoking in a survey of speciation theories. He's even provided a graphic to make sense of the relative emphasis of each.

Enjoy!

VOX DEI-BATE #10: NO 'BACK-TESTING' HERE

Vox’s characteristic skepticism regarding TENS’s ability to lead to testable predictions has been well-noted, but in this post he actually sticks his neck out with respect to the Miller presentation that I posted about earlier here. As you may recall, Miller presented the evidence that human chromosome #2 was produced by the fusion of two separate chromosomes, and argued that the existence of this telomeric event was a testable prediction. Vox, who wants to characterize such claims as ad hoc (or, as he puts it, ‘backtesting’) is not merely skeptical, but incredulous:

"Scott's example is the work done by Dr. Ken Miller, who posits the rather bizarre notion that evolution is not only busy creating new species by natural selection, but also making testable predictions. This prediction - for which he shows no evidence of having been made prior to the test - is that "the common ancestor had 48 chromosomes (24 pairs) and humans carry a fused chromosome; or ancestor had 23 pairs and apes carry a split chromosome."

Well, Vox, ask and ye shall receive. It turns out that the original prediction of interest was not based on genomic data (which did not exist back in the 1970's) but on perceived similarities in banding patterns between primate chromosomes. It was easy to determine significant homology in many of the chromosomes compared on the basis of those banding patterns alone. However, this alleged similarity did not address the fact that humans and the other great apes differed in the number of chromosomes.

(Hmmmm---what scenario could explain the difference in chromosome number, and yet be consistent with that working hypothesis of common descent?)

To the best of my knowledge, the first suggestion that human chromosome #2 might’ve been produced by the fusion of two chromosomes which exist separately in chimps was made in a paper "Comparaison de la structure fine des chromatides d'Homo sapiens et de Pan troglodytes" by LeJeune, Dutrrilaux, Rethore and Prieur which appeared in 1973. I don’t have the original, but the abstract for that paper can be seen here.*

Now, what should be mentioned to the non-specialist is that this was a fairly daring proposal back in 1973. Relatively few examples of what were called Robertsonian translocations were known at the time, and virtually none involving telomeres----whose well-known role as a buffer against copying mistakes during cell division had led to their being regarded as ultra-stable structures, the sort of chromosomal chunk least likely to recombine or fuse with another. As Holmquist and Dansis (1979) remarked, events like telomeric fusion were considered "discordant with classical cytogenetic theories, which assume all chromosome rearrangements to require at least two breaks, and consider centromeres and telomeres as immutable structures rather than structures determined by mutable DNA sequences."

In that context, we can appreciate the boldness of the 1973 paper. The scientists who made it were specialists in the effects of such events on human chromosome, and they were justifiably confident in their ability to interpret banding patterns: the lead scientist on that paper, Jerome LeJeune, was the discoverer of trisomy-21 (Down’s Syndrome). Nevertheless, as this pointed critique of an ID enthusiast notes, the inference of an event of telomeric fusion was not in itself evidence for common descent: "It’s the sequence, not the fusion, that tells us of our relatedness."

Quite so—and it was ultimately the completion of that sequence in the Chimpanzee Genome Project that provided us with the high level of detail needed to either falsify or confirm the original speculative hypothesis, which (if true) predicted that telomeric signatures would be identified. The identification of the telomeres within human chromosome #2 (the fulfillment of said prediction) was made in 1991 and summarized here.

Note the beautiful convergence over time of completely separate research programs!Cytogeneticists, prompted by evolutionary theory, provided the scientific community with a testable hypothesis. Molecular biologists put that hypothesis to test with genomic data, which not only confirmed the hypothesis (the fusion event) but provided powerful evidence for a recent common ancestor for Homo and Pan.

* Yunis and Prakash’s 1982 article in Science is probably a more accessible discussion of the research program at that time, as well as the logic behind the hypothesis of telomeric fusion.

THAT 'DARWINIST' LABEL

I had an exchange early in the comments of a previous thread that, when reread, seems relevant to my ‘debate’ with Vox.* A reader, evidently one with an ax to grind, wrote:

With the expectation of true rational discourse, I look forward to your posting of the true objective scientific delineation of the full scope of the Darwinian theory, vis a vis, the present ideological naturalist philosophy of Darwinism that presently filters and strangles life sciences.

I replied, in part:

While my thought is Darwinian, I don't really think that there is such a thing as 'the Darwinian theory'. As for 'Darwinism', this term appears in the writings of UK scientists as a gloss for 'evolution through natural selection', but that's usually not the sense that it's used in the USA, where it seems to be perceived as part and parcel of a belief system. I sense this is how you are using it, since you couple it with 'ideological naturalist philosophy', in the manner of Philip Johnson.

I'll interject here and remark that one of the reasons I've adopted the gloss ‘TENS’ as a shorthand for the modern theory is an attempt to avoid that source of confusion. My companion, however, seems to be still puzzled by my approach, replying:

You spoke of being Darwinian, implying agreement with Darwin's Theory, the rest is semantics. I encourage you to define it succintly to remove any confusion, especially the differentiation from the belief system that has perjoratively become known as Darwinism: Just the science, no ideology.

Sounds good to me, so I sent him a post meant to clarify exactly what my enthusiasm for Darwin actually implied:

To me, 'Darwinian' means that I look at life from the perspective of Charles Darwin: I think in terms of populations, interacting with their environment. I tend to interpret all changes to be, if not necessarily optimal, as a product of many forces, chief among them natural selection. I don't rule out the possibility of some other agency at work, but as a scientist I confine myself to natural causes as a formal matter.

This is not the same thing, however, as a metaphysical commitment. There is a difference between methodological naturalism and metaphysical naturalism. The former is the way that most things (not just science) are routinely accomplished. Plumbing, for example: the plumber does not typically invoke supernatural causes for the moisture on the floor or in the walls, but busies him or her self with the task for determining which pipe is amiss. We all routinely assume natural causes for almost all sorts of activity or phenomena; science merely codifies this assumption as a boundary condition for doing science.

That effectively ended the conversation, which leads me to believe my interlocutor was indeed of the Philip Johnson mode, routinely conflating the collective practice of science with a personal metaphysics. Which, as my example should make clear, makes as much sense as berating plumbers for their metaphysical blinders in choosing a spanner over a prayer book.

*It’s been so civil and we’ve agreed on so many points that it seems odd to refer to it as ‘debate’—but perhaps the fur will yet fly.

A RED-LETTER DAY, LITERALLY

Can a letter change your life? Sure it can! On this date in 1831, a recent graduate of Christ's College, Cambridge (Bachelor of Arts, Theology) returned home from several weeks of 'geologizing' in Wales with the Rev. Adam Sedgwick, only to find letters from one George Peacock and another of his former teachers, the Reverend John Henslow.

Charlie Darwin had been invited to serve as the ship's naturalist aboard H.M.S. Beagle, and, not incidentally, to as a consequence commit to being a class-appropriate companion for the vessel's brilliant but high-strung Captain, Robert Fitzroy, the grandson of a duke.This was thought wise, as the previous Captain, one Pringle Stokes, had committed suicide during the Beagle's previous voyage to South America.

Such facts, and the general hazards of travel at this period did not faze Darwin, who immediately accepted only to find to his chagrin that both his father and his sisters were vehemently opposed: it was, they thought, not only fraught with danger but another excuse for Charlie to not grow up and accept the responsibilities of the country parsonage for which his status-conscious father had groomed him. Fortunately, Charlie's uncle (Josiah Wedgwood, of pottery fame) had a little clout with Darwin, Senior and intervened successfully on his nephew's behalf! Who could guess that this chain of letters would lead Darwin down the difficult path of uncomfortable discovery, toward (in Tennyson's phrase) to 'nature red in tooth and claw' ?

I GOT MINE!

I finally got my copy of my Dad's new book. All I can say is, wow. Writing the kinds of books that my Dad specializes involves much more than generating text. There are all sorts of other considerations with how to handle illustrations and photographs, and Dad's made clear that, in past work-for-hire projects, his input into that part of the process was limited.

You can't say that about this book: it's a labor of love, and my father had lots of editorial control over this project. It is not only the most interesting work he's ever done, it is also the most visually arresting of his books. It is, in a word, a thing of beauty that draws admiration from folk who know nothing about the colorful history of motorcycling.

I should warn those who are interested, however, that this book is unlikely to pop up in bookstores any time soon. My Dad has chosen to directly market it himself! Those who want more information can e-mail the author at: beemer73@sbcglobal.net

VOX DEI-BATE #9

I'm going to tie up a loose end from a previous post before addressing the rest of Vox's most recent offering. Before I start, let me stress that I am not a mind-reader, and this is not amateur night at Sigmund's, and no personal criticism is implied. This is my attempt to understand Vox's general orientation, in order that both of our views get a fair shake. I would like to have Vox respond to this, to clarify or offer correction, before I address the questions that his most recent post raises---because I could be wrong here and I want to be fair.

Anyway, the loose end can be found in this quote from Vox's most recent post:

(Vox) Despite our varying degrees of trust in TENS, I think we are nevertheless beginning to find some common ground. I'm particularly interested to discover where Scott is going with the following statement; no doubt many of you are too:

(me) I think this observation has some bearing on some issues that Vox has raised in the past few posts as to how some 'evolutionists' have enlisted Darwin to 'attack religious faith', ridicule politicians who fail to say they 'believe in evolution', or attempt to suppress skepticism about TENS as unscientific.1

First of all, I don't believe that any of the above concerns are scientific questions, regardless of where we might stand. They are cultural concerns, and often politicized. The concerns as raised could be true, they could be false, but they would have no bearing on the question of whether or not TENS is the best model we have now, or likely to be the best model we have in the future.

Secondly, Vox has been very open about his lack of formal education in biology, particularly evolutionary biology, and much of his acknowledged sources are popularizations:

"I'm curious to see what sort of answers science has for someone who hasn't paid any more attention to the literature than reading four of Dawkins' books, plus "Darwin's Dangerous Idea" by Daniel Dennett."2

This feeds my impression that Vox's skepticism with respect to evolution is not so much with the discipline of evolutionary biology as practiced, but with the baggage that comes with books that are as much works of advocacy as they are expositions of science, especially those by Dawkins. In fact, I think that his beef is largely with Dawkins, especially Dawkins the popularizer of 'evolution-as-another-nail-in-religion's-coffin', who first makes a distinctive appearance in The Blind Watchmaker (1986). This is certainly the Dawkins that the guy in the pew is most likely to have heard of, especially since publication of The God Delusion (2006).

Again, I'm just speculating and Vox can correct me if he likes, but the money quote for me is this:

"....that it is scientifically irresponsible to argue that one must be either stupid or ignorant to possess doubts about TENS."

This is awfully reminiscent of a pretty famous quote from Dawkins in which he lays down the gauntlet, one that has been parroted ever since by outraged creationists (present company excluded, of course):

"It is absolutely safe to say that if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I'd rather not consider that)."

Now, if you're one of the outraged, you owe it to yourselves to read the full book review from which this passage comes, because the failure to nest it in its proper context does a great disservice to Dr. Dawkins. In the review, Dawkins goes on to say that he doesn't believe that his readers are likely stupid or insane, and talks about recent experiences in touring America, and concludes that his main impression was one of "sincere questions from intelligent people who really wanted to know because they had literally no education in evolution." 3

That's not a prejudicial statement. It's the truth. Surveys reveal time and time again that ignorance on this topic is widespread in North America. Even those who naively say they 'believe' in evolution often harbor profound misconceptions of what TENS is really all about. In fact, based on my experiences as a teacher, I believe that the misconceptions attached to the theory in the popular culture are at least as much of a barrier to its acceptance as any prior theological commitments on the part of its audience.

Now, recognizing that Vox may not have intended to paraphrase Dawkins (it just came out that way, perhaps?), let's break it down: what doubts does Vox really have, really, with TENS? He doesn't doubt that TENS "is, as he and others have said, the best model they've got right now." He acknowledges that he's unlikely to present an alternative model that would pass muster, and I suspect he knows that at present nobody else is in a position to do so, either.

Nor, to Vox's credit, does he play the creationist card of arguing that, in the absence of positive evidence for an alternative model, it is sufficient to bring negative arguments against evolution as grounds for rejection. Vox may not, by his own admission, know much about the biology but he's smart enough, I think, to recognize that virtually all of those negative arguments have been throughly addressed by people who know a lot more about the science than he does.

Besides, it's not really the science that bothers him. Vox understands that scientific claims are always tentative, always subject to review/modification/rejection in the light of new findings. He clearly is not losing sleep at night because the silly biologists who can't predict things the way they do in his field of economics don't have a better model. No, what gets Vox exercised is the uses to which the 'evolutionists' he knows about put that model. And that usage is clearly atheism. With that in mind, let's discuss some points of agreement.

" I can state with complete confidence that it is utterly absurd to attack religious faith on the basis of TENS..."

Well, I'm a believer, so I'm clearly not attempting to attack religious faith on any basis, yet I'm an enthusiastic evolutionary biologist. With Michael Ruse (someone Vox really needs to add to his reading list), I would answer 'yes' to the question 'Can a Darwinian Be a Christian?". Can any scientific theory, including TENS, 'prove' God's non-existence.? Of course not: that's excluded by the nature of science itself! As Vox himself has written, "those who attempt to enlist TENS as proof for things which cannot be tested have left the domain of science. "

So, in that sense I actually agree with Vox. If someone thinks that the fact of evolution conclusively 'proves' God's non-existence, that shows that they don't even understand how science works.4 On the other hand, Vox, 'Darwin's dangerous idea' does demolish the Argument from Design, whether we're talking about William Paley's watch or Michael Behe's claims of 'irreducible complexity.' Evolutionary biology might not 'disprove' God, but it cripples one of the better arguments that historically has been made for God's existence in the past, that of teleology. It provided the conceptual framework and the data to justify Hume's famous skepticism: no one who understands the history of this debate can be considered credible who does not acknowledge the devastating effect that Darwin's thought has on teleology.

So, in that sense I would say Vox is wrong: an attack on religion that does not rely exclusively on a rejection of teleology in its' attempt to unseat the Almighty is not absurd in its face. In his favor, I point out that the object of his wrath (Dawkins) has only recently found it necessary to buttress his traditional, evolutionary-based skepticism with other arguments----but I could care less about that myself because, as should now be clear, whenever Dawkins steps out of his evolutionary theorizing to argue toward God's non-existence, he is no longer doing science. Now, more Vox:

"....it is ridiculous to ask political candidates whether they "believe" in TENS."

I agree with Vox again, but not because one can reject TENS outright on the basis of science. It's that word 'believe' that I object to. Properly speaking, I don't 'believe' in evolution, either: that implies an affirmation of faith, but I don't need faith to accept that evolution is a fact, or that natural selection is a fact, or that in individual cases natural selection has been observed to lead to evolution, etc. No faith required! Rather, these are simply facts about the natural world that any credible model must acknowledge and account for. The question that was put to the GOP hopefuls many weeks back was crude to the point of being misleading, but (sigh) politics is often not about making logical arguments that use language properly, right? It's a shame that not one of them had the sophistication to point out the absurdity of the question, and in the process affirm that evolution is good science.

Finally, we come back to this: "...it is scientifically irresponsible to argue that one must be either stupid or ignorant to possess doubts about TENS as a theory capable of standing up to the conventional definition of the scientific method of hypothesis, testing and replicable observation."

I omitted the last clause in my prior discussion, because while I think that what partially motivates Vox's skepticism is his distaste for Dawkins and his disciples, what informs his actual argument is his understanding of theories. His 'back-testing' argument is an attempt to argue that, see, evolution can't do some of the things I think a truly scientific theory ought to do, so, while it can do some things, I feel justified in being skeptical about those things that can't be tested until I can see more confirmed predictions to a higher level of accuracy.

Well, obviously I'm not impressed by that argument. TENS is a robust theory in its proper domain, biology. The central claim (that evolution is caused by natural selection) is a hypothesis that in countless cases has been tested and verified. TENS potentially unites a vast number of different observations from different research programs in a powerful web of explanation. Many observations derived from TENS are manifestly replicable---in fact, so much so that they are rightly considered trivial.

Within that web of explanation there have been proposed many individual hypotheses, many of which are often difficult or impossible to test, or which subsequent research has falsified. Vox completely misreads the situation here in my judgment: his 'intuition' regarding a high margin of error and many falsified predictions derived from TENS leads him to be skeptical about as a whole, but the status of TENS as a scientific theory does not rest on the question of whether every application leads to testable predictions, but whether evolution by natural selection is a testable prediction itself. In fact, the falsification of many hypotheses, the debates within evolutionary biology on how to best conceptualize various items, all of these seeming 'defects' that creationists are constantly trying to hang their hats on are actually a sign of the robustness of TENS as a scientific theory. What Vox intuits as a weakness of our research program, ironically, is precisely what those of us who actually study biology regard as a strength!

I'm going to stop right here and give Vox a chance to correct any of my armchair psychoanalysis and ask his pardon in advance if I've mischaracterized him. I suspect that Vox and I are in substantive agreement that TENS is the only game in town, and that he is not actually urging anyone to reject TENS outright. Rather, he is skeptical about the applications of TENS to those things which are difficult or impossible to test, and deeply resents those who would employ such applications as personal weapons in the cultural wars. I sympathize, but I'm not here to defend such practicies, I'm here to defend TENS.

1) Even the claim that skepticism with respect to TENS is discouraged can be expected to have no long-term consequence if sufficient evidence emerges that is best explained by an alternative model! The only way to slow the self-corrective nature of the scientific enterprise is to enlist tyranny in behalf of some privileged belief system that feels threatened: geocentric interpretations of the Holy Scriptures in the case of Giordano Bruno, rejection of the state-sponsored Lysenko vernalization program by Nikolai Vavilov. Despite Bruno's execution and Vavilov's torture, the global scientific community persevered: both the geocentrism of the Church and the Lysenko's "genetics" are throughly discredited.

2) For all I know, two of the Dawkins books that Vox refers to could be The Selfish Gene (1976) or The Extended Phenotype (1982), which are deep, far-reaching books that, while accessible to laymen, can not really be said to be popularizations. These books are at best only tangentially concerned with defending the general correctness of the modern theory: rather, they discuss technical and conceptual challenges within evolutionary biology, and are addressed at least as much towards workers in the field as to the well-read layman. It would not surprise me if Vox had read these, he's certainly capable----but, as mentioned above, I don't think that this is the Dawkins that he has a beef with.

3) This mild-mannered take may be hard for some of you to square with the image that you may have of Dawkins. If so, watch this conversation between two old friends. And, at the risk of sounding like a name-dropper, I know from personal experience that Dawkins is really willing to reach out to anyone who is willing to promote honest engagement on such matters, even in the pews.

4) It might interest readers to learn that Dawkins has never made that claim, and he discusses the subtleties of this in The God Delusion.

CAUTION

If you are an educator, or if you care about education, you should be careful about clicking on the link. Don't do this on a full stomach. I'm warning you.

This is Miss SC on the problem of geographical literacy.

THIS SEEMS FAMILIAR

Lately, I've seen a lot of oblique arguments sent my way aimed at evolutionary theory: you know, it doesn't always make good predictions, it has a high margin of error, etc. One would get the impression that this is somehow news, or that the economists and engineers are pointing out some problems that biologists are unaware of. How sweet of them.

But, believe me, the ANOVA scenario above is brutally familiar to young biologists who want to devote themselves to publishable research. What actually goes into the literature has to survive intense scrutiny: it's not the actual science that these creationists are troubled by, it's the popularizations of science that they prefer to read (and, typically, misinterpret) that get their panties in a knot.

By the way, Jorge Chan's comic strip Ph.D is a hoot. Check it out!

QUAMMEN HAS FANS

Yes, it's the Seventh-Day Adventists, the original flood geologists, new and improved. Accept no substitutes. They've got another slick campaign for creationism headed to your local community. Check out this slick, powerful site which is essentially pitching a four-part seminar series prompted in part (they imply) by David Quammen's 2004 piece for National Geographic.


That issue sort of lured a lot of creationists into the mix with the sort of technique we associate with tabloids, posing a big, dramatic, suggestive leading question on the cover ('WAS DARWIN WRONG?'). When opened up, the very clear response of Quammen and National Geographic had to come as a let-down for all those young-earth, original-kind folks:



Anyway, I don't know how Quammen feels about it, but this latest SDA-sponsored effort fills me with misgivings. The Clovis SDA church sponsored the last creationist foray in my area back in February, and they somehow managed to give an entire week's worth of seminars (a revival meeting, really) on the Buchanan High School campus in my neck of the woods (Clovis, CA), all without identifying their sectarian origin in the local paper, which ran a full-page ad to plug the things in its 'Faith and Values' section. Not only was creationist Walter Veith featured taping his presentation for future resale at the event, but there was even an evening devoted to anti-Freemasonry conspiracy stuff.

Let's just say that I, some fellow science teachers and the rest of us were non-plussed at the whole affair (it went on for five consecutive evenings) and viewed the district's non-response on our concerns with alarm. Perhaps that has something to do with the CUSD board, which numbers among its members an Adventist (Dr. Susan Walker) who graduated from Loma Linda University, the SDA college which is affiliated with the flood geology-peddling Geoscience Research Institute.

In general, I like SDA.* Unlike a lot of fundy outfits, they have a strong academic orientation, and many SDA are highly educated. My family has SDA friends, people of the highest quality. But this latest bit better take place at their church, not on a public high school campus. I'm hip to their jive now.

**************UPDATE*****************

*PZ linked to me and said I'm being too kind to SDA. He's right about that, but when I think about it, PZ's probably going too easy on me, for a lot of reasons, not the least of which is that kooky SDA founder Ellen Price came out of some version of the kooky Methodism I subscribe too. So, glass houses and stones, and all that. I really appreciate PZ and anyone else who passes this information along, though.

In the meantime, I can't forget that SDA produced, among others, Ronald Numbers. For those of you who don't know, he's really the expert on the beginnings of flood geology, first actively promoted by an SDA named George McCready Price. Anyone who really wants to understand the origins of the modern creationist movement should read this book.