HOUSE-KEEPING ANNOUNCEMENT

If you didn't see, I added to my prior post below and greatly expanded it. Enjoy! I'm waiting for more comments or questions from Vox before I proceed....

VOX DEI BATE #5

Time prevents me from a full comment on Vox's most recent set of observations. I look forward to his discussion of my previous post, which compares two predictions concerning whether intermediates to modern whales would ever be found in the fossil record.

In the meantime, Vox writes:

"....we should have no problem finding one or two and demonstrating that they are a new species that did not previously exist, assuming that this is, in fact, happening."

It's been done, by Dobzhansky's group, in the early 1960's: you can read about it here. There are other examples, though the literature in this case is not as deep as the pallid piles of papers in Keynesian macroeconomics which seem to trouble Vox. That's because it's clearly science, and real science is hard.

(UPDATE)

Now, again, (and Vox has acknowledged that this is valid, I think) I don't want to get sidetracked in a 'turf war' between economists and biologists, because it's in no way central to the topic. But Vox is at pains to explain, based upon his experience, the relevance of the comparison in his original argument:


From what I've seen of evolutionary projections, its margin of errors are even greater than those seen in macroeconomics. Since this level of inaccuracy causes me to dismiss macroeconomics as a science, it leads me to similarly dismiss evolution. Obviously, if it can be shown that the macroevolutionary margin of error is smaller than that of macroeconomics, I'd be happy to reconsider. (my emphasis)

I think there's a basic error here: the map is not the territory! Vox is not arguing here that the theory of evolution by natural selection (TENS) has been falsified generally. Rather, he's saying that 'evolutionary projections', models based upon TENS, have a relatively low precision, which presumably leads to a certain level of inaccuracy. Well, that's true for a lot of things in science, not just specific models based on TENS. A high margin of error is not sufficient to disqualify a research program as unscientific, however, unless it can be shown that a different research program based upon a different model has a lower margin of error.

An example from the history of science should make this clear:

Johannes Kepler, like those astronomers who came before him, began with the belief that planets moved in perfect circular orbits. Problem: this hypothesis didn't fit the data, notably the 'wanderers' (planetai) that seemed to change direction. Like Ptolemy before him, Kepler trusted in epicycles, 'wheels within wheels' that would preserve the hypothesis of perfect circular motion. These models worked with a certain margin of error and, for most heavenly bodies, the discrepancies were so small once the epicycles were added that most felt they could be ignored---except, in Kepler's case, for the orbit of Mars. An exhaustive series of calculations based upon the best data available (Tycho Brahe's observations) led to a closer fit to the Ptolemaic model, but still with a certain margin of error that Kepler found unacceptable:


If I had believed that we could ignore these eight minutes, I would have patched up my hypothesis accordingly. But, since it was not permissible to ignore, those eight minutes pointed the road to a complete reformation of astronomy.

So, by analogy, Vox is in a similar predicament to Kepler at this stage of analysis. He's unsatisfied with the error rate, and---feeling confident (perhaps overconfident) that he's got the best data available, concludes there must be something wrong with the model. But was that really enough to unseat Ptolemy, whose properly-tweaked model still gave better 'predictions' than any other model up till that time? Of course not! Kepler was obliged to propose another model and show that it gave better results, with a lower margin of error.

Which he did, one based upon ellipses rather than circles, and in the process Kepler discovered some generalizations about the behavior of heavenly bodies which presaged Newton and which have since been described as his 'Laws of Planetary Motion'.

But the story doesn't end there! Both Kepler's Laws and Newton's Law still maintain a certain margin of error, albeit one lower by several orders of magnitude than, say, geocentric solar systems or Archimedes' statics. But the existence of these discrepancies did not automatically lead either of the former constructs to be rejected as science! These 'Laws' came to be seen in the 20th century as limiting cases of Einsteinian mechanics, whose margin of error becomes significantly lower at certain scales. In fact, no one would've been willing to embrace Einstein's thought, with all of its counter-intuitive moves, had there not been a 'trade-up' in precision!

So, Vox, you can play the part of evolutionary skeptic all you want to, but you can't expect the scientific community to join you in rejecting TENS on the grounds that you've given (its high margin of error) unless you can do what Kepler did and propose a testable explanation whose margin of error is significantly lower.

Now, Vox, I am guessing that you don't reject Keynesian macroeconomics out of spite or prejudice, but that you honestly feel that there are other models that do a better job of predicting economic behavior. That's not my bag, and again I'm disinterested in provoking a 'turf war.' What I want to know, Vox, is if you or anyone else has a better explanation for the history of life than TENS, a model that yields falsifiable predictions that, when observations become available, have a lower margin of error than TENS. Because, if you can't, then your skepticism remains an intuition, rather than sufficient grounds to reject evolutionary theory as science.

"THE NEW MOTORCYCLE BOOK'S HERE!"

(Repeat the above blurb in Steve Martin's manic late 70's delivery several times.)

Yes, the old man has received delivery of his latest book. You can see part of the new book's dust jacket behind the gentleman whose hand he is pressing, a friend who owns a warehouse. My father's better half is smiling in the middle, but I bet my Mom is probably wondering about how much profit Dad's going to realize from this venture. Unlike previous books, this venture's self-published and will not be available in book stores. More details to come!

VOX DE BAIT #4

More provocative questions from Vox....

Is it correct to say that "we just don't see clear evidence of speciation in the fossil record"? This appears to contradict what I have been taught about evolution since elementary school.

I can't really answer that, Vox, unless I know the context of the quote. We can certainly infer speciation in the fossil record, and there really are transitional forms.

This provides, by the way, a great opportunity to present a test case of a pair of competing predictions----one, from Darwin; the other, from the authors of the notorious textbook Of Pandas and People.

In the first edition of the Origin (1859), Darwin received a lot of criticism for one of his more 'far-out' suggestions, which appeared in Chapter 6 ("Difficulties On Theory"):

"... I can see no difficulty in a race of bears being rendered, by natural selection, more and more aquatic in their structure and habits, with larger and larger mouths, till a creature was produced as monstrous as a whale."

Now this quote clearly predicts the possible existence of intermediate forms between a carnivore that lived on land and a modern whale. Again, pretty far out for Darwin's day, and when Darwin made a number of changes in the second edition in an attempt to placate the sensibilities of his comtemporaries, he leaves this speculation entirely out. Writing nearly 130 years later, the authors (Kenyon and Davis) of Of Pandas and People (1989) remark:

"The absence of unambiguous transitional fossils is illustrated by the fossil record of whales. The earliest forms of whales occur in rocks of Eocene age, dated some 50 million years ago, but little is known of their possible ancestors. By and large, Darwinists believe that whales evolved from a land mammal. The problems is that there are no clear transitional fossils linking land mammals to whales. If whales did have land-dwelling ancestors, it is reasonable to expect to find some transitional fossils. Why? Because the anatomical differences between the two are so great that innumerable in-between stages must have paddled and swam the ancient seas."



In other words, clearly implying such 'transitional fossils' would not be found, because they don't exist. This is also a prediction, and we can now test it, along with Darwin's prediction: Hello, Phil Gingerich! Click on this fabulous link, and see the truly wonderful work of this scientist, who starting in 1981 (with Pakicetus) helped uncover many new fossils with transitional features between a land-based carnivore and modern whales . . . .

Now, do these examples, are they fulfillment of exhaustively precise scenarios, as in 'you're gonna find such-and-such a fossil in such-and-such strata at such-and-such a location, of such-and-such an age?' Of course not, but their existence, unknown both to Charles Darwin and the Panda authors, constitutes a test of their respective predictions.

And...as you can see....one fella's speculation is pretty robustly corroborated, whereas the claim that no transitional forms between land animals and whales has been pretty much----you should pardon the expression----blown out of the water:




I would be remiss if I did not also provide a link to this incredibly detailed, illustration-rich exploration of this topic by E. Babinski. And clicking here or on any of the whale fossil illustrations will take you to the UC Berkeley Museum of Paleontology's 'Understanding Evolution', a wonderful resource to which both Babinksi and myself are indebted.

VOX DEI BAIT #3

First of all, I added some stuff to the prior post.

Second of all, if you were expecting me to reply to any comments on Vox's site today, that's not going to happen during business hours. Don't have the time, and even if I did, I'd have to run an end-around the district's firewall to leave comments from my computer at school. Leave comments for me on my site, and I'll make a good-faith effort to always provide the appropriate context to which my response is based, as well as a link to Vox's latest offering.

Vox writes:

A change in the frequency of alleles within a population is the genetic definition of evolution. What is the genetic definition of speciation?

I'm not really sure we could define speciation in genetic terms without it being very awkward and disjointed. Speciation is usually defined in functional terms, according to the reproductive (or biological) species concept popularized by Mayr. That is, a species is defined as a population or populations which are only able to bear fertile offspring with one another in nature. You could, if you wanted to, express that genetically but why go to all that trouble? We know that there is a genetic basis for whom we are able to have fertile offspring with, and that should be enough for our purposes.

Note that species concepts are just that, concepts. If you're really interested in learning about some of the other ways of conceptualizing the elusive notion of 'species' you should really check out Wilkins's archive, especially this.

Are nucleotide substitutions to be regarded as the genetic equivalent to darwins?

Definitely not. Darwins are scalar quantities that represent measurable changes in traits, in the phenotype. Many nucleotide substitutions have absolutely no effect on the phenotype. Evolution as defined genetically can occur without speciation, without any sort of observable phenotypic trend in the population.

If not, what would be a reasonable definition of a "mendel" that would allow us to track the average rate of genetic evolution as one species transforms into another?

Nucleotide substitutions allow us to estimate rates in which new mutations become fixed in the population, but this has no direct correspondence with speciation. In fact, the higher the rate, the less likely the locus in question is under direct selection, and (as far as I know) the less likely it would contribute to any speciation event---based on what we know today. I add that caveat because the regulatory role of non-coding DNA is an active area of research, and it is always possible that we may find that certain introns might have a role in, say, stabilizing the genome if it is undergoing an episode of reorganization.

VOX DEI BAIT #2

Vox raises some interesting questions. I'm going to beg off on at least one:

3. Is the acceptable margin of error greater for economics or evolution? (It's much larger for both than people realize.) What margin of error is too great to allow a discipline to be reasonably considered a science?

This was prompted by unflattering comparisons between the two, some of which was aimed at tweaking Vox, who thinks he has some credentials in the former area. I don't want to get sidetracked by something like a turf war. I'm not sure that the margin of error is the issue in either case; it's just that both fields study complex phenomena that are more difficult to model than, say, perfectly round billiard balls moving on a frictionless surface. On with the show....

Do you understand the difference between a historical model and a predictive model? If you don't mind, would you quickly explain to those having problems understanding the difference why this is relevant to a discussion of evolution?

This is reminiscent of Charles Thaxton's distinction between origins science and operations science, which Sonleitner discusses here. (More vulgarly, Ken Ham is fond of asking his audiences "Were you there?") In general, historical models are based upon inference, rather than direct experimental test. There is nothing inherently unscientific about the former, as long as you are willing to accept that a higher burden of proof exists. Which is fine: extraordinary claims require extraordinary evidence. It might be added that claims that can be falsified by a single experiment are, often as not, trivial or (as in my above example with a frictionless surface) artificial.

And which type of model, in your opinion, is a better description of the current state of Neo-Darwinian theory?

I don't care for the term 'Neo-Darwinism'; to many Americans, it implies something like religious belief. I prefer the term 'modern synthesis' or 'modern synthetic theory' because this gives the real flavor of the enterprise as I know it. I think the question as posed is a false dichotomy. Simply put, as a synthesis the modern theory contains both historical and predictive elements, inference and observation, speculation and rigorous test.

Now, having said that, it's pretty important that evolutionary biologists (EB) should be at pains to distinguish between inference and experiment, etc. In general, the scientific literature itself is very good at making these distinctions in the discussion of results and their interpretation and popularizations of science are not. And that's a big part of the problem!

Here's an excellent article from the ASA (American Scientific Affiliation) website by Keith Miller that discusses this question. The author, a paleontologist and a Christian, concludes that the differences between the historical and 'hard' sciences in terms of testability are greatly exagerrated.

Is Talk Origins a reliable source? I seem to have come under an amount of criticism for relying on it. If it is unreliable, can you suggest an acceptable one?

The technical articles at Talk Origins seem pretty solid to me, and I don't hesitate to refer to them. I don't pay any attention to the other stuff that goes there, and I suspect that's what bothers some creationists. TO is assertively pro-evolution, and some of the legendary kerfuffles in its forums show partisanship (on all sides) at its worst, but that has no bearing on the scholarship in the technical articles, some of which is outstanding. There are few people who have considered more creationist arguments in more detail than Mark Issak, and I admire Doug Theobald's work, as well.

I conclude that pro-evo types should not, in my opinion, have any problem with Vox basing his arguments on anything at TO, but they certainly have a right to rake him over the coals if they think he's misrepresenting or misunderstanding the material he refers to.

Creationists who don't like TO because of its perceived partisanship might want to look at the ASA site. They have a searchable archive of their journal (Perspectives on Science and Faith) going back nearly 50 years, with lots of scholarship, that's a tremendous resource. Most of the authors are Christians, and they run the gamut between YEC's and full-blown evolutionary biologists. (Disclaimer: I'm a member myself)

Another good source for those who are wary of TO is the archives of the National Center for Science Education. It's a p'm a member of this organization, as well as ASA. There's a lot of detailed criticism of the leaders of the ID movement here. (Disclaimer: I belong to this outfit, too)

Well, I have to go earn a living now, I'll be back for some of Vox's other questions later!

NOT IN KANSAS, AGAIN...

Whenever I see someone asking for a 'trail' of transitional forms (and there are plenty), I know those who make this demand will never be satisfied. No matter how many fossils we find, they will always complain that there are some 'missing links'.

It is as if we have tens of thousands of movie stills showing July Garland in various locations in Oz, which can be arranged to tell a story of her arrival, quest and ultimate return to Kansas---and yet some of us insist that we have not 'proven' that there is any actual film called 'The Wizard of Oz'.

Instead (they claim) each and every frame must have been deliberately crafted by the still photographer, and the idea that they can be arranged to tell a moving story is just some fantasy we've all agreed to promote in order to deny the still photographer's existence.

VOX DE BAIT #1

And we're off, with slinging salvos between Vox and PZ.

PZ thinks Vox's argument is, well, phony. He claims that Vox has lifted a remark from Gingerich as to the amount of generations it might take to evolve an elephant from a mouse (Vox didn't specify sources in his original post), and he thinks that the argument depends upon a distorted understanding of how biologists measure rates of evolution. Whatever one thinks of this argument, I have to admit that I haven't heard this particular line of reasoning before. I wonder what Phil Gingerich might think about this? I think I shall ask him!

Vox, with an update to his original post, thinks PZ didn't read his argument very carefully and suggests that evolutionary experts should provide a prediction as to how long such a transition might actually take place, at the end of which time we should collect our Nobel Prizes.

At any rate, Vox used both a personal anecdote as well as this example as an explanation of the gnawing misgivings he has about evolution and natural selection. I'm still not sure what he thinks the actual status of these items shall be from his reply, but (no surprise) I think we can rule out any pan-adapationist orientation from Vox. Before I reply further, I think I would like to give Vox a chance to ask me any sort of follow-up question on this topic.

To be continued....

ZENO, MY HERO

If you're a veteran of the evo/creo wars, this post from Zeno is required reading. Seriously, you must read this: ICR is moving!

VOX DEI BAIT (Prologue)

Sorry if the title makes anyone cringe. I just couldn't resist.

I'm getting ready to kick off my exchange with Vox Day, who seems sympathetic to some sort of ID creationism. Before you get callouses from rolling your eyes too rapidly, I should say that Vox, who has his own little corner of cyberspace, has an interesting personal history that suggests that he's going to offer something new in this department, if only in flavor.

So, it's a debate of sorts---but I hope to actually learn something from the experience, and so I'm going to just throw some questions out there, initially, and encourage him to do the same. There's no point in belaboring the points where we either agree or (if we disagree) don't feel it matters that much one way or the other. And, even though I joshed about 'baiting' Vox in this post, I'm just naive enough to think that we can really have a meeting of the minds here, as opposed to mere street theatre. Here's hoping!

Anyway, here's my first set of thoughts for discussion: in your opinion, what is the status of evolution by natural selection as an explanatory model ? What sort of explanation is it? What, if anything, does it explain better than other models?

Standard disclaimers: the fact that some fellas are going to debate matters related to some item of science does not imply that there is actually a scientific debate about the matter in question.

I LIKE WENDEE

Wendee Holtcamp, that is. She's a professional science writer, a Ph.D candidate, the author of 'The Fish Wars' (a must-read for partisans in the evo/creo wars, I think) and she has a blog, here.

Here Wendee tries to see the forest for the trees where fundamentalism and faith are concerned. Check it out!

PLEASE JUNK THIS ARGUMENT

I'm warming up for my exchange with Vox Day by trading thoughts with some of his readership, and one of them repeated a trope that I hear a lot from people who profess to be interested in defending the integrity of science. They are concerned that 'evolutionary bias' may be preventing good science from being done: that is, that a current model for this or that phenomena, derived from evolutionary theory, is not going to be challenged even if false, etc.

That raises a number of points which we could debate another day: whether science is wedded to philosophical naturalism, as Philip Johnson has made a career of asserting, or the proper role of existing paradigms in guiding research programs, or whether astronomers have 'gravitational bias.' All interesting, but what I want to focus on is the 'junk DNA' version of this hypothesis. According to some, the suggestion that non-coding DNA was 'junk' was quickly embraced by scientists eager to deny design, and this bias harmed the practice of science.

Well. Larry Moran doesn't think much of this argument, and neither do I, but I actually had to research this for all of 15 minutes to place this it in context, and provide the facts needed for my reply, a truncated version of which follows:

" Introns were discovered by Sharp and Roberts's group at MIT in 1977, for which they were awarded the Nobel Prize (1993).

In 1978, Gilbert and others began interpreting this finding as implying that non-coding DNA is vestigial 'junk' with no function. The term 'junk DNA' is associated with two influential papers (Doolittle and Sapienza, Orgel and Crick) which appeared in Nature in 1980. The discussion of function in these papers was speculative, nuanced and there was a call for more research. These facts are often omitted by ID creationists eager to impute 'evolutionary bias.'

(T. Ryan Gregory is, if anything, even more alarmed at the way these ideas have been reported versus to how they were presented in the literature. He has some informative comments here, along with extensive quotes from the above papers demonstrating that they never ruled out functional explanations for non-coding DNA out of deference to evolution.)

That was less than 30 years ago. The necessary tools for testing these claims (PCR, DNA fingerprinting, etc.) did not exist at the time the Nature papers were published and they did not become widely available until the early 1990's.

Studies were published as early as 1992 that showed preferential sorting of 'junk DNA' within the genomes, and actual evidence of function for introns was published by 1994. By 2003, writing in Scientific American, W. Wayt Gibbs remarks, paraphrasing John Mattick, that the failure to recognize the importance of introns “may well go down as one of the biggest mistakes in the history of molecular biology.”

Yeah, well, it was a "mistake" that was corrected by the scientific community within less than two decades once the tools were developed to test the claim. Contrast that with the two millenia that Aristotelian essentialism hindered the emergence of population thinking in biology, or the long constraint that the church-endorsed Ptolemaic model held in astronomy.

I'm going to let Professor Moran have the last word, because he's so much more indignant than I am. Just remember, kids, that while individual scientists as a whole may be blinded to this or that piece of evidence (we're all human), the scientific community as a whole is always shining lights in dark holes, gradually bringing more and more of the natural world into sharper focus. Compared to the creationists, we are the one-eyed men, and that makes us kings.

TOO CLOSE FOR COMFORT

We're Number 1!

The San Joaquin Valley, that is, specifically the town of Arvin. This story, forwarded to me by my colleague Sean Boyd, isn't exactly news to those of us who live here.

When I came to Fresno County in 1980, you could see the mountains along its eastern perimeter virtually every day that was bright and sunny. Nowadays, that only happens in the 24 hours immediately following significant amounts of rain. Our air quality is abysmal, and unlikely to improve for decades. In fact, in Arvin's case, it's the nation's smoggiest, and we're too close for comfort.

Anyway, to provide some context for y'all who choose to read this story, I've made the graphic you see here. The green box is a blow-up of that region of Kern County and the red square in the center of the map is the approximate location of

Two personal anecdotes bear repeating here:

1) Sean Boyd, who worked in our region for over 25 years as a radio and TV weatherman, has the unusual distinction of being fired for (no lie) refusing to cook his weather forecasts to suit the political agenda of his bosses, which you can read about here;

2) My mother and I once spent a miserable day in retrieving my car (which had broken down on the main highway) only for hers to break down as well, with both vehicles on the side of the road. (Again, the map provides context) The Highway Patrol summoned the guy who owned the only towing business within an hour's drive, and he drove about 20 minutes to meet us and our two broken-down vehicles. He towed us to Arvin, where the cars were worked on by an ingenious (but almost certainly undocumented) Hispanic who did not speak English on a property owned by the tow truck guy---who was also the town's mayor and school superintendent. Let's just say they had us where they wanted us, and made us an offer to fix the cars that my mother couldn't refuse. Poor Mom. First, she got me for a son, and then this.