Backdoor ID?

I’m on record as saying I’m not opposed to kids learning about “Intelligent Design” in public school as long as it’s not presented as actual science. But here’s an interesting case: apparently a school in California positioned a class on ID as a philosophy course but then basically reeled off ID as science (with the help of videos that, the plaintiffs allege, “advocate religious perspectives and present religious theories as scientific ones”), without presenting much in the way of opposing views.

I’d like to know more about this, naturally, but given the information in the article this doesn’t sound at all kosher. If you’re basically offering a non-critical presentation of the ID material with noting else added, you’re probably violating church-state separation regardless of which class you teach it in. There’s a difference between describing and discussing ID as a social phenomenon, and just sitting the kids down and running a video. I mean, come on, ID people. At least try to pretend you’re attempting something other than indoctrination.

A good question here: How would you design a class, philosophy or otherwise, that discusses ID intelligently (heh) and without violating church-state separation? Personally, I think I would design a class called “Concepts of Creation,” which looks at the various ways humans have tried to describe the beginnings and progressions of things, including myths, history, and science. ID would fit in there as a modern creation story, but it would be in a context where it’s not presented as science, nor presented in isolation. It could be an interesting class, in any event.

80 thoughts on “Backdoor ID?

  1. I think your idea of “Concepts of Creation” would be great, if taught in the manner you suggest.I would suggest any future progeny of mine to indeed take such a class, so that they can make their own decisions based on ALL information available (although I hope any children of mine would indeed side with science). The question is, with ID’s history in our school system, would I ever believe the class is being taught in the manner you suggest?

    The ID people don’t want to teach it along anything else. It seems to me that ID only works in a vacuum, devoid of any other material that may suggest that no matter how you color it, it is STILL not science, and is just a face slapped on creationism to get it past any of those pesky rules, like say..the Constitution of the United States, for example.

  2. It seems to me that ID only works in a vacuum . . .

     . . . and, really, not even there. (It’s not just in comparison to other things that it isn’t science; it’s not science at all, in an absolute sense.) But I agree with your real point — that ID looks even marginally persuasive only when it’s all you know.

    How could someone design a public-school presentation of ID that would pass Constitutional muster? Well, John’s idea seems to be about the only one that might work; the recent Dover decision, though not nationally binding, strongly suggests that pretty much any attempt to teach ID itself is going to be tainted by the fact that any reasonable person would know something about its history and therefore recognize it as covert religious instruction.

    John’s plan would be tricky too, but it might work – if the full history of the ID movement were presented as neutrally as possible and if (as per Dover) the presentation didn’t single out the theory of evolution by natural selection for critique but treated all science “equally,” as it were.

  3. But why bother? Why bother teaching it in schools at all? It’s a creation myth, and it’s not even a very interesting creation myth. “Something made the whole world and everything in it. We don’t know who it was, or why. But we’re pretty sure that’s what happened.”

    Give me a break! If a new religion was founded based on that creation myth, they’d be laughed out of town. A good creation myth tells us something interesting about people. It tells us who they were, what they wanted, and what they were afraid of. Intelligent Design is the blandest, most boring creation myth imaginable. Keep it out of schools unless you want to encourage “nap time.”

    K

  4. Well, I didn’t say it was a good creation myth, merely that this would be an appropriate way to present it.

  5. You could throw it into a cultural anthropology class along with things like cargo cults.

    Mostly though, its a combination of a poor understanding of and willful ignorance of the last 20 years or so of biology. Hell, I’m sitting in a lecture right now where a guy is talking about the parts of our DNA that have basically remained unchanged since we were fish. Oh and some folks at CalTech went off and figured out how bees fly. It was in PNAS last month.

  6. Thought I’m definately opposed to teaching ID as a science class, I agree with John that it could be talked about intelligently in the class structure he mentioned. I am not well-versed in the particular course in question, but really, how long can you take to discuss the philosophical theory of ID? I would be livid if my kid sat in the class the entire semester learning about ID, even if it is an unbiased class. When it comes down to it, there simply isn’t enough unique material to cover over the course of a school term, it eventual erodes into a waste of time, regardless of which side of the fence you are on. That brings me back to John’s point…the ID has to be cut with something else, preferably information on other philosophical theories on how we got to where we are at.

    I also think that Byron brings up a good point about using it in a cultrual anthropology class, where the discussion of ID in terms of antropological means would make a lot of sense and potentially add significant understandinng to the reasoning behind it.

  7. In high school I took Greek mythology with a teacher who was a bit of a Bible-thumper. I still remember her explanation that those stories were just fantasy because everyone knows there’s only one God!

    The IDiots don’t want a class that would explain their ‘philosophy’ as just some made-up fairy tale. That wouldn’t be very convincing…

  8. Unrelated comment…I just wanted to say two things. First of all, I really enjoy reading your ‘whatever’. Secondly, I saw a copy of ‘Old Man’s War’ in the dealer’s room at a filk con over the weekend…I didn’t pick it up, but I’m definitely interested. :)

  9. Dispatches from the Culture Wars has a pretty good analysis of the class, including the first and second versions of the syllabus for the class. (http://scienceblogs.com/dispatches/2006/01/dover_part_2_with_a_twist.php)

    The teacher who is trying to organize the class is a gym teacher who also teaches geography and admits she isn’t qualified to teach the course. Her main qualification appears to be that her husband is a pastor.

    The thing I find most odd is her listing Crick (of Watson & Crick) to speak in the class. Never mind the fact that he’s DEAD…how did she expect for a rinky-dink class like this to pull down such a major speaker?

  10. It’s possibly an indication she doesn’t know enough about evolutionary theory to have an idea who to approach.

  11. > How would you design a class, philosophy or otherwise, that discusses ID

    Not sure, but I think it should involve paintball guns.

  12. Well, every class everywhere should involve paintball guns. I think that’s something everyone can agree on.

  13. The thing I find most odd is her listing Crick (of Watson & Crick) to speak in the class. Never mind the fact that he’s DEAD…

    I guess if she planned to have a panel discussion, she’ll be up the panel without a Crick.

  14. The only appropriate venue to discuss ID is a media studies class.

    For example, show the editorial stages through which “Pandas and People” was transformed from a creationist to an ID text. Show the advertising for the Kansas School Board elections, with it’s winks and nods to who’s a real Christian and who isn’t. Show how ID folks consistently try to cover up their real intentions, their own history as a movement, and, in the case of Dover, even their funding sources. (The money for the textbooks was raised through a church; the head of the school board pretended to forget this fact.)

    Then show how this well-funded movement hasn’t come up with a single peer-reviewed article (save one in an electrical engineering magazine, later withdrawn), or any experiments, or any science of any kind, and is therefore rejected by every professional scientific body in the country, and yet the media still gives us one “expert” for and against ID every time they cover the “controversy.” Compare this with previous campaigns to bury legitimate science with well-funded obfuscations like, “Does smoking really cause cancer? Experts disagree.”

    Then have the kids discuss how they as consumers (and future producers) of media can look behind simplistic public claims to the real agendas that inform such movements.

    After all, any school course or discussion that looks at ID in an historical vacuum, treating it as some kind of free-floating philosophical proposition, is meaningless.

  15. Your suggestion to give airtime to ID in a philosophy/comparitive
    religion class is I guess a version of Bush’s “teach the controversy”
    approach to doing an endgame around the Establishment clause.
    This only serves to give creedence to a theory without any basis
    outside of faith. Why don’t they offer a class discussing the
    sociological phenomenon that some people believe in a flat
    earth? It is a waste of time, and just muddies the water where
    the science is clear.

  16. I’m not suggesting such a class should be taught; merely that if one is going to teach it, this would be one way.

  17. Here are a couple of links on the subject

    LA Times, and

    Americans United Press Release

    From the Times article:

    “At a special meeting of the El Tejon Unified School District on Jan. 1, at which the board approved the new course, “Philosophy of Design,” school Supt. John W. Wight said that he had consulted the school district’s attorneys and that they “had told him that as long as the course was called ‘philosophy,’ ” it could pass legal muster, according to the lawsuit….

    An initial course description, which was distributed to students and their families last month, said “the class will take a close look at evolution as a theory and will discuss the scientific, biological and biblical aspects that suggest why Darwin’s philosophy is not rock solid. The class will discuss intelligent design as an alternative response to evolution. Physical and chemical evidence will be presented suggesting the earth is thousands of years old, not billions.”

    TK

  18. The class idea sounds interesting…but, man, the teacher who teaches that will need skin thicker than tank armor, nerves of ice, balls of steel, and a lawyer with the soul of a velociraptor.

  19. I mean, come on, ID people. At least try to pretend you’re attempting something other than indoctrination.
    To be fair, that’s what a lot of science class is. And to continue to be fair, what’s taught in science class has generally survived the rough-and-tumble of experiments and won out over the competition based on it’s merits; and what ID teaches hasn’t. Indoctrination in science class is reasonable: a scientist should be well versed in the controversies of his/her field, but will by necessity have to take many auxiliary theories for granted. But the indoctrination should be of scientific theories, not just scientific-sounding theories.

    Sounds suspiciously like science to me.
    Heh, that’s kinda the point of ID: to sound like science. The proponents would probably like ID to be a science as well, but nature isn’t cooperating.
    I rather suspect that the philosophy taught in that course will be as crappy as the science.

  20. I agree with those that say that ID shouldn’t be taught as science. It’s not science. The fundamental problem here is that the educational organisations are doing a bad job of teaching science, especially Darwin’s Theory of Evolution. Scientific research has revealed some of the fundamental mechanisms by which Darwin’s theory would operate (i.e. DNA, chromosones, and genes). Additional research has demonstrated that Darwin’s theory, as stated, is terribly inadequate to describe what we see in the fossil record. I read an article by Michael Crichton which pointed out that, based on the size of the DNA involved and the rate of errors in replication observed, mathematically speaking in all the eons since life can first be found in the fossil record we would only be arriving at the developement of organisms no more complicated than one celled bacteria. Yet most educational organizations treat the Theory of Evolution as essentially proven. When more and more science is proving the opposite. Darwin’s theory is clearly insufficient, by many orders of magnitude, to describe what we see when we visit the zoo.

    It’s this vacuum of science that will inevitably give rise to unscientific theories such as ID.

    Although, I do think that students should be taught some sort of comparative religion course. A course which would describe the fundamental tenets of the worlds major religions (Judaism, Christianity, Protestanism, Islam, and Hindu), and how they differ, along with their historical evolution. Religion has had vast influence on the course of human history. I don’t think you can adequately teach history if the students don’t have some basic understanding in that area. Especially in the Modern era, the differences in the rise of western civilization versus the stagnation of the nation of islam and the isolation of the chinese culture were profoundly affected by the dominant religions of the cultures.

  21. I read an article by Michael Crichton . . .

    Sure you did, and I’ve read the last ten years of Nature, and haven’t seen a single article remotely suggesting that evolution is “unproven.” So leaving Crichton behind, let’s quote some real scientists:

    “the massing evidence from paleontology, genetics, zoology, molecular biology and other fields gradually established evolution’s truth beyond reasonable doubt. Today that battle has been won everywhere–except in the public imagination.”

    That’s from Scientific American‘s round up of the state of biology, called “15 Answers to Creationist Nonsense”:

    http://www.sciam.com/article.cfm?articleID=000D4FEC-7D5B-1D07-8E49809EC588EEDF

    Sorry to be rude, but any time I see someone italicize the word “theory” and get all snap about it, it’s a clear sign they haven’t taken the first step in comprehending what science is or how it works.

    And no, reading articles by Michael Crichton doesn’t count. This debate isn’t like the shelf-life of Twinkies issue, where that thing you remember reading by some dude said they could, like, last forever. Which could totally be true, I guess.

  22. Scott,

    Your comment, “but any time I see someone italicize the word “theory” and get all snap about it, it’s a clear sign they haven’t taken the first step in comprehending what science is or how it works.”

    Is incorrect. I didn’t italicize the word “theory”. I italicized the title “Theory of Evolution”.

    Also, your comment, “So leaving Crichton behind, let’s quote some real scientists”

    Is pretty disrespectful of Michael Crichton, an author, who was educated as a scientist. Especially when you consider that the two or three articles of his that I’ve read in the last few years were published by Scientific American.

    You should look up his article on the politicalization of science. Pretty darn unscientific of you to simply toss out contrary evidence, but you can read alot about that in his article.

  23. Why did we go through all of the unpleasantness of school board rulings and court cases, when we just could have asked Michael Crichton in the first place? As a nation, we should feel pretty damned silly.

  24. Tim:

    “Is pretty disrespectful of Michael Crichton, an author, who was educated as a scientist.”

    There are lots of different kinds of scientists, Tim, and being one kind doesn’t make him an expert on all kinds of science, particularly when one’s primary job is not evolutionary science (Indeed, the problem with the few scientists who have thrown their lot in with ID is that they aren’t experts in the field of evolution, which causes them to suggest stupid things that actual evolutionary biologists whack at mercilessly). Indeed, being one sort of medical doctor (as Crichton is) doesn’t even mean one is competent in other fields of medicine, which is why, among other reasons, Senator Frist’s neurological diagonosis of Terry Schavio via five minutes of edited videotape was a particularly digusting incident of scientific incompetence.

    Michael Crichton’s primary job for the last three and a half decades has been writing; it does not follow that he is more competent in any scientific field than any other writer, regardless of the training he received back when I was born. For example, I would not necessarily assume he knows more about astronomy than I do; he has trained as scientist (or at least a medical doctor), but I’ve written a book on astronomy and he hasn’t. Also, writing general articles in Scientific American doesn’t compare with writing on-point articles on evolutionary theory in Nature, as the former is a consumer magazine of science while the latter is (if my memory does not fail me) an actual journal of science.

    Re: Politicization of science — as it happens, the politicization of science has nothing to do with the immense wall of factual information supporting evolutionary theory.

    Also, simply as a factual note, Scott’s just written a book in which evolutionary theory plays a rather large role, and there’s little doubt he’s well versed as any layman on current evolutionary thought. He’s not one who is going to be impressed with something you think you remember Michael Crichton writing about once, and for good reasons, among them the very probable fact that he knows at least as much about current evolutionary theory as Crichton, and probably more.

  25. Not to get into a catfight and bore everyone else, Tim, but this isn’t about me throwing out “evidence.” ID hasn’t produced a single peer-reviewed paper (save one in an electrical engineering journal many years ago, later withdrawn) so there isn’t any evidence to throw out—not evidence in the scientific sense, anyway.

    What Critchon is doing is publishing conjecture (and his own brand of charming right wing-ish crankery—he enjoyes dissing global warming as another one of those many conspiracies among scientists). Surely you’re not telling me that this unnamed, unlinked-to article you sorta remember actually offers data that threaten to overturn the pillars of modern biology? It seems like we all would have heard about that.

    You stated categorically that the Theory of Evolution has not been proven, and that “more and more science is proving the opposite.” That’s downright hooey. The fact of evolution has been repeatedly confirmed by observations, direct and indirect, in the lab and in the field, and is accepted by the overwhelming majority of scientists. The “Theory of Evolution” is a set of overwhelmingly accepted strategies for making sense of those facts and observations.

    You should look up his article on the politicalization of science.

    Argh. Does anyone here actually swallow that it’s those 99% of scientists who have politicized this particular issue? And not, say, folks like the Kansas School Board—i.e., politicians?

  26. I went to high school in North Carolina, and the teachers did the best they could not to raise anyone’s hackles–there were a couple of creationists in the class, but we were not allowed to argue the point. “It’s just a theory. It’s also the best theory that we have right now. You don’t have to believe it; you just have to understand it for the test. You may feel free, if you like, to believe in intelligent design.”

    I can’t say that the creationists in the class were altogether happy about it, but I didn’t see the indoctrination that creationists are whining about either–and that seems a fine way to teach intelligent design. (In ten minutes. And it seems wrong to allocate more than ten minutes of a biology class to it).

  27. Scott, as the Scalzi-approved local expert on evolutionary theory, I’m wondering if you can point me to any resources on a related topic. One of the biggest questions (curiosities, you might say) in my mind about evolutionary theory as an origin-of-speciation explanatory device is the question of how random genetic variations could lead to the widely varying chromosome counts in various species (this page, though clearly written from a position antagonistic towards Evolution, lists chromosome counts for assorted species). For example, humans have 46, alligators have 32, various species of fruit flies (genus Drosophila) have between 8 and 12, etc. Has there been work done investigating how dramatic changes like addition or deletion of whole chromosomes could feasibly lead to the generation of new species?

    For example, Down Syndrome, which is caused most frequently by trisomy of chromosome 21, represents a well known detrimental effect of chromosome number modification. Are you aware of any studies that have reported a beneficial effect from a modification in chromosome count (in any species, not just humans)?

  28. Scott,

    You seam to be laboring under the misapprehension that I believe in or support ID. You also seem to believe that Michael Crichton supports ID (I don’t know wether he does or doesn’t).

    I think Darwin’s Theory of Evolution was a brilliant leap of insight, especially considering the mammoth degree of ignorance, at the time it was proposed, regarding the mechanisms of inheritance of individual traits. I also think that Newton’s Laws of Motion were a brilliant leap of insight, especially considering that they probably were one of the more significant factors that led to the Modern Age. But, I also think that we should have open minds enough to accept that when science starts to reveal evidence that a theory might not be kosher, we can agree to accept that. Just as, in the late 19th century, science revealed that the speed of light was constant and therefore, Newton’s Laws of Motion weren’t the last word on the subject.

    I am certainly willing that adaptation accounts for variation within a species, especially over time. But, to my knowledge (based on statements of other people long before I ever heard of ID) we’ve never observed adaption causing inter-species differentiation. Also, when scientist use observed evidence and mathematics to prove that ‘random changes’ cannot account for the variations we see in flora and fauna of our world or its fossil record by many orders of magnitude, I have to logically conclude that something else is going on.

    That said. I’m not stating that that proves ID. I repeat myself. ID is not science. I’m saying that when facts start to contradict something. Saying that something is proven, only creates a credibility gap that encourages unscientific theories (like ID) to come out of the woodwork. This isn’t the first time the scientific community rejected contrary evidence rather than have its world shaken. Physicists unanimously rejected the first evidence that the speed of light was constant. It took Einstein to straighten it out for them.

    Michael Crichton’s point was that when scientist reject contrary evidence and take political sides it doesn’t give us the ‘truth’, it just gives us bad science.

  29. Brian:

    “Are you aware of any studies that have reported a beneficial effect from a modification in chromosome count (in any species, not just humans)?”

    You don’t need Scott to answer this, you just need to use the search engine at talk.origins:

    “Effects of chromosomal duplication: Duplicating only one chromosome is generally disadvantageous; an example in human beings is Down’s syndrome. Having multiple copies of all of the chromosomes is known as polyploidy. Polyploidy is rare in fungi and animals (although it does occur) and is common in plants. It has been estimated that 20-50% of all plant species arise as the result of polyploidy.”

    It’s that last sentence that answers your question.

    (references at the linked page)

    Tim:

    “But, to my knowledge (based on statements of other people long before I ever heard of ID) we’ve never observed adaption causing inter-species differentiation. ”

    This sounds like the “microevolution v. macroevolution” thing to me, which is dealt with over at (once again) talk.origins. Tim, if you’ve never been to talk.origins, it’s a very useful site, with all the cites and facts and information on these matters you’d want.

    But to repeat: there’s no evidence that the theory of evolution “might not be kosher,” and there’s certainly no competing theory that stands up to the repeated scrutiny evolutionary theory with withstood.

  30. Warning: This is boring until I get to the part about mosquitos.

    Brian:
    Yes, countless new species of plants have arisen as a result of polyploidy, a special kind of evolutionary shift that happens when the chromosome count multiplies by two, or sometimes more! (de Wet, J. M. J., 1971. Polyploidy and evolution in plants. Taxon 20: 29-35.). It is believed that 40% or more of angiosperm species are a result of polyploidy.

    If plants don’t float your boat, check out fish speciation: Schultz, R.J., 1980, Role of polyploidy in the evolution of fishes, See Ref. 13, 313–40. There are also some mammalian examples.

    For an overview:
    http://www.as.wvu.edu/~kgarbutt/QuantGen/Gen535_2_2004/Polyploidy.html

    Tim-
    Sorry if I suggested you were an IDist. I merely meant to say you were making an extraordinary claim (crisis in modern biology) with less-than-extraordinary evidence (half-remembered, unsited article by sf writer).

    But, to my knowledge (based on statements of other people long before I ever heard of ID) we’ve never observed adaption causing inter-species differentiation.

    Argh. You should look these people up and call “hooey” on them. Inter-species differentiation has been observed on countless occassions, especially in situations in which a founder population was separated from the rest of its species by the advent of a new environment (suddenly emergent freshwater lakes are very popular).

    For a wicked-cool example, check out Byrne, K. and R. A. Nichols, 1999. Culex pipiens in London Underground tunnels: differentiation between surface and subterranean populations. Heredity 82: 7-15.

    Here’s the Cliff’s Notes version: A new species of mosquito, Culex molestus, speciated from Culex pipiens as a result of isolation in the London Underground! (An entire benighted species that has never seen the light of day . . . Bwa-ha-ha-ha.) These are legitimately different species, in that they can’t interbreed, have different habits, posses marked genetic differences, etc. And the whole differentiation took place in modern times, with many a sample taken along the way.

    That’s the saddest part about our education system, that no one lets students explore extremely cool examples of evolution like that one–immediate, understandable, and verifiable. Too much talk of monkeys, I suppose.

    But whatever the Scalzinator says, I ain’t no expert. For a vast clearinghouse of Creationist/IDist debunkings that sites peer-reviewed articles in almost every case, check out:

    http://www.talkorigins.org/indexcc/list.html#CB700

  31. Also, Tim (et al.), it’s important to remember that no one here is insulting Crichton when they criticize things he says. Science training or no, if he says things which do not make any sense or are unscientific, it’s only fair and right that this be pointed out.

    More to the point, one of the keystone proponents of ID is Michael Behe, who is an actual scientist. Nobody cut him any slack either, and nor should they.

  32. Also, species is an abstract, human concept. It’s an idea that exists only in the minds of taxonomists to accomodate categorization–such is its primary (and largely only) utility.

    Species doesn’t exist in nature, but as an arbitrary definition to assist categorization. As such, there are many different formal definitions.

    For instance, there’s the Biological Species Concept, which is based around the idea of reproductive isolation. But as this is inapplicable to extinct organisms, a morphologic and/or biogeographic definition tends to be favored by paleontologists.

    And, really, there’s nothing particularly more special about reproductive isolation than, say, the number of cervical vertebrae or skull shape variations an organism might have. Any biological criteria are ultimately determined by the genome itself; both morphology and reproductive isolation are thoroughly involved in survival–saying one matters more than the other is meaningless.

    Essentially, what Darwin offered was an explanation for diversity. Species–as a concept–is just a way to keep track of it all (which occasionally provides it’s own challenges). So you see, anyone who bases any kind of denial of evolution on reproductive isolation of critters–reveals that they do not understand what taxonomy is, or why taxonomists do what they do.

  33. Jeez…you wander in looking for a bloggy nightecap of cat pictures and maybe a book pimp or two…

    *head hurts* going to bed now…apparently 25 IQ points smarter than when I got here. *ouchie*

  34. Scott Westerfield,

    I want to thank you for the references, but I wouldn’t concede that interspecies adaption can accomodate the vast diversity we see in the flora and fauna of our world and the incredibly diverse evidence we see in the fossil record. I objectively differ that adaptation can explain such remarkable changes in the evolution of species which are evident in the fossil record. I will concede that would eliminate maybe one or two orders of magnitude in the difference we see behind the objective evidence and the predictive mathematics.

    I additionally want to emphasize that that was not my primary critique against the complete truth of Darwin’s Theory of Evolution. My main point was that bioligists’ evidence combined with mathematicians’ prognostications were so tremendously far apart from the reality which exist at your local zoo, that Darwin’s supposition that ‘random changes’ can account for the underlining diversity that we see in the historic biosphere.

    In my understanding one of the greatest hints that future scientific discoveries will be made is when current experiments fail the generally accepted math. If the orbit of Neptune had lived up to accepted calculations we would never have discovered Pluto (I’m sure John will attest to this). If the observation of sub-atomic particles had agreed with Newtonian physics Einstein would not have derived the counter intuitive theories that bedrocked 20th century physics.

    I think that that ‘truth’ of evolution will ultimately be discovered in some underlining discovery of an ‘ordering influence’. I don’t have any clue or supposition of what area of biology or chemistry where this ‘ordering influence’ will be discovered, but I’m sufficiently open minded to accept that when ‘the math doesn’t work, the theory is flawed’.

    The thing the that bothers me most about this debate is that so many people on both sides refuse to accept the simple, and humbling, reality that ‘We just don’t know the absolute truth’. We seen this repeatably throughout the history of western civilization and we’re still there.

  35. Tim:

    I objectively differ that adaptation can explain such remarkable changes in the evolution of species which are evident in the fossil record. . . . I additionally want to emphasize that that was not my primary critique against the complete truth of Darwin’s Theory of Evolution.

    I don’t know what you mean here. Darwinian theory doesn’t depend on any particular account of what causes the background rate of mutation or how it does so. If (as you seem, more or less, to be suggesting) it turns out that the mutations with which natural selection works are in some way caused by an “ordering influence” . . . well, possibly, but that fact doesn’t in any way tell against Darwinian theory. You might as well criticize the theory for not providing a separate account of the electromagnetic force.

    If your only point here is that in order for the evolution we see in the fossil record to have occurred, there must have been (e.g.) a much higher mutation rate than previously believed, then you should be aware that this point can be made entirely within current Darwinian theory.

    The only “math” that doesn’t “add up” is that if you assume too low a mutation rate (or other source of fresh genetic variation), you can’t account for the diversity we actually see. Fine; evolutionary theorists make arguments like this all the time. Suggesting that this is a shortcoming of the theory itself is like suggesting that because the value of the gravitational constant is not what we previously thought, therefore there’s something “incomplete” about the accepted theory of gravitation. Any “incompleteness” here is of a very uninteresting sort that doesn’t in any way call into question the acceptibility or in-principle satisfactoriness of the theory itself.

    p>In general, your point seems to be that because there’s something a theory doesn’t tell us, therefore the theory is “incomplete.” What you neglect is the fact that there are only certain questions we expect a theory to answer.

  36. I don’t tend to post about this subject again until I have checked out Scott Westerfield’s, and John’s references (education takes time).

    But some things are too absurd to pass up.

    Scott Elyard,

    species is an abstract, human concept

    No. It is a scientifically based concept.

    species A category of biological classification ranking below the genus, comprising of related organisms, or populations capable of interbreeding

    Emphasis mine.

    When trying to survey the real world, we as rational beings must draw rational lines, otherwise our comparisons and observations would be meaningless.

  37. OK, I lied.

    Scott Ryan,

    Darwin’s Theory of Evolution states that the evolution of life takes place through the effects of adaptation and the ‘random changes’ that affect that life.

    If it is scientifically proven that the above statement cannot be true, then the theory is not wholy true.

    If the error of what is predicted to what is observed is within a few magnitudes, than it’s concievable that the error is attributable to measurement error (i.e. the mutation rate is incorrect, or the advantageous/disadvantageous rate is incorrect). When the results disagree by many orders of magnitude, one must assume that, either our capacity to measure the phenomenon is flawed, or our original premise is flawed.

    Regardless of which is true. When predictions fall so far from our observed reality, the basis of the predictions are worthless.

    Again I state. What fundamental shortcoming do we have that just cannot admit the simple, and humbling, reality that ‘We just don’t know’.

  38. There is evidence that for some species the evolutionary mutation rate is much higher than previously thought. This article from Nature in August 2004 offers evidence of a mutation rate in C. elegans that is ten times higher than previous estimates. (Sorry, they charge for the full text online, but you can find the back issue in your local library.)

    Here we provide a direct and unbiased estimate of the nuclear mutation rate and its molecular spectrum with a set of C. elegans mutation-accumulation lines that reveal a mutation rate about tenfold higher than previous indirect estimates and an excess of insertions over deletions. Because deletions dominate patterns of C. elegans pseudogene variation our observations indicate that natural selection might be significant in promoting small genome size, and challenge the prevalent assumption that pseudogene divergence accurately reflects the spontaneous mutation spectrum.

    And as for the variation in chromosomal counts, from what I understand it comes down to how much reproductive energy a species is capable of expending to maintain its DNA. For some of the simplest organisms there is often a need to strip down to only that information necessary to procreate, whereas higher organisms carry excess baggage in their chromosomes (although there is new evidence that this excess, once considered ‘junk’, is crucial for diversity within a species).

    (Sorry – no citation for that last bit. I can elaborate later, but for now I have to get to work.)

  39. species A category of biological classification ranking below the genus, comprising of related organisms, or populations capable of interbreeding
    That’s a very common definition, but it’s also incorrect. There are quite a number of examples of separate species that are capable of interbreeding but do so very rarely or not at all in practice. Whether two groups form separate species is to some extent an arbitrary decision.
    Now, according to Gould, the grey areas are actually somewhat rare (at least in the animal and plant kingdoms): either the putative species are interbreeding a fair bit or extremely rarely, with few exceptions.

  40. I read an article by Michael Crichton which pointed out that, based on the size of the DNA involved and the rate of errors in replication observed, mathematically speaking in all the eons since life can first be found in the fossil record we would only be arriving at the developement of organisms no more complicated than one celled bacteria.
    I can’t find that particular article. But I have seen similar analyses, and they tend to make a number of mistakes. For instance, many presume only pointwise mutations. Mutations which copy stretches of dna around (which does happen) are likely to be very important.

    Another common mistake is calculating the wrong thing. The a-priori chance of my asking my computer to give me the number of seconds after midnight precisely 36288 seconds after midnight today is also low. But it happened. Similarly, the a-priori chances of humans evolving through natural selection is probably extremely low. But that doesn’t imply any problem with the theory of natural selection. The more relevant probability is the likelyhood of complex/smart organisms evolving through natural selection given a few billion years. If it’s very unlikely then the theory has a problem. Thing is, that is a very difficult thing to calculate.

  41. Yeah… my only question, so where is this Math that supposedly trips up up the Theory of Evolution. Tim keeps quoting it, but does it actually exist?

    Besides, math depends on inputs and assumptions… math can say anything. I’m an engineer, I know this.

    Math can even be made to lie. That’s what statisticians are for.

  42. Does anyone remember the old creationist argument about moon dust? The one where they claimed that because the assumed rate of moon dust accumulation determined by NASA (at the time) was such that, had the moon existed for as long as (non creationist) scientists said, it would therefore have like 7 feet of dust on it everywhere, and the lander would have sunk into it? They claimed that this disproved the alleged old age of the universe, and supported young earth creationism.

    The problem, of course, with this reasoning, is that adjusting the rate of moon dust accumulation provided a better data fit than adjusting the entire age of the universe from billions of billions of years down to a couple thousand. And of course scientists did just that.

    I don’t know, that just seemed relevant about now.

  43. Tim:

    “What fundamental shortcoming do we have that just cannot admit the simple, and humbling, reality that ‘We just don’t know’.”

    That’s not true of science at all, actually. Scientists will happily tell you that there is quite a bit that we don’t know, and indeed, it’s at the places where we don’t know things where some of the most interesting science is being done — just ask a string theorist about that.

    The thing is that what we don’t know does not negate the things we do know — in the case of evolutionary biology, what we don’t know about its processes does not imply that the information we do have that’s been exhaustively research and confirmed is somehow in doubt.

    Or, to put it more simply: Just because we don’t know some things does not mean we don’t know anything.

  44. Darwin’s Theory of Evolution states that the evolution of life takes place through the effects of adaptation and the ‘random changes’ that affect that life.

    Well . . . Darwin’s theory states that evolution and speciation occur through natural selection among traits that have differing effects on reproductive success. The theory doesn’t require any specific source of variation for those traits, and the word “random” in this context simply means that it’s something the theory isn’t supposed to explain.

    In fact, strictly speaking, Darwin’s theory doesn’t even require that the variations be genetically based — although our current neo-Darwinian synthesis does claim (and show) that natural selection does occur at the genetic level. In principle, natural selection could occur among non-genetic traits as well without invalidating the theory.

    If it is scientifically proven that the above statement cannot be true, then the theory is not wholy true.

    Not really. If it’s scientifically proven that natural selection can’t fully account for the diveristy we now observe because the requisite variation did not or could not occur, then the theory simply doesn’t fully account for all the diversity we observe. The theory is still sound and correct; all that changes is the range of phenomena it can successfully explain.

    Again I state. What fundamental shortcoming do we have that just cannot admit the simple, and humbling, reality that ‘We just don’t know’.

    State it as often as you like; this isn’t science’s problem.

  45. When trying to survey the real world, we as rational beings must draw rational lines, otherwise our comparisons and observations would be meaningless.

    Well, that’s not true. Drawing arbitrary lines makes things easier to communicate (hence Linnean taxonomy in the first place).

    But just because we set up names for, say, 8 colors doesn’t mean that intermediary colors between the named colors doesn’t exist, or that it is impossible to talk about them.

    In fact, the opposite is true.

    Take common ancestry. It’s simple enough to talk about shared ancestry without invoking candidate ancestors. This is, in fact, the basis for phylogenetic taxonomy. So, for example, we can define a clade by its evolutionary extremes. The definition is arbitrary:

    The definiton of Aves is the most recent common ancestor of Archaeopteryx and Passer and all of their descendants.

    But useful. See? We just talked about a huge number of organisms without needing to invoke the name common ancestor of all of them–since that information is unknowable for extinct organisms; additionally, we have a functional definition of a large group of organisms which has greater utility than naming every possible candidate species for the group and having to revise it later because molecular evidence displaces a few of those species.

    Should it be later shown (for e.g.) that Archaopteryx is not a bird, the definition can be revised to reflect that. (But now we’re going way afar afield of the topic.)

  46. Tim, in your post addressing Scott Ryan, you say:

    “Regardless of which is true. When predictions fall so far from our observed reality, the basis of the predictions are worthless.”

    Apparently, you are unaware that evolution by natural selection has been rather wildly successful on the basis of it’s predictions.

    In fact, no legitiamtely competing theory has been so productive or practical, which is, in part, why there is no other competing theories anymore.

    Perhaps you might be interested in genetic algorithms. Or the obvious applications to medicine. Or the fact that early in the 20th century, a prediction was made that a four-winged stage would be discovered in the evolution of Avian flight. In 2001, Microraptor gui, a four-winged dromeosaurid, was discovered in China (anyone interested can e-mail me for PDF).

    Can you tell me about successful predictions made by “modern” competing theories?

    I can’t find any. At all.

  47. Andrew Wade:

    That’s a very common definition, but it’s also incorrect. There are quite a number of examples of separate species that are capable of interbreeding but do so very rarely or not at all in practice.

    And from the other direction: of course not every two members of the same species are fertile with one another (even if they’re of the opposite sex). Talking about a “population capable of interbreeding” without saying anything about pairwise fertility is loose shorthand at best.

  48. Faith is all well and good. I have it every time I purchase a lottery ticket.

    Using it to describe the universe is just about the silliest idea I’ve ever heard because the answer to every question is that god said so and he knows best, so love it and learn to live with it.

    Religion (and ID) has the same answer to every question. Science’s answer is: Let’s have a look and see if we can figure out how such and such works.

    Everytime faith has been left behind and the bother was made to figure out how things worked we’ve progressed (with relatively few deaths resulting). Until all other probably theories have been exhausted and the evidence indicates nothing except a devine hand we can keep ID in a glass case with a little label that says “Break in case of Rapture”.

  49. So much is revealed by definitions of terms. The most annoying one (to me) in this debate is the word THEORY. Some folks read it as premise or hypothesus. Others as a title. Others think it’s a fact. People often use multiple meanings for theory in the same sentence. Without realising it.

    Then there’s the problem of the colloqual use of the phrase “Darwin’s Theory of Evolution”.

    Evolution is a fact. See references sited above. I’m particularly fond of the book “The Beak of the Finch”. Talk to Crighten about why a different flu shot is made every year. Viruses change, people have gotten taller over the centuries, and inland grizzlies (400lbs) are from the same ancestral stock as coast grizzlies (bloody huge).

    Evolution by Means of Natural Selection is a theory. This is the point where ID’ers have a toe hold. Perhaps it ain’t Nat’l Selection, but whatever causes the evolution currently looks like it to scientists in the field. They could be wrong. Einstien could be wrong about what causes gravity too, but gravity is.

    Darwin, by the way, was generally 75% wrong in his book “Origin of Species” (which wasn’t about origins, btw, and had way to much pidgeon stuff). The 25% right, though, was the bit that begged for experimentation.

    -Rita (not trained in that field of science, but a careful and logical reader of words)

  50. If the error of what is predicted to what is observed is within a few magnitudes, than it’s concievable that the error is attributable to measurement error (i.e. the mutation rate is incorrect, or the advantageous/disadvantageous rate is incorrect). When the results disagree by many orders of magnitude, one must assume that, either our capacity to measure the phenomenon is flawed, or our original premise is flawed.
    Or, as I suspect, the method from getting from premise to prediction is flawed. But ok, perhaps the theory of evolution through natural selection is flawed. To echo Scalzi, many scientists would that the theory is not quite right, and indeed there are many variations on the theme of Darwin’s theory to try and bring it closer to observations. But that doesn’t mean that Darwin’s theory is worthless: there are many predictions that it gets right.

    If the orbit of Neptune had lived up to accepted calculations we would never have discovered Pluto (I’m sure John will attest to this).
    That’s actually a great example for this discussion. In that case it turned out not to be Newton’s Theory of Gravity that was incorrect, but the “observations” (the number of planets). Whereas in the case of Mercury, it turned out to be the theory itself that was incorrect. But Newton’s theory is _not_ worthless. And it’s not just small errors either: when it comes to the near neighborhood of black holes either it is basically useless. But for, say, orbits around the Earth, I believe it is still in use.
    Now Newton’s theory has been superceeded by another theory, whereas Darwin’s theory has not been superceeded (it has, however been modified). That may yet occur for some denotations of “superceed”.
    None of this helps ID (and Tim hasn’t been claiming otherwise). ID, as I know it, is basically young-Earth creationism in drag, and it doesn’t conflict just with Darwin’s theory, but also “Evolution” (a/k/a the tree of life) and Geology. (Darwin’s theory predicts a certain pattern of change in life on the planet, but that pattern (Evolution) can be considered as a theory in it’s own right (sans mechanism), and there is a great deal of observational evidence for it.)

  51. Well, in any social science class religeon is taught. If there are spiritual aspects that relate to science in a science class then teach it otheriwse there are many different clases that already tech religion. I am also more into private schools because the government cant get it’s head out of it’s ass.

  52. Rita:
    Evolution is a fact.

    Evolution by Means of Natural Selection is a theory.
    Hrrm, I don’t think it’s improper to call the observation that species change gradually over time and have common ancestors (Evolution) a theory. But it would be somewhat unusual to describe it as a theory, and it is definitely a fact as well.

  53. Erm, screwed up the quoting a bit there.

    In any event Rita does have a point. If IDers wish to challange “Evolution through Natural Selection” they have a chance (or at least would if they were competant). But if they wish to challange “Evolution” (and many of them do), the evidence is so strong there really is no chance.

  54. Checking Crichton’s Wikipedia entry, I find some interesting quotes:
    Crichton has commented that “belief without a factual basis is more akin to faith. Faith alone is not a proper foundation for scientific belief.” This in an apparently famous speech to Caltech on the idea of consensus science and junk science. Certainly doesn’t sound like someone making a case for ID. The whole of the speech, which can be found here:
    http://www.crichton-official.com/speeches/speeches_quote04.html

    Is a screed against SETI and global warming, from 2003, that some in the ID movement would like to co-opt, because it criticizes parts of the scientific establishment. Some of the speech has been proven to be demonstrably wrong (predating the hurricane season of 2004, for example, or the finidings that the artic IS shrinking by NASA). However, in that same speech, Crichton specifically says he defines Science as having a TESTABLE HYPOTHESIS. He disdains SETI for having an equation at its root which can take a result of 0 or a number in the billions of billions and still be true.

    What is funny is that how ID proponents take part of Crichton’s quote out of context, to put it forth as saying that the Establishment is keeping them down…and ignoring the ‘science is testable and hard facts’ aspects of the speech.

  55. “But some things are too absurd to pass up.

    Scott Elyard,

    species is an abstract, human concept

    No. It is a scientifically based concept.

    species A category of biological classification ranking below the genus, comprising of related organisms, or populations capable of interbreeding

    Emphasis mine.”

    Tim, check out the existence of ring species if you think that species is a clear-cut concrete feature of the real world that exists independent of human judgment.

    By the way “abstract, human concept” is not necessarily contradictory to “scientifically based concept“.

  56. Seems I screwed up the linkage (and now I don’t have them handy)

    Some of the things in the article, which I didn’t include are the lack of credential for the teacher, the short-notice on which the class was based and that she is the wife of a creationist pastor.

  57. John and Scott,

    Thanks for the links and citations for the various polyploidy stuff. John, had I previously known of talk.origins, I would’ve looked there. Mea culpa… sorta. :-)

  58. Andrew Wade,

    Sorry. I went looking for the article, also, trying to use as many specifics as I could remember from it, but I can’t find it anywhere (I wanted to get the reference regarding the math prediction). I don’t remember when I read it (lousy memory for time). It may no longer be available.

  59. I went searching for the article I mentioned several days ago and couldn’t find it. So I went to advanced searche to look for some other article on the same subject. I found a recently published article (November, 2005) by Dr. Gerald Schroeder
    an M.I.T. trained scientist. Unfortunately, I didn’t like the article because I kept finding it on these Jewish religious sites. The article does a much more detailed description of the problem with randomness than the one that I read (but I just don’t like where he goes after he makes that point) and it gives the reader a good understanding of what I meant by ‘many orders of magnitude’.

    I actually agree more with a pull quote he has from one the book references in the article. From Life’s Solution : Inevitable Humans in a Lonely Universe (Cambridge University Press, 2003) by Simon Conway Morris he quotes, “It is my suspicion that research might reveal a deeper fabric to biology…”.

    This is along the line of argument I was originally trying to make. That somewhere within the mechanism of DNA replication or gamete creation (two processes that seem to be reasonably robust) there exists the equivalent of a check sum function that prevents a random change from being reflected in the outcome unless it yeilds at least a potentially correct outcome. I certainly don’t have a sufficient understanding of microbiology or organic chemistry to have any clue how this might work, but if such an animal exists I bet there’s a Nobel prize for the person that explains it.

    The article also has another book reference that sounds pretty fascinating. A Guided Tour of the Living Cell (W.H. Freeman & Company, 1984) by Christian De Duve sounds like a pretty good read.

  60. Scott Westerfeld,

    I tried to get follow up on your reference:

    Byrne, K. and R. A. Nichols, 1999. Culex pipiens in London Underground tunnels: differentiation between surface and subterranean populations. Heredity 82: 7-15

    But, I couldn’t find any site which would allow me to read any more than the brief abstract without paying for a subscription. Ashame. The abstract did make it sound like it would have answered many of the questions that I would have regarding inter-species differentiation.

  61. From the article:
    “In brief, randomness cannot have been the driving force behind the success of life. Our understanding of statistics and molecular biology clearly supports the notion that there must have been a direction and a Director behind the success of life.”

    And, of course, it isn’t. Dr. Schroeder’s article is worthless because it rests upon the canard/strawman that all evolution is nothing more than postulated randomenss, which isn’t true. All he’s done is reveal that he knows absolutely nothing about how evolution works, and, for that matter, the people he’s quote mining to support his viewpoint.

    Mutation is random. But Evolution is more than mere duplication errors, frame shifts, and the like. A random mutation doesn’t always result in fatalities, which can demonstrated by inducing polydactyly in mice embryos. So Dr. Schroeder is wrong.

    And if not all mutations are fatal, a small percentage of mutations can be useful. And since heiritability plays a major factor in inheritance, there’s an easily verified record of useful mutations stored within the DNA of every living organism. Acting as a filter on that is natural selection. In fact, this whole point was made rather excellently in the introduction to The Blind Watchmaker (Dawkins, 1986).

    Tim, I recommned you start lurking on http://www.pandasthumb.org/ and actually start reading those talk.orgins FAQ articles. I’d recommend the same to Gerald Shroeder as well, but as he’s quoted by a certain Discovery Institute, I suspect that he already has been made aware of them.

    If the published date on your link is correct (2005), he just doesn’t care that he’s wrong. Accuracy, I’ve found, is of little interest to these people. Scholarship and basic honesty are routinely sacrificed in the name of pushing a sloppy excuse for darkness and ignorance in the name of science.

  62. The fundamental mistake Dr. Gerald Schroeder makes is here:

    Nature has the option of choosing among the 10 to power of 260 possible proteins, the 3 million proteins of which all viable life is composed. In other words, for each one correct choice, there are 10 to power of 254 wrong choices!

    Those are not all wrong choices. A great many of those combinations, even if they had never appeared in the history of life on this planet, would have worked perfectly well if they had done so. And many, many more, would have worked “somewhat”.
    There are further problems with the analysis. The Neo-Darwinian model of evolution is not “pick a 200-amino acid long peptide string and see if it works as a protein”, it’s “modify a functional[1] 200-amino acid long peptide string and see how well it works. Repeat.” And it is certainly not “pick a 200-amino acid long peptide string and see if it is one of these sequences: …” Yet Dr. Schroeder uses the last model in his analysis. Why he does this I don’t know as he provides a good explanation of the Neo-Darwinian model right in the first paragraph.

    [1] Unless you’re talking about abiogenesis, which is admittedly a bit of a puzzle without a God to kickstart the whole thing.

    This impossibility of randomness producing order is not different from the attempt to produce Shakespeare or any meaningful string of letters more than a few words in length by a random letter generator …

    Add mutation and a selection function and you can do exactly this: produce Shakespeare from randomness. I wrote a program that did exactly this about a year back: it started with a random string, produced point-wise mutations, and selected by how close the result was to Hamlet. It worked too: I didn’t wait for it to produce a perfect version of Hamlet, but the result was readable. Random mutations+selection can demonstrably produce order. (Now as a model for the evolution of genes it’s pretty bogus: no transposition mutations, and a selection criteria of “Hamlet” rather than the more appropriate “English text”.)

    Either our knowledge of statistical probability is skewed …

    <snark>His knowledge of statistical probability is skewed: Not all of the proteins in in life is 200 amino acids long (as his calculation assumes), and the number of amino-acid sequences extant in humans is far higher than 50,000. (Any particular human may have about 50,000 amino-acid sequences, but they do vary slightly from human to human.). He’s calculating the wrong thing, and he can’t even do that correctly. Doctor he may be, but it’s hopefully not of anything that involves statistics.</snark>

  63. As a follow up: my program would have produced Hamlet eventually, but it would have taken more generations than are available on Earth. (I think I calculated it to about a month of computer time.). The article you talked about may have done a similar analysis with genes. This is why I think transposition mutations are so important. The thing is proteins have hierarchal structure to them: they’re composed of alpha-helixes and beta sheets. I don’t know about beta sheets, but alpha-helixes should correspond pretty well to amino-acid sequences. So if you transpose a sequence corresponding to an alpha-helix (and probably other structures as well), an alpha helix may well show up in the corresponding position in the expressed protein. Proteins may well be evolved as much by copy-and-pasting bits of structure around as they are by point-wise mutations. And more than that, proteins don’t have to be generated from scratch: they can be copied from existing proteins and modify to taste. There is evidence for this sort of thing in the genomes: multiple copies of protein genes, genes jumping around the genome, and genes for proteins performing different functions that look suspiciously similar (as if they were evolved from a common ancestor gene). Unfortunately I don’t have a citation for the Scientific American article.

  64. There is evidence for this sort of thing in the genomes

    Copy and paste design that is. It’s not really evidence of evolution through natural selection; Although it’s considered bad practice, copy & paste with subsequence divergence does occur in intelligently designed computer code. As Rita said, life evolved, but there is a toe-hold for debate about the mechanism behind that evolution. Computer code evolves too.
    That being said, it’s not much of a toe-hold. The pattern of evolution of computer code is rather different than that of species. Codebases split (fork) and diverge (e.g. speciate), but they also copy code amongst each other, sometimes in considerable quantities. In the plant and animal kingdoms this does not occur at all much above the species level. This is explained in the Neo-Darwinian theory by the absence of mechanisms[1] for transferring genetic information between species that cannot interbreed. I have heard of no explanation for this with regards to Intelligent Design.
    Contrast, say the evolution of unix to that of fish, I think. Now one can leave out the horizontal transfers from the first diagram to get a tree (such as this one for languages). But scientists have been looking for such “horizontal transfers” of genetic information in the plant and animal kingdoms (and between kingdoms) and they don’t appear to occur in any quantity. So one couldn’t create a diagram like the one for unix for animals. (It would be very difficult to identify genes doing this. But bits of phenotypes jumping around would show up in the fossil record, and all examples of this turn out to be convergent evolution instead.)

    [1] Some viruses can carry bits of host genome around with them. But it’s not a very efficient way of spreading genes around. However, many bacteria will quite happily incorporate any old DNA around into their genomes, which is why I keep referring to the plant and animal kingdoms where this does not occur.

    As for an ‘ordering influence’, that’s not incompatible with the fossil record. But neither do I think such an explanation is needed. (It would, of course, have to be developed a lot more to be useful and really testable).

  65. “But bits of phenotypes jumping around would show up in the fossil record, and all examples of this turn out to be convergent evolution instead.”

    Well, to the extent that can be surmised at any rate. Most extinct DNA is unavailable for direct analysis.

    Convergence is the simplest explanation.

  66. Hey Tim, I thought of an even better example where subtle, random mutations in Hox genes would produce directly beneficial morphologies: vertebrae. This is cool. Trust me.

    See, morphogenesis of cervical vertabrae (CVs) are controlled by variations within Hox genes in vertebrates.

    As you can probably guess, Hox genes can vary considerably from one genus to the next. (We know this is the same gene amongst taxa because the gene controls growth of the same structures in all of these disparate genera, without exception.)

    So, for example, some animals (like synapsids (the group that gave rise to mammals), for instance), might have a set number of CV–which in the case of almost all synapsids is seven. Whales have seven neck bones. Humans have seven neck bones. Giraffes have seven neck bones.

    But in diapsid reptiles, the level of variation in the number of CVs is rather extreme. Diapsids have six at minimum. Archosaurs have a minimum of eight. Swans have more than twenty. There’s even an elasmosaur (an euryaspid diapsid) with 71 cervical vertebrae!

    Giraffes have long necks because their CVs are distended along the axial. Giraffes further extend their reach by having disproportionately long legs–so much so, that adults must splay their forelimbs outwards in order to bend down far enough to get a drink. Much less disproportionate are the limbs of sauropods, which have rather shorter legs than even most theropods.

    Sauropods are able to attain height by having way more vertebrae than their distant, convergent cousins the giraffes.

    So for these two major groups (diapsids and synapsids), two very different results from different, random mutations were then successfully passed onward through their respective lineages. In neither case did these mutations kill off the lineages. Birds, crocs, lizards, snakes, Sphenodon and mammals are still with us today.

    Now it must be fairly obvious what possible advantage having a longer neck might have. Being able to reach food is pretty important. The fact that sauropods have long necks and giraffes have long necks is an example of convergence.

    But the fact that the long necks stem from some random changes made to the same gene (but differently in the case of each group), is powerful evidence that they have a common ancestor.

  67. “But bits of phenotypes jumping around would show up in the fossil record, and all examples of this turn out to be convergent evolution instead.”
    Well, to the extent that can be surmised at any rate.

    Yeah, true. And with the success of the theory of evolution, convergent evolution as an explanation isn’t even going to be questioned in many cases. So my argument is more than a bit circular.
    But indulge me a little weaseling. Many jumping phenotypes would be dismissed as convergent evolution, but not all. Put a reptilian jaw on a mammal species and a paleontologist would notice. They would not throw out evolution right away of course, but it would be a puzzle and puzzles in science get noticed. (If it happened in only one skeleton the puzzle would merely be “which reptile did this jaw come from?” — an assumption that two skeletons got accidentally mixed. But if it kept happening with the same species, now that would attract attention).

  68. “And with the success of the theory of evolution, convergent evolution as an explanation isn’t even going to be questioned in many cases. So my argument is more than a bit circular.”

    Though when it is contested, it can get pretty intense (cf. the response to the birds are dinosaurs theory by the “birds are not dinosaurs” group).

    “But if it kept happening with the same species, now that would attract attention).”

    It would indeed! At which point there would need to be more evidence to clarify the relationships of:

    synapsids to reptiles
    synapsids to mammals
    the newly discovered taxon within/exclusive of each of the above.

    Since convergence by itself tends to merely be noise in data being parsed by the cladistic analysis, legitimate synapomorphies will reveal relationships only if there is enough of them to drown out the noise.

    Too much noise (or not enough data to begin with) will not adequately reveal phylogeny.

  69. Andrew:
    In any event Rita does have a point. If IDers wish to challange “Evolution through Natural Selection” they have a chance (or at least would if they were competant).

    There’s the rub. It is not just ID, but anyone with a competing, testable hypothesis that could have a toe-hold. “A scientific theory,” as my physics prof loved to say, “is like a heavyweight-boxing champion: If you want to unseat it, make sure your guy is stronger.”
    Keeping the analogy, ID may wish to unseat the current theory of evolution, but they don’t even have a boxer, much less one on the card.

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