Thursday, October 8, 2009

The Elaborate Biological Clock

The biological clock influences many biological processes, but now researchers are finding that the influence goes both ways. John Hogenesch, Steve Kay and co workers have pieced together a multi-level genetic network associated with the cell's biological clock. Hogenesch's diagram of the network (above) illustrates how biological processes provide feedback to the clock. As Hogenesch explains:

Clock biologists all appreciated that the communication went one direction--from the clock to biological processes--but I don't think anyone anticipated that there would be this level of integration with cell metabolism and the cell cycle, or all these other pathways impinging on clock function.

Of course this level of sophistication was not anticipated by evolutionists because, like the Epicureans, they believe those "veering atoms" just happened to create the most complex structures known. And now that the biological clock's elaborate genetic network is better understood, evolutionists believe it just built up due to a series of mutations that just happened to occur. Amazing.

This might seem improbable but remember, we're not allowed to be incredulous regarding evolution. After all, it is a fact.

48 comments:

  1. Thank you for your very interesting Blog! I was wondering if you would write about the "power" or less of it, of the natural selection. In the last few month, a lot of stories have come up that disprove the effect of NS on animals features such as the paons' tail, the giraffe neck and now a new study show that sexual selection (see this new article: http://www.newscientist.com/article/dn17932-inferior-males-get-lucky-with-the-birds.html?DCMP=OTC-rss&nsref=life)doesnt necessarily select for the "fitest".

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  2. yet these scientists with all their "faith" in evolution made a very interesting discovery. do you think they would have made the discovery faster if they were skeptical of evolution? that's an interesting hypothesis that can be tested by comparing the productivity (roughly, per capita # of papers) produced by evolution skeptics and everyone else. what do you think the result would be? I sense a p<0.000001, with the t value not favoring you.

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  3. @Khan: who is an evolution sceptic here?

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  4. here's an example:
    http://i962.photobucket.com/albums/ae108/dmso74/behe_carroll.jpg

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  5. So, your saying someone is right if they get more citations in a certain period of time? Emperor - clothes.

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  6. it means that they're being productive scientists and are making important new discoveries that others are following up on. if you're not cited or are not publishing papers,it means the opposite. got it?

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  7. or you have been "expelled" - get it?

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  8. Khan:

    What would the result of a similar study have been at the time of Galileo, Newton, Pasteur? Your argument is irrelevant.

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  9. I think my use of the word 'silly' to describe these posts is getting old... if someone has a better word...

    So, let's see: circadian biologists find that the systems controlling the daily rhythm has a large amount of feedback. Somehow, this is interpreted as a failure of evolution and its predictions (what?) as it somehow demonstrates one way in which it's reasonable to be incredulous of evolution. Because "evolutionists" (biologists) expect unknown aspects of biology to be simple ("veering atoms") by default.

    Ladies and gentlemen, I humbly present you with the straw man fallacy...

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  10. Shirakawasuna:

    Once again, you seem to be making pronouncements about logical fallacies which actually apply to your own posts, rather than the article in question.

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  11. Shirakawasuna: I agree, your silly posts are getting rather old.

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  12. Shirakawasunaand et Khan:
    Besides the fact that none of your comments make any real sense and that none of them actually present anything of interest for this article (and most others), you persist. Why?

    If you have nothing to offer other than denial then either wake up and smell the pizza or get lost.

    Ex. Shi says, "Somehow, this is interpreted as a failure of evolution and ...it somehow demonstrates one way in which it's reasonable to be incredulous of evolution."

    What is your point exactly other than 'somehow' remarks?
    If you understood anything at all of statistical mechanics applied to biological systems, the implications of coded information or algorithmic content in the genome, etc. you wouldn't even be making such foolish remarks.

    "Because "evolutionists" (biologists) expect unknown aspects of biology to be simple ("veering atoms") by default"

    Apparently you didn't get the meaning of "...but I don't think anyone anticipated that there would be this level of integration with cell metabolism ..."

    Expecting the "unknown" and 'not anticipating' high levels of integration are 2 very different things. IDists expect the contrary - more and more evidence of tightly integrated function and information. That's an indicator of designed systems.

    No Darwinist, using neo Darwinian theory as guidance, has any reason to expect high levels of integration of this kind since such "complex feedback loops" are something engineers plan and build - not something one expects of random processes.

    On the contrary, simplicity and disorder are what one SHOULD find if things came about through random processes + NS - not tight functional integration.

    The fact that this simplicity has practically never been found - rather deeper and deeper functional integration is what we find all the time - should give you a clue - but obviously doesn't because your minds are on hold.

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  13. Brian, Anonymous, if you have something to point out and demonstrate, do it. Cornelius is quite plainly telling us that it's a good reason to be incredulous of evolution because his straw man idea of "evolutionists" involves them assuming and expecting the 'veering atoms' to be responsible for complex biological processes as opposed to, you know, complex biological mechanisms. Because that surely follows from evolutionary theory, right? The investigators all said so? They explained it in the paper? It's implied?

    Nope, just a cheap straw man.

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  14. Hitch, a lot of your post was contentless derision without any listed justification, so I'll just address the parts where you say something specific enough for me to care.

    "Expecting the "unknown" and 'not anticipating' high levels of integration are 2 very different things. IDists expect the contrary - more and more evidence of tightly integrated function and information. That's an indicator of designed systems."

    You managed to mangle what I was referring to with "uknown", it seems, as "expecting the uknown" is hardly what I listed as the contrasting position of "evolutionists" (biologists). I'll remind you of exactly what he said: "[evolutionists] believe those "veering atoms" just happened to create the most complex structures known." This is his given reason for why they didn't expect such integration and it's jamming false words into biologists' mouths. It's a common and dishonest piece of rhetoric: biologists think life 'just happens', evolution 'just happened', as if the primary focus of biology isn't figuring out the intricate mechanisms by which both things proceed. Hopefully I don't need to mention that they obviously recognize the intricate systems involved, they're the ones repeatedly discovering and investigating them.

    If expecting integration is a prediction of ID, then it is not separate from the predictions of evolutionary theory and provides no means of independent testing. Biological systems are already known to go through centralized pathways, which makes sense for 'decision-making' in cells. One could point at the actions of cAMP, responding to all kinds of stimuli, for just one example. Its effects can vary, however, as the proteins and other messengers which affects its concentration are subject to evolutionary forces.

    It's getting convoluted, but hopefully you get the point: centralized pathways make sense in light of evolution. Hopefully I won't even have to mention that they don't actually work like human systems, what with brownian motion and all that.

    "That's an indicator of designed systems."

    It's also an indicator of biological pathways, if by indicator you mean property of. Of course, there's plenty of designed systems which lack that quality as well... You would surely then jump to the conclusion that biological pathways look designed, but you it'd be just that: a jump.

    "No Darwinist, using neo Darwinian theory as guidance, has any reason to expect high levels of integration of this kind since such "complex feedback loops" are something engineers plan and build - not something one expects of random processes."

    Wrong. Huge numbers of biological feedback systems emerge from the basic properties of molecules: the chemistry of concentration, competition for active sites. These are not fantastically-intricate methods of control, they are simple and straightforward: does a molecule compete for the active site of carrier protein X? It has a potential use in regulation, subject itself to natural selection for different levels of competition, bonding, manufacture, etc. What was not expected, actually, was the simplicity of the chemistry behind the systems, at least in terms of how the individual molecules act with one another, but this had nothing to do with evolutionary theory's predictions (nor ID's so-called predictions).

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  15. "On the contrary, simplicity and disorder are what one SHOULD find if things came about through random processes + NS - not tight functional integration."

    Why? I'd like to see you demonstrate where random process (mutation, etc) constrained by selection should produce disorder. I expect a definition of disorder, btw, which is rigorous.

    "The fact that this simplicity has practically never been found - rather deeper and deeper functional integration is what we find all the time - should give you a clue - but obviously doesn't because your minds are on hold."

    The integration is a form of simplicity: it's the routing of decision-making processes of the cell/organism through a central pathway. It involves a large number of different molecules feeding into the system, but the alternative involving so much input is to have separate systems for each, independently evolved.

    Thanks for calling them "Darwinist[s]", though. It really shows your level of education on the matter.


    All of this misses the point, however. Cornelius claimed/implied that "evolutionists" (biologists) expect biology to 'just happen' as a result of their ideas of evolutionary theory and are therefore surprised when integrated systems are discovered. Integrated meaning taking input from a number of sources and putting them through a central pathway. He's wrong: none of his claims follow from evolutionary theory and he's inserted the nonsense about 'veering atoms' into other peoples' mouths. He has a straw man when he uses that dishonest premise to imply that it's therefore reasonable to doubt evolution. He's knocked down a paper tiger.

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  16. Shirakawasuna:

    Regarding the purported "straw man", Dr. Hunter has offered a hypothesis about why the biologists in the study did not anticipate the high level of integration which they found in the cell's biological clock. You may disagree with his hypothesis, but you can't reasonably claim that he mischaracterized any argument that they made. In fact, your incredulous caricatures of Hunter's position are much more deserving of the epithet.

    Hunter also did not put the words "veering atoms" in anybody's mouth. He took those words from the mouth of Epicurus, an ancient Greek philosopher whose ideas on matter and existence were probably not too different from your own. Hunter obviously used this quote as a symbol, a literary device representing unguided mechanistic naturalism, as it has been accepted down through the ages.

    Why should you take exception to the term "veering atoms," anyway? I am sure you believe that while the complex biological processes were indeed produced by complex biological mechanisms (no one disputes this) these mechanisms were in turn produced by the emergent properties of unguided molecules, composed of, yes, "veering atoms".

    The question is this: what is reasonable to expect from such unguided processes? If you were not already pre-committed to an atheistic worldview, would you truly have predicted that non-living matter could organize itself into the amazing collection of nanotechnology we see in these microscopic cells, given any amount of time?

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  17. Ugh, my browser messed up so I have to rewrite my response.

    Brian: you're presenting a picture of Dr. Hunter's post where all he did was say that the biologists think these processes came about by evolution and that it was "unguided mechanistic naturalism", that "veering atoms" is somehow a substitute for a nuanced and accurate picture of evolutionary history on a molecular level. I have to disagree (I'll quote when appropriate).

    "Regarding the purported "straw man", Dr. Hunter has offered a hypothesis about why the biologists in the study did not anticipate the high level of integration which they found in the cell's biological clock. You may disagree with his hypothesis, but you can't reasonably claim that he mischaracterized any argument that they made. In fact, your incredulous caricatures of Hunter's position are much more deserving of the epithet."

    He left the misrepresentation of "evolutionists" and the summary of what the circadian biologists did a little separate. As people here are touchy if you make connections, I made my criticism without even connecting the two together. If you want to assume that he's in fact referring to the circadian biologists as the "evolutionists" he portrays, the post is even worse. I think it's clear he was including the biologists in his criticism, but he used enough insinuation that I didn't want to get into that argument.

    I took issue with the "hypothesis", if it can be called that, concerning "evolutionists", where he flat out states his pedantically derisive opinion of their assumptions, ideas, and conclusions. He tells us that for them, the "'veering atoms' just happened to create the most complex structures known." Aside from being a reference to shoddy design arguments, it's an intense oversimplification of a biologist's opinion of the mechanisms of a cell and its evolution as well as existing organisms' evolutionary histories. He uses it, quite obviously, because it makes them look like simplistic fools making stupid predictions based on evolution, when they've done/been none of that in this situation. Perhaps he would say it has more to do with the ideas than them being fools, but the caricature fits and they would have to be for the claim to be true. That isn't the only problem in the post, but it's enough to earn him some deserved insolence.

    "Hunter also did not put the words "veering atoms" in anybody's mouth."

    Wrong. He explicitly said, "[evolutionists] believe those "veering atoms" just happened to create the most complex structures known." I am aware that it's a reference to Epirucreans and the implication is not at all improved by acknowledging that: it furthers the idea that the "evolutionists", who you are now acknowledging includes the circadian biologists, hold such simplistic ideas or something similar to them. No evidence offered, just pedantic derision.

    It is also not a reference to "unguided mechanistic naturalism", it is a reference to random atomic processes creating the thing in question, as Epicureanism held for all kinds of things. There is more than random molecules to evolution, as you should know. It's hardly a fair characterization of evolution's mechanisms.

    "Why should you take exception to the term "veering atoms," anyway?"

    Pedantic note: I don't mind the term, I take exception to its application here.

    "I am sure you believe that while the complex biological processes were indeed produced by complex biological mechanisms (no one disputes this) these mechanisms were in turn produced by the emergent properties of unguided molecules, composed of, yes, "veering atoms"."

    Yes, but Dr. Hunter didn't have such a nice explanation of biologists or "evolutionists" considering complex biological processes with complex biological mechanisms, nor did he reference emergent properties. He presented them as simplistic while using phrases like "just happened".

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  18. "The question is this: what is reasonable to expect from such unguided processes?"

    A huge number of things, many of them dependent on things we don't yet know in molecular biology. First and foremost you expect homology from common descent and that is widely demonstrated. Of course, common descent isn't usually described as 'unguided', but if you ignore it in your criticism you're failing a rather important and basic aspect of biology. There is also selection, a nonrandom process integral to evolution's mechanisms, from which you expect (in different populations) variations on themes and adaptation, among other things. On a molecular level, you expect conservation of the most basic and necessary genes across clades, for example. I'm not sure why I'm even listing all of this, but you asked.

    "If you were not already pre-committed to an atheistic worldview, would you truly have predicted that non-living matter could organize itself into the amazing collection of nanotechnology we see in these microscopic cells, given any amount of time?"

    Oh my, how ridiculous. Pre-committed to an atheistic worldview? No, if I'm pre-committed to anything, it's basic skepticism and an appreciation for rational thought and induction. Atheism or something like it is a natural outcome of that, not a foregone conclusion. Of course, you're also getting rather personal. I could also speculate (with more insight, if I say so myself) as to why ID advocates almost inevitably have an evangelical background, but I haven't. Their arguments and misinformation are easy to knock down without even pointing that out.

    Now then, what's the alternative to this 'pre-commitment' I apparently have? Being a theist? Are you asking me if I think non-living matter would 'organize itself' (terrible, biased phrasing) into life if I were a theist? I don't know where to begin with that. Is the subject suddenly abiogenesis? Are we discussing some new kind of biological Vitalism? I haven't a clue. I suspect that you're inserting a complaint you have with me personally or some views you suspect that I hold rather than keeping to the actual subject matter.

    Last point: the "veering atoms" sentence is bad enough, but he also wrote this:

    "And now that the biological clock's elaborate genetic network is better understood, evolutionists believe it just built up due to a series of mutations that just happened to occur. Amazing."

    I'm requoting it, but I didn't think it would been necessary. Look at what he's saying: he wants you to think that biologists/"evolutionists" think the circadian rhythm's genetic network (input/output system) "just" came about due to "a series of mutations that just happened to occur". I'll generously assume that the first "just" doesn't mean only, but do you think that's an accurate depiction of biologists'/"evolutionists'" ideas of evolution, particularly the evolution of an intricate and complicated biological system over a period of billions of years? I have a number of things to say if you answer, "yes", but hopefully you now realize that he's presented his opposition in a simplistic fashion, so simplistic that his post is mostly one big straw man.

    He ends his post by yet again mentioning how reasonable it is to be incredulous. How do you think his post demonstrates this, even partially, even if your interpretation is right?

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  19. Edit: 'billions' -> 'millions'.

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  20. Shirakawasuna and folks:

    I haven't read all your comments, but thought I would respond to a couple.

    "he flat out states his pedantically derisive opinion of their assumptions, ideas, and conclusions. He tells us that for them, the "'veering atoms' just happened to create the most complex structures known." ... it's an intense oversimplification of a biologist's opinion of the mechanisms of a cell and its evolution as well as existing organisms' evolutionary histories. [etc, etc]"

    It is interesting to see evolutionists protest when their theory is described. The Epicureans appeal to naturalism to resolve such issues as the problem of evil parallels precisely moves made in the Enlightenment that laid the groundwork for nineteenth century evolutionary thought.

    The fact that evolutionists hypothesize *histories* is entirely beside the point as it does nothing to reduce their dogmatic appeal to naturalistic explanations. Do you think the Epicureans did not imagine *histories* as well?

    Now of course all of this would be a moot point if evolutionists had compelling explanations. Of course they don't, but people believe they do. For those people, no skepticism will make much sense.


    "First and foremost you expect homology from common descent and that is widely demonstrated. Of course, common descent isn't usually described as 'unguided', but if you ignore it in your criticism you're failing a rather important and basic aspect of biology. There is also selection, a nonrandom process integral to evolution's mechanisms"

    This is the usual evolutionary interpretation of the evidence. It is rare for evolutionists to present a theory-neutral view of the evidence. The paradigm is so entrenched that evolutionary interpretations become *the* scientific interpretations.

    For instance, the claim that homology is widely demonstrated is an incredible canard. We could also say evidence for geocentrism is "widely demonstrated." But in fact convergence in biology is massive (no, that is not hyperbole), and evolutionists have no good explanation for it. They once said lightning couldn't strike twice, and then when repeated designs were discovered they chalked it up to the wonders of evolution. No finding ever can be allowed to have an alternate explanation even considered, no matter how strained the evolutionary explanation becomes.

    Then we have this typical bit of denial:

    "common descent isn't usually described as 'unguided' "

    Evolutionists not only avoid terms such as "unguided," but in fact they actively use teleological or Lamarckian language. It's always "the fantastic design arose due to meet this or that need," not "the fantastic design arose from unguided variation and so was then selected."

    And finally, the ultimate absurdity:

    "There is also selection, a nonrandom process integral to evolution's mechanisms"

    Selection never created anything. It only kills off the bad designs. The kangaroo, oak tree and sparrow all had to be created one step at a time by unguided, directionless forces and events. Selection did not bring about *any* of those steps -- it only kills off the losers. The sooner evolutionists stop fooling themselves about this the better.

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  21. "It is interesting to see evolutionists protest when their theory is described."

    You didn't describe evolutionary theory, you pulled out an Epicurean reference and implied that biologists/"evolutionists" don't expect complex/increased integration as a result of the "veering atoms" cop-out. It's simply not true, it's your unevidenced assertion.

    The small bit of history on the Enlightenment is irrelevant, scientists/"evolutionists" are not so simplistic as you imply. You seem to want to back away and elucidate now that your implications have been realized, that you were trying to imply that this integration was not expected as a result of such simplistic thinking.

    "Now of course all of this would be a moot point if evolutionists had compelling explanations. Of course they don't, but people believe they do. For those people, no skepticism will make much sense."

    There is a difference between skepticism and mere doubt. Skepticism is built into science, as you should know: claims are fought out before and after publication, during conferences, in the lab, via correspondence. They aren't accepted without evidence, there are always critics of unfounded explanations.

    Now then, "evolutionists" don't have compelling explanations? How about the overwhelming homology between organisms which "just happens" to create overlapping phylogenies? No? How about the conserved regions of the genome, which "just happen" to be the housekeeping genes. No? Are you still opposed to selection as a mechanism? Take it up with computational biologists and CS experts who use selection algorithms to improve engineering. Yet another unevidenced assertion you have, there.

    Are you implying that I or someone else should explain the findings of circadian biologists or show how it's predicted by evolutionary theory? If so, why?

    "This is the usual evolutionary interpretation of the evidence. It is rare for evolutionists to present a theory-neutral view of the evidence. The paradigm is so entrenched that evolutionary interpretations become *the* scientific interpretations."

    I'm not sure what the problem is, here. Interpreting the evidence is precisely how theories and hypotheses work, their success at explanation and prediction are what matter and in that regard evolution has been a resounding success.

    "For instance, the claim that homology is widely demonstrated is an incredible canard. We could also say evidence for geocentrism is "widely demonstrated.""

    Yes, you could. The accuracy of a scientific claim is contingent on the evidence and its explanatory value, something which is hardly missing for homology and entirely lacking for geocentrism.

    "But in fact convergence in biology is massive (no, that is not hyperbole), and evolutionists have no good explanation for it."

    It's nowhere near as huge as homology and the explanations for it, when it exists, are two-fold: 1) convergence is incomplete. There are very similar phenotypes, but they often have different functions or advantages when you actually look closely. I believe you remember your attempt at comparing thylacines to wolves, don't you? 2) When there is convergence, and it can be strong, it is due to similar selective pressures. I don't think I need to get pedantic to point out the similar environmental pressures on say... dolphins and ichthyosaurs as large, originally tetrapod sea carnivores (textbook example).

    "They once said lightning couldn't strike twice, and then when repeated designs were discovered they chalked it up to the wonders of evolution."

    I would expect evidence for such an assertion. It's not like even Darwin was unaware of convergence, he spent huge amounts of time studying barnacles, a subject of controversy at the time due to possessing their hard shells (they were often classified as molluscs) but with competing evidence that they were arthropods. Darwin set out the very basics, was well-aware of convergency, yet you claim the thinking was "lightning couldn't strike twice" i.e. no convergence?

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  22. Go ahead and strain it, we'll see what happens.

    "Evolutionists not only avoid terms such as "unguided," but in fact they actively use teleological or Lamarckian language."

    Nonsense. Biologists/"evolutionists" use the word "unguided" to describe evolving populations all the time. It's simply rare to hear someone describe common descent as unguided. They do often use telic language as do chemists and other scientists: describing dynamic objects as 'wanting' to do something or 'trying' to do something is a convenient simplification and comes naturally to us anthropomorphizing apes. I can't think of examples of Lamarckian language being used by actual biologists nor any "evolutionists" who have even very slight education in evolutionary theory.

    "It's always "the fantastic design arose due to meet this or that need," not "the fantastic design arose from unguided variation and so was then selected.""

    You seem to have an erroneous notion about how things referred to as 'designed' in biology are thought to have arisen. That particular telic phrase is used for systems which surely arose through a series of mutations, not a single one, with selection acting at all times. That would be the more detailed way to describe the probable evolutionary history of a 'designed' biological aspect (neglecting genetic drift for the moment). Not one 'big' change and selection acting on it (that's more of a developmental biologist's bag).

    "Selection never created anything."

    Except for antennas superior to those of human design (don't give me nonsense about a selection algorithm being so 'design' that it doesn't count). It also does a fine job at ensuring that antibiotic resistance will remain a serious threat to public health, among other easy examples. Selection trims down variation by 'favoring' (increasing in frequency) those phenotypes which have greater reproductive success.

    "It only kills off the bad designs."

    Far too vague for me to agree or disagree. Is a slightly less successful "design" "bad"? See my short summary of selection above: it acts on existing variation within a population, increasing in frequency those phenotypes which do better. The origin of variation is a separate subject.

    "The kangaroo, oak tree and sparrow all had to be created one step at a time by unguided, directionless forces and events."

    You mean "evolved" rather than created, right? In that case, then yes you're right! That's the conclusions of evolutionary theory and its mechanisms, although there's still plenty of room for *actual* disagreement on the relative impact that the different evolutionary forces have had or how they affected a particular clade. It's a form of modern uniformitarianism (not to be confused with phyletic gradualism) whereby current modes of adaptation are used to extrapolate probable mechanistic origins of life we see today, including kangaroos, trees, and sparrows. By the way, evolutionary theory also holds that those three groups hold common ancestry, so rather than merely being "created" step-by-step, their ancestors branched off from one another down separate evolutionary paths.

    "Selection did not bring about *any* of those steps -- it only kills off the losers."

    And thereby increases the 'winners'. That's the nice thing about selection... you can use it all the time to do great things. You can use it to enrich cultures of bacteria, for a simple and easy-to-understand example, by adding conditions they would experience in their normal environments. Staph epi can be enriched by adding it to a high-saline mannitol environment. This is closer to 'species-sorting' than natural selection, but the idea is the same: kill off the 'losers' and the frequency of 'winners' increases.

    "The sooner evolutionists stop fooling themselves about this the better."

    I'm not sure how I'm fooling myself by understanding the basics of selection, could you elaborate?

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  23. A last, simple approach: what do you think of selection with respect to Richard Lenski's ongoing long-term E. coli experiment? Is using a new carbon source "just killing off the losers"?

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  24. One more comment (I can't help myself): does anyone else find it strange that I have to explain the power of selection to someone with credentials in computational biology?

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  25. Shirakawasuna:

    Thank you for replying to my comment above. Sorry it has taken so long for me to respond. There has been a lot of water under the bridge since then. I may comment on some of the things you said, but meanwhile, your last comment raised an intriguing question:

    "Does anyone else find it strange that I have to explain the power of selection to someone with credentials in computational biology?"

    The answer to this question must be "yes."

    Indeed, I can't imagine that even you yourself really believe that Dr. Hunter doesn't know as much as you do about the subject, or even more. As you say, the man has a Ph.D. in Biophysics and Computational Biology.

    So, the deeper and more important question is this:

    If Dr. Hunter does understand all of these things we are discussing, including the process and power of natural selection, the emergent properties of matter and the complexity of the biological systems which produce biological features, then why is he skeptical of the Neo-Darwinian paradigm which dominates biology today?

    How do you explain this?

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  26. Brian,
    perhaps reading the Biola Doctrinal statement, which Cornelius, as even an adjunct, non-tenure-track instructor must adhere to, will shed some light:

    http://www.biola.edu/about/doctrinal-statement/

    and you say evolution is religious?

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  27. Brian, I'd like to leave my comment on having to explain this to Dr. Hunter as it stands. Speculating about how he could possibly be so undereducated while receiving said Ph.D. on his own blog is inappropriate. His own demonstrations stand on their own, it is a wonder that he can act like he does.

    It is also not particularly amazing that there are a small handful of "skeptics" (ID advocates) with credentials. We aren't talking about an entire field of science, as they oppose, but of individuals, often with religious motivations or biases to begin with, who adopt very poor argumentation which align quite nicely with that past. Jonathan Wells specifically obtained his Ph.D. so that he could use credentialism, although I don't accuse Dr. Hunter of such a thing.

    I suppose I contradicted myself by speculating a bit, eh? My speculation was entirely in explaining how a few individuals could obtain credentials in a subject while wrongly arguing against some of its elements.

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  28. Khan:

    "and you say evolution is religious?"

    The Biola statement is no different than what a typical evolutionist (eg, Francis Collins, Ken Miller, etc) would accept.

    The important point that you are missing is that evolution is religious not because evolutionists hold religious beliefs, but because the evolutionary position (ie, evolution is a fact) entails religious assumptions.

    So why are you advocating a religious theory?

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  29. Cornelius,
    no offense but that is flat-out wrong. would Ken Miller ever accept that God specially created humans, and that they do not share a common ancestor with other organisms (bottom of explanatory note)? that God created "kinds" of organisms? give me a break.

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  30. Khan:

    Read it more carefully--that's not part of the Doctrinal Statement.

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  31. so are you saying the explanatory note is wrong?

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  32. and, if so, how do you interpret this: "The Old and New Testament are without error or misstatement in their.. record of historical facts. They are without error or defect of any kind." Does Genesis count as a record of historical fact?

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  33. Religious assumptions of evolution, eh? I realize you wrote a book on this (Title o' the blog), but I seriously doubt it's cogent. Perhaps you'd like to list an example which wouldn't also have a 'damning' correlary in geology?

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  34. Khan:

    "how do you interpret this: 'The Old and New Testament are without error or misstatement in their.. record of historical facts. They are without error or defect of any kind.' "

    That is usually understood to be an essential of the Christian faith--held by evolutionists and creationists alike.

    The idea that there are no errors or misstatements leaves a wide berth for interpreters. IOW, evolutionists do not hold that there are errors or misstatements in the Bible, they simply interpret it differently than creationists. Both make strong theological arguments, but from different perspectives.

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  35. you are completely ignoring my central question. I understand, perhaps your part-time instructoship and access to the Biola library is on the line.

    the explanatory note right below this doctrinal statement explains what it means, i.e. that god created "kinds" of organisms, and that man does not share common ancestors with other organisms. so, again, is this explanatory note wrong?

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  36. From the explanatory note:

    "The existence and nature of the creation is due to the direct miraculous power of God. The origin of the universe, the origin of life, the origin of kinds of living things, and the origin of humans cannot be explained adequately apart from reference to that intelligent exercise of power."

    The explanatory note, telling us what it is:

    "In addition, the following explanatory notes indicate the organization’s understanding and teaching position on certain points which could be subject to various interpretations:"

    So wait, you seriously think Ken Miller believes in specially-created "kinds"? Seriously?

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  37. Khan:

    ***
    the explanatory note right below this doctrinal statement explains what it means, i.e. that god created "kinds" of organisms, and that man does not share common ancestors with other organisms. so, again, is this explanatory note wrong?
    ***

    As I've already explained the portion of the explanatory notes to which you are referring is not a doctrine position.

    Doctrinal positions are essentials. Jesus died for your sins, that is not negotiable -- I don't care how many transitional species are discovered.

    But in addition to essentials, there are non essential points. Sometimes it is a good idea to take a position on such non essentials, for instance if it helps to establish a teaching approach, as is indicated in this case.

    What do I think of this? I don't take a strong position on non essentials, except for opposing obviously false positions. For instance in this case, evolutionists interpret evolution as God's creation tool because they believe that God would never have created this world (for various reasons).

    I trust you can see that God's using naturalistic mechanisms is not the problem here, but rather the problem is the mandating of this due to a false position (ie, God would never have created this world).

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  38. Shirakawasuna & Khan:

    You both seem to be playing coy.

    Come now, state your position clearly. Which of the following statements best summarize your views?

    a. Dr. Hunter does not understand current evolutionary thought. Although he has obtained his Ph.D. in Biophysics and Computational Biology, and has written several books critiquing evolutionary theory, he has still somehow failed to understand the basic principles of modern evolutionary theory. This seems to be what Shirakawasuna is insinuating.

    b. Dr. Hunter understands evolution, but purposefully conceals what he knows for ulterior motives. Khan seems to suggest that Dr. Hunter secretly believes in evolution, but conceals this in order to keep his job at Biola.

    Both of these statements are obviously absurd, but I can't derive another meaning from the statements you've made.

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  39. Cornelius,
    so, again, is the explanatory note wrong? this is now the 3rd time i've asked.

    Brian,
    you obviously have not met many PhD's. people who get these degrees in a particular topic tend to be very focused on that particular topic and thus tend to be lacking in other, even closely related, areas. it would not be at all unusual for a Ph.D. ecologist, for example, to not know much biochemistry and likewise it's not surprising that a Ph.D. biophysicist wouldn't understand evolution.

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  40. ps Brian,
    did you know that every faculty member at Biola has to agree with every aspect of both the doctrinal and teaching statements expressed on that page? they have to submit this agreement in writing as a condition for hire. so either Cornelius agrees with every one of those statements (including the one about God creating "kinds" of organisms) or he lied to get his job. what is absurd about that?

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  41. Brian: "Shirakawasuna & Khan:

    You both seem to be playing coy."

    I'm attempting to avoid insulting Dr. Hunter, which you seem to want to draw me into. He holds scientifically indefensible positions, uses vague implication rather than proper, academically-honest arguments, and repeatedly illegitimately impugnes the reputations and intellectual vigor of entire established fields of science. Take from that what you will, I'll continue expressing surprise at the fact that he does what he does with the credentials he's obtained and pointing out the problems with his posts, which is the limit of my incivility on someone else's blog.

    I needn't accept one or another of your options, which are more personal than I'm going to go on this blog. If you're still wondering how a small handful of people can hold strange and inaccurate positions, despite having academic credentials, I'm not sure how much more I can explain...

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  42. Brian: As you can see, Khan doesn't mind being that personal, so you can get your fix of personalisms there ;).

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  43. Khan:

    "so, again, is the explanatory note wrong? this is now the 3rd time i've asked."

    And I've already answered. But rationalists cannot understand anything but rationalism.





    "did you know that every faculty member at Biola has to agree with every aspect of both the doctrinal and teaching statements expressed on that page?"

    No, I didn't know that.

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  44. I guess "yes" or "no" is too "rationalist" an answer to expect. and if i'm wrong about Biola, you need to correct the wikipedia entry. but i know now i can't expect a yes or no answer to that question either.

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  45. From the 'Spiritual and Doctrinal Review Form':
    "If the candidate’s responses are congruent with the Doctrinal Statement and Explanatory Notes, check “Acceptable” below. As per guidelines in the Faculty Handbook, “if the initial reading by the reviewer reveals doctrinal discrepancies or related underlying conceptual difficulties with the university’s doctrinal Statement or Explanatory Notes, the reviewer will conduct a personal interview with the tenure candidate."

    Clearly, the Explanatory Notes are taken seriously and are not merely mentioned for clarity on the university's position, leaving acceptance of the notes completely up to faculty with no repercussions - rather than being immediately 'Acceptable', you are pushed into an interview due to "concerns", the same as would occur if you rejected the main portion of the Doctrinal Statement.

    Again, no, Ken Miller would not agree with the statement. Second, Khan is quite accurate in his implications and you have failed to adequately address the issue, Dr. Hunter. You have, as seems to be a pattern, asserted your accuracy without actual demonstration of the facts.

    If there's still any doubt, there is this from Biola's Provost Search page:

    "Biola University's Doctrinal Statement remains the foundational document, regarding the theological position of Biola University. From its inception, Biola's position has been and remains Christian, Protestant, and theologically conservative. Prospective and existing employees must affirm that their personal theological beliefs are in agreement with the Biola Doctrinal Statement. A prospective or an existing employee's church affiliation will be considered in determining his or her understanding of and compliance with Biola's theological position."

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  46. Khan:

    I am familiar with the phenomena of the ph.D. in one topic being less familiar with phenomena outside of his focus of study. This can't explain Dr. Hunter, who has written three books on the subject of evolution. I was hoping for a more thoughtful reply.

    I am at least grateful that you gave me a plain answer, unlike Shirakawasuna, who apparently doesn't mind making insinuations, but plays shy when asked to state his accusations plainly.

    For the record, I didn't think both of the two options I provided were insulting, nor were you limited to choose one of them. These were just the positions you both seemed to hold.

    Both options seemed ridiculous to me, and I hoped that one or both of you would repudiate them and supply better explanations for Dr. Hunter's interpretation of the evidence, given his academic credentials.

    Neither of you made any attempt to do so. Rather, Khan seemed to embrace these thoughtless attitudes, and Shirakawasuna seemed content to insinuate that they could be true, while giving the appearance that he is taking the high road.

    All that being said, I confess myself mystified by this new road you are going down. Exactly what do you two hope to establish by all of these citations from Biola University's Doctrinal Statement? What are you trying to say?

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  47. Brian: "I am at least grateful that you gave me a plain answer, unlike Shirakawasuna, who apparently doesn't mind making insinuations, but plays shy when asked to state his accusations plainly."

    I'm not playing shy, I'm refusing to directly state what options follow from the shoddy performance we keep getting from Dr. Hunter. Let's just leave it at this: none of them are flattering and I would prefer to focus on the topics at hand and the many weaknesses of these posts. I merely expressed wonder at someone with experience in computational biology attempting to claim that natural selection doesn't "create" anything as if it wasn't just about the oldest creationist canard on the book, ignoring variation and the consequences of changes in allele frequency. I listed multiple examples of selection at work, which were ignored...

    The best I can come up with is that he did nothing at all relating to fitness, but even *I* am aware of the applications of selection as an undergrad...

    Finally, I'm not "taking the high road", I'm only asserting one standard here: I won't do it on his own blog. I'll gladly go into detail what the likely contingencies are elsewhere, if you're very much interested.

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  48. My only interest in Biola's Doctrinal Statement is that Dr. Hunter claimed Ken Miller would accept it. He wouldn't. He also seems to have gotten ancillary facts about it wrong...

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