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Tag Archives: evolution

On the weekend of September 9, I and a fellow member of the Center for Inquiry attended a creationism “conference” (I’d have called it a lecture series, but hey, whatever). My overall impression is that if this is all that creationists have, evolutionary theory is not at all in jeopardy. Of course, I never thought it was. I just wanted to experience what people who believe the Earth is a mere 6,000 years old and that dinosaurs co-existed with humans had to say. The whole thing could only be accepted by those who have drunk the Kool Aid. There was nothing convincing in anything I saw, and some stretched my credulity well past the breaking point. Read More »

Something I’ve been wanting to tackle for a long time is Alvin Plantinga’s Evolutionary Argument Against Naturalism which he presented to a Christian lay audience in an article published online in Christianity Today. Here’s a spoiler: it’s awful. According to Plantinga,

As I see it, this is a whopping error: evolution and naturalism are not merely uneasy bedfellows; they are more like belligerent combatants. One can’t rationally accept both evolution and naturalism; one can’t rationally be an evolutionary naturalist. The problem, as several thinkers (C. S. Lewis, for example) have seen, is that naturalism, or evolutionary naturalism, seems to lead to a deep and pervasive skepticism. It leads to the conclusion that our cognitive or belief-producing faculties—memory, perception, logical insight, etc.—are unreliable and cannot be trusted to produce a preponderance of true beliefs over false.

I have no problem with skepticism. I think everybody should be a skeptic. For those who don’t, I’m offering up the Brooklyn Bridge… Cheap!

Nor do I have a problem with anything in that last long sentence. Our memory is quite fallible. So is our ‘logical insight’, since it is based on heuristic and not rigorous logic. It just happens to work most of the time and is fast, and for the times it doesn’t it typically doesn’t matter. For instance, our natural instinct when out in the dark we hear a rustling in the bushes our impulse is to take flight. But whether the rustling in the bushes is a real danger (the tiger that Plantinga likes to use) or a prankster is not considered by our subconscious. With the former, our chance of survival increases because we don’t go over to the bush to check the source of the disturbance. With the latter, we just feel foolish. In both cases, our lives continue.

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I have just finished Jerry Coyne’s book on the fact of evolution entitled Why Evolution Is True. I say fact, of course, since there is no longer any discussion of whether evolution happened in biology. Not because evolution is dogmatically unquestionable, as evolution deniers will say, but because such a discussion is utterly pointless. 

He begins the book by describing what evolution is (itself often misunderstood) and a bit about systematics. It’s a good basic description of how phylogenetic trees are built from a comparative morphology point of view. He moves on to some interesting examples of visible evolution in the fossil record, discussing the near-continuous changes in radiolarians and foraminiferans, some of the recent fossil evidences for various transitions such as the aquatic-terrestrial tetrapod transition, dinosaur to bird, and (with good reason, as Jerry demonstrates, the darling of modern paleontology) land-sea mammalian transition.

Jerry continues with some of the earliest evidences of evolution that was discussed in The Origin, such as vestigial organs and atavisms, as well as something somewhat more modern – evidence from pseudogenes. Embryology is also strong in this chapter and he clearly describes what “phylogeny begets ontogeny” means, with examples. This easily leads into, of course, how bad design occurs. I’ve always enjoyed examples of clearly inept design, and here Jerry gives some of the more famous ones like the tortuous path of the aortic arches in humans and how such a ridiculous ‘design’ arose from contingency dictated by our evolutionary past. 

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The concept of Irreducible Complexity (IC) and, by extension Intelligent Design (ID) as a whole, is a defeatest and slothful concept. It’s proponents whine and wail that things are too complicated to have arisen through blind natural processes so don’t even bother to try to understand it. What kind of attitude is that? If everyone in history had this outlook we would still be throwing rocks to catch dinner. Science as we know it arose because there were those who did not accept that dogmatically-given answers are immune from being questioned. In other words, what we know as modern Science arose in spite of Religion and most definitely not because of it.

And – trust me on this – I did not need the opinon of Judge Jones III, as correct as it was, to know that ID is NOT Science. In Science, we deal in explanations that offer insight into the mechanisms of processes, not simply substituting another expression for “I don’t know”, like “a magic man done it”, and trying to pass it off as somehow being a satisfactory answer when it answers exactly nothing. How do we know when something is ‘too complex’ except when given as a ‘just so’ story? And ‘just so’ stories are as dogmatic as it gets. In Science we systematically work to divest ourselves of dogma, not embrace it!

In the Kitzmiller v. Dover case, Dr. Michael Behe was front and center for the defense trying to put forward the idea that this idiotic concept ‘explains’ the complexity of cellular structures that he feels (without ever presenting any data to corroborate his belief) could not come to be through the blind machinations of natural selection.

Poppycock. Behe tries to appeal to ignorance, which is not a logical argument at all. This is true in every single example supposedly supporting IC he has ever given. But his argument is never any more than throwing up his hands in self-fulfilling defeat at a real explanation. At the Kitzmiller trial, he was forced to admit that he was not even familliar with the relevant literature! This is the height of intellectual dishonesty, and because Behe espouses such nonsense his colleagues have completely (and rightly) disowned these nonsensical ideas (and let’s face it – him). This underscores a basic difference between ID (or should I say ‘cdesign proponentsists’?) and Evolution proponents in that the latter actually work to gather evidence in support of hypotheses while the former do nothing but sponge off the gullible by telling the faithful what they want to hear.

Today I’m going to discuss what proponents of ID consider the poster child for their position and why it is really far-and-away better represented by evolution.

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Every molecule in your body has a story to tell. This tale is about hemoglobin, the class of oxygen-binding molecules that make oxygen transport in complex creatures such as us possible. Hemoglobins are proteins that contain the heme moiety, a planar molecule binding iron (Fe) and maintaining it in the +2 oxidataion state (denoted Fe(II)).

Hemoglogins in the Animal Kingdom
Hemoglobins in almost all vertebrates is a heterotetramer (that is, four (‘tetra’) individual of different (‘hetero’) proteins) composed of two α-globin and two β-globin polypeptides (a fancy word for proteins). The heme part is bound in a pocket formed by structure of each globin unit. The movement and interactions between the subunits increases hemoglobin’s ability to bind oxygen.

Hemoglobin structure

Hemoglobin structure

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Of late a lot of hubbub has brewed over Richard Lenski’s latest paper on the laboratory evolution of citrate-eating E. coli (PNAS 105(23):7899-7906 (2008)). Lenski figures very prominently in Carl Zimmer’s overview of E. coli research entitled Microcosm, and for good reason. For those that don’t know of the content of the current paper, for the last 20 years Lenski and his students have been growing bacteria (starting from a single bacterium and creating 12 lines) and periodically freezing samples (every 500 generations or so) to see if these bacteria evolve in the lab. At the time this paper was published, over 44,000 generations had passed.

Periodically, the frozen ‘fossil’ bacteria can be thawed and DNA compared over time. Since the bacteria are cloned and reproduce asexually, only natural selection and genetic drift can act on the gene populations, greatly simplifying analysis. Previous to this paper, changes in growth rates, reduced lag phases when the bacteria were transfered to a fresh culture medium, reduced peak population densities and larger cell sizes relative to their ancestors were reported. Most populations evolved increased DNA supercoiling.

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The web blogsite MySpace does not have a Science section. I find that rather insulting, being a scientist. The world makes use of the benefits of Science to such an extent that the MySpace gods are completely oblivious to their dependence on it. In a sense, this jaded attitude is in part responsible for the rise of pseudoscience and spirituality. In my book, a spiritual person is a flake. Where does Deepak Chopra get off telling us that scientists have hijacked the term ‘quantum mechanics’ as if it were spiritual gurus and not physicists that were its developers? He’s got it backwards! It is HE that has hijacked it and made it out to be something which it is most definitely not. Quantum healing my ass! What a rube. Anyway, this article is cut and pasted from the Australian Skeptics website and is an excellent discussion on Shannon information and the increase in information in the genome. Why don’t creationists get it? This is so much more fascinating than the banal god-dunn-it!

Speaking of them, why are they so dishonest when going out to interview scientists? PZ Myers ran into the same problem when Ben Stein filmed that train wreck. I’ll lay money down that Richard is totally up front with his motives. Creationist propagandists, on the other hand, always seem to use underhanded tactics.


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Some time ago, PBS aired an episode of Nova entitled ‘Judgement Day’. It was, in my estimation, an excellent discussion of what went on in the town of Dover when creationists attempted to inject their inanity about how life came to be into a Science class.  I highly recommend watching it, as it was an accurate depiction of what went on in the subsequent lawsuit.  And, yes, I have read both the trial transcripts and the judge’s decision, so I am in a position to make such a judgement call. 

The program re-enacted a number of highlights from the trial. Michael Behe, the only member of the Discovery Institute of those originally scheduled to appear, was supposed to be the defence’s star witness. It turned out he was an unwitting wringer for the prosecution. Behe is an example of one of the most interesting properties of creationists (or intelligent design) proponents: their inability to change their ideas in the face of overwhelming evidence. Behe has been repeatedly told why his concept of ‘irreducible complexity’ and the examples he gives for it are completely bogus, yet he has never changed his tune. And this was why he was totally demolished on the witness stand. Of course, Behe produced his pet example of irreducible complexity, the bacterial flagellum.

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There are many out there that refuse to accept that the same science which is used to convict criminals can also be used to demonstrate conclusively that humans evolved from common ancestors with chimpanzees, which evolved from common ancestors with great apes, etc. Very strange, since lay people are so trusting of the former. I’m going to write here about a story about one gene, out of the many thousands of similar stories in our genome, the NANOG gene. For those that are interested in molecular studies of evolution, with particular reference to human evolution, I strongly recommend Daniel Fairbanks Relics of Eden. This is a great primer for how molecular biology is applied to the problem of evolution. The following information is contained within Chapter 5 and Appendix 1 of Relics of Eden.

What is NANOG?

NANOG is a homeobox gene which encodes a transcription factor critical in development. In other words, it is a regulatory gene. The products of this gene allow cultured stem cells to divide indefinitely without differentiation (to become specialized cell types). It becomes activated shortly after conception.

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I’ve grown up believing that you should not speak ill of anyone, but then, I don’t lie, either. The subject of this blog is Kent Hovind, or ‘Dr. Dino’; a man that, without ever having met, I completely loathe. No, it goes beyond that, and I will now tell you why.

Yesterday, I downloaded a debate that was made available on the Infidel Guy website between Mr. Kent Hovind and Dr. Massimo Pigliucci which originally aired in 2001. Dr. Pigliucci most ably defended evolution with a great deal more patience than I would have had. I have little patience for stupidity (which is why I never found ‘Friends’ funny at all) and have to fight the urge to stop my hand from smacking topside of the head anyone suffering from this all too common affliction. Mr. Hovind would receive a great deal less gentle attention in my presence.

It is apparent that Mr. Hovind is unhappy at being called ‘Mr.’ and feels that his ‘degree’ from an unaccredited university demands that the title ‘Dr.’ be used when addressing him:

‘… I have a doctor’s degree also, though it’s not from an accredited university but I don’t think that matters…’ 

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