Responding to Bob

30 05 2007

Every now and then I get a comment that needs some clarification (and maybe some good ‘ol refutation). I did this quite often during my early blogging days at ProgressiveU, moving long discourses out of the comments and moving them to the front page so that everyone could benefit from what the writer had to say (and hopefully from my response). Hence, I’ll be responding line by line to a recent comment by “Bob G” on my post “Creation Museum Aftermath“, and my regular readers will probably get a new post or two out of it on the topic of color change in animals (if I can muster up something good on such a complex topic, that is). Anyway, what Bob has to say will appear in b-quote format, my responses in the usual format.

You are both partially right about the chameleon. The adaptation of transitory color change is for the primary purpose of camouflage in the chameleon, the squid, octopus, etc. The use of the attribute has secondary use for hiding, predation, and communication. Which came first? I would argue for camouflage. One has only to observe geckos at my Florida home. White on white substrate, black on black substrate, etc. However, its throat bag is always red for communication purposes. The squid has intricate color used for communication, but when under predation or stalking, it goes drab. When used for territorial ambitions, it flashes every color under the sun.

Here, Bob was referring to my comment that Denyse O’Leary (as well as NY Times columnist Edward Rothstein) didn’t know what they were talking about when it came to color changes in chameleons (Family Chamaeleonidae). There are lots of little critters called “chameleons” because of their ability to change from brown to green, but these are anoles, lizards belonging to the Family Polychrotidae (I even had a few when I was kid). True chameleons often hunt their prey by acting like a stick (in fact they use the same jerky-motions employed by praying mantis on the hunt) and do not change colors to blend in with their environment. Rather, true chameleons change color to show their mood or can be used as an indicator of health; going blue, lime green, and orange all over isn’t going to help you hide from predators or camouflage you when hunting prey.

Little anole lizards, however, do change color based upon illumination as well as to mood (particularly excitement/aggression). They lack the vibrant color combinations of true chameleons, but they can still go between a dark chocolate brown to brilliant emerald green (with the characteristic ruby dewlap, too). Cephalopods are a whole other matter, not only changing color but texture as well, and they use their dazzling quick-change abilities to hide, communicate, and even “hypnotize” prey. I’ll write more about their abilities in the future, but for the present moment it’s safe to say that true chameleons and “New World” anoles go about color change in different ways.

As a much published and patented scientist (biochemist – AND RU undergraduate – “upstream red team”), I am amused by the need for scientists to organize into camps; I used to call it scientific colonization, but now I feel that it may be just a common herd instinct.

This is a fairly general statement; are we speaking of big ideas in science (we are accept gravity because of a herd instinct) or smaller issues? I assume that what Bob meant was when it comes to creation vs. evolution scientists are usually in either one camp or another, but there seems to be a fair bit of diversity when it comes to divine intervention and science (ranging from young earth creationism to ID to theistic evolution to atheism, with lots of different views in-between). For my own part, I see no reason to infer divine intervention when there is no evidence of being any. Answers in Genesis knows this well, which is why they refuse to think about anything without including the Bible; if we look at nature, forgetting religious doctrine or dogma, no divine purpose or plan is apparent. The book of Job tells us that if we listen, nature will speak to us, even teach us, but looking at nature in and of itself there is no semblance or vestige of design.

Bottom line: Darwin and Ken Ham are predominantly dead wrong! But some of their ideas are borne out in principle and fact. Their basic underlying premises are demonstrably refutable. By the way, a recent volume of Nature (v.446/15 pp246ff.) has a great tribute on the 300th anniversary of Linnaeus. From that review, one can readily see that the idea of species is totally fabricated.

I think the comparison of Ham and Darwin is a rather false dichotomy; what has Ham ever done to help bring understanding about the natural world (and no, a Creation Museum does not count)? If we are to make comparisons, then why not Owen, Huxley, Steno, Mantell, Buckland, Lyell, Agassiz, Lamarck, Buffon, Cuvier, or even Ussher vs. Darwin; at least then we’re comparing apples to apples, in a sense. Darwin was wrong about plenty of things, but science has overturned some of his ideas through finding out more about nature; Ham is wrong because his arguments run counter to observations from the natural world. While Darwin has transformed into something of an icon to some, he is important to remember (if for no other reason) because he scientifically showed evolution to be real and credible; previously it was mere rumor and required someone to come along and show it to be real. To the best of my understanding, natural selection, sexual selection, and other ideas that Darwin put forward are still very much legitimate, so I don’t see why we should discount Darwin as predominantly wrong.

So the “Origin of the Species” did not have to be that long a book. It just had to say that man invented species, and Linnaeus was the inventor. For example, the Galopagus finch’s beak was not a step toward evolution into a new species. It was a result of differentiation of an already present gene in the genome, so this is an ANTI-evolutionary adaptation that prevents the need to “evolve” into another beast. This is referred to as “genetic spread” in the genome of a “species”. The genome of a vertebrate especially is so vast, and many genes cooperate to produce the phenotypic variation we see. To top it all off, there are “nonsense codons’ that were thought to be inactive, but become activated by an external stimulus. This can then alter phenotype. Let’s give a round of applause to laMarck.

Lots of people aren’t especially happy with On the Origin of Species (at least not until the more poetic parts at the end), but I would disagree; it had to be a long book. Darwin had to back up his assertions with evidence, and if I were him I’d probably right a thick book as well. Darwin could not simply put out a 20 page memo and expect everyone to accept his ideas, especially during the time of prominent scientists like Richard Owen; if he was going to prove his point, it was going to take a lot of work and a lot of examples from his own experience and that of others familiar with artificial selection and how animals can change. While it is well known that what actually constitutes a “species” has been exceedingly hard to nail down, it is not entirely arbitrary either.

I also must admit that I’m a bit confused by the “ANTI-evolutionary adaptation” statement, and it hints at baraminology (God created different “kinds” that have some sort of genetic barrier that keeps them from evolving into new species/forms). In order to pick this one apart, we need to get a little more specific. By now most people are familiar with the work of Peter and Rosemary Grant, and they have shown that populations of finches on the Galapagos islands experience changes in beak size/shape based upon seasonal changes (which in turn influences food availability). As in one case, when only a few, hard seeds were left, only birds with larger beaks could feed and so there was a directional selection towards birds with larger beaks (and this change, of course, was heritable, so the beak size of the populations offspring changed as well). If the environmental pressure that caused the large-beaked birds to be favored continued, we’d see a continuation of the trend and possibly even see the birds change in other aspects in response to a changing ecology; there is no contention about this. Such pressure was never manifested, however, and so finch beak sizes seem to change in response to wet years and dry years, the cycle causing differing beak sizes to be favored at different times, and the birds are quickly adapted. No one is suggesting that a macromutation would be required in one generation or the birds would have to change into a new kind of “beast”; there is enough existing variation to adapt the birds in response to their environment, and this is hardly “anti-evolutionary.” If there is indeed some kind of genetic ceiling that does not allow for speciation, the burden of proof is on the creationists.

I must say now that I am a Christian, and believe in the design of man by a Supreme Being. BUT I do not place myself with Young Earthers. I have met very few “IDers” who believe the earth is young. No one knows how old the earth is. The tautology of dating fossils by the strata, and then the strata by the fossils leads to these stretches of the imagination. Then “validation” of other technologies sets in, such as radiometric dating, magnetic orientation, etc., to arrive at the date that is already accepted. Using Ken Ham’s personal beliefs in a young earth or the dragon mythology to discredit the ID group is using straw man agruments, and is patently unfair.

I’ll tackle the last comment first; I didn’t say that ID advocates believe as Ham believes, but they have been awfully quiet about his funhouse. Like I said in my initial post, if ID advocates are so concerned about sound science, why don’t they speak up? Intelligent design is predominantly based in Christian doctrine, and I’m finding that, more often than not, believers in ID use creationist arguments (like baraminology) to fill gaps not spoken of by the likes of Wells, Behe, Dembski, etc. There is nothing unfair about stating the fact that the Discovery Institute and proponents of ID usually do not make disparaging remarks about creationists because of the “Big-Tent” strategy they need to keep their support, and judging from the comments/posts at places like Uncommon Descent and Overwhelming Evidence creationists arguments are often tied up with intelligent design.

The assertion that “no one knows how old the earth is” is also incorrect. While relative dating is important to paleontology, it is not the only technique we have, and until we had radiometric dating we had no idea how old the earth truly was. Prior to absolute dating technology, “deep time” was divided up into sections based upon fossil content (in fact, mass extinctions helped to make natural boundaries in the timescale), and multiple independent tests have over-and-over-again confirmed an earth that is approximately 4.6 billion years old. This wasn’t some number arrived at from fossils and then “confirmed” with later techniques; in G.G. Simpsion’s The Meaning of Evolution he states that the oldest rocks then known were about 2,000,000,000 years old, although there could be older rocks (and we’ve found them, confirming our hypothesis). Even prior to that, when stratigraphy was first conceived by William “Strata” Smith, Smith’s student calculated the earth to be about 96 million years old. Evolution even entered this debate when Lord Kelvin tried to show that evolution didn’t have enough time to progress by calculating an earth about 20-40 million years old, but the assumptions on which he based his calculations later were shown to be wrong (i.e. he didn’t account for heat generated by radioactive rocks in the earth, but how could he? Radioactivity wasn’t discovered until 1896, shortly before his death). Simply put, prior to absolute dating techniques we had no way of knowing how old the earth really was, and relative dating tells us that some things are older than others but does not give us the date at which they were deposited. Absolute dating and relative dating work together to make sense of the strata; absolute dating is not crammed into a pre-existing paradigm at all.

BUT, apart from gradualism that Darwin said was his achilles heel, Darwin had a lot of correct things, so let’s not throw out the baby with the bath.

Just to make a quick note, much is made of “gradualism” and the lack thereof, but I think there is a bit of semantic misunderstanding going on here. While the term has come to mean “slow change,” when I see the word “gradual” I can’t help but think of “gradations.” Being that (outside of polyploidy, perhaps) big saltational changes are not known to occur in evolution, of course it would move forward by “gradations,” but the speed at which it does so is variable. I can’t conceive of any evolutionary “speed limit” that all life must obey without variation, so I would personally like to divorce the notion of “gradual” from “slow” as it is confounding this issue.

In the Bible, God separated the animals by their “kinds” not species. And I believe these “kinds” are still the same, but with genetic elements lost, not gained, over time. So the genetic spread becomes sparser. This has been shown unequivocally with humans, in which a lot of the genome was lost by hardship ages ago, so the recombination variety has become paltry over time. That is why species are not necessarily created (mutation = death is the rule so far in experimentation), but become extinct over time. That is why there are hundreds of “species” going extinct each year, and will continue to do so.

It’s unfair of me to associate Ken Ham’s ideas about dragons (on which ID is mum), but yet here comes baraminology once again. The point Bob is trying to make here has recently been put forward by creationists like John C. Sanford in his horrible book Genetic Entropy and the Mystery of the Genome. The general idea is that God created everything perfect, but after the Fall sin, death, etc. came into play and so creatures have been “degrading” ever since. Sanford expresses this towards the end of his book showing how the lifespan of mankind has been dwindling since Adam and Eve were cast out of Eden, but this is a rather poor argument. If we’re to play along and take the Bible literally, God put a limit on man’s age in Genesis 6:3 to no more than 120 years (which has been broken, by the way), which skews the results. Even if we were to discount this, would mankind eventually lose years off the upper limit until we were no longer able to reach reproductive maturity? Or would we all go from birth to adulthood in, say, 5 years time? Such notions are not consistent with reality and the “declining age model” does nothing to disprove evolution, an old earth, or any other scientific claim.

We also must consider what is meant by “degrading.” Does this mean reduced reproductive vigor or ability to speciate? Apparently not, given the diversity of life long after whenever the “creation even” occurred. Creatures like ammonites don’t play by these rules either, naturally gaining complexity in their crenelations (and even uncoiling into some odd shapes) before they ultimately went extinct 65 million years ago. Bob’s idea also plays into a sort of Platonic ideal from which all animals descended; of course God would have made the first ones perfect, but given what evolution has shown us there must have been very few “created kinds” if at all. It’s odd that Bob points out that the “species” concept is entirely man-made, but misses the point that created “kinds” are also arbitrary and created by man. Where would you divide fish from tetrapod, archaeocete from true whale, dinosaur from bird? In fact, created “kinds” work to say “don’t look behind the curtain” when it comes to established evolutionary transitions, attempting to separate naturally occurring transitions.

If there is some kind of genetic ceiling or barrier to evolution, then it is up to creationists to prove its existence. We know populations can speciate, so what is holding life on earth back from speciating so many times that it looks entirely different from a previous ancestor while still carrying along some inherited characteristics (homologies)? In order for baraminology to work, speciation must be denied, and given that we know speciation to occur, the pseudoscience becomes untenable. The only safe created “kind” would be the earliest common ancestor from which all life arose, but that would require oodles of evolution and so that stance is rejected by creationists. Bob’s argument above also reminds me of the “Bad genes or bad luck?” problem that David Raup presents in his excellent book Extinction. It’s not an either/or question, and mutations are not exclusively bad. Indeed, mutation is often discussed as if there was only one kind, but there are in fact many and it’s important to know what genetic material is being mutated and whether there’s another intact copy of that same information that will keep a potentially lethal mutation from killing an organism. Hell, if mutations were always bad, always degrading organisms, than how could some bacteria come to have the ability to break down nylon (a synthetic material not in existence until the middle of the last century)? There is certainly more to the picture than the simple “most mutations are bad” argument.

So, I think the safest course is to not follow the groups, be they evolutionists or crationists, but to use scientific method and common sense to arrive at a question that no one can ever suitably answer.

Appreciated advice, but the problem is that nature does not work by “common sense.” “Common sense” is (to play with the order a little) what people “sense” in “common,” and would be no different from going along with a consensus for its own sake. As I’ve written before, I am such a strong adherent to evolution because of my own experience; I have not been indoctrinated or brainwashed, but have looked into the claims of ID/creationism and evolution long and hard. Not surprisingly, evolution always comes out on top. Sure, there are plenty of things that I don’t yet understand and when I come across such a notion I try my best to grasp it, but I am not simply adhering to evolution because anyone told me to.

Sorry for the rambling discourse, I hope y’all get the drift.

Bob from Exeter NH
PS. Great web site!

Thank you for the compliment and the comment Bob. I have to say, however, that even though you claim not to be a young earth creationist you seemed to take some potshots at the science that has determined the age of the earth and introduced the creationist argument of baraminology at least twice. This is why intelligent design irks me; if they would just come out and say they were creationists, or at least embraced some creationist arguments even, then I would still vehemently disagree but at least I could say they were being forthright. At present, however, they seem to be noncommittal about lots of important issues like the age of the earth, what deity intervened and when, etc. Hardly scientific at all, really. If anyone pushes those issues aside, tries to say “Oh, we don’t need to know that” I have to wonder how much they really care about understanding the world we find ourselves in. While many people who identify themselves as intelligent design supporters get frustrated when I call them creationists, I really don’t know what else to conclude; ID is essentially creationism “lite” (or micro-creationism, if you please), and often times any old mish-mash of creationist belief is used to plug the holes not filled by top ID advocates.

In any event, I recognize ID as a different “species” in the genus “creationism”; it might have a few different attributes, but the homologies are still so prevalent that there can be no mistaking its affinities.




12 responses

30 05 2007
Chris Harrison

Nice concluding paragraph. Very clever.

I read Bob’s comment a couple of hours ago, and I think it’s even more odd the second time I read it.

I see “genetic entropy” is becoming the standard trump card for ID/creationists these days.

In the Bible, God separated the animals by their “kinds” not species. And I believe these “kinds” are still the same, but with genetic elements lost, not gained, over time.

This is problematic, then. Because the gain of genetic “elements” has been recorded. As I understand him, any gene that happens to be duplicated will qualify as “gain” of a genetic element. Of course, if my previous discussions with IDists are any indication, Bob has a different meaning for the word “element” than what I’m thinking. For a scientists, such imprecise word choice is surprising. What is a “genetic element”, exactly?

So the genetic spread becomes sparser. This has been shown unequivocally with humans, in which a lot of the genome was lost by hardship ages ago, so the recombination variety has become paltry over time.

Our species does have limited genetic variability, when compared to say, our cousins, the chimps, but the explanation I’ve seen for this involves no magic or any “falling”.

Our species is relatively young, and so mutation and thus genetic variation has not had as much time to cull as compared with older species, like chimps. Established populations are routinely seen to possess increased genetic diversity than recent ones. With respect to humans, the fossil record tells us that humans originated in Africa, and then radiated out from there. Looking at genetic properties of Africans, indeed we find higher variability there than the rest of the world.


That is why species are not necessarily created (mutation = death is the rule so far in experimentation), but become extinct over time. That is why there are hundreds of “species” going extinct each year, and will continue to do so.

The above is largely incoherent as written, but I think I understand him to be saying that mutations are only bad, which is completely false.

One only needs to look at antibiotic resistance to realize how inane this assertion is.

30 05 2007

Thanks for the comment, as always, Chris. I know you’re a lot more familiar with the genetics angle of things than I am (I’m doing my best to catch up!) so I definitely appreciate your contribution. I just find it interesting that lots of ID advocates day “No, this isn’t creationism” but rely on YEC arguments when pushed. In a way, I could more understand a YEC that believes the world is 6,000 years old than someone who says YEC’s are wrong, but most scientists are wrong in saying it’s 4.6 billion years old; if both “sides” are wrong, then what’s the answer and where is that information coming from?

30 05 2007
Chris Harrison

I think most IDists, are deliberately noncommittal about the age of the Earth. They usually don’t want to adhere to YEC beliefs because of the political ramifications, but they’d prefer not to fall in line with those “Darwinists” as much as possible. And of course, as you mentioned, they rarely criticize YECs because they know where most of their support stems from.

I guess that 2% of ID proponents are truly concerned with building a scientific theory.

31 05 2007

Our species is relatively young

I like everything else you said, Chris, but this is flat-out wrong.

ALL SPECIES are exactly the same age – pick any two species, and trace back to their last common ancestor – the time between the extant species (now) and that ancestor (then) is exactly the same regardless of which branch you trace back. Since all life on Earth can be (putatively) traced back to a single common ancestor, then all species on Earth are the same age, something like 3.8 billion years old. Is the sea urchin Strongylocentrotus purpuratus an “old” species because we can find urchin fossils that date back 100 million years?

Morphologically-modern Homo sapiens may appear in the fossil record only a few tens or hundreds of thousands of years ago, but this is not equivalent to H. sapiens being younger than, say, Pan troglodytes – we shared a common ancestor at some distinct point in the past, perhaps 7 million years ago. Were chimp populations held in stasis while the human lineage was morphologically diverging?

The relatively low species-level genetic variation within humans stems from a populaton bottleneck sometime in the last 100 000 years, combined with a very rapid dispersal across the globe. Chimps (aside: which species? Bonobos or Chimpanzee?) apparently did not experience such a bottleneck, at least not until modern times when habitat destruction and predation by humans led to a population decline. We have the genetic variation you’d expect in a K-selected large mammal species stemming from a small population some few thousands of generations ago.

Back on-topic: Nicely done, Brian. I think it’s very interesting to see the mix of literalist biblical thinking combined with some of the Discovery Institute’s talking points. The old (and rather stupid) canard about stratigraphy and fossils shows up right alongside the more recent (but still stupid) all mutations are bad point.

I guess that 2% of ID proponents are truly concerned with building a scientific theory.

I’m not convinced that your measurement is signficantly different from zero. I’d ask for a larger sample size, but that would be asking you to spend more time talking to cretinists… I don’t wish you to hurt yourself.

31 05 2007

Thanks Martin; I think it’s interesting to see the combination of various ID factors with creationist ideas, with ID saying “there’s nothing religious about this” the whole time. What I think is even more interesting, however, is the lack of background creationists have when it comes to evolution; scientists are constantly admonished for not understanding creationism or ID, but many spend plenty of time reading creationist literature while many creationists I’ve encountered are essentially unfamiliar with any substantial amount of literature on evolution. Hell, half the time I feel like I’m more familiar with their claims and the origin of certain creationist ideas than they are!

31 05 2007
Chris Harrison

Thanks for the correction Martin. Do you by chance have any papers on this 100,000 years old bottleneck? I’d be interested if you did.

31 05 2007

Thanks Martin
Thanks for the correction Martin.

You two are both way too nice. It’s freaking me out! I show up here, rant and rave rudely in a long, rambling comment, and you guys say “thanks”! I’m Canadian, and both of you are Yanquis… I thought the angry/polite thing was supposed to be the other way around. I’m so confused…

Do you by chance have any papers on this 100,000 years old bottleneck?

Not on me, sorry. I’ll do a quick search in WoS here…

Fay and Wu (1999) is a math-heavy examination of the discordance in genetic variation between mtDNA and nuclear markers, with the conclusion that this discordance is not incompatible, and may actually be highly consistent with a “recent human bottleneck”. They don’t give a nice round number for when this bottleneck was supposed to have happened, at least not in my quick read through.

Lahr and Foley (1998) is a much more in-depth look at the entire issue of the origins and current patterns of distribution of Homo sapiens. It’s 40 pages long, though, so I didn’t read beyond the abstract.

I have the PDF for the Fay and Wu (1999) paper (I was wrong, above – I did have it on me! Well, on my computer’s harddrive), it’s just a short “Letter to the Editor” in Molecular Biology and Evolution; email me and I’ll send it to you if you don’t have access. Yearbook of Physical Anthropology seems not to have electronic editions, but the U of Guelph library has it in hard-copy. I’d be happy to snail-mail a copy to someone if it’s not otherwise available (do undergrads at your universities get interlibrary loan priviledges for journal articles?). Both papers cite lots of other probably-relevant studies.

Literature Cited:
Fay JC, Wu CI (1999) A human population bottleneck can account for the discordance between patterns of mitochondrial versus nuclear DNA variation MOLECULAR BIOLOGY AND EVOLUTION 16 (7): 1003-1005
Lahr MM, Foley RA (1998) Towards a theory of modern human origins: Geography, demography, and diversity in recent human evolution YEARBOOK OF PHYSICAL ANTHROPOLOGY 41: 137-176

31 05 2007

You two are both way too nice. It’s freaking me out!

Well, if it bothers you that much Martin, then I guess I should be honest. I’ve tolerated your comments on here in an order to keep the peace of what the glorious Senator Brownback has called our “atheistic theology,” but I just can’t keep up the Big-Tent charade anymore. Here I am, just trying to have a good time, but oh no, a Canadian has to show up and ruin the fun, eh? The famous documentary Strange Brew opened by eyes years ago, and I simply cannot tolerate this internet immigration anymore.



Sorry about that, a troll from OE hijacked my blog, but I’m back in control now. Yes, it’s horribly true that I am not nearly surly enough, so thank you for pointing that out. Darn it, I’ve done it again. You’re righ… confound you Martin! Now I’m stuck in a shame spiral…

31 05 2007
Chris Harrison

Thanks for the references.

And a much larger and extended thanks for tipping me off to the “interlibrary loan privileges”, cos I just found out I have access to the full text of every article in Blackwell Synergy, Google Scholar, Science, SpringerLink, Wiley InterScience and a bunch more cool journals.

So now I’ve all 40 pages of “Towards a theory of modern human origins: Geography, demography, and diversity in recent human evolution” open in pdf format. Sweet

24 03 2011


31 05 2007

So now I’ve all 40 pages of “Towards a theory of modern human origins: Geography, demography, and diversity in recent human evolution” open in pdf format. Sweet

24 03 2011

if you read this you are gay and have no life!!!

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