Nathaniel Abraham — Competence Without Belief?

_{William Dembski

December 7, 2007

Evolution}

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The case of Nathaniel Abraham — a biologist who does not “believe” in evolution, got fired for it, and is now suing his erstwhile employer — is getting some play in the press (see Boston Globe and Chronicle of Higher Education). The question this raises is whether it is legitimate to fire someone who knows all that he needs to know about evolution to successfully practice his discipline but still does not believe in evolution. More generally, to be a member of the guild, do you have to believe something that you are capable of successfully applying? One of the commenters at the Chronicle of Higher Education remarked that you can’t continue to employ a mathematician who believes 1 plus 1 equals 3. But what if the mathematician says, “In fact, I believe 1 plus 1 equals 3, but I realize that most of you think it equals 2, and I know why you think that, so, to keep peace in the family, I’ll just play along”? It seems that BELIEF and COMPETENCE are two separate things — one can be competent in handling an idea without believing in it.

Compare the case of Nathaniel Abraham with the case of a high school student reported a long time ago here.

Comments

JJ- Creationists were the first to predict the universe had a beginning. How do you think the atheists felt when science confirmed that prediction?Joseph_{December 9, 2007
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My, my so any argument that evolution--as understood--has not provided the differentiation power resemblesBaraminology, it is nothing less than Creationists, because Creationists use arguments based on this concept. Well, some atheists still don't recognize the Big Bang because it "sounds like" Creation ex nilho. So resemblance is not a solid methodology. The resemblance of inevitable conclusions (should they be inevitable) and religious theology is not proof that the idea itself is automatically religious.jjcassidy_{December 9, 2007
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Patrick, GAW does so on purpose. He(?) cannot take the questions head-on. Arthur Murray and Fred Astair would be very proud of him(?). 1 new protein-to-protein binding site since Darwin wrote "On the Origins or Species..."- and that was in HIV which isn't even considered a living organism. With that very underwhelming evidence on their side is it any wonder why it is paramount to their case to try to talk past the opposition? BTW I apologize for my poor choice of words. Now I realize that the only reason gaw and Sally_T are here is to try to get one or more of us to lose our tempers so that we get banned.Joseph_{December 9, 2007
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I just read the whole exchange and I believe GAW and Joseph/BA77 are talking past each other. Let's see if I can help. GAW, There are 2 categories: 1. Claims that everyone agrees upon. This includes the fact that under certain conditions a deleterious mutation may have positive benefits. TEO does not include diretionality, so that's fine. An example is the one protein-binding site developed by HIV:
the viroporin is not some new molecular machine. There is no evidence that it exerts its effect in, say, an ATP- or energy-dependent manner. Rather, similar to other viroporins, the protein simply forms a passive leaky pore or weak channel. (4,5) This situation is probably best viewed as a foreign protein degrading the integrity of a membrane, rather than performing some positive function.
BA77/Joseph are probably considering this from an engineering perspective, and they're looking for non-deleterious mutations which have positive functions. 2. Claims about Darwinian mechanisms for which there is no positive evidence. Or at least claims where there is debate. This is the "Darwinian paradigm". Joseph/BA77 probably include universal common descent and other claims in here. Joseph/BA77, GAW is not making these distinctions. In his mind evidence for category 1 is evidence for category 2 and thus category 2 would be useful for medical research.Patrick_{December 9, 2007
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GAW, Let's see GAW, all "beneficial" mutations (as you nearsightedly refer to them) to bacteria, to develop antibiotic resistance, are shown to break something in the bacteria: http://www.trueorigin.org/bacteria01.asp of special note: Table I. Mutation Phenotypes Leading to Resistances of Specific Antibiotics. Antibiotic - Phenotype Providing Resistance Actinonin -Loss of enzyme activity Ampicillin -SOS response halting cell division Azithromycin -Loss of a regulatory protein Chloramphenicol -Reduced formation of a porin or a regulatory protein Ciprofloxacin -Loss of a porin or loss of a regulatory protein Erythromycin -Reduced affinity to 23S rRNA or loss of a regulatory protein Fluoroquinolones -Loss of affinity to gyrase Imioenem -Reduced formation of a porin Kanamycin -Reduced formation of a transport protein Nalidixic Acid -Loss or inactivation of a regulatory protein Rifampin -Loss of affinity to RNA polymerase Streptomycin -Reduced affinity to 16S rRNA or reduction of transport activity Tetracycline -Reduced formation of a porin or a regulatory protein Zittermicin A -Loss of proton motive force So you say, a wounded bacterium marches forth to await rescue from a changing environment and to finally develop meaningful complexity? Let's see what actually happens to bacteria that have been subject to the environmental stress for over 250 million years: Bacterium fossils, in salt crystals, dating back as far as 250 million years have had their DNA recovered, sequenced and compared to their offspring of today (Vreeland RH, 2000 Nature). “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; (The Paradox of the "Ancient" Bacterium Which Contains "Modern" Protein-Coding Genes) http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637 and this: 30-Million-Year Sleep: Germ Is Declared Alive By MALCOLM W. BROWNE Published: May 19, 1995 But Dr. Cano and his former graduate student Dr. Monica K. Borucki said that they had found slight but significant differences between the DNA of the ancient, amber-sealed Bacillus sphaericus and that of its modern counterpart. http://query.nytimes.com/gst/fullpage.html?res=990CEFD61439F93AA25756C0A963958260&sec=&spon=&pagewanted=2 Thus GAW, the bacteria shows only a very slight but significant difference between ancient and modern, which all but rules out contamination. Yet at the same time, the mutation rate, to account for the slight difference, is far to slow to fit into any evolutionary mo^dels. OOPS, again on evolution GAW! Hmm, I bet the evidence fits, like a tee square, into the ID/Genetic Entropy mo^del though, once the math is thoroughly fleshed out for the ID/Genetic Entropy mo^del. Dang GAW, where is this almighty evolution stuff you keep harping about? Mighty bashful stuff you got there buddy!bornagain77_{December 9, 2007
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From the paper getawitness provided:
However, recent evidence suggests that bacteria may play a more active role in the mutation of their own genomes in response to at least some DNA-damaging agents by inducing proteins that actually promote mutation [7–15].
That sure sounds like Dr Spetner's "built-in responses to environmental cues" to me. It could also be a form of EAM.Joseph_{December 9, 2007
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BTW, if YECs, using nothing but baraminology to guide them, could reach the same scientific inference as the paper you site, then it proves “Darwinian principles” had nothing to do with it.
This is all so confusing to a noob like me. Joseph, are you saying that baraminology would lead to all the same conclusions as Darwinism?-poachy
I am saying that approaching research with a Darwinian presupposition is useless- ie it does not help the researchers. And that is obvious if one can approach the same research without it or with a completely different presupposition and the end result is similar or exactly the same. Ya see bacteria "evolving" into bacteria fits nicely into the YEC scenario. And when people start using a loss of functionality as evidence for Darwinian evolution, they have lost the debate. That is because you cannot keep taking away and hope to construct more useful complexity.Joseph_{December 9, 2007
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BA77, Maybe I'm misunderstanding you. Earlier you wrote, "The bacteria are designed to mutate under stress, and will always be out competed by the original bacteria in the wild once the stress is removed." But what you call "stress" is environment. There's no such thing as increased fitness outside of an environment, so there's no such thing as an "improved" bacteria outside of an environment. The "stresses" of the environment are always implicated. So if the mutations improved the fitness in the new environment, the mutations improved the fitness, period.getawitness_{December 9, 2007
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BTW, if YECs, using nothing but baraminology to guide them, could reach the same scientific inference as the paper you site, then it proves “Darwinian principles” had nothing to do with it. This is all so confusing to a noob like me. Joseph, are you saying that baraminology would lead to all the same conclusions as Darwinism?poachy_{December 9, 2007
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BA77, where have I lied? In fact I pointed out that mutation was beneficial to E. coli in the paper I cited. Yet you have said that there's no such thing as a beneficial mutation. Clearly those are in conflict. Maybe the paper is wrong. My copy of Sanford is awaiting me at interlibrary loan, and I'll pick it up tomorrow and read it. But where have I lied? That's a pretty strong accusation.getawitness_{December 9, 2007
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BTW, if YECs, using nothing but baraminology to guide them, could reach the same scientific inference as the paper you site, then it proves "Darwinian principles" had nothing to do with it. And seeing there are immunologists, biologists and geneticists who are YECs the answer is "Yes".Joseph_{December 9, 2007
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GAW, Can't you be honest about even one thing in science? Do you even know that you are lying to us and to yourself? Or are you truly so deceived as to believe the shallow crap that you spout? GAW, You are playing a far dea^dlier game with the truth than you can now realize. A very serious game that has a very serious cost associated with it, that I assure you, you do not want to pay for in the %bornagain77_{December 9, 2007
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Joseph, The paper did in fact use Darwinian principles, but you keep repeating the most expansive notion of the ToE (with your own quirky vocabulary) as though tht shows otherwise.
Where in the paper did it say that it used Darwinian principles? Also my vocab isn't quirky- it happens to coincide with what is being debated.
You keep demanding that I must show that “all organisms are related via universal common descent via culled genetic accidents.”
That is false. I said you have to show that the scientists used that principle for that is the theory of evolution.
There are two issues here: (1) universal common descent, and (2) the mechanism.
And where in the paper did it say that we expected X occured due to genetic accidents?
You don’t even buy common descent, against all evidence, so convincing you of a mechanism is a lost cause.
The "evidence" for universal common descent is genetic similarities. IOW there isn't any data, evidence or observations that can account for the physiological and anatomical differences. Similarities can also be explained by common design and convergence.
I wonder if you also deny the consensus on global warming and HIV/AIDS.
I bet you ignore all the data which shows the warming is NOT caused by humans.Joseph_{December 9, 2007
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My apologies for this off-topic response but the following must be addressed:
Re Kevin Trudeau: I’m sure some of his advice is fine, as it seems to be folk wisdom. Some is obviously dangerous hogwash, such as that cancer is not caused by the sun but by sunblock.
Kevin tells you what hours are the safest to go out and get some sun. He also states that going out at the wrong times can lead to skin disease such as melanoma. It is also verified by science that getting some sun is essential to our bodies. Sunblock- unless it is some all-natural, toxin-free brand, then it contains toxins. Science has also verified that, through the process known as osmosis, whatever you put on your skin gets into your body. And science has verified that toxins can and do cause cancer. All Kevin is saying is that the more toxins you put into your body the better the odds are that you will get cancer.Joseph_{December 9, 2007
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Joseph, The paper did in fact use Darwinian principles, but you keep repeating the most expansive notion of the ToE (with your own quirky vocabulary) as though tht shows otherwise. You keep demanding that I must show that "all organisms are related via universal common descent via culled genetic accidents." There are two issues here: (1) universal common descent, and (2) the mechanism. You don't even buy common descent, against all evidence, so convincing you of a mechanism is a lost cause. (Here your credulity regarding Kevin Trudeau and YEC "arugments" is telling.) I have begun to think you like anti-establishment views just to be rebellious. I wonder if you also deny the consensus on global warming and HIV/AIDS.getawitness_{December 9, 2007
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getawitness, You have NOT shown that the paper used Darwinian principles. In order to do that you have to tell us what that finding has to do with all of life’s diversity owing its collective common ancestry to some unknown population(s) of single-celled organisms via culled genetic accidents? Either do that or admit it doesn’t. And again I NEVER said that evolution is useless for research. I said the theory of evolution is useless for research. There is a HUGE differeence between evolution and the theory of evolution: From the “Contemporary Discourse in the Field Of Biology” series I am reading Biological Evolution: An Anthology of Current Thought:
Evolution can be described with a seven-word phrase: genetic change, over time, within a population. page 6 (bold added)
Whereas the theory of evolution states that all organisms are related via universal common descent via culled genetic accidents.Joseph_{December 9, 2007
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One more thing getawitness. You point to examples of antibiotic resistence as affirming Darwinism while stating that everything can be used to argue design. Everyone believes in both mutations and antibiotic resistence. Darwinism is an extrapolation based on such things. It looks like everything can be and is used to argue for Darwinism.pk4_paul_{December 8, 2007
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"The main response is to argue that these findings could be explained by design. Sure, they could. Everything could be explained by design. But the discovery, which may lead to new ways of fighting antibiotic resistance, was made using Darwinian principles." Darwinian principles are based on selected but random mutations. The discussed responses of prokaryotes entail non-random responses. That's the design indicator. Not everything points to design. Just logical indicators.pk4_paul_{December 8, 2007
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The funny thing is, BA77 simply asked me to point to a study that made a significant finding using Darwinian principles. I pointed to such a study. The main response is to argue that these findings could be explained by design. Sure, they could. Everything could be explained by design. But the discovery, which may lead to new ways of fighting antibiotic resistance, was made using Darwinian principles. Nobody found anything using an ID approach. Sure you can try to co-opt it after the fact. But the scientists made this findng -- and if confirmed, it is signifcant -- using evolutionary principles. Which gives the lie to Joseph's claim that evolution is useless for research. Hijack the paper all you want for design. That doesn't change who found it, and how: evolutionists, using Darwinian principles.getawitness_{December 8, 2007
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pk4_paul, I phrased it poorly. From the Romesberg lab website:
The worldwide emergence of bacteria that are resistant to available antibiotics threatens to undo the dramatic advances in human health witnessed in the second half of the last century. This development is especially troubling considering that no new class of antibiotic has been introduced in over two decades. As a result, it is critical to understand the molecular origins of resistance. For antibiotics derived from natural products (i.e. vancomycin), resistance is most often due to the acquisition of genes from other bacteria that encode enzymes capable of inactivating the antibiotic, modifying its target, or increasing its export out of the cell. However, enzymes that modify synthetic antibiotics such as quinolones, sulfonamides, and trimethoprim do not exist in nature, and resistance to these antibiotics requires mutation of genes already present in the bacterial genome.
In other words, resistance to these synthetic antibiotics can't evolve through horizontal gene transfer.getawitness_{December 8, 2007
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getawitness: (from linked paper): "However, recent evidence suggests that bacteria may play a more active role in the mutation of their own genomes in response to at least some DNA-damaging agents by inducing proteins that actually promote mutation [7–15]. If the acquisition of antibiotic resistance-conferring mutations also requires the induction of these proteins, then their inhibition would represent a novel approach to combating the growing problem of drug resistance." This seems clear to me, and doesn't conflict with Behe's TEOE findings with E. coli, HIV and Plasmodium. Certain bacteria may have a mechanism to increase their own mutation rate in order to combat poisons in their environment through selection. This mechanism itself probably is part of the basic bacterial genome design and didn't originate with modern antibiotics. It would be just another intricate subsystem that NDE would require to be explained gradualistically. Any such adaptively increased mutation rate would still be random with respect to fitness, and result just in various induced defects a tiny percentage of which might just happen to be favorable in the presence of the antibiotic. The observed long term results with bacterial cultures have still failed to produce innovative new structures, despite this new mechanism being perhaps part of the bacteria's armament. The immune system incorporates a very sophisticated version of this in deliberately generating antibody site mutations in response to antigens. I didn't notice Behe trying to deny the use of a form of RV + NS in the immune system. It is actually part of an apparent IC system, which still demands a gradualistic explanation.magnan_{December 8, 2007
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That’s why bacteria can’t “borrow” resistance genes from other bacteria as happens commonly. So for resistance to emerge in these cases, it has to be a novel mutation — because it’s a novel threat. You're not familiar with horizontal gene transfers? Novel mutations? What textbook did you get that from?pk4_paul_{December 8, 2007
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Mutations are not good for any organism. No. Mutations can be good for E. coli. E. coli is an organism. You missed the point. Less than one per cent of genetic changes survive the repair process. The enhanced likelihood of changes surviving during environmental stress is evidence for design.pk4_paul_{December 8, 2007
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GAW, The bacteria are designed to mutate under stress, and will always be out competed by the original bacteria in the wild once the "stress is removed. This conforms to Genetic Entropy and has never been violated. (See super germs are really superwimps, by answers in Genesis) Again how does this prove evolution true if it does not improve over the original e-coli?bornagain77_{December 8, 2007
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Thanks, by the way, for explaining your filter. It's amusing to see what words must be modified. "Model"? "Dominate"? The imaginations of the people who made that thing! My goodness.getawitness_{December 8, 2007
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BA77, What the mutations do is evolve resistance to synthetic antibiotics. That's crucial, because the terrific effectiveness of synthetic antibiotics depends on their novelty. That's why bacteria can't "borrow" resistance genes from other bacteria as happens commonly. So for resistance to emerge in these cases, it has to be a novel mutation -- because it's a novel threat. Behe is not studying malaria or E.coli in the lab. The Edge of Evolution, while an interesting book, reviews the work of others and makes (IMO) exaggerated claims from that review.getawitness_{December 8, 2007
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GAW, I don't own the computer I use, so someone else has it set up to prevent por^no from being displayed in front of sensitive eyes. I dug out Dr. Behe’s EOE book and found what he had to say about E-coli. pg. 141-142 In the early 1990’s Lenski and coworkers began to grow E.coli in flasks; the flasks reached their capacity of bacteria after about 6 or 7 doublings. Everyday he transferred a portion of the bugs to a fresh flask. By now over thirty thousand generations of E. coli, roughly the equivalent of a million years in the (supposed) history of humans, have been born and died in Lenski’s lab. In each flask the bacteria would grow to a population size of five hundred million. Over the whole course of the experiment, perhaps ten trillion, 10^13, E coli. have been produced. Although ten trillion sounds like a lot(it’s probably more than the number of primates on the (supposed) line from chimp to human), it’s viryually nothing compared to the number of malaria cells that have infested the earth. In the past fifty years there have been about a billion times as many of those as E. coli in the Michigan lab, which makes the study less valuable than our data on malaria. Nonetheless, the E coli. work has pointed in the same general direction. The lab bacteria performed much like the wild pathogens: A host of incoherent cahnges have slightly altered pre-existing systems. Nothing fundamentally new has been produced. No new protein-protein interactions, no new molecular machines. As with thalasswemia in humans, some large evolutionary advantages have been conferred by breaking things. Several populations of bacteria lost their ability to repair DNA. One of the most beneficial mutations, seen repeatidly in separate cultures, was the bacterium’s loss of the ability to make a sugar called ribose, which is a component of RNA. Another was a change in a regulatory gene called spoT, which affected in masse how fifty-nine other genes work, either increasing or decreasing their activity. One likely explanation for the net good effect of this very blunt mutation is that it turned off the energetically costly genes that make bacterial flagellum, saving the cell some energy. Breaking some genes and turning others off, however, won’t make much of anything. After a while, beneficial changes from the experiment petered out. The fact that malaria, with a billion fold more chances gave a pattern very similar to the more modest studies on E. coli strongly suggests that’s all Darwinism can do. So tell me exactly, GAW, how are these a "beneficial mutations", as you so eagerly put them (Got to plug Darwinism, with whatever junk you can I guess), going to, in any conceivable fashion (I would say reasonable but I've given up on you ever being reasonable), change a bacteria into a fish? I need a good bedtime story so go on with your fairy tales.bornagain77_{December 8, 2007
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pk4_paul,
Mutations are not good for any organism.
No. Mutations can be good for E. coli. E. coli is an organism.getawitness_{December 8, 2007
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BA77, I don’t get it. Mutations are good for E.coli. They help it resist antibiotics. That’s shown by the paper. We don’t fight mutations in E. coli because we want to help it; we fight mutations in E. coli because we want to fight it. In fact, as the paper argues, the bacteria sets the stage for beneficial mutations under certain conditions. getawitness, you just made a prima facie case for intelligent design. Mutations are not good for any organism. That is why the genomes of all cellular organisms come replete with intricate and complex genomic repair mechanisms. Mutations are nothing more than unrepaired genetic errors. Only a very small percentage of genetic errors see the light of day. Some occassionally benefit an organism. In prokaryotes this often happens when a cellular structure, that interacts with a pathogen, is affected by a mutation. If either the rate of genetic errors accelerates in response to environmental pressures or repair mechanisms are adjusted to permit this, one can rightly suspect an adaptive design built into cellular processes involving mutations. IOW- design.pk4_paul_{December 8, 2007
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Admit you are a NA^ZI pig?
Only when you explain your NA^NY filter.getawitness_{December 8, 2007
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