Pop quiz (no cheating!)

_{Paul Nelson

February 23, 2009

Biology, Evolution, Intelligent Design}

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To take the quiz — or to play along — here’s your background information, and no cheating by looking into cell biology textbooks or using Google or PubMed.

1. Topoisomerases are essential enzymes, found in all organisms, which solve topological problems arising from the double-helical structure of DNA.

Now, assume:

2. All organisms on Earth share a common ancestor, the Last Universal Common Ancestor (LUCA).

OK — quiz time. Given (1) and (2), what should we expect to find, with respect to the homology of topoisomerases, when we examine organisms descended from LUCA in different parts of the Tree of Life?

Multiple choice:

A) Homologous topoisomerases

B) Non-homologous topoisomerases

C) Can’t say.

Make your best guess, and then go here:

[This paper is open access.]

Don’t miss the authors’ comment 12 lines down, in the right-hand column, first page.

Agree or disagree?

Comments

Seems to me like the authors' claim is falsifiable (and, moreover, false). If we hold falsifiability to be a criterion for what constitutes science, then surely they made a scientific statement?Hoki_{February 26, 2009
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I totally agree that ID does not say that an intelligent designer would only have constructed one type of each topoisomerase. This is simply the old "no designer worth his salt objection". But why wouldn't their claim come to rest under Patrick's ID-compatible hypotheses?Hoki_{February 25, 2009
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Well, when i first read the quiz, i was going to answer "C) Can't say". Why? Alternative A appears to be the correct one. But i reasoned that it is impossible to tell if i haven't read anything about the specific genes i question. Some of them could have been subject to horizontal gene transfer, thus obstuficated the the direct homology. Then i read the Introduction in the paper, and what did i read? "we will conclude that there was lateral gene transfer when the enzyme is only present in some members of the domain and branches within another domain in phylogenetic trees." I feel so smart;)Pyramide_{February 25, 2009
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“the distribution of topoisomerases families and sub-families among modern organisms is not congruent with the universal tree of life based on 16S rRNA sequence comparison (with the trinity Archaea, Bacteria and Eukarya).” If there is this type of discontinuity in genetics then the burden of proof is on the evolutionist. They must give a reason why. In this article they give the reason why as “lateral transfer” of genetics through a certain type of virus. The job now is to disprove this hypothosis. One way is to examine the local genetic environment and detect problems with this theory. If the virus is inserted randomly into a genome, then we should see this type of pattern in the genomes. On the other hand if we see a continuity of topoisomerases between genomes then we should discount the “lateral transfer” theory.Tim AJ_{February 25, 2009
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The authors hypothesize:
“An intelligent designer would have probably invented only one ubiquitous Topo I and one ubiquitous Topo II to facilitate the task of future biochemists. The reality turned out to be quite different, and more interesting.”
To the authors: "Your Intelligent Designer is too small". Compare the chimpanzee and giraffe, shrew and whale, ant and rhinoceros. Would not this lead to the following hypotheses? One design principle of an Intelligent Designer is: "Provide for high complexity using combinations of components." The authors have clearly never played "Hide and Seek" either themselves or with their children. Otherwise they would recognize the value of progressively harder challenges towards maturing children while making it enjoyable. (Or would never admit to it.) This experience could be summarized in another Design Principle: "Provide enough simple systems to encourage biologists, and provide numerous complex systems to challenge them." Applying these to topoisomerases raises the following hypotheses for design regarding topoisomerases: 1) "Form topoisomerases with sufficient complexity to form a wide variety of systems." 2) "Form topoisomerases with enough simplicity to encourage biologists in their discovery, and with enough of diversity to challenge them." Design hypothesis 1) could be disproved by showing that all systems could be formed from two ubiquitous Topo I and Topo II topoisomerases. Design hypothesis 2) Could be disproved by showing that topoisomerases are too simple to provide a challenge. i.e. that they fit into Darwin's neat "tree of life." Objection 2 appears to be dismissed by:
"the distribution of topoisomerases families and sub-families among modern organisms is not congruent with the universal tree of life based on 16S rRNA sequence comparison (with the trinity Archaea, Bacteria and Eukarya).”
PS curious use of "trinity". From the growing evidence of highly specified complexity in biochemical systems, a third Design Principle might be hypothesized: "
Provide sufficient complexity to refute all theories that life could have occurred without an Intelligent Designer."
DLH_{February 24, 2009
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Don’t miss the authors’ comment 12 lines down, in the right-hand column...
This confused me for a while... I believe it should say "on the right-hand side of the column"? In my browsers there is only one column... Anyway, thanks Paul for giving us the heads-up -- a valuable service from one who reads the literature to those who don't.lars_{February 24, 2009
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An intelligent designer would have probably invented only one ubiquitous Topo I and one ubiquitous Topo II to facilitate the task of future biochemists.
That is the secret handshake that is required to remain in good standing with the scientific community when you publish a paper that ID supporters are going to love. It is also an admission of insecurity. It is always the papers that are the most damaging to Darwinism that get an explicit disclaimer of intelligent design. It reminds me of the the classic "nothing to see here" scene in Naked Gun. Here is a link to a 30 second clip if you don't know what I am talking about. http://www.youtube.com/watch?v=rSjK2OqrgicJehu_{February 24, 2009
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Agreed with all the above about the theological basis for these panda's-thumb-like "a designer wouldn't have done it this way" arguments. The remarkable thing, though, is that this peer-reviewed, Darwinist paper asserts that the designer hypothesis makes a testable prediction! And then of course, it's a prediction that's abundantly confirmed (and sometimes disconfirmed) -- homology. If these authors would follow their reasoning to its conclusion, there is an awful lot of homology out there supporting the conclusion that there is a designer. So let's add this to the list of peer-reviewed publications supporting ID... :-p Too bad it's baloney.lars_{February 24, 2009
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An intelligent designer would have probably invented... I can't count the number of times I've looked at some computer code (even my own that I had not visited in quite a while) and thought: "That's a dumb way to do it! There's a much simpler, easier, and more efficient way to do it." I modify the code, and when I run it the program goes down in flames and leaves a big smoking hole in the ground. Upon further reflection I discover that the original code really was the best, or even the only way to do it. Biologists who speculate about how an intelligent designer would have done something should do it their way and see how it works, as proof that their speculation is valid. They might be in for some big surprises.GilDodgen_{February 24, 2009
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TSD,
Counter-question: How does the “science” of ID determine what an intelligent designer would and would not do?
Straight ID theory does not provide those answers since it's about design detection. But I'm presuming you're asking about mechanisms or "how did the actor act" which is the realm of ID-compatible hypotheses.Patrick_{February 24, 2009
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“An intelligent designer would have probably invented only one ubiquitous Topo I and one ubiquitous Topo II to facilitate the task of future biochemists. The reality turned out to be quite different, and more interesting.” Yes, this is by far the most annoying part to me. Basically they only bring up ID to take a free jab at it and move along. But they provide absolutely no basis for what they are saying. I could just as easily say "An intelligent designer would have probably made things look just like they evolved." If you think ID is such useless crap, why even bring it up in a paper such as this? I would not have gotten away with doing something like this when working on undergraduate papers, much less in graduate work. I suppose this is how it goes though when you feel great disdain for your opponents. You just say whatever you want and don't worry about there being any actual truth behind it.Leslie_{February 24, 2009
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Methinks they dost protest too much!
First they ignore you, then they laugh at you, then they fight you, then you win. (We are here ^)Lutepisc_{February 24, 2009
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@uoflcard: My definition would be: "In order to get good evidence for evolution we need to apply evolutionary thinking on the test results; randomly change the results and select the ones that support our theory" Then in order to see if it's good evidence your definition should apply.critiacrof_{February 24, 2009
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"And how, pray tell, does the researcher come by this scientific knowledge of what an intelligent designer would or would not do?" Simple answer: he didn't. It is speculation on his part. "So, here’s my challenge to any Darwinists reading this: please describe for us in detail how you know scientifically (not philosophically, metaphysically or theologically) what an intelligent designer would or would not do." I can think of no way to do it. Counter-question: How does the "science" of ID determine what an intelligent designer would and would not do?TSD_{February 23, 2009
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Evolution’s motto has become, “Any evidence is good evidence if it supports evolution.”
My modification would be: "Any evidence is good evidence of evolution...we just have to imagine how it could be good evidence."uoflcard_{February 23, 2009
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An intelligent designer would have probably invented only one ubiquitous Topo I and one ubiquitous Topo II to facilitate the task of future biochemists. The reality turned out to be quite different, and more interesting
How in the world can this author scientifically comment on the probability of what an intelligent designer would have done?uoflcard_{February 23, 2009
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As I recall, the late Stephen Gould (God rest his soul)started his book The Panda's Thumb with a comment that "odd arrangements" and "funny solutions" were "not the stuff of a wise creator", or something close to that. (Sorry, don't have the book right here for the exact words, but that is definitely the gist.) The only problem was Gould never got round to telling us how he knew what a wise creator would or wouldn't have done. He certainly didn't provide any references to any scientific research studies that confirmed his hypothesis, and as far as I know, he never did such studies himself. This is the old "God wouldn't have done it that way" argument. P-1 We observe odd arrangements and funny solutions in biological systems. P-2 God would not have done things that way Conclusion: therefore evolution did it. What is a theological premise doing in what is supposed to be a purely scientific argument? Same for the authors of the paper cited in the OP...what is a metaphysical statement doing in what is supposed to be a purely "scientific" research study! I mean, why bring up ID at all? Methinks they dost protest too much!DonaldM_{February 23, 2009
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Domoman: Please include references. When the search engines land on UD for this quote, we want to be sure that the authors get full credit:
Um, Bill, you forgot to add the words "for their stupidity" at the end of your statement!DonaldM_{February 23, 2009
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Domoman: Please include citations. When the search engines land on UD for this quote, we want to be sure that the authors get full credit: Chevance, F.F.V., and Hughes, K.T., Coordinating assembly of a bacterial macromolecular machine, Nature Reviews Microbiology, 6, 455-465, (June 2008).William Dembski_{February 23, 2009
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DonaldM, lol It's pretty pathetic isn't? This reminds me of the joke of an article by some evolutionists, writing in Nature Reviews Microbiology, on the bacteria flagellum. They said this:
“Finally, it seems that the bacterial flagellum is a structure of great complexity. In an attempt to understand why, it is not necessary to resort to intelligent designers, because surely a designer would have fashioned a simpler structure and gene regulation system."
Hmm, they should answer your question too, DonaldM. lol Thanks to id.com.au for providing this laughable quote last year. :)Domoman_{February 23, 2009
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“An intelligent designer would have probably invented only one ubiquitous Topo I and one ubiquitous Topo II to facilitate the task of future biochemists. The reality turned out to be quite different, and more interesting.”
And how, pray tell, does the researcher come by this scientific knowledge of what an intelligent designer would or would not do? So, here's my challenge to any Darwinists reading this: please describe for us in detail how you know scientifically (not philosophically, metaphysically or theologically) what an intelligent designer would or would not do. Who has conducted the relevant research studies to confirm this hypothesis and in what peer reviewed scientific journal were these research studies reported? The logic seems to be something like this. P-1 Biological systems exhibit trait T P-2 - An intelligent designer would not have done it that way Conclusion: therefore evolution did it! And THIS is SCIENCE????!!!????!!!DonaldM_{February 23, 2009
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Dembski:
Evolution’s motto has become, “Any evidence is good evidence if it supports evolution.”
May I suggest, rather, that for evidence to qualify as evidence, it must contain a tale that shows its support of evolution.bFast_{February 23, 2009
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Thanks Paul for posting this. What nonsense. Either Darwinism is doomed or our civilization is doomed for buying such nonsense: "An intelligent designer would have probably invented only one ubiquitous Topo I and one ubiquitous Topo II to facilitate the task of future biochemists. The reality turned out to be quite different, and more interesting." Similarity and homology has traditionally been the tell-tale sign of evolutionary connection. Now homology is supposed to be diagnostic of design and the evolutionary picture is more interesting and complicated, requiring many different Topos. Evolution's motto has become, "Any evidence is good evidence if it supports evolution."William Dembski_{February 23, 2009
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I would also pick A) assuming common ancestry. However... “As in the case of other enzymes working with DNA, such as DNA polymerases, the distribution of topoisomerases families and sub-families among modern organisms is not congruent with the universal tree of life based on 16S rRNA sequence comparison (with the trinity Archaea, Bacteria and Eukarya).” The evidence isn't congruent with the universal tree of life. However, there is a universal tree of life. Therefore, we need to imagine a way the evidence can still fit with a universal tree of life. “An intelligent designer would have probably invented only one ubiquitous Topo I and one ubiquitous Topo II to facilitate the task of future biochemists.” An intelligent designer would've designed things to look like everything came from a common ancestor. The evidence is incongruent with common descent. Therefore, there is no intelligent designer. Or...Maybe an intelligent designer would have invented multiple non-homologous topoisomerases to give future biochemists a clue?pharmgirl_{February 23, 2009
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I'd pick A) if I accepted the second premise and believed in neo-Darwinism. I didn't really read the article though, it looks rather complicated, or at least too long to keep my interest in reading it all the way through. I skipped to the conclusion though, and it suggests "that most topoisomerase families and subfamilies originated in the viral world predicts." Personally this sounds like a load crap in my opinion. :P Now, if it could be suggested that viruses could be the result of genetic entropy within topoisomerase families and subfamilies (essentially, their opposite conclusion) I might buy it. But this..., nah. However, I'm basically out of my league in understanding this (at least, as of now), so don't take my comment too seriously. Maybe with a molecule's worth of salt. xDDomoman_{February 23, 2009
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