Pharyngula

Egnor responds, falls flat on his face

Posted by PZ Myers on February 24, 2007
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The other day, the Time magazine blog strongly criticized the DI’s list of irrelevant, unqualified scientists who “dissent from Darwin”, and singled out a surgeon, Michael Egnor, as an example of the foolishness of the people who support the DI. I took apart some of Egnor’s claims, that evolutionary processes can’t generate new information. In particular, I showed that there are lots of publications that show new information emerging in organisms.

Egnor replied in a comment. He’s still completely wrong. The Discovery Institute has posted his vapid comment, too, as if it says something, so let’s briefly show where he has gone wrong.

In addition to showing that PubMed lists over 2800 papers relevant to his question, I singled out one: an analysis that showed that insecticide resistance in mosquitos was generated by a mutation of an acetylcholinesterase gene, and that they also had a duplication of the gene—this is a classic example of how to generate new information. Duplicate one gene into two, and subsequent mutations in one copy can introduce useful variants, such as resistance to insecticide, while the original function is still left intact in the other copy.

Egnor foolishly rejects this, claiming it does not address his challenge, with a shift of the goalposts that he doesn’t seem to realize still leaves me scoring.

So what’s the threshold, quantitatively? It seems to be a threshold of information generating capability. But the information in living things is specified; it does things, specific things. In that sense, it differs completely from Shannon information, which is a measure of randomness and the extent to which a message can be compressed. Shannon information is not relevant to biological information.

Notice the sneaky move. He’s going to demand a quantitative measure of an information increase, but at the same time, he’s going to argue that mathematical measures of information, such as Shannon information, can’t be used. He’s saying “Give me a number, but you aren’t allowed to use any procedures that produce a number”—heads he wins, tails I lose.

Unfortunately for Egnor, I didn’t say anything about Shannon information; a gene duplication itself represents an increase in Shannon information, of course, but that wasn’t my point. I gave him an example of a change in genetic information of a specific organism that “does things, specific things”! The mosquitos have a new property, pesticide resistance, and they achieved it by adding a new gene, a copy of an old one with significant changes. It answered his demands, both the old one on the Time blog and the new one in his comment, perfectly.

His other tactic was to claim that my search of PubMed as invalid and didn’t meet his requirements.

Regarding your PubMed literature search, I must not have used the words ‘Information’, ‘Measurement, and ‘Random’ often enough in my discussion with Mike Lemonick, and you thought I said ‘gene’ ‘duplication’ and ‘evolution’. I understand; we all make mistakes. If you actually want to answer my question, type ‘information’, and (not ‘or’!) ‘measurement’, and ‘random’, and the name of the species in which you wish to look for experimental measurement of information generation by random processes.

I did a PubMed search just now. I searched for ‘measurement’, and ‘information’ and ‘random’ and ‘e coli’. There were only three articles, none of which have any bearing on my question. The first article, by Bettelheim et al, was entitled ‘The diversity of Escherichia coli serotypes and biotypes in cattle faeces’.

Anybody who uses a database search function knows that there is a skill to defining search terms; you’re going to be frustrated if you use the terms that you think everyone should be using, rather than the terms that they actually use. It’s an astonishing bit of hubris that Egnor can design an incompetent search that by his own admission fails to turn up any relevant articles, and he thinks that is superior to my search, based on knowledge of terms that relevant researchers in evolutionary biology would use, that turned up over 2800 good articles. The real test is to look at the articles you get, and see if they answer your question; Egnor did not do that. My search turned up articles describing mechanisms of evolution of new proteins and whole new clades by genetic and molecular processes; he apparently prefers to close his eyes to that and instead tailor a search that excludes anything that might conflict with his preconceptions.

Nick Matzke has also thrown in his two cents on that thread, and it’s a good reply so I’ll promote it here.

Michael Egnor, despite being cited fawningly yet again on the DI blog, has yet to respond to my simple answer to his silly question about the origin of new genetic information.

Here’s my answer again:

The Discovery Institute blog just linked to this thread, so I am just now coming to it.

Regarding Egnor’s question about the ability of random mutation and natural selection to produce new genetic information —

Michael Egnor is just ignorantly repeating some of the dumbest lines from the ID propaganda manual. This paper explains the origin of new genetic information, reviewing 20+ examples where the origin of new genes with new functions has been reconstructed in detail:

Long M, Betran E, Thornton K, Wang W. (2003). The origin of new genes: glimpses from the young and old. Nature Reviews Genetics. 4(11):865-75.

The paper is free online in various places — as is Manyuan Long’s vita, which contains dozens of papers specifically on this topic.

Egnor has probably never read this paper or any similar work, which is why he has such a beknighted view of the relevant science. Dr. Egnor: admit you were wrong on your very first argument, and that the headquarters of the ID movement, the Discovery Institute, was also wrong in praising your argument here, and let’s start this discussion over.

(PS: Regarding gene duplication — sure, an exact duplicate isn’t “new” information. But after duplication — sit down for this shocker — mutation and selection can change a copy. Now you have two genes with divergent sequences and different functions. This is new information in anyone’s book.

As for a “limit” — why should anyone think there is any particular limit to the amount of information this process can generate? If evolution can generate three new genes (known as of 2003) in the Drosophila melanogaster genome in 3 million years (see Long et al. 2003, Table 2), it can obviously do much more with millions of species and billions of years. Any arbitrary line can be crossed by saying “add one more new gene”. Game over, man.)

(PPS: Dr. Egnor, did you ever work on animal models in any of your training or research as a neurosurgeon? Just why do you think humans share so many anatomical details with other animals, anyway?)

Egnor is not only wrong, but he’s pretty damn arrogant about it—how else to explain someone who is proud of the fact that he knows nothing about a subject, and is proud of his inability to find sources that would correct his ignorance, even when they’re pointed out to him directly? He’s like Michael Behe, in that we can plop mountains of information in front of him, and he’ll just blithely claim it doesn’t exist.

The saga continues with another rebuttal.

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Comments

  1. #1 David Marjanovi?
    February 24, 2007

    In addition, transposable elements are directly recruited by host genes

    Sugarbear, I’ve been studying molecular biology for 5 years now, and I still don’t understand what you mean. Transposable elements are recruited?!?

    You see, I get the idea that you don’t understand that you don’t understand what you’re talking about. Maybe you should go to a university library, open the humongous gray paperback called “Molecular Biology of the Cell” (first of the many authors: Alberts), and spend the next couple of weeks reading it 5 h a day. Then come back and tell us about how the trees are arranged regularly in the grove.

    Life is a huge mess. If there was any design, it was Stupid Design. Creationism is blasphemy. :-)

  2. #2 David Marjanovi?
    February 24, 2007

    Google for “RNA world” and then spend the rest of the day reading the results.

    You have a lot of work ahead of you before you can declare ID irrelevant to science. The problem is that the more science advances the weaker the evolutionary explanations become.

    The problem is that the longer you don’t bring your knowledge up to date you don’t know squat about what the evolutionary explanations are.

    Like Sugarbear, you are so arrogant as to believe that everyone is as ignorant as you.

  3. #3 Torbjörn Larsson
    February 24, 2007

    DI proclaim loudly: ‘Just because science blogs has answered Egnor’s question any number of times, don’t think we won’t present a particular uninterested response as a weakness. Oh, and since he is a “professor of neurosurgey [sic]” we will claim you are responseless.’ I think they have to rethink that strategy now, silently.

    Salvador Cordova has taught Egnor well. Always try to project an affable atmosphere while stabbing opposite discussion participants in the back.

    “I believe in evolution as much as you do, in the sense that living things have changed over time. … I think that some aspects of living things, particularly the specified information in biological molecules, are more reasonably explained as the consequence of design.”

    The obvious contradiction doesn’t bother Egnor. Nor does the problem of distinguishing aspect from aspect. Instead he is perfectly willing to conflate science with pseudoscience. Perhaps for him cancer is tissue as much as brain tissue – and a neurosurgeon can as well leave it in there.

    “There isn’t any area of medicine that makes much routine use of evolutionary biology”

    Except that cancer and their treatments rely heavily on evolutionary effects. Perhaps Egnor need some help with PubMed searches here too. I’m sure we can oblige in that case.

    Oh, and neurosurgeons doesn’t bother much with the background behind tissue matching either. After all, our heart surgery colleges are perfectly willing to transplant any animal heart. It was probably just bad luck that the patient that got a baboon instead of a chimp heart immediately died from rejection in spite of a “class A” match. ( http://query.nytimes.com/gst/fullpage.html?sec=health&res=9A0DE6DE1F39F934A25752C1A962948260 )

    “Doctors don’t deal much with evolutionary biology, since eugenics went out of fashion.”

    That is another Cordova specialty, take an issue that has been appropriated by political or other means (here medical) and pretend that it was the fault of science.

  4. #4 Torbjörn Larsson
    February 24, 2007

    Continuing the comparsion between Cordova and Egnor into the science, his grasp is as feeble as Sal’s. Yes, it is actually that bad! The neurosurgeon part doesn’t seem to help, contradicting DI’s claims here or on its list. Nothing new there, of course.

    This philosophical conundrum isn’t anything new in science. We don’t know where the laws of physics come from either, but that doesn’t preclude the scientific inference that there are laws of physics.

    Philosophical conundrums doesn’t apply in science. Since Egnor is perfectly willing to embrace pseudoscience uncritically, it isn’t too surprising he has problems with distinguishing philosophy from science either. He obviously doesn’t know what science is.

    But in this particular case science can contribute to philosophy. There have been two main strategies used in the search for a fundamental theory, for a long time now. Either it is uniquely constrained, i.e. there is only one set of fundamental laws and parameters that works. Or it is not uniquely constrained, so random chance played some part in us observing the universe that we do. This should be well known even for scientist illiterates such as Egnor and Cordova.

    Newton’s demonstration of a ‘clockwork’ physical world that adhered to mathematical laws played an important role in the rise of Deism in the 18th century.

    If so, deism is now gutted.

    ‘Free will’ is a folk psychology concept, and is not a problem for either philosophy or neuroscience. It is now known that we construct our view of our immediate ‘plans’ and actions after the response is initiated. So this end of the determinism problem is disempowered – we can have free will in a deterministic setting.

    On the other end of the determinism problem, physics has also learned that it leads to unpredictive chaos. And underneath the classical deterministic regime lies quantum mechanics, without chaos but now known to instead lead to outcomes with genuinely stochastic character. So physics both eats the cake and keeps it when it comes to ‘clockwork’ determinism.

    The conclusions that we can draw from science that constrain philosophy and religion is quite different today, for obvious reasons. I’m sure Egnor would be illuminated here if he decides to take a further look on Pharyngula.

    But the information in living things is specified; it does things, specific things. In that sense, it differs completely from Shannon information

    I’m sure that no neurosurgeon thinks when looking at reconnecting nerve tissues, “what information increase will this make to my patient”. The proper question is probably “how much function will I restore”.

    Biology is primarily about function. Others have delved into the information issue in great depth, but I would add two things.

    First, if we want to complement the primary picture that evolution deals with, we can look at structure and information on several levels that is ignored by Egnor. (Or is it ‘Egnored’? :-) Phylogenetic trees is a structure, with information, that is generally produced on several levels, from molecules to species. Allele frequencies is another structure, with information, that is produced over populations.

    Second, such structures are predicted without any recourse to physical information theory. But if we tried that route, we would probably end up using other measures than KC complexity in most cases. For example, a measure that describes neural networks (and perhaps lateral gene transfer) should maximize between complete regularity and complete irregularity, with connections on all order of ranges. There are several such measures.

  5. #5 Torbjörn Larsson
    February 25, 2007

    Obviously there is little use in continuing answer Egnor, since he isn’t interested in understanding the answers. But it is always a good thing to show curious bystanders what science says.

    I asked for a measurement of new information, not anecdotes about new functions.

    Here the three basic mistakes are repeated:
    - Evolution theory predicts function without discussing information.
    - Scientific theories are not “just-so” stories but makes testable predictions.
    - There is no unique measure of information.

    Since several others have explained the confusion Egnor have about information measures, I will only add two things.

    First, it is known that no single information measure can capture all structures. ( See for example http://adsabs.harvard.edu/abs/1990Natur.344..705M .) Second, as Mark Chu-Carroll noted on his blog “Good Math, Bad Math” Egnor can’t ask for specific values of information outside Shannon information that is the only uniquely defined such measure.

    Physical information theory, of the sort used in classical physics and quantum mechanics seems more apt,

    There is very little use of information theory in physics and computer science outside some specific uses. Especially QM has very little done in this regard.

    One should think that this fact would tip creationists that they are following a chimera.

    Darwinism, understood as the theory that RM+NS accounts fully for biological complexity, doesn’t have squat to do with the practice of modern medicine.

    Again, since several have explained the confusion Egnor have about evolution (which he typically confuses with Darwinism, and Darwinism with RM+NS) and his distasteful continuing mention of eugenics, I will only add a few things.

    First, nobody suggests that practicing modern medicine means practicing evolutionary biology. What we can claim is that medicine is compliant with evolutionary predictions. For example, that tissue matching may be necessary and that tissues from related species match better.

    Second, modern medicine in fact uses evolutionary methods. Some medicines are now developed by test tube evolution.

    Third, a scientific theory isn’t dogma. This is something a creationist can’t easily understand, but science has progressed since Darwin’s introduction of evolutionary theory. It makes no sense to refer to Darwin’s books for help on modern scientific knowledge.

    Fourth, Egnor is (surprise, surprise!) making an old quotemining of Darwin. Darwin didn’t claim that the smallpox vaccine was regrettable. He was describing that evolution is still taking place in the modern society:

    “I have hitherto only considered the advancement of man from a semi-human condition to that of the modern savage. But some remarks on the action of natural selection on civilised nations may be worth adding. This subject has been ably discussed by Mr. W. R. Greg,* and previously by Mr. Wallace and Mr. Galton.*(2) Most of my remarks are taken from these three authors.
    [ ... ]
    There is reason to believe that vaccination has preserved thousands, who from a weak constitution would formerly have succumbed to small-pox. Thus the weak members of civilised societies propagate their kind. No one who has attended to the breeding of domestic animals will doubt that this must be highly injurious to the race of man. It is surprising how soon a want of care, or care wrongly directed, leads to the degeneration of a domestic race; but excepting in the case of man himself, hardly any one is so ignorant as to allow his worst animals to breed.
    [ ... ]
    The surgeon may harden himself whilst performing an operation, for he knows that he is acting for the good of his patient; but if we were intentionally to neglect the weak and helpless, it could only be for a contingent benefit, with an overwhelming present evil. We must therefore bear the undoubtedly bad effects of the weak surviving and propagating their kind; but there appears to be at least one check in steady action, namely that the weaker and inferior members of society do not marry so freely as the sound; and this check might be indefinitely increased by the weak in body or mind refraining
    from marriage, though this is more to be hoped for than expected.     [Bold added.]”
    ( http://www.infidels.org/library/historical/charles_darwin/descent_of_man/chapter_05.html )

    Oh, and if Egnor reads this, PZ spells his name Myers.