Re: [asa] Behe's Math... was Arrogance

From: Iain Strachan <igd.strachan@gmail.com>
Date: Tue Aug 21 2007 - 15:14:22 EDT

Hi, I've not read Behe's book, so can't comment authoritatively.

However, you mention "successful mutation rate" as part of the
calculations. I'm wondering if this rate is computed on the assumption that
the mutation probability is the same for any nucleotide in the Genome.
(This is the way one operates when doing a genetic algorithm). However, if
one reads, for example Lynn Caporale's excellent book "Darwin in the Genome"
(which is refreshing in other ways in that she doesn't bash religion), one
finds that mutation rates are anything but uniform, but are often
concentrated in mutation "hotspots", where the rates are many times higher
than in other spots. It is noted in the book that certain sequences of
nucleotides make mutations much more likely than others, because of their
propensity to fool the proof reading mechanisms. Also, one thing that seems
to prevent mutations is "mirror palindromicity", where you get a sequence
followed shortly by its reverse complement (e.g. AGGC .... GCCT).
Apparently, during the copying process, one strand of DNA is copied
immediately (the leading strand) and the other one is only copied later (the
lagging strand). During this time, such sequences can double over into a
hairpin (also called a "stem loop"), so that the reverse complement
sequences temporarily pair up. These sections have an extremely low
mutation rate, and the mutations are concentrated at points where they don't
match up (hence are much higher).

If mutation rates are in fact much higher than when you average things out,
and concentrated in a few small regions, then does this not affect the
validity of calculations based on uniform mutation rates?

Iain.

On 8/21/07, John Walley <john_walley@yahoo.com> wrote:
>
> So now that we are all in agreement that "the malaria example is a great
> example of evolution under strong selective pressures", this problem boils
> down to a simple mathematical calculation.
>
> We simply take the number of generations of malaria organisms in that 50
> year time frame and divide by 8 and we get an estimate of how many selected
> mutations per population size and number of generations, and this gives us a
> rough estimate of a successful mutation rate to expect in other organisms,
> at least microbes. Granted the rate depends on a multitude of factors and
> may change in advanced life but it gives us a starting point.
>
> Behe then compares this to the population size of primates and the number
> of mutations needed just to get from chimps to humans in the timespan that
> they have both been on the earth and it is not even close. And nevermind for
> now the fact that more than just single mutations are needed, but ones that
> add additional base pairs as well.
>
> As a physicist Pim, wouldn't you agree that this is a scientific way to
> analyse this problem and arrive at whether or not random mutation and
> selection could explain evolution without some other intervention like
> Design?
>
> This mathematical analysis should answer the question for us once and for
> all about Design. Either it is not needed or Behe is right and the power of
> random mutation is "fanciful Darwinian speculation".
>
>
>
> ----- Original Message ----
> From: PvM <pvm.pandas@gmail.com>
> To: John Walley <john_walley@yahoo.com>
> Cc: AmericanScientificAffiliation <asa@calvin.edu>
> Sent: Tuesday, August 21, 2007 1:56:58 PM
> Subject: Re: [asa] FYI: Arrogance, dogma and why science - not faith - is
> the new enemy of
>
>
> Again we are running into a misunderstanding here as to what evolution
> should do and can do. There may be cases, as is the case here, that
> evolution takes more time, and yet, despite all odds, evolution took
> only 45 years or so to find one to eight independent solutions to the
> problem, likely involving two or more mutations. Mutations which made
> the parasite immune to chloroquine. We have seen the same for many of
> the other medicine. In fact, the malaria example is a great example of
> evolution under strong selective pressures.
>
> So we have all that is needed: A succsesful solution, mutations, and
> all in a reasonably short period of time. Surely that should put to
> rest any of the confusing claims by Behe?
>
> Sure, we did not see new structures arise or much added complexity
> although complexity was added. Two mutations, perhaps a few more where
> all that was needed. And evolution found the solution independently in
> 5-8 cases.
>
> You mentioned in another email how this solution was sloppy because it
> reduced the viability of the organism, but it didn't. It actually
> increased the success of the organism in an environment full of
> chloroquine.
>
> I believe Behe's example shows that we scientists need to do a better
> job explaining evolutionary theory.
>
> The simple fact is that processes of variation and selection can
> trivially increase information and thus complexity in the genome.
>
> Of course, science has to explain a lot of information added, this is
> why it takes time and meticulous work, and while ID does nothing to
> add to our knowledge other than to argue that the mosquito parasite
> must have been designed (because of our ignorance as to how it
> achieved something Behe "calculated" to be impossible).
>
>
>
> On 8/21/07, John Walley <john_walley@yahoo.com> wrote:
> > In the case of malaria you have both of what you need, variation and
> selection. And agreed you have a mechanism as well.
> >
> > But Behe is correct when he observes that at least in the case of
> malaria "evolution doesn't do very much".
> >
> > John
> >
> >
> >
> > ----- Original Message ----
> > From: PvM <pvm.pandas@gmail.com>
> > To: John Walley <john_walley@yahoo.com>
> > Cc: AmericanScientificAffiliation <asa@calvin.edu>
> > Sent: Monday, August 20, 2007 10:34:22 PM
> > Subject: Re: [asa] FYI: Arrogance, dogma and why science - not faith -
> is the new enemy of
> >
> >
> > But mechanisms for adding complexity exist, all that is needed is
> > variation and selection. So your objection seems to be flawed. There
> > are mechanisms for evolution, although I am not sure what you mean by
> > naturalistic evolution...
> >
> > On 8/20/07, John Walley <john_walley@yahoo.com> wrote:
> > > Of course random mutation is observed in nature. You must have missed
> the
> > > "what Darwinism purports it to do part".
> > >
> > > Why would we expect new complexity to be added? Maybe because that is
> the
> > > heart of Darwinian evolution that we are discussing. If there is no
> > > mechanism for adding complexity, life would still be protocells or as
> Behe
> > > says, Designed.
> > >
> > > Vacuous goes both ways. It is logically vacuous to defend naturalistic
> > > evolution without any mechanism for it.
> > >
> > > John
> > >
> > > -----Original Message-----
> > > From: asa-owner@lists.calvin.edu [mailto:asa-owner@lists.calvin.edu]
> On
> > > Behalf Of PvM
> > > Sent: Monday, August 20, 2007 12:42 AM
> > > To: John Walley
> > > Cc: AmericanScientificAffiliation
> > > Subject: Re: [asa] FYI: Arrogance, dogma and why science - not faith -
> is
> > > the new enemy of
> > >
> > > <quote>Regardless, showing that random mutation or other naturalistic
> > > processes is not observed in nature to do what Darwinism purports it
> > > to do is valuable and relevant, albeit inconvenient for some, even if
> > > it is arrived at by theological motivation.</quote>
> > >
> > > But random mutation is observed in nature as are many other
> > > naturalistic processes. I believe that you be surprised to find out
> > > how concepts of development, variation, selection are very powerful
> > > natural processes, which are actually observed.
> > >
> > > While it may be Behe's goal to show that there are limits to Darwinian
> > > theory, I feel that he has done little to support your more
> > > extravagant claim that he has shown that random mutation or other
> > > naturalistic processes is not observed in nature. In fact, such a
> > > claim seems rather vacuous. In fact, if you are familiar with Behe, he
> > > fully accepts that these processes can explain the evolution of life
> > > however, he insists that some 'intelligence' is still needed to get it
> > > all started.
> > > Although, such a position seems strangely self defeating.
> > >
> > > JW- This is the "fanciful Darwinian thinking" Behe points out. It
> > > may be trivial to show how complexity can be produced but it is
> > > theoretical, just like Behe's Design argument. In the longest running
> > > empirical study of evolution known to man, that of malaria, zero new
> > > complexity was added.
> > >
> > > What is so theoretical about showing that observed processes of
> > > variation and chance can explain the increase in complexity and that
> > > in fact experiments seem to support this. As far as malaria is
> > > concerned, the interesting strawman is why one would expect new
> > > complexity to be added? In fact, even that minor claim seems to be
> > > contradicted by science.
> > >
> > > It also seems to me you are inflating a little the 'malaria'
> > > experiment. Pandasthumb and other science sites have shown clearly
> > > what is wrong with Behe's claims.
> > >
> > > http://www.pandasthumb.org/archives/2007/07/reality_1_behe.html
> > >
> > > http://www.pandasthumb.org/archives/2007/06/of_cilia_and_si.html
> > >
> > > So how does Behe explain all this?
> > >
> > > <quote>"Here's something to ponder long and hard: Malaria was
> > > intentionally designed. The molecular machinery with which the
> > > parasite invades red blood cells is an exquisitely purposeful
> > > arrangement of parts."</quote>
> > >
> > > Wow...
> > >
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> > >
> > >
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> > >
> >
>
>
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>

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Received on Tue Aug 21 15:14:36 2007

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