Re: [asa] FYI: Arrogance, dogma and why science - not faith - is the new enemy of

From: PvM <pvm.pandas@gmail.com>
Date: Tue Aug 21 2007 - 00:29:52 EDT

More on Behe.

First of all a comment by Nick Matzke which really deserves to be a
posting by itself. Behe used a dubious number 1 in 10^20 as the
foundation of his argument and then suggests that the likelihood of a
double mutation becomes exceedingly small. What is even more
disturbing is Behe's suggestion that evolution should find a solution
to any problem given to it. However, evolution is constrained by laws
of phyiscs and thus unless relevant variations arise, the present
chloroquine resistance is all evolution may have to offer.

And yet, we observe countless different phenotypes in Malaria which
coincide quite nicely with geological location, suggesting that God is
either quite busy modifying these malaria genomes, or perhaps that
Behe's argument is flawed. Indeed, the actual science strongly
suggests that Behe is wrong.

See for instance

Pooja Mittra et al Progressive Increase in Point Mutations Associated
with Chloroquine Resistance in Plasmodium falciparum Isolates from
India The Journal of Infectious Diseases 2006; 193:130412

Or

Genetic diversity and chloroquine selective sweeps in Plasmodium
falciparum Nature, Volume 418, Issue 6895, pp. 320-323 (2002).

<quote>Widespread use of antimalarial agents can profoundly influence
the evolution of the human malaria parasite Plasmodium falciparum.
Recent selective sweeps for drug-resistant genotypes may have
restricted the genetic diversity of this parasite, resembling effects
attributed in current debates to a historic population bottleneck.
Chloroquine-resistant (CQR) parasites were initially reported about 45
years ago from two foci in southeast Asia and South America, but the
number of CQR founder mutations and the impact of chlorquine on
parasite genomes worldwide have been difficult to evaluate. Using 342
highly polymorphic microsatellite markers from a genetic map, here we
show that the level of genetic diversity varies substantially among
different regions of the parasite genome, revealing extensive linkage
disequilibrium surrounding the key CQR gene pfcrt and at least four
CQR founder events. This disequilibrium and its decay rate in the
pfcrt-flanking region are consistent with strong directional selective
sweeps occurring over only approximately 20-80 sexual generations,
especially a single resistant pfcrt haplotype spreading to very high
frequencies throughout most of Asia and Africa. The presence of
linkage disequilibrium provides a basis for mapping genes under drug
selection in P. falciparum.
</quote>

In fact, there appear to be more than 2 foci now that our ignorance
about the genome is ever reducing.

But the statement: Selective sweep, in 20-80 sexual generations, now
that is an interesting possibility.

In other words, the foundation for Behe's claims seem to be quite
shaky at best, a mostly unsubstantiated estimate of probabilities,
ignoring other evolutionary processes, the existence of single
mutation chloroquine resistance and so on.

----------
http://scienceblogs.com/pharyngula/2007/06/behes_edge_of_evolution_part_i.php#comment-456458

Here is how Behe gets the 1 in 10^20 number:

p. 57:

<quote>
    How much more difficult is it for malaria to develop resistance to
chloroquine than to some other drugs? We can get a good handle on the
answer by reversing the logic and counting up the number of malarial
cells needed in order to find one that is immune to the drug. For
instance, in the case of atovaquone, a clinical study showed that
about one in a trillion cells had spontaneous resistance.15 In another
experiment it was shown that a single amino acid mutation, causing a
change at position number 268 in a single protein, was enough, to make
P. falciparum resistant to the drug. So we can deduce that the odds of
getting that single mutation are roughly one in a trillion. On the
other hand, resistance to chloroquine has appeared fewer than ten
times in the whole world in the past half century. Nicholas White of
Mahidol University in Thailand points out that if you multiply the
number of parasites in a person who is very ill with malaria times the
number of people who get malaria per year times the number of years
since the introduction of chloroquine, then you can estimate that the
odds of a parasite developing resistance to chloroquine is roughly one
in a hundred billion billion.16 In shorthand scientific notation,
that's one in 1020.

The relevant notes on p. 281:

    13. White, N. J. 1999. Delaying antimalarial drug resistance with
combination chemotherapy. Parassitologia 41:301-8.

    14. Gassis and Rathod. 1996.

    15. White. 1999.

    16. White, N. J. 2004. Antimalarial drug resistance. J. Clin.
Invest. 113:1084-92.

    17. White. 1999.

If you read the key paper, White 2004, you see only:

<quote>
    "Resistance to chloroquine in P. falciparum has arisen
spontaneously less than ten times in the past fifty years (14). This
suggests that the per-parasite probability of developing resistance de
novo is on the order of 1 in 10^20 parasite multiplications."
</quote>

    [Ref 14]
    Su, X., Kirkman, L.A., Fujioka, H., and Wellems, T.E. 1997.
Complex polymorphisms in an approximately 330 kDa protein are linked
to chloroquine-resistant P. falciparum in Southeast Asia and Africa.
Cell. 91:593-603.

I see nothing explicit in Su et al. 1997 about less than 10 origins,
or a 1 in 10^20 probability. This is probably what White was looking
at:

<quote<
    CQR (chloroquine-resistant) P. falciparum parasites spread
steadily from two foci that originated 40 years ago in South America
and Southeast Asia after the massive use of chloroquine for nearly a
decade. The African continent was spared for a time, until CQR
parasites entered East Africa in the 1970s and subsequently swept
across the continent. Today, CQR malaria is present in nearly all
malarious regions except certain areas of the Middle East, Central
America, and the Caribbean. This steady and inexorable march of
chloroquine resistance from two foci is in contrast to the expansion
of pyrimethamine-resistant P. falciparum strains, which contain simple
point mutations in dihydrofolate reductase-thymidylate synthase that
have been selected many times ([42]). The rare events of chloroquine
resistance therefore suggest that the genesis of CQR P. falciparum was
complex, requiring a special combination of multiple mutations.
</quote>

Apparently the resistance allele is the Dd2 allele of the cg2 gene.
But Su et al. 1997 suggests recombination, which of course Behe never
mentions:

<quote>
    Constitutive expression of the cg2 gene in both CQR and CQS
parasites highlights the importance of structural polymorphisms in the
chloroquine resistance mechanism. In contrast to CQR parasites, CQS
parasites from Asia and Africa have a variety of different cg2
alleles. Most of these alleles contain some but not all of the
polymorphisms found in CQR parasites and may have existed
independently in geographically distant regions prior to the
development of chloroquine resistance. The particular combination of
polymorphisms in the Dd2 cg2 gene may therefore have come together by
recombination to form an exact structure necessary for chloroquine
resistance.
<quote>

This is pretty thin gruel on which Behe bases his 1 in 10^20 estimate
for the origin of chloroquine resistance, which is used throughout The
Edge of Evolution!

Behe says on page 59,

<quote> Let's compare the two numbers for the odds of achieving
resistance to atovaquone, where just one mutation is needed, versus
chloroquine, where (presumably -- since if a single mutation could
help, chloroquine resistance would originate much more frequently) two
are needed. The odds are, respectively, one in a trillion (1012) and
one in a hundred billion billion (1020). The ratio of the two numbers
shows that the malarial parasite is a hundred million times (108) less
likely to develop resistance to chloroquine than to atovaquone. This
is reasonable since the genome size of the malarial parasite is in the
neighborhood of a hundred million nucleotides. The implication is that
if two amino acids in a protein have to be changed instead of just
one, that decreases the likelihood of resistance by a factor of about
a hundred million.

    Even though the odds are tremendously stacked against it, P.
falciparum was able to develop chloroquine resistance because there
are an enormous number of parasitic cells (about a trillion) in an
infected patient's body, and about a billion infected people in the
world in a year. So the parasite has the population numbers to get
around the terrible odds. Spontaneous resistance to atovaquone can be
found in roughly every third sick person.17 Spontaneous resistance to
chloroquine can be found perhaps in every billionth sick person, and
since there are usually close to a billion sick people on the planet
every year or so, that means chloroquine resistance is usually waiting
to be found in at least one person, somewhere in the world, at any
given time.
</quote>

He doesn't even know if it really is two mutations that are necessary
to cause chloroquine resistance! It might be several mutations for all
he knows, or it might just be that the number of different resistance
events detected by researchers in the wild is much smaller than the
number of resistance events that actually occur (consider the filters:
1. Not all beneficial mutants survive, many will die in their host; 2.
Many beneficial mutants will lose out in the race to "selectively
sweep" the population; 3. Researchers will mostly only detect the few
mutants that have successfully swept to a large proportion of the
regional population). Or it could be that the rare event is a
recombination event or something else.

And yet CQ resistance by the (assumed!) "double mutation", with
probability 1 in 10^20, is Behe's central measuring stick throughout
the book! Incredible...

PS: Now, looking at the literature:

    Previous work from this and other groups has implicated eight or
nine different pfcrt mutations in the development of CQ resistance
(4). The sequential accumulation of these mutations plausibly explains
the observed genetics and epidemiology of CQ resistance (see the
figure). So why did CQ last so much longer than SP as a frontline
antimalarial? First, four sequential mutations in the dhfr gene--which
encodes dihydrofolate reductase, an enzyme essential for parasite
folate metabolism and targeted by the drug pyrimethamine--appear
sufficient for SP resistance (5). These four mutations accumulate much
faster than the nine required for CQ resistance. Second, CQ persists
at therapeutically useful concentrations for a much shorter period
than SP, leading to lower selection pressures for resistance (6).
Third, CQ resistance may involve genes other than pfcrt, such that
sexual recombination during the malaria life cycle breaks down genetic
combinations, slowing resistance (7, 8). The putative involvement of
other genes remains controversial. [...]

    Resistance to CQ probably arises through the sequential
accumulation of mutations (see the figure). The first mutations spread
because they confer increased tolerance to CQ on parasites, enabling
them to infect humans sooner after drug treatment--for example,
mutation 4 allows parasites to infect people 6 days after treatment
rather than 7 days. The relatively rapid elimination of CQ means that
these are rather weak selective forces (6) and that the spread of
these first mutations will be slow. Eventually, mutation 8 arises,
which allows the parasite to survive therapeutic levels of CQ. Once
above this threshold, the selective advantage conferred by this
mutation becomes enormous and the pfcrt haplotype (now containing
several sequentially acquired mutations) spreads rapidly across
geographic regions where CQ is in common use. This appears to have
occurred four times for CQ resistance: twice in South America, once in
southeast Asia, and once in Papua New Guinea (see the viewpoint by
Wellems on page 124) (10). The mutations may not have equal effects:
mutations K76T and Ala220 --> Ser (A220S) appear to be the most
reliable markers predicting CQ resistance. There are three plausible
explanations for this: (i) If the mutations can be acquired in any
sequence and K76T and A220S have large effects, then they will have a
stronger correlation with resistance; the problem with this argument
is that they rarely, if ever, occur alone and invariably occur with
other "lesser" pfcrt mutations. (ii) Mutation acquisition may follow a
set sequence with K76T and A220S near its end. (iii) These are the
pharmacologically important mutations. The other mutations are
optional--they may have a small effect on CQ tolerance, or compensate
for impaired protein activity after the acquisition of the K76T or
A220S mutations, or encode resistance during the transmission stages
of the malaria life cycle.

    From: I. M. Hastings, P. G. Bray, S. A. Ward (2002).
"PARASITOLOGY: A Requiem for Chloroquine." Science 4 October 2002:
Vol. 298. no. 5591, pp. 74-75. DOI: 10.1126/science.1077573

(Behe cites this paper as ref #1 of Chapter 3 but apparently ignores
its discussion of how malaria evolved.

So it looks like resistance actually occurs by the gradual
accumulation of several mutations, and that what you are seeing in the
wild is not a few rare double-mutation events, but instead a few
much-evolved strains that have accumulated a large number of
resistance mutations.

PPS:

    In addition, none of the Philippine isolates with A144T and L160Y
mutations (n = 48) carried the A220S mutation very commonly seen in
CQR parasites elsewhere.

    [...]

    This study confirms that at least two founder events of
chloroquine resistance have occurred in the Pacific region, one in PNG
and one in the Philippines, and demonstrates that under chloroquine
selection pressure, P. falciparum parasites with various genetic
backgrounds have developed chloroquine resistance independently by
mutating different positions in the pfcrt gene.

From Chen et al. 2005. So A220S, which is one of Behe's required
chloroquine resistance mutations, is not actually required. (I should
add that Kenneth Miller tipped me off to this.)

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Received on Mon, 20 Aug 2007 21:29:52 -0700

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