Re: Jeff's posts in MT Digest 78

I think this jeremiad should probably come to an end and we should all get
back to tuning, but I'll reply to Jeff's most recent posts.

Re Dawkins: Dawkins is an extreme selectionist (more about this later), but
on most things, he's spot on. The statement you quoted is a little on
the extreme
side. Read Ronald Numbers' book "The Creationists" for a sympathetic treatment.
Also, the last episode of the PBS Evolution series is short on science, strong
on sociology of belief, and deals sympathetically with Wheaton college students
who find learning about evolution a challenge to their faith.

Re Linton: Not true, Shigella dysenteriae turns out to be E. coli which
has picked
up virulence plasmids. This is a clear case of how organisms can
increase their
complexity by simple genetic means.

Re HIV: Nobody claims that HIV becomes a new species in the bodies of
victims. All that is claimed is that drug resistance arises by mutation during
treatment and that relaxing the selection allows the remaining wild type
viruses
to outgrow the mutants. Because the viral load is ne low, the immune
system can recover some function. I agree that it is a poor example, but
it does
illustrate mutation and selection in circumstances of public interest.

Re Skeptical Dissent: This means nothing more than that 100 not very
well known
scientists out of several hundred thousand in the US alone are willing
to publically
proclaim their ignorance. I would take such a list more seriously if
the signees were
from the National Academy of Sciences or were the heads of the major
biological societies and editors of the peer-reviewed journals. Note
that many are from religious colleges
or are fields quite distant from evolutionary biology.

However, depending on the circumstances of the poll, I might agree with
it, though
I believe it is deliberately and dishonestly designed to confuse the
public as to
the real status of evolutionary theories.

The question as posed omits other known evolutionary mechanisms,
particularly those which INCREASE the genetic complexity of organisms, a
point ignored by ID and IR theorists. These mechanisms include gene
duplication (and amplification), exon shuffling, chromosomal doubling,
hybridization, horizontal transfer (natural gene transfer by viruses,
free DNA, etc.) and sub-cellular symbiosis. The statement also ignores
neutral mutation, genetic drift, and allopatric speciation (aka
punctuated equilibrium in the weak sense) an other known mechanisms of
evolutionary change. The drafters of the question should take the 2nd
part seriously themselves.

The list is an interesting mix to say the least. Hearn is a theistic
evolutionist, but not a young earth creationist. He was featured on the
last episode of the Evolution series on PBS. Behe is a legitimate
biochemist (I have one of his DNA papers in my files), but has gone off
the deep when with ID/IR theory. Many of the other scientists are from
fields other than evolutionary biology or biochemistry.

As for Schaefer, Nobel Prize nominations are made only by previous
winners and their deliberations are secret. Anyone else can nominate
anybody for a Nobel Prize, but only official nominations by Nobel
laureates count.

Tipler is not even a supernaturalist as he believes that God is a
material supercomputer
that gets its energy from a special type of anisotropic collapse of the
whole universe after the expansion due to the Big Bang has stopped and
reversed into the Big Crunch. He also believes that this supercomputer
can simulate as finite state automata every intelligent being that will
ever exist in the universe and that what we call Resurrection and
Immortality are simulations in this machine. Furthermore, he believes
that this supercomputer sends messages backwards in time (advanced
potentials) to tweak evolution so some intelligent species builds it.
Somehow I don't think this is creationists have in mind when they ask
that alternatives to Darwinian evolution be taught in schools.

I met him at a Skeptics Conference at Cal Tech a few years ago, joined
him for lunch, and have read his book, "The Physics of Immortality."
The physics makes sense and the theory is testable. However, the most
recent cosmological data indicate that the expansion is speeding up, not
decreasing, and that there is not enough matter in the universe to cause
it to collapse.

Except for Dembski and Fana, I didn't see any names I immediately
recognized, so I don't anything about the rest of them and don't have
time to look them up. In any case, appeals to authority are unimportant
in science.

Whether evolution erodes people's faith has no bearing on whether it
occurred or not. The Bible also implies that the world is flat and that
pi is 3, but hundreds of millions of Christians and Jews accept the
rotundity of the earth and the transcendentality of PI. People can
modify their faiths to accomodate the findings of science and
mathematics. Haverstick's post shows how he has done it and the
evolutionist Stephen Jay Gould has written a book recently about
reconciling the two "magisteria" as he calls them.

You missed the point about the fruit fly data, only a very small
fraction of which was shown on PBS. These studies show that the basic
mechanisms determining the body plans of vertebrates and arthropods are
the same, something that special creation does not predict.
There is an immense literature on homeotic genes, hox boxes and the like
and the homologies between the genes themselves, their chromosomal
organization, and their functions are clearly apparent. The so-called
evolutionary dead ends or monsters are simply the means by which the
genes were first identified. It is often easier to look at pathologies
than the normal states because what observe differences due to loss or
gain of functions. This methodology is uncontroversial.

Similarly the basic control genes for eyes are the same in both phyla.
Dawkins has reported that eyes have evolved independently from primitive
light sensitive patches at least 20 times in different lineages, but the
basic control mechanisms have been conserved since the Pre-Cambrian when
the basic body plans evolved and diverged. We have a whole series of
eyes of differing design and complexity. Computer simulations suggest
that it would take only about 100,000 generations to go from an eye spot
to an eye as complex as that of a vertebrate or octopus.

Similarly, birds and dinosaurs have been shown to be very closely
related and are now classified in the same family. There are dinosaurs
with feathers as well as birds with teeth, bony tails, and wing claws.
For some time it has been known the chick cells in culture can be
induced to make tooth proteins; now we know that even more genes in the
tooth program have been retained as chick embryos can make tooth buds,
although adult birds no longer have teeth.

All of these data show that we can understand "irreducibly complex"
systems, given enough data and a modicum of imagination. Frankly, IR and
ID are pseudoscience and have been refuted numerous times as they are
basically "arguments from ignorance." Just because Dembski and Behe
can't imagine how eyes or the immune system (which by the way, has been
shown by Doolittle at UCSD to simpler homologs in invertebrates ),
doesn't justify giving up, saying we can never understand how they
evolved, and therefore claiming that God must have designed them. The
mathematics are irrelevant because the assumptions are wrong -- "GIGO."

--John