Group

I have now read Schneider's paper Schneider T.D., "Evolution of
biological information," Nucleic Acids Research, 2000, Vol. 28, No. 14,
pp.2794-2799. http://nar.oupjournals.org/cgi/content/full/28/14/2794) and
here is my preliminary critique of it:

1) "Schneider's paper is misleadingly titled: "Evolution of biological
information". But it is just a *computer* simulation. No actual
*biological* materials (e.g. genomes of nucleic acids, proteins, etc) were
used, nor does Schneider propose that his simulation be tested with *real*
genomes or proteins. He even uses the word "protein" in quotes:

"Here this method is used to observe information gain in the
binding sites for an artificial `protein' in a computer simulation of
evolution." (p.2794).

So even if it be granted (which I don't grant) that Schneider's computer
simulation has shown how information can be generated "from scratch":

"That is, the necessary information should be able to evolve from
scratch." (p.2794)

Given that gene duplication is common and that transcription and
translation are part of the housekeeping functions of all cells, the
program simulates the process of evolution of new binding sites
from scratch." (p.2796)

it would not be *biological* information. *Computer* electrons and
photons are not *biological* DNA and proteins. The substrates are *very*
different. Nor is *computer* random mutation and natural selection
*biological* random mutation and natural selection (it is significant that
only once in the entire paper - see below - does Schneider use the words
"natural selection" of his model, everywhere else he uses the single word
"selection", indicating that he knows it is not *real* biological "natural
selection). It only becomes *real* biological information and random
mutation and natural selection, when the simulation is tested in the *real*
world, using *real* DNA, proteins, with *real* mutations and a *real*
environment does the selecting. It is significant that Schneider does not
propose this, presumably because he knows it wouldn't work..

Note that the page numbers are from the PDF version, which is different,
due to placement of Schneider's graphs, from the HTML version

2) By "from scratch" Schneider means "with zero information" (pp.2794,
2795). But he contradicts himself by admitting that he "needed [to] code
the recognizer into the genome":

"We need to code the recognizer into the genome so that it can co-evolve
with the binding sites. Then we need to apply random mutations and
selection for finding the sites and against finding non-sites." (p.2794).

But coding recognition into a genome is hardly "begin[ning] with zero
information" in that genome (this comes up again later)!

3) Schneider continues to mislead, by claiming that "the simulation will
match the biology at *every* point" (my emphasis):

"To simulate the biology, suppose we have a population of
organisms each with a given length of DNA. This fixes the genome
size, as in the biological situation. Then we need to specify a set of
locations that a recognizer protein has to bind to. That fixes the
number of sites, again as in nature. We need to code the recognizer
into the genome so that it can co-evolve with the binding sites.
Then we need to apply random mutations and selection for finding
the sites and against finding non-sites. Given these conditions, the
simulation will match the biology at every point." (p.2794)

which is *false*, unless he build an *exact* replica of an entire ecosystem,
containing "a population of organisms" subject to "random mutations and
selection". Remember what Darlington said that the reason computer
weather models get it wrong is because they do not *faithfully* simulate
the weather and evolution is *far* more complex than the weather.

"To turn from propaganda to reality, there is a conspicuous
dichotomy in the reality and predicting power of mathematical
models. We see this in what goes on around us from day to day.
The precision with which mathematics and computers can put men
on the moon, within a few 100 m of a predetermined point at a
range of something like 400 000 km or - million miles, is an
example at the reality of mathematical models when all significant
factors are known and can be precisely quantified. On the ether
hand, failure of mathematics and computers to predict weather
accurately even at short range is an example of the unreality of
mathematical models when significant factors are not all known or
can not be precisely quantified. This dichotomy extends to
mathematical models of evolution. The precision with which they
can describe and predict simple Mendelian processes or the
outcomes of population-growth and competition experiments in
glass jars proves the reality of the models in artificially simple
cases in which factors are few, known, and quantifiable. On the
other hand, the factors concerned in real cases of organic evolution
are more numerous and more difficult to identify and measure than
the factors that determine weather. Mathematical models of real
evolutionary processes may therefore be even more wrong than
weather predictions. But while bad weather predictions are
promptly falsified by visible events, bad mathematical models of
evolution are not, because evolution cannot be seen as weather can.
So, erroneous models of evolution may be uncritically accepted.
This is not just a remote possibility but a frightening probability,
frightening because the wrong conclusions are likely to be applied
to man with consequences incomparably more disastrous than
having a picnic rained out." (Darlington P.J., Jr., "Evolution for
Naturalists: The Simple Principles and Complex Reality," John
Wiley & Sons: New York NY, 1980, p.40).

And as Von Neumann showed (as pointed out by Yockey), the
*minimum* self-replicating system has to have an "information content ...
in the range of hundreds of thousands to several million bits":

"John von Neumann ... was interested in a robot that had a control
message of sufficient information content that it could direct its
own actions and reproduce itself. ... Let us think of the protobiont
as a kind of von Neumann self-replicating machine (von Neumann,
1966). The built-in set of instructions that directs its action has an
information content and is analogous to a genetic message. Von
Neumann (1966) thought that there was a minimum degree of
complexity below which the process of selfreplication is
degenerative. Above this level, the process of self-replication was,
as he put it, explosive. Thus the complexity of the built-in
algorithm must be sufficient to allow the operation of the robot but
it must also have an additional information content sufficient to
allow it to self-replicate. ... The protobiont, like the self-replicating
robot, must have a genome of sufficient complexity both to
metabolize and to self-replicate. ... Let us consider how the
information content of the set of instructions incorporated in the
von Neumann machine leads us to an estimate of the minimum
information content of the protobiont. What is the smallest
information content in the instructions required to direct the
actions and replication of the protobiont? We may draw our
estimates of its minimum information content from the genomes of
the most primitive free-living organisms in order to ascertain the
lowest threshold the various scenarios for the origin of life must
attain. ... The ... minimum information content of the protobiont
must be in the range of hundreds of thousands to several million
bits. Scenarios on the origin of life must show how a complexity of
that magnitude, which is characteristic of organisms, was generated
(Yockey, 1977c, 1981)." (Yockey H.P., "Information Theory and
Molecular Biology," Cambridge University Press: Cambridge UK,
1992, pp.243-244)

So either Schneider's simulation smuggles in an "information content of
[its] protobiont ... in the range of hundreds of thousands to several million
bits" or it is not even a simulation of a minimum self-replicating system.

4) Schneider even admits that his simulation" may not be representative of
all biological systems":

"Because half of the population always survives each selection
round in the evolutionary simulation presented here, the population
cannot die out and there is no lethal level of incompetence. While
this may not be representative of all biological systems, since
extinction and threshold effects do occur, it is representative of the
situation in which a functional species can survive without a
particular genetic control system but which would do better to gain
control ab initio." (p.2794).

In fact the only "biological system" he mentioned in his paper was
"human":

"For example, human splice acceptor sites contain ~9.4 bits of
information on average (6)." (p.2794)

but the above is not "representative of [human] biological systems". In fact
it is "not ... representative of" *any* "biological systems" that "half of the
population *always* survives each selection round", and "the population
*cannot* die out" because "there is *no* lethal level of incompetence."
(my emphasis). Moreover, there is *no* "functional species [that] can
survive without a ... genetic control system"? So this is not *even* a
"simulation" of a "biological system", but a *caricature*! It is a "model" in
the sense that the cardboard box in the cartoon "Calvin and Hobbes" was a
model of an "airplane":

"It seems to be characteristic of the human mind that when it sees a
black box in action, it imagines that the contents of the box are
simple. A happy example is seen in the comic strip `Calvin and
Hobbes' .... Calvin is always jumping in a box with his stuffed
tiger, Hobbes, and traveling back in time, or `transmogrifying'
himself into animal shapes, or using it as a `duplicator' and making
clones of himself A little boy like Calvin easily imagines that a box
can fly like an airplane (or something), because Calvin doesn't
know how airplanes work. In some ways, grown-up scientists are
just as prone to wishful thinking as little boys like Calvin. ... When
a merely verbal [or even mathematical-SEJ] picture is painted of
the development of such a complex system, there is absolutely no
way to know if it would actually work. When such crucial
questions are ignored we leave science and enter the world of
Calvin and Hobbes. ... it's one thing to say an organism has a
completed, functioning system, and another to say how the system
developed. ... in the end, it is a hop in the box with Calvin and
Hobbes. ... Calvin and Hobbes stories can sometimes be spun by
ignoring critical details ... ." (Behe M.J., "Darwin's Black Box: The
Biochemical Challenge to Evolution," Free Press: New York NY,
1996, pp.23, 95, 137, 177)

but the above is not "representative of [human] biological systems". In fact
it is "not ... representative of" *any* "biological systems" that "half of the
population *always* survives each selection round", and "the population
*cannot* die out" because "there is *no* lethal level of incompetence."
(my emphasis). Moreover, there is *no* "functional species [that] can
survive without a ... genetic control system"? So this is not *even* a
"simulation" of a "biological system", but a *caricature*! It is a "model" in
the sense that the cardboard box in the cartoon "Calvin and Hobbes" was a
model of an "airplane":

"It seems to be characteristic of the human mind that when it sees a
black box in action, it imagines that the contents of the box are
simple. A happy example is seen in the comic strip `Calvin and
Hobbes' .... Calvin is always jumping in a box with his stuffed
tiger, Hobbes, and traveling back in time, or `transmogrifying'
himself into animal shapes, or using it as a `duplicator' and making
clones of himself A little boy like Calvin easily imagines that a box
can fly like an airplane (or something), because Calvin doesn't
know how airplanes work. In some ways, grown-up scientists are
just as prone to wishful thinking as little boys like Calvin. ... When
a merely verbal [or even mathematical-SEJ] picture is painted of
the development of such a complex system, there is absolutely no
way to know if it would actually work. When such crucial
questions are ignored we leave science and enter the world of
Calvin and Hobbes. ... it's one thing to say an organism has a
completed, functioning system, and another to say how the system
developed. ... in the end, it is a hop in the box with Calvin and
Hobbes. ... Calvin and Hobbes stories can sometimes be spun by
ignoring critical details ... ." (Behe M.J., "Darwin's Black Box: The
Biochemical Challenge to Evolution," Free Press: New York NY,
1996, pp.23, 95, 137, 177)

Neo-Darwinism co-founder of Julian Huxley warned against this tendency
of "Darwinism" to grow "more and more theoretical" and being satisfied
with mere "paper demonstration[s]", that have "little contact ... with the
concrete facts of cytology and heredity, or with actual experimentation":

"And finally Darwinism itself grew more and more theoretical. The
paper demonstration that such and such a character was or might
be adaptive was regarded by many writers as sufficient proof that it
must owe its origin to Natural Selection. Evolutionary studies
became more and more merely case-books of real or supposed
adaptations. Late nineteenth- century Darwinism came to resemble
the early nineteenth-century school of Natural Theology. Paley
redivivus, one might say, but philosophically upside down, with
Natural Selection instead of a Divine Artificer as the Deus ex
machina. There was little contact of evolutionary speculation with
the concrete facts of cytology and heredity, or with actual
experimentation." (Huxley J., "Evolution: The Modern Synthesis,"
[1942], George Allen & Unwin: London, 1945, reprint, p.23)

5) Schneider gives no actual details of his Ev program's source code, so it
can be checked against what Schneider claims for it. In his "MATERIALS
AND METHODS" section Schneider refers to a website:

"Sequence logos were created as described previously (5). Pascal
programs ev, evd and lister are available from
http://www.lecb.ncifcrf.gov/~toms/ . The evolution movie is at
http://www.lecb.ncifcrf.gov/~toms/paper/ev/movie (p.2795).

Dembski has delved into Schneider's code and gives an example of
"Schneider ... fine-tuning his evolutionary algorithm to obtain the results
he wants":

"In the Nucleic Acids Research article we have been discussing, he
does not list the source code for the program underlying his
simulation. For that code he refers readers to the relevant web
address. The source code is revealing and shows that Schneider
had to do a lot of fine-tuning to his evolutionary algorithm to make
his simulation come out right. For instance, in the crucial
paragraph from his article that I quoted above, Schneider remarks
parenthetically: "To preserve diversity [of organisms], no
replacement takes place if [the number of mistakes is] equal."
Schneider's Pascal source code (which appears not in his Nucleic
Acids Research article but at a separate web location) reveals why:
"SPECIAL RULE: if the bugs have the same number of mistakes,
reproduction (by replacement) does not take place. This ensures
that the quicksort algorithm does not affect who takes over the
population. (1988 October 26) Without this, the population quickly
is taken over and evolution is extremely slow!" Schneider is
here fine-tuning his evolutionary algorithm to obtain the results he
wants. All such fine-tuning amounts to investigator interference
smuggling in complex specified information." (Dembski W.A.,
"No Free Lunch: Why Specified Complexity Cannot Be Purchased
without Intelligence," Rowman & Littlefield: Lanham MD, 2002,
pp.217-218. Emphasis in original)

This alone invalidates Schneider's entire Ev program as a faithful
simulation of the "Evolution of *Biological* Information". By artificially
constraining the program by a "SPECIAL RULE" (and I expect that this is
not the only one), Schneider has smuggled in his own human *intelligent
design* information into his program.

6) Schneider's simulation is of "a genome size of 256 bases" which has "a
set of 16 binding sites":

"To test the hypothesis that Rsequence can evolve to match
Rfrequency, the evolutionary process was simulated by a simple
computer program, ev, for which I will describe one evolutionary
run. This paper demonstrates that a set of 16 binding sites in a
genome size of 256 bases, which would theoretically be expected
to have an average of Rfrequency = 4 bits of information per site,
can evolve to this value given only these minimal numerical and
size constraints. " (p.2795)

but he does not reference any actual *biological* genome that has "16
binding sites in a genome size of 256 bases".

7) Schneider says that "A section of the genome is set aside by the
program to encode the gene for a sequence recognizing `protein',

"A section of the genome is set aside by the program to encode the
gene for a sequence recognizing `protein', represented by a weight
matrix (7,15) consisting of a two-dimensional array of 4 by L = 6
integers." (p.2795)

On p.2796 this "gene" is only "125" bases long. There are AFAIK *no*
biological genes 125 bases long, nor are their organisms that have "a
genome size of 256 bases" with a gene of 125 bases. So again, this is
*not* a "simulation" of a *real* "biological" organism.

8) Schneider says that "the number of mistakes made by each organism in
the population is determined":

"The organisms are subjected to rounds of selection and mutation.
First, the number of mistakes made by each organism in the
population is determined. Then the half of the population making
the least mistakes is allowed to replicate by having their genomes
replace ("Kill") the ones making more mistakes." (p.2795)

Dembski comments on this point (see tagline) that "Schneider purports to
have generated biologically relevant information, and thus CSI ... `from
scratch'" but "he [has] smuggled in CSI .... Within this crucial paragraph,
the crucial sentence is: "The number of mistakes made by each organism
in the population is determined." Who or what determines the number of
mistakes? .... Schneider's [simulation] ... identifies target sequences
implicitly through the choice of fitness function. ... by tying fitness to
number of mistakes, Schneider guarantees that the gradients of his fitness
function rise gradually and thus that his evolutionary algorithm converges
in short order to an optimal computational sequence ..."

9) Schneider says of his graph in Figure 2b (p.2797):

"This roughly-sigmoidal rapid transition corresponds to (and the
program was inspired by) the proposal that evolution proceeds by
punctuated equilibrium (18,19), with noisy `active stasis' clearly
visible from generation 705 to 2000 (Figs 2b and 3)."

This is also misleading (indeed *ridiculous*) for Schneider to claim that
this has anything to do with what Gould and Eldredge, who are mentioned
at references "(18,19)" meant by "punctuated equilibrium", which was at
the *species* (or higher) level, not at the gene level.

10) Schneider say his "ev model" "starts with a completely random
genome", yet it has "transcription and translation [that] are part of the
housekeeping functions of all cells":

"An advantage of the ev model over previous evolutionary models,
such as biomorphs (20), Avida (21) and Tierra (22), is that it starts
with a completely random genome, and no further intervention is
required. Given that gene duplication is common and that
transcription and translation are part of the housekeeping functions
of all cells, the program simulates the process of evolution of new
binding sites from scratch. The exact mechanisms of translation
and locating binding sites are irrelevant." (p.2796)

But this raises the issue that *real* "biological" genomes don't reshuffle
their bases into order, like Schneider's simulation does. Also,
"transcription and translation ... functions" are hardly "from scratch",
"start[ing] with a completely random genome" "with zero information"
(pp.2794, 2795) , but even in the simplest bacteria are at least 50
molecular machines with *immense* CSI. If Schneider's Ev program
carries out these "transcription and translation ... housekeeping functions"
then it is imparting that CSI into its output. So far from "The exact
mechanisms of translation and locating binding sites are irrelevant", if
Schneider's simulation does not faithfully represent them, then it is his
simulation that is "irrelevant"!

11) Schneider only once calls what his model is simulating, "*natural
selection*", in a figure caption:

"Figure 2. Information gain by natural selection. (a) Number of
mistakes made by the organism with the fewest mistakes plotted
against the generation number."

In the rest of the paper he uses the single word "selection". I take this as a
tacit admission that his model is not a simulation of *real* biological
natural selection.

12) Even if Schneider did eventually test his computer simulation against
the real world and it worked, on his own admission it would just be
"microevolution":

"Microevolution can be measured in haldanes, as standard
deviations per generation (25-27). In this simulation 4.0 ¤ 0.4 bits
evolved at each site in 704 generations, or 4.0/(0.4 x 704) = 0.014
haldanes." (p.2797)

However, as Gould pointed out (and it is his "punctuated equilibrium" that
Schneider claims his model represents), macroevolution (e.g. " the most
profound structural transitions in the history of life") is not just
"microevolution (flies in bottles) extended":

"Orthodox neo-Darwinians extrapolate these even and continuous
changes to the most profound structural transitions in the history of
life: by a long series of insensibly graded intermediate steps, birds
are linked to reptiles, fish with jaws to their jawless ancestors.
Macroevolution (major structural transition) is nothing more than
microevolution (flies in bottles) extended. If black moths can
displace white moths in a century, then reptiles can become birds
in a few million years by the smooth and sequential summation of
countless changes. The shift of gene frequencies in local
populations is an adequate model for all evolutionary processes - or
so the current orthodoxy states." (Gould S.J., "The Return of the
Hopeful Monster," in "The Panda's Thumb: More Reflections in
Natural History," [1980], Penguin: London, 1990, reprint, pp.155-
156)

I should again point out here that I would not personally be bothered if it is
eventually shown that RM&NS can increase biological information. That
would still just be microevolution. And as evolutionists from Goldschmidt
(and before) have pointed out, there are *plenty* (if not *all*) major
transitions that have yet to be explained by the "accumulation and
selection of small mutants", e.g.:

"At this point in our discussion I may challenge the adherents of
the strictly Darwinian view, which we are discussing here, to try to
explain the evolution of the following features by accumulation
and selection of small mutants: hair in mammals, feathers in birds
segmentation of arthropods and vertebrates, the transformation of
the gill arches in phylogeny including the aortic arches, muscles,
nerves, etc.; further, teeth, shells of mollusks, ectoskeletons,
compound eyes, blood circulation, alternation of generations,
statocysts, ambulacral system of echinoderms, pedicellaria of the
same, enidocysts, poison apparatus of snakes, whalebone, and,
finally, primary chemical differences like hemoglobin vs.
hemocyanin, etc. Corresponding examples from plants could be
given." (Goldschmidt R.B., "The Material Basis of Evolution,"
[1940], Yale University Press: New Haven CT, 1982, reprint, pp.6-
7)

I have in the past used the example of a newspaper "The Sunday Times"
misprinting its front page "The Sundry Times". I had previously thought
that "not even the most ardent Darwinist would seriously propose that this
tiny increase in information, extrapolated over millions of years, could
ever write even a newspaper, let alone something different like a book"
(indeed a "30 volume ... *Encyclopaedia*") but after reading Schneider's
paper I am now not so sure that there are not some "ardent Darwinist[s]
[who] would seriously propose it!":

=================================================
http://groups.yahoo.com/group/CreationEvolutionDesign/message/12869
From: "Stephen E. Jones" <sejones@...>
Date: Mon Mar 28, 2005 3:36 pm
Subject: Re: 1. Combined response(s) 28-Mar-05; 2. PE 8.3. "Cell ...
Information" [...]
Most creationist/IDists commit the mistake of arguing that `evolution'
(whatever that means) *cannot* increase information, which means not
even by 1 bit. Then all an evolutionist needs to do is show that a mutation
can increase information by 1 bit, and the evolutionist has won. My
approach is to argue that natural processes (I don't concede that natural
processes are *necessarily* `evolution'-they could equally be creation, i.e.
Progressive Mediate Creation), barring a genetic miracle (e.g. see tagline)
which would equally be supernatural creation/design, cannot plausibly
increase genetic information of *sufficient quantity and quality* to
account for *macro*-evolution (there is no need to dispute it could be
micro-evolution).

I have given the example in the past of a malfunction in a newspaper
printing press that produces the misprint "The Sundry Times". That is only
1 bit of information and "not even the most ardent Darwinist would
seriously propose that this tiny increase in information, extrapolated over
millions of years, could ever write even a newspaper, let alone something
different like a book":

--------------------------------------------------------------------------
http://www.asa3.org/archive/evolution/200005/0152.html
Re: Note of appreciation From: Stephen E. Jones (sejones@...)
Date: Sun May 14 2000 - 17:36:03 EDT [...]
While *some* increases of information (in a technical
Information Theory sense) may be generated by gene duplication, and then
random mutation and natural selection, this has not been shown to be of
sufficient quantity, quality or timeliness, to " produce changes associated
with macro-evolution".

An example I use is one of our local newspapers "The Sunday Times".
Say 100,000 identical copies of it are produced. There is only 1 bit of
information content for the whole 100,000 copies.

Now suppose one copy had a misprint "The Sundry Times". This would be
another 1 bit of information. It might even have some `survival value' in
that the word "Sundry" means something else (as opposed to "Sundxy".
But AFAIK not even the most ardent Darwinist would seriously propose
that this tiny increase in information, extrapolated over millions of years,
could ever write even a newspaper, let alone something different like a
book. [...]
--------------------------------------------------------------------------

Yet, as Dawkins reminds us: "*Each* [cell] nucleus ... contains a digitally
coded database larger, in information content, than all 30 volumes of the
Encyclopaedia Britannica put together" (my emphasis):

"Again, this is characteristic of all animal and plant cells. Each
nucleus ... contains a digitally coded database larger, in information
content, than all 30 volumes of the Encyclopaedia Britannica put
together. And this figure is for *each* cell, not all the cells of a
body put together. ... When you eat a steak, you are shredding the
equivalent of more than 100 billion copies of the Encyclopaedia
Britannica." (Dawkins R., "The Blind Watchmaker," [1986],
Penguin: London, 1991, reprint, pp.17-18. Emphasis in original)

Paul A (and his naturalistic ilk) would presumably have us believe that not
only the biological equivalent of a newspaper was produced by a series
1 bit misprints like the "r" instead of "a" in "The Sundry Times," but the
biological equivalent of a "30 volume... Encyclopaedia"! [...]
=================================================

13) Schneider lets slip that there is another unrealistic element in his (and
indeed all) computer simulations in that it (they) "does not correlate with
time":

"Because a computer simulation does not correlate with time, the
haldane and darwin can be combined to give units of bits per
generation; in this case 0.006 ¤ 0.001 bits per generation per site."
(p.2797)

14) Schneider claims "The ev model quantitatively addresses the question
of how life gains information ... without any other external influence,
thereby completely answering the creationists":

"The ev model quantitatively addresses the question of how life
gains information, a valid issue recently raised by creationists ....
The ev model shows explicitly how this information gain comes
about from mutation and selection, without any other external
influence, thereby completely answering the creationists." (p.2797)

Well, when Schneider's simulation is actually tested with *real* "life" (e.g.
a bacterium), and under *real* mutation and natural selection it gains
information, then, and only then, would "creationists" be favourably
impressed. But if they are like me, they would already be impressed (but
unfavourably) that Schneider does not mention in his paper that his
simulation should now be so tested in the *real* "biological" world.

15) Continuing to mislead (perhaps himself: "The first principle is that you
must not fool yourself-and you are the easiest person to fool" - Feynman)
Schneider claims that his "ev model" "fits Behe's (34) definition of
`irreducible complexity' exactly":

"The ev model can also be used to succinctly address two other
creationist arguments. First, the recognizer gene and its binding
sites co-evolve, so they become dependent on each other and
destructive mutations in either immediately lead to elimination of
the organism. This situation fits Behe's (34) definition of
`irreducible complexity' exactly ("a single system composed of
several well-matched, interacting parts that contribute to the basic
function, wherein the removal of any one of the parts causes the
system to effectively cease functioning", page 39)..." (p.2797)"

But a "recognizer gene" of "125" bases, is hardly what Behe had in mind
by `irreducible complexity' (interestingly Schneider puts it in single
quotes, as though even he realises that it isn't), given Behe's examples of
IC being "a single system composed of several well-matched, interacting
parts", such as the bacterial flagellum and the blood-clotting cascade, etc)!
It is also interesting (and significant) how many evolutionists ignore
Behe's proposed examples of IC and invent their own as straw men to
more easily knock down.

16) The unrealism of Schneider's model is shown by "the mutation rate of"
a *virus* "HIV is ... 10 times slower"

"Second, the probability of finding 16 sites averaging 4 bits each in
random sequences is 2^-4 x 16 5 x 10^-20 yet the sites evolved
from random sequences in only ~10^3 generations, at an average
rate of ~1 bit per 11 generations. Because the mutation rate of HIV
is only 10 times slower, it could evolve a 4 bit site in 100
generations, ~9 months (35), but it could be much faster because
the enormous titer [10^10 new virions/day/person (17)] provides a
larger pool for successful changes. Likewise, at this rate, roughly
an entire human genome of ~4 x 10^9 bits (assuming an average of
1 bit/base, which is clearly an over­estimate) could evolve in a
billion years, even without the advantages of large environmentally
diverse world-wide populations, sexual recombination and
interspecies genetic transfer." (pp.2798-2799)

17) Schneider's extrapolation above from a *computer simulation* of "256
bases" (so-called), to "at this rate, roughly an entire human genome of ~4 x
10^9 bits ... could evolve in a billion years" is just absurd. As though
humans are just a "HIV" virus writ large! And remember in Schneider's
simulation, for it to work, "half of the population always survives each
selection round ..., the population cannot die out and there is no lethal
level of incompetence." However, this was evidently too much for even
Schneider (or one of his reviewers) and as an afterthought he concedes that
"this rate is unlikely to be maintained for eukaryotes"! (p.2799).

18) Finally, Schneider concludes, "contrary to ...Spetner ... the ev program
also clearly demonstrates that biological information .. can rapidly appear
in genetic control systems subjected to replication, mutation and
selection":

"So, contrary to probabilistic arguments by Spetner (32,36), the ev
program also clearly demonstrates that biological information,
measured in the strict Shannon sense, can rapidly appear in genetic
control systems subjected to replication, mutation and selection
(33)." (p.2799)

Well, Spetner in his works cited by Schneider, gave examples of a lot of
*real* "biological information", i.e. actual *organisms* complete with
species names. When Schneider tests his *computer* model against *real*
organisms and it produces *real* "biological information" of the amount
predicted, then I am sure that Spetner (like me) would be impressed, but
not before. Indeed, I don't know about Spetner, but as for me, there are so
many *obvious* fallacies in this paper, that I have no confidence in
Schneider's judgment. He strikes me as someone who has not learned
Feynman's "first principle ... that you must not fool yourself-and you are
the easiest person to fool":

'The first principle is that you must not fool yourself-and you are
the easiest person to fool. So you have to be very careful about
that. After you've not fooled yourself, it's easy not to fool other
scientists. You just have to be honest in a conventional way after
that. I would like to add something that's not essential to the
science, but something I kind of believe, which is that you should
not fool the layman when you're talking as a scientist. .... I'm
talking about a specific, extra type of integrity that is not lying, out
bending over backwards to show how you're maybe wrong, that
you ought to have when acting as a scientist. And this is our
responsibility as scientists, certainly to other scientists, and I think
to laymen. For example, I was a little surprised when I was talking
to a friend who was going to go on the radio. He does work on
cosmology and astronomy, and he wondered how he would explain
what the applications of this work were. `Well,' I said, `there aren't
any.' He said, `Yes, but then we won't get support for more
research of this kind.' I think that's kind of dishonest. If you're
representing yourself as a scientist, then you should explain to the
layman what you're doing and if they don't want to support you
under those circumstances, then that's their decision. One example
of the principle is this: If you've made up your mind to test a
theory, or you want to explain some idea, you should always decide
to publish it whichever way it comes out. If we only publish results
of a certain kind, we can make the argument look good. We must
publish both kinds of results." (Feynman R.P., "Cargo Cult
Science," in "`Surely You're Joking, Mr Feynman!': Adventures of
a Curious Character," [1985], Unwin Paperbacks: London, 1990,
reprint, p.343)

and so Schneider's Ev program is just another example of what Feynman
called "Cargo Cult Science"!

[...]

Steve

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"In reading Schneider's article, and more generally when confronting
Darwinian scenarios that purport to generate CSI for free, I always go back
to my days as a graduate student in mathematics teaching undergraduates
trigonometry. When it came time to grade their tests, I always had to watch
that they did not trick me by purporting to establish a trigonometric
equality when in fact they did not have a clue why one trigonometric
expression was equal to another. What students would do is write one
expression at the top of the page, the other at the bottom of the page. Then
they would manipulate the top expression, transforming it line by line
down the middle of the page. Next they would manipulate the bottom
expression, transforming it line by line up the middle of the page. In the
middle of the page the transformed top and bottom expressions would
happily meet, offering no clue how they were related. My challenge was to
find where the unwarranted leap occurred (i.e., where the transformation
from one expression to the other could no longer be justified). I find
myself in a similar position analyzing Schneider's article and Darwinian
scenarios like his. Schneider purports to have generated biologically
relevant information, and thus CSI, for free (or "from scratch" as he
prefers). The No Free Lunch theorems, however, tell us this is not
possible. Where, then, has he smuggled in CSI? The precise place where
he smuggles it in is not hard to find if one knows what to look for. Here is
the crucial paragraph in his article: The organisms [i.e., the computational
sequences in phase space] are subjected to rounds of selection and
mutation. First, the number of mistakes made by each organism in the
population is determined. Then the half of the population making the least
mistakes is allowed to replicate by having their genomes replace ("kill")
the ones making more mistakes. (To preserve diversity, no replacement
takes place if they are equal.) At every generation, each organism is
subjected to one random point mutation in which the original base is
obtained one-quarter of the time. Within this crucial paragraph, the crucial
sentence is: "The number of mistakes made by each organism in the
population is determined." Who or what determines the number of
mistakes? Clearly, Schneider had to program any such determination of
number of mistakes into his simulation. Moreover, the determination of
number of mistakes is the key defining feature of his fitness function. For
this function optimal fitness corresponds to minimal number of mistakes.
We have seen all this before, to wit, in Richard Dawkins's METHINKS IT
IS LIKE A WEASEL simulation (see section 4.1). To be sure, Schneider's
simulation is more subtle. But the parallels are unmistakable. Like
Dawkins's simulation, Schneider's simulation starts with a randomly given
"genome" and requires no further intervention. Unlike Dawkins's
simulation, Schneider's does not identify an explicitly given target
sequence. Even so, it identifies target sequences implicitly through the
choice of fitness function. Moreover, by tying fitness to number of
mistakes, Schneider guarantees that the gradients of his fitness function
rise gradually and thus that his evolutionary algorithm converges in short
order to an optimal computational sequence (optimality being defined in
relation to his fitness function). Although once the algorithm starts running
there is no intervention on the part of the investigator, it is not the case
that
Schneider did not intervene crucially in structuring the fitness function. He
did, and this is where he smuggled in the CSI that he claimed to obtain
from scratch." (Dembski W.A., "No Free Lunch: Why Specified
Complexity Cannot Be Purchased without Intelligence," Rowman &
Littlefield: Lanham MD, 2002, pp.214-215)
Stephen E. Jones, BSc (Biol). http://members.iinet.net.au/~sejones
Moderator: http://groups.yahoo.com/group/CreationEvolutionDesign
& http://groups.yahoo.com/group/ProblemsOfEvolution/ Book: "Problems
of Evolution" http://members.iinet.net.au/~sejones/PoE/PoE00ToC.html
& http://members.iinet.net.au/~sejones/pe00cont.html
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