Re: Lack of evolution (computers and living things)

On Jun 12, 1:14 pm, Prof Weird <pol...@xxxxxxxxxxxxxxxxxxxxx> wrote:
On Jun 12, 3:01 pm, Seanpit <sean...@xxxxxxxxx> wrote:





This technical paper [excerpts below] was submitted for presentation
at the Genetic Programming 1997 Conference (GP-97) held 13-16 July at
Stanford University, where Susumu Ohno was the scheduled keynote
speaker. Only two of six reviewers recommended accepting it. Maybe
that's not bad for a paper that questions the possibility of achieving
one of Genetic Programming's highest goals.

http://www.panspermia.org/computr2.htm

Yes, this paper is over 10 years old.  However, the questions raised
by this paper have yet to be answered by any new relevant
demonstration(s).
_______________________________

Chandra Wickramasinghe has compared the Darwinian account of evolution
to saying that all of world literature came from the book of Genesis
by occasional typos and paragraph swapping.

So - the OPINION of a mathematician/astronomer about biology is more
relevant that those of biologists ?

Why not?

Professor of Eugenics (= white superiority) Ronald Fisher had no
degree in biology or mathematics. He held an ordinary B.A. degree in
astronomy - nothing else. But IIRC Richard Dawkins called Fisher the
greatest scientist since Darwin.








[snark] And Argument from Faulty Analogy is SOOOOO convincing .... [/
snark]

The mechanism discussed
here is analogous to stipulating that every text along the way was
viable as literature. Such gradualistic series have not been shown to
be possible in written text or computer programs. Nor have they been
shown to exist in biology. If this is how new genes are supposed to
evolve, the mechanism remains to be demonstrated.

Too bad the mechanism HAS been demonstrated; it's just that
creationuts frantically begin waving their hands and whining to dispel
the evidence.  Arguments from analogy don't hold when the analogotes
aren't too similar.



Computer Programs
1) One well-known computer program that purports to mimic evolution is
the one by Richard Dawkins that creates "biomorphs". The program
generates stick figures that resemble insects, trees, bats, spiders,
etc. The figures show a certain amount of variety as they evolve. But
the evolution is by artificial selection, and nothing like gene
duplication occurs.

In this case,  the difference between 'artificial' selection and
'natural' selection is about the same as 'six eggs' vs 'half a dozen
eggs'.

And WHY would gene duplication be necessary for such a simple
program ?

Instead, only nine or sixteen variables (in
different versions) are allowed to wander within narrow ranges. These
few variables occupy a tiny fraction of the "genome" that generates
the biomorphs, which includes Dawkins's application program and the
necessary parts of the computer's operating system. The sequence space
explored by Dawkins's program is tightly confined and every member of
it is functional. Saying that this process represents evolution is
like saying that the song "Happy Birthday" evolves whenever it is sung
for a different person. Certainly, nothing analogous to a new gene is
created by Dawkins's biomorphs.

WAS IT EVER THE INTENT OF THE BIOMORPHS PROGRAM to do what you are
whining it failed to do ?



2) The program by Tom Ray called Tierra is also well-known. It starts
with a species that originally has 80 instructions. The creatures
multiply and evolve until the computer's storage capacity is full.
From then on the population is controlled by killing off creatures
ranking lower on a fitness scale. One common outcome is the evolution
of parasitism. Parasitism is known to be important in biological
evolution. But the evolution of parasitism does not necessarily
require any new genes — the genes of the parasites and hosts already
exist beforehand. True, biological genomes that become related in this
way may in fact require new genes to make them compatible with each
other. But in Tierra, nothing suggests that anything analogous to a
new gene is ever created.

You REALLY shouldn't rely on cherry-picked ten year old papers :

"Evolution of biological complexity", Adami C, Ofria C, Collier TC,
PNAS 97(9): 4463-4468, April 2000

"Automatic design and manufacture of robotic lifeforms", Lipson H,
Pollack JJB, Nature 406 : 974-977, Aug 2000

"Further examples of evolution by GENE DUPLICATION revealed through
DNA sequence comparisons", Ohta T, Genetics 138 : 1331-1337, Dec 1994

"Macroevolution simulated with autonomously replicating computer
programs", Yedid G,Bell G, Nature 420 : 810-812, Dec 2002



3) John Koza's models of evolution, called Genetic Programming, start
with selected algorithms that are shuffled and duplicated to create
new subroutines. The subroutines are bred for their ability to solve a
basic problem. While it is possible for an evolved subroutine to
contain more algorithms than its parent, there is no suggestion that
any new algorithms are created in Koza's process. All of the necessary
algorithms — and some that may be unnecessary — are supplied from the
outset. Therefore, this evolutionary process more nearly mimics Cosmic
Ancestry than Darwinism!

RiiIIiiIIIiIGHT !  Starting with a program that CANNOT PERFORM certain
logical operations, they evolved programs that could do several
complex logical operations (that were irreducibly complex to boot !)

"The evolutionary origin of complex features", Lenski RE, Ofria C,
Pennock RT, Adami C, Nature 423: 139-144, May 2003

"Evolving inventions", Koza JR, Keane MA, Streeter MJ, Scientific
American 288(2): 52-59, 2003  Starting from just a wire, the program
used random variation filtered by functional selection to EVOLVE
circuits more efficient and more complex than anything a human could
come up with.

[snark]But the FACT that it succeeded is NOT proof that it actually
succeeded in a way that creationuts will accept ... [/snark]







4) The fourth computer program is different from the other three
because it was intended not to model evolution but to automate the
updating of software — and it was never implemented. At the Second
Artificial Life Conference held February 5 - 9, 1990, in Santa Fe, New
Mexico, Harold Thimbleby of Scotland proposed that updates to existing
computer programs could be distributed and installed automatically by
computer viruses (Kelly). Such a virus would contain code that would
a) recognize a host needing the upgrade, b) provide and install the
upgrade, and c) from there, infect other computers also needing the
upgrade. Here the computer analog of new genes for evolutionary
improvements would be inserted from elsewhere by viruses, as in Cosmic
Ancestry. That this process could work in computers was not disputed
at the Santa Fe conference. And in biology, that viruses can spread by
infection and insert their own genes into their hosts' genome,
including the germline, without harm, is already known. Ohno himself
mentions that viruses are a possible mechanism behind biological
evolution and he says viruses would be the only way to transform whole
populations at once (Ohno, p 55).

Discussion

We have believed since before Darwin that biology does not have a
different set of rules from the rest of science. If Darwinian
evolution works, it should be possible to mimic the process in
software. By whatever mechanism, Ohno's or other, computers should be
able to mimic what biological evolution has done. In the discussion
above, we have focused on the creation of new genes that code for new
functions.

More broadly, if a software model of evolution is possible, ordinary
personal computers should be able to evolve wholly new, unexpected
features that are somehow advantageous to them or their software. For
example, computers might acquire the ability to activate other helpful
programs, network with other computers, use the telephone, identify
and disarm harmful viruses, automatically backup themselves, survive
crashes, etc. All of these improvements would require new computer
code. Since computer programs are transferred constantly, and
duplicated, and mistakes are inserted occasionally, just as in
biology, the opportunity for existing computer programs to evolve by
the Darwinian method is already in place.

Of course, in the marketplace, computers have acquired these and many
other new abilities, but not in a closed system. To mimic Darwinian
evolution, they would have to evolve improvements without input from
programmers, starting with only programs already available. To suggest
that computers ever might evolve significant improvements this way
seems farfetched. Why? Can computers, without the input of new code,
write for themselves any programs with fundamentally new meaning? Is
there any example of an improvement to personal computers that was
written by the unguided random duplication, mutation and recombination
of existing code? Or, is the Darwinian account of the evolution of
biological improvements equally farfetched?

Argument from faulty analogy.



Returning to the narrower original question, can any computer model of
Darwinian evolution produce the analog of new genes?

Yes - as listed in a few of the above papers.  And findable with a
search, were one actually interested in learning ....

Initiating standard posturing :

If not, perhaps
we should wonder if the Darwinian mechanism is sufficient to produce
new genes on Earth, or whether another source for them is necessary.

Production of new genes observed on Earth :

"Evolution of vertebrate steroid receptors from an ancestral estrogen
receptor by ligand exploitation and serial genome expansions",
Thornton JW, PNAS 98 (10): 5671-5767, May 2001

"Evolution of anti-freeze glycoprotein gene from a trypsinogen gene in
Antarctic notothenioid fish", Chen L, DeVries AL, Cheng CC, PNAS 94 :
3811-16, April 1997

"Positive Darwinian selection after gene duplication in primate
ribonuclease genes", Zhang J, Rosenberg HF, Nei M, PNAS 95: 3708-3713,
Mar 1998

"Origin of new genes and source for N-terminal domain of the
chimerical gene, jingwei, in Drosophila", Long M, Wang W, Zhang J,
Gene ...

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Ray


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