Re: Challenge for Darwinists - Protein Synthesis

Richard Forrest wrote:
Wall Of Sleep wrote:

allanm wrote:

Wall Of Sleep wrote:


allanm wrote:

Wall Of Sleep wrote:


<snip>

Statistically, all variation in an initially varying population will be
eliminated (in the absence of mutation) in (4 * population size)
generations.

So looked at either way - the origin of a sequence or the fate of
variants in a derived population - the existence and persistence of
variation proves the historic reality of ongoing mutation.



It would seem to me that the forces of nature are working against random
mutation at every turn then. I'm still totally unconvinced that this
vehicle can be the driving force behind the millions of unique
biological systems we see today.


<snip>

I'm afraid you've missed my point then. What I described is not a
preservative force but part of the inexorable force for *change*. You
assume that mutants will *always* be eliminated. But they have (at
least) the same chance as every other allele of becoming the 'norm'
as variants are lost.

Consider this:

A population of just 4 individuals. A single diploid gene. Lets label
each gene individually, one from each parent:

Aa
Bb
Cc
Dd

If each different gene were a different variant, we would, by the
inexorable loss of variation I described, end up with all A, or all a,
or all B...... etc etc. Each ancestral gene has an exactly equal chance
of becoming the 'norm', and the other 7 will go. The existence of
variants is thus evidence of the historic action of mutation in
*opposition* to the tendency to homogenize.

Lets then take a theoretical future homogeneous population resulting
from this effect - all A, say.

A neutral mutation arises , A*. It too has an exactly equal chance of
becoming the 'norm' further down the line. So 1 in 8 random neutral
mutations will become 'fixed' - the population becomes all A*.

Then from that position, 1 in 8 times, a further mutation, A**, becomes
fixed..... How does a population manage to stay the same against this
backdrop of mutation and elimination of 'competing' variation?

And this is without any natural selection. Stick that in the picture
and we have a means by which a mutational change can buck the stats. It
no longer has to make do with an equal chance. Selection can work both
ways, of course. Good ideas get a bunk up. But equally, bad ones get
their chance knocked below equality - a preservative force, against
change but also against deterioration. (And, this slightly ups the
chances for the other variants that are 'better').

Multiply this argument up over the whole genome, factor in the
continual variation of the fitness 'landscape' due to external
factors, and you may (I hope) see that the combination of mutation,
statistical factors and selection renders stasis highly unlikely. Or at
the least, get some flavour why people who work in this field don't
seem to share your misgivings.


The problem with this scenario is that it doesn't work! Dog breeders
have been using artificial selection for hundreds of years now and have
never come up with anything that can be called a new species.



Try getting a Great Dane and a Chiwawah to breed.


Are you suggesting they are different species?



The most intense experiments were done with Drosophila and nothing
viable came of their efforts - certainly nothing that resembled a new
species. After thousands and thousands of generations, with intense
mutation inducers, all they came up with were - Drosophila.


Except where they have, of course.
http://www.pnas.org/cgi/content/abstract/101/33/12232



"We suggest that duplicated genes that have yet to evolve a stable function at the time of speciation may be candidates for "speciation genes," which is broadly defined as genes that contribute to differential adaptation between species."

Notice the "may be". I see no real substance here.






"In the best-known organisms, like Drosophila, innumerable mutants are
known. If we were able to combine a thousand or more of such mutants in
a single individual, this still would have no resemblance whatsoever to
any type known as a [new] species in nature." Richard B. Goldschmidt,
"Evolution, As Viewed by One Geneticist," American Scientist, January
1952, p. 94.


Wow! A reference from 54 years ago!
Of course, no work has been done in the field of genetics since then.
Or has it?


"Most mutants which arise in any organism are more or less
disadvantageous to their possessors. The classical mutants obtained in
Drosophila usually show deterioration, breakdown, or disappearance of
some organs. Mutants are known which diminish the quantity or destroy
the pigment in the eyes, and in the body reduce the wings, eyes,
bristles, legs. Many mutants are, in fact lethal to their possessors.
Mutants which equal the normal fly in vigor are a minority, and mutants
that would make a major improvement of the normal organization in the
normal environments are unknown." Theodosius Dobzhansky, Evolution,
Genetics, and Man (1955), p. 105.


Getting closer. This is only 51 years old. Hell, I was born by then!

Evidently they weren't aware of the paper published in 2004 which
showed them wrong.
How silly of them.

Mind you, perhaps it's this other 2004 paper they didn't know about:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15304653&dopt=Citation


Same as above paper?


Or this 2001 paper:
http://www.pnas.org/cgi/content/abstract/98/23/13195


"Substantial genetic differentiation, as great as among species, exists between populations of Drosophila melanogaster inhabiting opposite slopes of a small canyon. Previous work has shown that prezygotic sexual isolation and numerous differences in stress-related phenotypes have evolved between D. melanogaster populations in "Evolution Canyon," Israel, in which slopes 100-400 m apart differ dramatically in aridity, solar radiation, and associated vegetation. Because the canyon's width is well within flies' dispersal capabilities, we examined genetic changes associated with local adaptation and incipient speciation in the absence of geographical isolation. Here we report remarkable genetic differentiation of microsatellites and divergence in the regulatory region of hsp70Ba which encodes the major inducible heat shock protein of Drosophila, in the two populations. Additionally, an analysis of microsatellites suggests a limited exchange of migrants and lack of recent population bottlenecks. We hypothesize that adaptation to the contrasting microclimates overwhelms gene flow and is responsible for the genetic and phenotypic divergence between the populations."

I noticed no mention of any attempts to breed the two "species" to see if their resultant offspring would be fertile. Which brings me to this: what definition of "species" are they using? Is it the broad definition of "differences", or is it the classic definition of "able to produce fertile offspring"?


Or this 1993 paper:
http://links.jstor.org/sici?sici=0014-3820(199304)47%3A2%3C432%3AFSIDPA%3E2.0.CO%3B2-L


Could not access this one.


Or even this 1982 paper:
http://links.jstor.org/sici?sici=0014-3820(198201)36%3A1%3C132%3AMEFISI%3E2.0.CO%3B2-1


Or this one either.


Or this 1995 paper:
http://www.pnas.org/cgi/content/abstract/92/7/2519


"It is generally believed that Drosophila melanogaster has no closely related species with which it can produce the viable and fertile hybrids that are essential for the genetic analysis of speciation. Following the recent report of molecular differentiation between a Zimbabwe, Africa, population and two United States populations, we provide evidence that strong sexual isolation exists between the D. melanogaster population in Zimbabwe and populations of other continents. In the presence of males of their own kind, females from most isofemale lines of Zimbabwe would not mate with males from elsewhere; the reciprocal mating is also significantly reduced, but to a lesser degree. The genes for sexual behaviors are apparently polymorphic in Zimbabwe and postmating reproductive isolation between this and other populations has not yet evolved. Whole chromosome substitutions indicate significant genetic contributions to male mating success by both major autosomes, whereas the X chromosome effect is too weak to measure. In addition, the relative mating success between hybrid and pure line males supports the interpretation of strong female choice. These observations suggest that we are seeing the early stages of speciation in this group and that it is driven by sexual selection. The genetic and molecular tractability of D. melanogaster offers great promise for the detailed analysis of this apparent case of incipient speciation."

Note "would not mate" is not "can not mate" or more importantly "cannot produce fertile offspring" - hence the conclusion that this might be "the early stages of speciation", rather than real speciation. These are real desperate attempts to find speciation IMO.


Or this 2001 paper:
http://www.mamb.ru/lib/lib_ru/scienc11.pdf

"The power of sexual selection to drive changes in mate recognition traits gives it the potential to be a potent force in speciation. Much of the evidence to support this possibility comes from comparative studies that examine differences in the number of species between clades that apparently differ in the intensity of sexual selection.We argue that more detailed studies are needed, examining extinction rates and other sources of variation in species richness. Typically, investigations of extant natural populations have been too indirect to convincingly conclude speciation by sexual selection. Recent empirical work, however, is beginning to take a more direct approach and rule
out confounding variables."

Still no real speciation - only "the potential to be a potent force in speciation". Not the same thing. Again, grasping at straws IMO.



Or this 1980 paper:
http://links.jstor.org/sici?sici=0014-3820(198007)34%3A4%3C730%3AAMGIOS%3E2.0.CO%3B2-J


I cannot access any of these "jstor" links.


Or this 2002 paper:
http://mbe.oxfordjournals.org/cgi/content/abstract/19/4/472


"The divergence of Drosophila pseudoobscura from its close relatives, D. persimilis and D. pseudoobscura bogotana, was examined using the pattern of DNA sequence variation in a common set of 50 inbred lines at 11 loci from diverse locations in the genome. Drosophila pseudoobscura and D. persimilis show a marked excess of low-frequency variation across loci, consistent with a model of recent population expansion in both species. The different loci vary considerably, both in polymorphism levels and in the levels of polymorphisms that are shared by different species pairs. A major question we address is whether these patterns of shared variation are best explained by gene flow or by persistence since common ancestry. A new test of gene flow, based on patterns of linkage disequilibrium, is developed. The results from these, and other tests, support a model in which D. pseudoobscura and D. persimilis have exchanged genes at some loci. However, the pattern of variation suggests that most gene flow, although occurring after speciation began, was not recent. There is less evidence of gene flow between D. pseudoobscura and D. p. bogotana. The results are compared with recent work on the genomic locations of genes that contribute to reproductive isolation between D. pseudoobscura and D. persimilis. We show that there is a good correspondence between the genomic regions associated with reproductive isolation and the regions that show little or no evidence of gene flow."

This is an attempt to guess at past events and not an empirical test of speciation.


Or this 1993 paper:
http://links.jstor.org/sici?sici=0014-3820%28199312%2947%3A6%3C1637%3ALEOSWH%3E2.0.CO%3B2-T&size=LARGE


Again...

Or this 2004 paper:
http://evol.allenpress.com/evolonline/?request=get-abstract&issn=0014-3820&volume=058&issue=08&page=1856



"Recent studies suggest that chromosomal rearrangements play a significant role in speciation by preventing recombination and maintaining species persistence despite interspecies gene flow. Factors conferring adaptation or reproductive isolation are maintained in rearranged regions in the face of hybridization, while such factors are eliminated from collinear regions. As a direct test of this rearrangement model, we evaluated the genetic basis of hybrid male sterility in a sympatric species pair, Drosophila pseudoobscura pseudoobscura and D. persimilis, and an allopatric species pair, D. pseudoobscura bogotana and D. persimilis. Our results are consistent with the proposed model: virtually all of the sterility factors in the former pair are associated with three inverted regions, whereas sterility factors are present in the collinear regions in the latter pair. These findings indicate recombination and selection may have eliminated sterility factors outside the inverted regions between D. p. pseudoobscura and D. persimilis, suggesting chromosomal rearrangements may facilitate species persistence despite hybridization."

What does this mean: "by preventing recombination and maintaining species persistence despite interspecies gene flow"?
How is "interspecies gene flow" possible?


Gee! How stupid of them not to know what was going happen in the next
half-century of genetic research!

Silly scientists!


I see nothing in the above papers that contradicts the findings of these "old" scientists. You may read more into the newer findings than I do however.



"The clear-cut mutants of Drosophila, with which so much of the
classical research in genetics were done, are almost without exception
inferior to wild-type flies in viability, fertility,
longevity."-*Theodosius Dobzhansky, Heredity and the Nature of Man
(1964), p. 126.



Getting closer: this one is only 42 years old.


"Out of 400 mutations that have been provided by Drosophila
melanogaster, there is not one that can be called a new species. It does
not seem, therefore, that the central problem of evolution can be solved
by mutations."-*Maurice Caullery, Genetics and Heredity (1964), p. 119.



Still 42 years old


"The decisive step in evolution, the first step toward macroevolution,
the step from one species to another, requires another evolutionary
method than that of sheer accumulation of micromutations. "
-- Richard B. Goldschmidt
GOLDSCHMIDT, R.B. (1940) The Material Basis of Evolution. Yale
University Press, New Haven.




Oh dear! You've slipped: this is 65 years old.


"We have long been seeking a different kind of evolutionary process and
have now found one; namely, the change within the pattern of the
chromosomes. ... The neo-Darwinian theory of the geneticists is no
longer tenable. "
-- Richard B. Goldschmidt
GOLDSCHMIDT, R.B. (1940) The Material Basis of Evolution. Yale
University Press, New Haven.


As is this one

--
"Are we to believe that mere chance can accomplish that which has proven
quite impossible for the enlightened scientist to achieve? I regard
that notion as absurd!" John A. Davison, Ph.D. - AN EVOLUTIONARY
MANIFESTO: A NEW HYPOTHESIS FOR ORGANIC CHANGE
http://www.uvm.edu/~jdavison/davison-manifesto.html


Well bully for John A. Davison.
What a pity that this is simply an argument from incredulity.

Such an argument has no place in science.

Creationism couldn't exist without such arguments.


Have you read his manifesto? If not, then read first and make derogatory comments afterward please.


--
"Are we to believe that mere chance can accomplish that which has proven quite impossible for the enlightened scientist to achieve? I regard that notion as absurd!" John A. Davison, Ph.D. - AN EVOLUTIONARY MANIFESTO: A NEW HYPOTHESIS FOR ORGANIC CHANGE
http://www.uvm.edu/~jdavison/davison-manifesto.html

.

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