Re: Darwin, NeoDarwinian Taboos, and the Explanation of Evolution

On Nov 30, 12:43=A0am, CNCa...@xxxxxxx wrote:

In relation to the first NeoDarwinian tenet, Charles Darwin believed
that changes in the environment induce inherited changes in living
beings and these changes are not always random but may be directed:
He started to believe there was an acquired variation mechanism
in evolution. He didn't believe it at first, but a lot of biologists
gave him data that we now recognized was wrong. He even wrote a book
about the "pangenes" necessary to transmit an acquired characteristic.
However, he stated again and again that the "acquired characteristic"
type variation was usually a minor part of evolution. Although he
thought it could exaggerate a characteristic already in existence, he
realized that it couldn't create a characteristic that wasn't there to
begin with. Only a mutation random with respect to its function can
create a new characteristic.
This is what is missing from your description. Random doesn't mean
without cause. The random that he was talking about is the randomness
that comes with application.
A giraffe may stretch its neck, cause stress on it body, and
generate adrenaline which does something nasty to it gametes that
causes a mutation. Stress, whatever causes it, may cause a dysfunction
that causes a mutation. Thus, one can't say that the mutation doesn't
have something to do with the giraffe stretching its neck. However,
the form of the mutation may have nothing to do with the neck.
I'll make my point another way by now stating something that may
sound contradictory. On the genetic level, not the individual level,
all mutations are acquired characteristics. If the DNA sequence of a
gene is changed, then all descendents of the gene will carry the same
change. On a purely gene centric level, ALL variation is acquired
directly from the environment. In a sense, Lamarkian evolution applies
to individual genes. However, the phenotype of the individual is
separate from the genes. The mutation of the gene has nothing to do
with how the gene is expresed in the individual. Therefore, the rate
of occurrence of any mutation has nothing to do with the survival
value of that mutation.
The trisomy that causes Down's syndrome is pretty much a lethal
gene. However, it is one of the most common mutations there is. It is
really caused by assymmetric meiosis, and hence is a form of
assymmetric recombination. One cell gets two copies of the same
chromosome.
Down's syndrome may be caused by environmental factors, but it is
still a random mutation. Its frequency has nothing to do with the
utility of the mutation it self. Its frequency has nothing to do with
the amount of reading done by the parents. The parents can be PhD
physicists and with minors in history and still get a child with
Down's syndrome. The parents can be illiterate and too lazy to work,
and still have a child with Down's syndrome. The probability of
mutation has nothing to do with the activity of the parent. And once
the mutation occurs, the chances are high (not 100%) that their
children will have it. Whatever gamete gets that extra chromosome
carries Down's syndrome. Whether the Down's syndrome victim has
children is a matter of natural selection. The selection is not
random. But the mutation certainly is.

=3D93Changed conditions generally induce mere fluctuating variability, bu=
t
sometimes they cause direct and definite effects.=3D94 (The Origin, 1872,
p. 131)
The variability may fluctuate, but the type of variation does not
correlate with conditions. If you expose an organism to small amounts
of nuclear radiation, one may get a type of mutation called a knock-
out mutation. A gene may be destroyed by the radiation. However, the
mutation doesn't automatically protect the organism from nuclear
radiation. Knock-out mutations, especially when a HOX gene is knocked
out, results in bizarre forms. Almost always they are lethal, although
sometimes they don't express themselves at all. The larva can have an
eye where the leg is supposed to be, or something else. It may not
express itself at all, because it is recessive.
Never the less, the fact that it was caused by nuclear radiation
doesn't mean the expression of the gene has anything to do with
nuclear radiation. There is a small probability it may help against
radiation, and a small probability it may make the juvenile more
sensitive to nuclear radiation. However, there is no correlation
between the cause of the mutation and the form the mutation takes.
Yes, modern science has found exceptions where Darwin and
contempories were a little bit right. There are special cases where
the organism can induce a certain change in the DNA sequence of the
child. In biolgoy, every rule has a few exceptions. However, it is
safe to say that the mjority of variation is random WITH RESPECT TO
THE CONDITIONS THAT CAUSED IT.
Cold weather does not induce a change in genetic sequence that
results in warmer coats. Maybe the hormone balance in the mothers womb
induces a gene to express itself with warmer coats. That is sort of
stretching Lamarkian evolution a bit. However, if you want to force
the definition you can do so. To a large degree, the change in genetic
sequence produces a change in phenotype with no correlation to the
cause of the change. Cold weather usually does not result in warmer
coats. It can be better or worse eyes, it can be a change in milk
production, it can be a cancer. But the phenotype will usually not be
better suited to cold weather. This remains a rule that to a very
large extent is true. Evolution is caused by random mutations to a
very large degree.

In relation to the second NeoDarwinian tenet that use and disuse of
organs have no influence on the evolution of living beings because
they do not induce corresponding changes in genes, Darwin=3D92s stance ha=
s
been diametrically opposite.
This time you are taking Darwin out of context. Darwin in "Origin
of the Species" says that unused traites tend to vary with time.
Unused traits are not subject to natural selection because they aren't
used. So random mutations that effect these traits tend to accumulate.
Thus, an unused trait is more likely to show large variation that
other more used traits. Random mutations will make different versions
of the unused trait. However, sometimes some variation will make the
trait useful for some other function than it was originally used. So
vestigial organs aren't likely to dissappear entirely. They may come
back with a different function. Or morph into many neutral forms. Wide
variation is the mark of an unused feature. Dissppearance is very
rare.
Yes, he mentions some traits he thinks disappeared due to lack of
use. Again, he adopted the acquired characteristic fallacy in later
editions of "Origin." However, these were exceptions. In fact, traits
don't dissppear cmpletely unless they are dangerous in the new
environment. The eyes of cavefish probably dissappear because of the
prevalence of eye infections in caves. If a sensitive organ like the
eye can't be used, it becomes a liability. Why have an eye that
another fish can poke if there is not enough light to see? So the eye
dissappears. Without a disadvantage, a trait can last a long time.
Note that the gene itself of a vestigial trait can last forever.
If another gene suppresses the expression of that gene, it has no
advantage or disadvantage.
He believed and presented examples that use and disuse of organs can
lead to inherited enlargement or vestigialization and loss of
structures, even not necessarily with the aid of natural selection:
He was mostly wrong with these examples. However, he gave plenty
of examples where a random mutation caused a certain feature. He was
pretty much right with those.

=3D93There can be little doubt that use in our domestic animals
strengthens and enlarges certain parts, and disuse diminishes them;
and that such modifications are inherited.=3D94 (The Origin, 1859, p. 134=
)
He was wrong here. Breeding strengthens and enlarges certain
parts, not use. "Little doubt" has turned into "wrong."
For one of his better attempts, read the part about the breeding
of steers. He points out that the taste of steers is developed by
breeding the siblings of the steer, not the steer itself. Obviously,
use and disuse can not be important in this case. In this, Darwin was
right on.

and

=3D93Disuse, aided sometimes by natural selection, will often tend to
reduce an organ, when it has become useless by changed habits or under
changed conditions of life.=3D94 (The Origin 1859, p. 479)
The third neoDarwinain tenet, presently known as Dollo=3D92s law, posits
that a lost trait cannot reappear after long periods of time because,
in the absence of selection on genes responsible for the trait, over
time these genes will mutate to such an extent that would become
nonfunctional. This neoDarwinian tenet also is nonDarwinian. The
author of =3D93The Origin=3D94 has shown the contrary to be true and atte=
mpted
to explain why:

=3D93When a character which has been lost in a breed, reappears after a
great number of generations, the most probable hypothesis is not that
the offspring suddenly takes after an ancestor some hundred
generations distant, but that in each successive generation there has
been a tendency to reproduce the character in question, which at
least, under unklnown favourable conditions gains an ascendancy.=3D94 (Th=
e
Origin 1859, pp. 160-161)
This quotation of Darwin's has nothing to do with Dollo's Law.
Most people who read Darwin (myself included) immediately associate
this paragraph with recessive genes. Yes, a recessive gene can hide
itself for generations until it meets its equivalent partner in an
individual. Look up recessive and ominant. Yes, even some dominate
genes can hide until conditions are right for expression. Look up
plasticity. Traites do come back after generations. Darwin anticipated
Mendal with that regard.
Dollo's Law is something else. Dollo's Law has more to do with
what you mentioned earlier about traites separating. In recombination,
two genes close together on a chromosome can remain together a long
time. They may even become the defining characteristic of a species.
The two genes may one day be separated by crossover. It may be almost
impossible to bring those to genes back together. If this happens to a
number of genes, the descendents may wind up to be completely
different from the ancestor. The chances of breeding an ancestor look
alike is almost impossible. Thus, evolution doesn't go backward. This
has little to do with mutation and a lot to do with recombination.
Evolution doesn't reassemble old parts.
The classical example is the whale. The whale embryo has
phyrengial openings. In the whales fish ancestors, this these gaps
probably corresponded to gills. However, the whale is now using them
for other functions. The whale has jaws, and organs for making sound,
etc. So it never recreated gills. It just holds its breath.
I just read about electric eels. So I have to use this
fascinating creature as an example. An electric eel can't breath
underwater. Its ancestor probably had an open air bladder that acted
like a lung. All teolost fish have the remains of an air bladder
originally useful in respiration of gaseous air. Goldfish breath
gaseous air using their air bladdr. However, the electric eel now
lives in environments where the water contains little air. So it has
evolved vascularized cheeks to absorb air. It didn't redevelop its air
bladder by constant use. It developed a completely different type of
cheek to breath air. This was random mutation. If acquired
characteristics were routinely inherited, one would expect the air
bladder of the electric eel to again become functional as an air
absorber.

It is clear that neoDarwinians needed not simply to revise Darwin but
remove from his theory three fundamental tenets. This was done for a
good reason. In their effort to utilize the discovery of genes and the
gene theory they had to sacrifice at the altar of the neoDarwinism
three Darwinian tenets (changed conditions can directly and in a
definite way influence evolution of organic world, use and disuse of
organs can influence their evolution by enlarging and vestigializing/
losing them, respectively, and evolution is reversible).
Now, what is the epistemological status and the scientific validity of
the neoDarwinian theory, three quarters of a century after its first
appearance?
Yep, neoDarwinian theory is incomplete. The great synthesis is
still going on. What else is new?

Alfred Wallace, the co-author of the theory of natural
selection, observed that Darwin accepted the action of non-
selectionist factors and admitted that there are =3D93unknown causes at
work and that natural selection is the most important but not the
exclusive means of modification.=3D94 (A. Wallace, 1880 The Origin of
Species and Genera. Nineteenth =A0Century.http://www.wku.edu/~smithch/wal=
lac=3D
e/S322.htm).
Does the gene and the gene theory represents the causes of evolution
that Darwin did not know?
He definitely didn't have the knowledge we have about genes today.
However, I think he paid more attention to development. I think the
next Great Thing is the merging of gene theory and development.

A succinct validation of the neoDarwinian explanation of evolution
could be reduced to the answer one would give to the following
question:
Has the genecentric idea, i.e. the idea that the evolution of organic
world is ultimately determined by evolution of genes, found any
experimental or theoretical support?
Yes, a good part of evolution occurs at the gene level. However,
as I said before, ALL mutations are acquired characteristics at the
gene level. To really get a grip on evolution, we have to understand
the association between genes and the individual's development.
Without rushing to conclusions, a review of all the experimental and
theoretical work conducted during a century has failed to prove the
idea.
You are mixing up "proven with exceptions" with "disproven."
Great progress has been made showing how much of evolution is
associated with genes. I think current research is showing that other
things are important.
Look up the word "evolvability." There is a phenomenon where a
purely "gene centric" model is deficient. I think you will read a lot
about "evolvability" in the future. However, this still doesn't make
"gene centric" research wrong. Its just there is more to come.
We still have not a single experimental proof that the evolution
of a trait has been induced by the evolution of one or more genes.
This statement is nonsense. The differences between traits are
mediated by genes. Different traits have different traits associated
with them. There is ample evidence that changes in DNA sequence are
associated with evolution. Now, people are doing research on gene
networks. I think this is going to result in a far larger picture of
evolution.
To
the contrary, adequate experimental evidence shows that various
characters have evolved despite the fact that genes involved in the
development of these characters remained functionally unchanged.
The expression of these genes has changed a lot. The DNA sequence
in regulatory genes has changed a lot. Haven't you read about HOX
genes?
For
such examples read chapter 14, 15, 16, 17 of my recent book Epigenetic
Principles of Evolution or go tohttp://www.epigeneticscomesofage.com
Thanks for the link.

.

Loading