Richard Harter's demolition of modern synthesis

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z@z

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Jul 25, 1999, 3:00:00 AM7/25/99
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Richard Harter's ORIGINAL DEMOLITION [1]:

| ... However he is pointing at a fundamental problem with the
| modern synthesis. Basically, it is broken. The gist of the matter is
| that there aren't enough genes.
|
| The conflict which the synthesis purportedly resolved was a dispute
| between the naturalists and the population geneticists as to the nature
| of heredity as to whether it was soft or hard, i.e., whether variation
| was continuous or discrete. The compromise was effected by the
| observation that soft inheritance (continuous variation) is emulated by
| hard inheritance (discrete variation) if a trait is the cumulative
| result of a number of genes.
|
| Continuous variation (or emulation thereof) is necessary for the
| Darwinian model of natural selection which supposes a process of the
| accumulation of small advantages. It is, moreover, that which is
| observed for many traits.
|
| The catch is that there aren't enough genes. The human genome has
| approximately 70,000 genes. If genes are to determine traits
| quasi-continuously it will take 10-20 genes to control one trait which
| means that the number of traits controlled by the genome is on the order
| of 5,000 traits OR LESS.
|
| The observation that genes affect many traits and vice versa is not
| cogent; the issue is one of degrees of freedom. Likewise appeals to
| self-organization are not to the point; self-organization can elaborate
| the effects of genes but the variation must be supplied by the genome.
|
| It is relevant to point out that a gene on average consists of a
| thousand base pairs, thereby supplying many bits of information.
| However most of this supply of information is a mirage. The vast bulk
| of a protein is devoted to folding up into the right shape. The region
| of interest is the hot spot which only consists of a handful of amino
| acids. It should also be noted that a fair percentage of the genome is
| devoted to house-keeping machinery for the eukaryote cell.
|
| The problem then is that a few thousand (or less) evolvable traits is
| not enough to account for the evolution of the morphology of human
| beings and our fellow vertebrates. It does seem to be true that the
| synthesis accounts for the evolution of bacteria (and presumably the
| monera) - the number of traits to be governed is much smaller and the
| effects of the genome are strictly localized. However the synthesis was
| developed to account for the evolution of the metazoa and the metaphyta*
| in terms of population genetics and this, manifestly, is what it does
| not do.

* was 'phytozoa' in the original post (corrected in [2])

Reply of PZ Myers [3]:

| Oops. Can I offer a few ways out of this little 'enigma' you've proposed,
| that there aren't enough genes to account for all the supposed traits
| organisms express?
|
| 1. The combinatorial argument. N genes don't code for just N traits, they
| can code for 2^N traits. That is, one gene allows for 2 possible cell
| states, 2 allow for 4 states, 3 allow for 8, etc.

Chris Ho-Stuart objects [4]:

| No so. Traits are not states; and one organism can have a number of
| distinct traits. If (simplifying enormously) traits are either present
| or absent; and are independent, and if genes are binary as you suggest
| then N genes can code for N traits.

| 2. The regulatory argument. What's critical in defining a cell is its
| regulatory state -- and any one gene may have a large number of regulatory
| sites. (OK, it's a variant of #1...)

Richard Harter objects [5]:

| This doesn't work, essentially for the reason that Chris points out.

| 3. The development argument. Genes aren't adequate to specify an organism--
| there are also significant influences from the cytoplasm and the environment,
| and each cell has an independent history that influences gene expression.

Richard Harter objects [5]:

| This also doesn't work although the issues are subtler. The problem is
| that development is not heritable. Consider a parent organism creating
| an egg. The parent not only passes on a genotype, it also passes on an
| environment in which the child organism will develop. Fine, this
| apparently is information that is not in the child's genotype.
| Consider, however, what happens when the child in turn creates an egg.
| It must supply the same developmental environment to its offspring. Now
| where does that information come from? There are two possibilities.
| One, which is actually the case, is that the information is encoded in
| the genome. (I.e., a mother inherits genes from her mother that
| "describe" how to create the eggs environment. There is some
| interesting genetics there.) The other, which is not the case, is that
| it has recorded somehow the information about the environment given it
| and sets up the same environment for its offspring. The latter
| possibility, if it were to occur, would be a form of direct Lamarckian
| inheritance.
|
| Your "solution" does apply to the reproduction of cells. That is, when
| a cell divides, the two daughter cells do inherit the system state of
| the parent. It does not apply to the case of reproduction of metazoa.
| Plants are a bit messier.

| What it amounts to is that your argument was a rather more subtle and cleverer-
| than-usual variation of the creationist demand that we show "fin genes" that
| get turned into "arm genes". You were making an unrealistic assumption that
| there is some kind of simple one-to-one mapping of genes to discrete
| morphological traits, and there isn't one. There is no "arm gene". ...

Richard Harter objects [5]:

| No, I am not making that assumption and I pointed out that I am not
| making that assumption. It is given that there is a messy map from the
| genotype to the phenotype (and even that the phenotype is a function of
| the environment as well.) The key is the number of degrees of freedom,
| i.e., the dimensionality of the two spaces. If there are N dimensions
| in gene space they can determine at most N dimensions in trait space.
| This is not changed by the messiness of the mapping.

| Does this spell trouble for the "change in allele frequencies" mantra? Sort of,
| I think. Ultimately, it's all going to come down to some messy molecular
| biology, but for now there is more complicated stuff going on than we can
| understand. Look at beak size in those finches, for instance -- it's variation
| that can be quantified with a few simple parameters, but all the underlying
| biology is a total mystery. How is shape and size of a beak specified? I
| doubt that there is a "beak gene" anywhere in the bird. There are genes that
| somehow specify growth rates in certain bones, genes that define adhesivity
| in migrating tissues, genes that allocate cells to certain fates. You can
| measure beak length, but there are a thousand sneaky changes beneath that
| that you don't see at all -- and who knows which one is the genuinely
| significant one that selection sees.

Richard Harter objects [5]:

| Even so. The biology isn't a total mystery, of course. The biologist
| chappies have been making progress in untangling this tangled web but
| there is very much more unknown than is known.
|
| As far as I can tell, the modern synthesis as originally formulated is
| broken. Darwinian natural selection was invoked as a mechanism to
| explain the evolution of the phenotype. At the level of the organism it
| really doesn't matter what the sources of variation are; natural
| selection (and other factors) operates on the heritable variations in
| the phenotype. Likewise the formulas of population genetics work where
| they can be seen to be applicable (principally in bacteria populations).
| The marriage between the two is very much a shotgun wedding and it does
| seem that the bride was never pregnant by the groom.
|
| That said, the issue of "not enough genes" is not resolvable by an
| annulment. The resolution may be that the number of traits (the
| dimensionality of trait space) is much smaller than we assume.

[1] http://www.deja.com/=dnc/getdoc.xp?AN=504215969
[2] http://www.deja.com/=dnc/getdoc.xp?AN=504236234
[3] http://www.deja.com/=dnc/getdoc.xp?AN=504246163
[4] http://www.deja.com/=dnc/getdoc.xp?AN=504270443
[5] http://www.deja.com/=dnc/getdoc.xp?AN=504303417


Wolfgang Gottfried G.


The most scientific alternative to the modern synthesis:
http://members.lol.li/twostone/E/psychon.html

scientific = having a concise and transparent conceptual basis and
a strong predictive power

PZ Myers

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Jul 26, 1999, 3:00:00 AM7/26/99
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In article <7nfphv$35d$1...@pollux.ip-plus.net>, "z@z" <z...@z.lol.li> wrote:

>Richard Harter's ORIGINAL DEMOLITION [1]:
>

[snip]

>
>The most scientific alternative to the modern synthesis:
>http://members.lol.li/twostone/E/psychon.html
>
>scientific = having a concise and transparent conceptual basis and
> a strong predictive power

Yikes. With all respect to Harter, I don't think it is quite right to
claim that he has personally demolished the modern synthesis -- I think
it is pretty well agreed upon by lots of people that it is incomplete, to
say the least. It's also rather strange to try and imply some serious
problem by citing a few people disagreeing about something on a usenet
newsgroup...Harter, Ho-Stuart, and I probably agree on many more things
about evolution than we disagree on, and I suspect that one of those points
of concordance is that your "psychon theory" is an extraordinarily silly
bit of lunacy.

Even if he had 'demolished' the synthesis, it wouldn't add a scrap of
support to your goofy ideas. And if I had demolished his demolition with
my argument, it wasn't in support of some dogmatic status quo.

--
PZ Myers


Bwana

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Jul 27, 1999, 3:00:00 AM7/27/99
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<one HELL of a SNIP>

> | That said, the issue of "not enough genes" is not resolvable by an
> | annulment. The resolution may be that the number of traits (the
> | dimensionality of trait space) is much smaller than we assume.

Maybe that information contained is not even directly accessible. It may be
stored in an encrypted format (or compressed, which may be the same thing).

Bwana


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