Re: Is the complexity of evolutionary change explainable?

hrvoje-d wrote:

*** the big answer :) part 1 ***

I've seen many posts that are saying that I am not competent in the
area of genetics and those that are questioning that the alhorithm is
an analogy to nature. Here I'll try to explain it, not strictly
mathematically but so it can be seen that the analogy is good enough
for the conclusions I wrote.

First of all: literature.

I think that we can agree that the major publication on genetics which
includes microevolution should explain (at least roughly) how the
mutation rate that is determined by research can be responsible for
changes in the complexity between species.

I came across a great, brilliant book (600 pages) that is the
literature for students at universities for studing genetics. That is
"Robert H. Tamarin: Principles of Genetics, sixth edition, McGraww-Hill
1999). In that book there is the chapter "Evolution and Speciation" in
the pat 4: "Quantitative and Evolutionary Genetics". I read that
chapter thorouly AND UNDERSTOOD IT. And does it put the mutation rate
in perspective in the fashion "to change the shape of the hand roughly
x changes in y genes are required, considering the determined mutation
rate of 10^-8 and the population of z with migration etc. : NOT AT ALL.

Of course not. One chapter in a genetics textbook is not the answer to
your questions. People are talking about the primary literature here. A
genetics text is the wrong place to look for population genetics,
anyway. There are population genetics texts, but more than that, there
is a huge body of work contained in scientific journals. And that's what
you need to be looking for.

Finding the answer to your specific question about what changes the
shape of a hand is a major research program that we have just begun --
the term is evolutionary developmental genetics, or evo-devo. Most work
these days is on more basic features of organisms that arise much
earlier in development than hand shape, but there is progress being
made. And of course we need to know the genes and mutations involved
before the second part of your question can be answered for that
specific set of genes.

More generally, the question is whether current mutation rates can
account for differences between species. That much is obvious; yes, they
can. Most of those differences, however, don't affect the phenotype.

In general, you will need to refine your question before it can be dealt
with scientifically.

Here is the summary:

First it's saying about some basic ideas of the evolutionary theory.
Then it's discussing about Mechanisms of cladogenesis: reproductive
isolation an allopatric, parapatric and sympatic speciation. Theese are
all discussions on a macro-scale and are not about the bond between the
genome that is coding the characteristrics. Then comes another
macro-scale discussion about phyletic gradualism versus punctuated
equilibrium. Then there is a subchapter "genetic variation". Here it's
saying about: maintaining polymorphysms; heterozygote advantage,
heterozygote advantage, frequency dependant selection; maintaining many
polymorphysms, multilocus selection models and Kimura's hypotesis of
neutral alleles. ALL THOSE DISCUSSIONS are dealing with perserving the
diversity in the genome, NOT CREATING IT: what kind of selection should
exsist not to destroy the diversity of alleles (genes on the homolog
chromosomes); whether to select one gene (or a group of them) based on
it's fitness or, because this leads to the decline in diversity, all
genes should be considered neutral (Kimura). Then it's saying about
effect of genetic drift and migration on that diversity (again, all
traits exsist in the genome) Computer models of theese problems are
included. Mutation is considered as follows: "probability of dominant
alleles mutating to recessive and vice versa" Hey! How can they mutate
in such a complex way? One gene contains 300 nucleotides on avarage,
and the mutation rate is 10^-8!

No, one gene contains hundreds of thousands of nucleotides on the
average, if we're talking about eukaryote genomes. But most of those are
in introns. But let's go with your figures. If the mutation rate is
10^-8/nucleotide/generation, and the population size is a conservative
10^4, then the probability that some mutation will occur in that
300-base gene somewhere in the population in this generation is around
3%. In order to make an allele recessive, the most common way is to make
it non-functional. There are many mutations that would do this. Without
knowing the protein involved we can't come up with a good estimate of
the proportion, but I would bet it's likely to be at least 10% of them.
So the chance of a mutation to a recessive allele in this population is
around 0.3% per generation. Sounds likely enough to me.

It's not saying about that probability
in nature, just assuming the numbers for calculating the conditions of
equilibrium (balance) for example.

Then finally I thought I will find the mutation rate put in the
perspective in the chapter "DNA variation" but NO. There it's only
saying about the differences measured between species, and determining
the rate of changes in the genome. NOT MENTIONING HOW this changes
could occur with the mutation rate that is determined in nature!

As it happens, it fits just fine. Since most mutations are neutral, the
mutation rate (in individuals) should equal the substitution rate (in
the population). The number of differences between humans and chimps,
for example, is 35 million. If we suppose a separation of about 5
million years, with half the changes in each lineage for a total of 10
million years worth of evolution, and a genome of 3 billion bases, we
get a mutation rate of (3.5 x 10^7) / (3 x 10^9) / 10^7 per year, or
about 10^-9 per year. If a generation is 25 years, this is about 2 x
10^-8 per generation, or about the number you cited. Of course very few
of these mutations have any effect on phenotype.

Ok, I said, I'll find it elsewhere, on the Internet, but no! But on
http://evolution.berkeley .edu I did find under "Big issues"
(unsolved): "How does evolution produce new and complex features?"

http://evolution.berkeley.edu/evosite/evo101/VIIBigissues.shtml

It is not explained as I can see - not even roughly.

It's a question too big to be explained in one paragraph. We know some
things about the process and not others. Be more specific.

.

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