Re: Propping up the theory of Evolution

On Fri, 4 Jul 2008 06:53:10 -0700 (PDT), hersheyh
<hersheyhv@xxxxxxxxx> wrote:

On Jul 4, 12:57 am, rick_so...@xxxxxxxxxxx wrote:
On Jul 4, 5:36 am, hersheyh <hershe...@xxxxxxxxx> wrote:



On Jul 3, 11:05 pm, rick_so...@xxxxxxxxxxx wrote:

The amount of genomic difference between chimps and humans is about
what one would expect *if* the entire difference were due to fixation
of selectively neutral traits (in the 97% of our genomes that is
relatively sequence-irrelevant).  Actually, the amount of difference
is a little less than that expectation.  That is because of
selection.  Most selection is selection *against* change.  The number
of sites that differ between chimp and human that can be clearly
identified as having a selective pressure *for* change can be numbered
to be in the range of 50 or so sites (none a protein coding region).

What is 97% of 2 billion if there are 2 billion bits of information in
a strand of DNA?

The haploid human genome is about 3 billion nucleotides long, not 2
billion.  Meaning that us diploids have twice that number.  And the
DNA is not in a single strand, but divided into 23 chromosomes in the
haploid genome (that's 23 pairs, or 46, in the diploid).

Thats 40 million bits of information.

97% of 2 billion is not 40 million by any math I am aware of.  That
97% is a rough estimate of the amount of DNA that has no effective
sequence constraint because it does not code for proteins (or some
regulatory sequences).  So 3% would be the measure of the 'bits' that
have some constraint.  3% of *3* billion is about 90 million
nucleotides.  Since this is the part under some sequence constraint
only because it encodes protein, even this part is not under severe
constraint, because much of protein sequence can change without undue
consequence.

We are not like monkeys, and
whoever wrote that 40 million bits of code would tell you that nature
by itself, cannot write a 40 million bit meaningful essay by random
chance, by merely producing random characters, as you would suggest.

The part that is under strong constraint is almost identical in humans
and chimps.  Typical human and chimp homologs of proteins differ in
only an average of two amino acids. About 30 percent of all human
proteins are identical in sequence to the corresponding chimp
protein.  No one wrote the DNA; it was passed on from parent to child
in both lineages from a nearly identical sequence in the last common
ancestor.  The relative *lack* of difference in coding regions even
compared to the small total difference (almost all selectively
neutral, meaning that it is without functional effect) is due to the
conservative nature of selection.

If you are suggesting that you still believe in garbage DNA well thats
not what recent studies suggest. There is no junk DNA. It is just that
people do not know what it is used for.

First, I did not call it "junk" or "garbage" DNA. I said it was DNA
in which sequence was more-or-less irrelevant and thus sequence which
can change so much as to be essentially unconserved. [Even protein-
coding regions can change in a neutral or near neutral fashion, both
because it is a fact that only a small fraction of amino acids are
invariant (typically at the active sites) when you look at the same
functional protein across species, and because of the degeneracy of
the genetic code. And that is without looking at introns. In fact,
in organisms which have the longest time since a common ancestor (e.g,
E. coli and human) the change in protein (and hence DNA) sequence is
so great that one can only identify that they were derived by common
descent because the protein with that function has the same 3-D
*shape* (protein function is determined by shape and a few specific
aa's).

I am fully aware that enhancers and other regulatory regions are
*embedded* within these non-coding regions. Which is why I used the
value of 3% rather 1.5% (1.5% is the fraction of the human genome
*actually* involved in coding protein sequences). Enhancers and other
regulatory elements are typically small stretches of sequence since
they have to interact with proteins and microRNAs and other small
elements. Moreover, there is actual experimental (remove a sequence
and see if there is any effect) and field (mutations that delete large
chunks of non-coding DNA exist in nature) evidence that much of the
DNA present in vertebrates is dispensible and, if it did have a
purpose at one time, no longer does. Certainly the fugu's (like the
Danio, a fish) relatively parsimonious genome which discards a large
fraction of this non-coding DNA is evidence that much of it is
dispensible.

http://www.fugu-sg.org/
http://genome.jgi-psf.org/Takru4/Takru4.home.html

Although far too technical for you, the following, which discusses the
important role of duplication (and subfunctionalization) in evolution
is a relatively important idea that has made use of the small (1/8 the
size of humans, but with roughly the same number of coding sequences)
fugu genome.

http://genomebiology.com/2007/8/4/R53

And that is also what the two articles you cite say. Apparently
reading with understanding is beyond your capabilities. Perhaps that
is because you lack sufficient background to comprehend them. Or
perhaps you thought I could not read them and understand what they
really said, even thought they are news articles (which sometimes do
get things wrong)?

http://www.eurekalert.org/pub_releases/2006-03/jhmi-jdm032306.php

In this article the authors specifically point out that the sequences
have changed so much they are unrecognizable.

"The notion that mutations in enhancers play a role in human disease
progression has been difficult to confirm because usually enhancers
are located in the 98 percent of the human genome that does not code
for protein, termed non-coding DNA. Unlike DNA sequences that code for
protein, non-coding DNA, sometimes referred to as "junk" DNA, follows
few rules for organization and sequence patterns and therefore is more
difficult to study."

"Traditionally, DNA sequences are thought to have to look similar to
function similarly; this is how scientists identify genes in other
species, a strategy best used for studying similar species. From an
evolutionary standpoint, the last common ancestor of human and
zebrafish lived more than 300 million years ago. Because DNA sequences
in each species have changed over time, traditional methods of
comparing DNA sequences between humans and zebrafish have failed to
identify any potential enhancers around the RET gene because the DNA
sequences differ too much."

IOW, the regulatory elements either are or are embedded in sequences
that are sequence-indifferent. This is either because the regulatory
elements are themselves sequence-indifferent, the regulatory elements
are small and embedded within sequence that has no role, have co-
evolved with the binding or interacting material to the point of not
being identifiable, or some combination of the three. [My bet is that
smallness is the major reason.]

http://www.eurekalert.org/pub_releases/2007-04/sumc-dn041907.php

In this paper, the authors explicitly state that most transposons do
not produce a useful function and that *most* simply become
pseudogenes of no function. IOW, chance mutation by transposition
produces all kinds of variants and *selection* then retains only those
or the specific parts of those that, by chance, have some added
utility. Whatever that is, it is not the way that "intelligent
design" works.

"The 10,402 sequences studied by Bejerano, along with David Haussler,
PhD, professor of biomolecular engineering at UC-Santa Cruz, are
remnants of unusual DNA pieces called transposons that duplicate
themselves and hop around the genome. "We used to think they were
mostly messing things up. Here is a case where they are actually
useful," Bejerano said.
He suspects that when a transposon is plopped down in a region
where it wasn't needed, it slowly accumulated mutations until it no
longer resembled its original sequence. The genome is littered with
these decaying transposons. When a transposon dropped into a location
where it was useful, however, it held on to much of the original
sequence, making it possible for Bejerano to pick out."

Rick is completely incapable of understanding your exposition so I
must assume that you write it mainly for people like me who really do
appreciate the education.


.

Relevant Pages