GENEALOGY-DNA-L Archives

Archiver > GENEALOGY-DNA > 2006-12 > 1166828193


From: "John McEwan" <>
Subject: Re: [DNA] Eye color, lactose intollerance, height,and many other traits...
Date: Sat, 23 Dec 2006 11:56:33 +1300
In-Reply-To: <001f01c725db$a70f45d0$6400a8c0@Ken1>


Dear Ken

You asked
.........
. All DNA has some function, it is just that some is much
> more critical than other bits.

How could you possibly know right now that all dna has some present
function?
.........

We know some things and we can infer some aspects as well.
1) As stated about 1% of mammalian DNA codes for proteins and is
typically highly conserved across species.
2) Around 7% tends to be conserved across closely related species
suggesting that this codes for functions that are consistent across
species
2) There is quite a bit of the total DNA (10-20%?) that is highly
repetitive and does not code for proteins that are on the ends or middle
of chromosomes (telomeres and centromeres) and are involved in a number
of processes, typically associated with cell replication. i.e. it has a
structural function and the repetitive sequence is conserved to some
extent across species. However, while a specific individual repeat may
be of little importance the structure as a whole is essential.
3) As has discussed on this list there is a weak DNA sequence signal
that guides where histones (DNA binding proteins) bind or do not bind.
This aids packing of the DNA. It has to be packed correctly and
appropriately so certain segments can be transcribed to RNA (including a
stupendous amount that never produces protein) or blocked from
transcription. This function can be disrupted by large scale insertions
or deletions and there are a number of well known instances of this
associated with inappropriate transposon insertion into less conserved
regions.
4) Some sequence may simply act to space the functional units at
appropriate physical and genetic distance from each other i.e. the
sequence is not important, but the physical separation is. Examples
include having the right spacing between segments of DNA that
transcription factors bind to so that there is the correct number of
turns in the DNA so the proteins can interact.
5) DNA regions on a larger scale are segmented into regions that differ
in composition of the bases present, these blocks have function and
influence the type and activity of the genes present in this larger
matrix.
6) recent evidence suggests that a very large fraction of the genome is
transcribed (i.e. it makes RNA) which is then processed in ways yet
poorly understood to control expression, but this involves histone
binding, their chemical modification and various RNA segments that in
turn influence RNA transcription and translation of RNA into protein.
6) On a larger scale the structure and spacing of DNA functional units
differs markedly between say animals, plants and bacteria. However
within various groups and subgroups these structural features are
consistently conserved across the genome to a degree that simply cannot
occur by chance and must therefore have a functional underpinning. This
is an active research area and many theories have been proposed.
Examples include why are many protein and non protein encoding genes
spliced and organised into exon and intron units in eukaryotes (species
with nucleic)? In plants the structure of these, the size of the introns
and the "gaps" between the transcribed units is quite different from
animals. This cannot exist and be conserved for millions of years solely
by chance. It has to have a functional value even if we don't as yet
know exactly what it is.
6) At the trival level a single base may be essential solely because it
holds two segments of DNA together and without it the cell cannot
replicate correctly.

The point I was originally making is there is some members of this list
have a very simplistic view of the human genome that it consists solely
of ~1% of protein coding bits that are the "genes" and the rest is
"junk" that has NO function. Also the markers DNA genealogy companies
use are located in this junk (which in itself is not solely true) and
therefore the variation observed in them has NO effect on the
individual.

I hope the above points I have made at least demonstrates that this view
of mammalian genome structure and function is outdated and should be
discarded into the dustbin of history. Regards DNA marker status in
genealogy having NO influence on the individuals phenotype or observed
traits, this is also NOT true and increasingly will become less so.
People on this list have already discussed large scale sequencing for
genealogical uses, this obviously has to also encode information about a
persons phenotype. The most extreme example currently is people
sequencing their entire mitochondrial genome. It is simply not true that
all the known variants observed in the entire mitochondrial genome have
NO effect on an individuals phenotype. On the Y chromosome an extreme
example is where many Y STRs are nulls indicating a large scale
deletion. Every person taking a test has to realise that the results
make identify something they were not expecting even if that percentage
is very low. However, lets be realistic, most people if they are >50 and
have children probably don't really care anyway. Little they can be told
will be a surprise to them.

Cheers and Merry Xmas

John McEwan








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