Re: Junk DNA

On Tue, 03 Jul 2007 10:56:46 -0500, Dick <remdickhm@xxxxxxxxxxxxx>
wrote:

On Mon, 02 Jul 2007 13:07:01 -0400, r norman <r_s_norman@xxxxxxxxxxxx>
wrote:

On Mon, 02 Jul 2007 10:18:51 -0500, Dick <remdickhm@xxxxxxxxxxxxx>
wrote:

On Sun, 01 Jul 2007 17:04:46 -0400, r norman <r_s_norman@xxxxxxxxxxxx>
wrote:

On Sun, 01 Jul 2007 15:49:50 -0500, Free Lunch <lunch@xxxxxxxxxxxxxx>
wrote:

On Sun, 1 Jul 2007 21:47:03 +0200, in talk.origins
"Rolf" <rolf@xxxxxxxx> wrote in <5eqhngF3a38ijU1@xxxxxxxxxxxxxxxxxx>:

"spintronic" <spintronic@xxxxxxxxxxx> wrote in message
news:1183312778.628142.234290@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Anyone left in here brave enough to call non coding regions, "Junk
DNA"?


I am very familiar with junk; back in the good old days when I was building
radio receivers and transmitters, my junk box was a valuable source of
components. And needless to say, whenever a piece of equipment was torn
apart - it all went into the junkbox (again).

I wouldn't be surprised if many of those non-coding sections of DNA are
very much like your electronics junk box.

I had just such a junk box for many, many years. Finally I realized
that almost everything in it really was junk and got rid of it all.

Once a component had been soldered and unsoldered several times, the
leads got shorter and shorter and the body became damaged by heat from
the soldering iron. You also couldn't easily distinguish between
still usable parts and damaged parts; the electrolytic capacitors were
all shot, the tubes were certainly bad, the connectors noisy and
erratic, many of the screws and nuts were stripped. Semiconductors
were often burned out. You can call a "spare parts bin" a "junk bin",
but the fact remains, junk is junk.

I got a laugh at the Junk box. I kept much of my junk over many years
and many moves. Technology changed from crystals, to tubes to
transistors and then ICs. Funny thing happened, I found old radios
needing repair at flea markets and some of the old stuff fit in.

I find a problem applying the analogy to junk in the DNA. I get the
impression DNA is capable of keeping its genes clean and backups
(redundancy) around to make repairs.

Is the parts box very good as an analogy?

There is a real problem in trying to put humanizing analogies onto
something as strange as the genome: you tend to believe in the
analogy and forget about the facts. And it is certainly not
established that DNA is capable of keeping its genes "clean". If it
were, there would be no junk!

Saying that a lot of DNA is a "parts box" of potentially useful
functions is as bad as called it "junk" with no use. The fact is that
DNA sequencing is such a new technique and we are now overwhelmed by
such an enormous mass of undigested data that we are really grasping
at trying to understand just how cells use DNA to do their work.

I deliberately wrote that last sentence in place of saying "grasping
at understanding just what DNA means". The DNA sequence is NOT a
"book" to be "read" containing "instructions" or "blueprints". It is
a molecule that does indeed contain some coding sequences that can be
"read" to produce an amino acid sequence. It also contains other
sequences that are "recognized" as control elements. But we are just
starting to get a real understanding of how even a prokaryotic cell
uses its single DNA molecule, let alone how a eukaryotic cell manages
it complex chromosomal content. The stuff we can identify as being
actually "read" and "used" is a tiny portion of the total. Much of
the stuff we cannot find any use for is incredibly variable which
suggests that the specific sequence has no important function. There
are long stretches of repeating sequences that really seem to have no
function and, most important, there are organisms (puffer fish) that
seem to live quite well without all that material.

I do appreciate this response. At times I wonder if I do understand
the complexity. I use the computer Bios as an analogy to
understanding DNA. Something has to be a beginning point at boot up.
In the bios, it may as simple as returning the processor to zero
address to get it on track. I don't understand, after cell division
how the transcription mechanism knows where to first read the new DNA.

I do hope I am using transcription correctly. I understand the DNA is
passive and there are specialized proteins which find needed gene
locations, then read them, then assemble, with more assemblers, the
appropriate proteins. From here it gets so hazy as functioning
progresses into specialized instructions. How these new cells get
positioned, and know how to pick out specific specialized instructions
so as to be a liver cell, a heart, etc. and assemble within a
structure provided by other cells, well, I am sure you understand my
dilemna.

So, I try to focus on something simple such as how the flagellum might
get its motility, one step at a time. But, even that becomes a
quagmire. It seems every simple step involves complicated steps until
I am back to abiogenesis.

I really hope there is life after death and there is an opportunity to
ask questions. I suppose that would be even worse than just going to
sleep, but I hate to think my life just ends. What a waste.

One very important thing to keep in mind is that modern mechanisms are
highly elaborated and specialized and refined, no doubt far different
from the original evolutionary pathway. Also you must keep in mind
that there are several different kinds of flagellar motors in
existence. The eukaryotic one is totally different from the
prokaryotic and the archean one sufficiently different from the
eubacterial one to suggest independent evolution. There is also more
than one kind of bacterial flagellum but I am not sure how they may be
related evolutionarily.

Another essential thing to keep in mind is that the "reading" or
"interpretation" of the DNA by the cell is highly controlled by
materials inside the cell. That is the basis for cell
differentiation: different cell lines of the same organism, hence
different cell lines that contain exactly the same DNA, read different
genes and express them differently. There are chemical modifications
(methylation) of the DNA molecule, itself, plus specific proteins that
bind to the DNA and control what gets transcribed and what does not.

There really isn't any particular "boot up" process in a cell
comparable to what a computer goes through. For the eukaryote cell,
where the DNA is in a complex physical form called the chromosome, the
DNA must be in a particular state or configuration and the cell must
contain the proper machinery and control elements. Only then does the
DNA get read and interpreted properly. At that point, it doesn't
really matter exactly what part of the DNA is read first. It is a
highly distributed process, with multiple sites being transcribed
simultaneously. Of course it is also a highly sequential process
because the gene products produced by reading one segment can then
bind to other regions of the DNA (or bind to proteins involved in the
transcription control) to influence which regions of DNA can be
transcribed next. There is no such thing as starting with a "dead"
cell, injecting it with DNA, and kick starting it into life. That is
why genetic manipulation always involves injecting the new DNA into a
fully functional cell that already contains the appropriate control
elements in the appropriate state. That is also why stem cells are
such a big issue: they are the cells whose control elements are
appropriate to produce any cell type.

Prokaryotes work somewhat differently because their genetic material
is a naked DNA molecule. However they have similar regulatory and
control machinery.

It is virtually certain that the earliest cells didn't have all this
complex regulatory machinery. All the cell needs to do to stay alive
is produce the appropriate proteins. Even the parts of such a complex
system as the modern bacterial flagellum are self assembling: make
the proteins and the thing forms spontaneously because of the pattern
of protein-protein binding rules inherent in the amino acid sequence
of the component parts. So if you don't have complex differentiated
cell types and you don't have a complex developmental pattern, as is
the case with bacteria, you just make all the proteins that are coded
and it really doesn't matter where you start. There are usually some
kind of negative feedback patterns so that when you have enough of
some particular protein, you stop making that one.

.