Re: Sorry, no fish in the DNA tank

On Nov 18, 6:58 pm, Greg Guarino <g...@xxxxxxxxxxxxx> wrote:
On Mon, 17 Nov 2008 14:46:36 -0800 (PST), spintronic

<spintro...@xxxxxxxxxxx> wrote:
On Nov 17, 2:32 pm, Greg Guarino <g...@xxxxxxxxxxxxx> wrote:
On Sat, 15 Nov 2008 10:01:22 -0800 (PST), spintronic

<spintro...@xxxxxxxxxxx> wrote:
This "proposed" minimal genome, has 151 genes


I see no indication that the authors think that their proposed
cell is the minimum possible unit of life,

Whoever said that.

A common and tiresome tactic.


No, no tactic. It simply was not their intention, and I never said it
was.


Given that the real number of required genes is closer to ~350, Their
*guess* is hopeful at best.

http://www.pnas.org/content/103/2/425.abstract

nor that such a thing  is even their goal.

I guess in your "long" and extensive read, you forgot to read the
title
of the paper. Here let me remind you;

It's entitled; "Towards synthesis of a minimal cell".

And there you go again. It sure sounds like you are saying that the
researchers are trying to find something like the minimum possible
cell. If not, what are you trying to say?


There are a few groups trying to answer a very simple question.

What is the smallest number of genes required for a self-replicating
cell.

Their are 2 methods employed,
bottom up(which appears to be the approach of the 151 gene
*projection*)

I say again *projection*.

top down (venters team. Which found about ~350)

The top down approach basically throws geans out of the genome, until
the cell is no longer functional. Usign this approach, the more genes
you throw out, the more constrained you are to limited enviroments.

Again, its at about ~350 the more genes they throw out, the more
limited the enviroment is the cell can survive in.



What did they say that the reason was for the "extreme dependence on elaborate laboratory
reagents and conditions for viability"?

Partly, to ease the concerns of the public and the politicians.

I still haven't read the whole thing, but I didn't see anything about
the public or politicians. The do elaborate on the safety precautions:

"It is important to note that a minimal cell would be intentionally
fragile. For example, the vesicle would be easily lysed and the small
molecule feeding mix would be highly specialized indeed (including
unstable cofactors such as N-5,10-methenyltetrahydrofolate and
S-adenosylmethionine). These built-in safety features will prevent a
minimal cell from replicating outside the laboratory. "

This supports the idea that the fragility is intentional, rather than
natural.


There are many ways to make a cell dependent upon a lab. All you have
to do is knock out a gene the cell can't survive without, and supply
that protein/chemical manually.

There is no need to say fragility goes hand in hand with dependance,
the fragility is independent of it's dependance.

It is fragile because it has hardly any genes/tools to survive in the
big wide world.



But *mainly* because that's the way it is.

I suspect there's some truth in this, now. But assuming that your
actual point has something to do with the possibility of natural
abiogenesis (if it doesn't, please let us know what it is),

My point is simple.

If a minimal cell has 151 -> ~350 genes. And it is *minimal*.
How the fluff did it evolve?



would not the natural environment of the early Earth be missing perhaps the most
lethal danger to our minimal cells, meaning other decidedly non-minimal organisms?

Theres a whole load of steps before this stage. You are (supposedly)
meant to have a whole ocean of ribozymes, now how do you get 151 ->
~350 *specific* proteins into a cell in one go.

And then how do you get the instructions in the genome at *precisely*
the same time?

And your *early Earth* is not as user friendly as you think, no ozone,
radiation, ......



For instance, the authors speculate that a very
simple lipid membrane might suffice to form a compartment for their
cell. Presumably that is nowhere near enough protection in the rough
and tumble world of organisms with a several billion year head start,
but before those organisms existed?


You need transport proteins for the lipid mambraine.

Otherwise you get crap in, and the good's leak.



I suggest you read
this,http://www.pnas.org/content/103/2/425.abstract

And then this,

http://en.wikipedia.org/wiki/Mycoplasma_laboratorium

From this article I see where you got the 381 genes from, again
supporting the idea that you think this has something to do with the
minimal unit possible for life, with implications for the possibility
of abiogenesis. I suggest (quite seriously)  you write to the Venter
Institute and ask if they think their work supports either of those
contentions. I suggest also that you avoid using the word "stupid" in
your letter. No everyone is as "evolved" as I am. :)

When your done, well talk more on the reasons why it is a fact, that
the
fewer the genes the greater the enviromental constraints.

I see no reason to argue with the concept that early self-replicators
might be able to survive only in a very specific environment, very
much like the one they were in.

Greg Guarino

.

Relevant Pages

  • Re: Minimum Cell?
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  • Re: epigenetics
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  • Re: epigenetics
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    (talk.origins)
  • Re: Where does information come from?
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  • See the future of biotechnology
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