Re: Sorry, no fish in the DNA tank

On Tue, 18 Nov 2008 15:48:52 -0800 (PST), spintronic
<spintronic@xxxxxxxxxxx> wrote:

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.

I have yet to see evidence that either of the groups you mention has
this as their goal. It seems clear that the 151 group wants a tool to
aid in biotechnology.

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.

Both are starting with genes from existing life forms, so the most
that could be said is that they have (possibly) found the smallest
working combination of the particular modern genes they decided to
try.

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.

Assuming that is correct, the fair conclusion seems to be that a
synthetic organism that is very little like the earliest cellular life
is fragile in the world of 2008.

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?

I would say that your entire premise is wrong. I strongly doubt that
either team would say they think they have found the minimum possible
cell, or even the minimum possible genome size for a cell. Surely none
of the modern genes they used were present in the earliest
replicators. Surely the Venter team, whose work you seem to prefer,
understands that even the smallest natural genome they could find is
separated from the earliest cells by billions of years of evolution.

I suggest again that you write to them politely and ask if they think
that their work supports the idea that a primordial cell needed to
have 350 genes at a minimum, and if such a determination is the goal
of their research. I think that there is at least some chance that
someone would take the time to reply, especially if you work hard to
write your question in an interesting way. Then you can share the
reponse with the rest of us.

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.

As I don't imagine anyone is suggesting such a scenario, it doesn't
seem like a useful question.

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

Ditto

Greg Guarino

.

Relevant Pages

  • Re: Minimum Cell?
    ... What must the cell be able to do? ... Note that mitochondria have only a half-dozen genes related to ... It is generally believed that hydrogenosomes are ...
    (talk.origins)
  • Re: epigenetics
    ... production of a pine tree but when put into a human egg cell would ... PAX gene into leg cells of a fly causes the formation eyes in the leg. ... It's because of the other genes ... "responsible" for producing eyes of whatever type. ...
    (talk.origins)
  • Re: epigenetics
    ... production of a pine tree but when put into a human egg cell would ... PAX gene into leg cells of a fly causes the formation eyes in the leg. ... It's because of the other genes ... "responsible" for producing eyes of whatever type. ...
    (talk.origins)
  • Re: Where does information come from?
    ... in the cell. ... describe the sequences of bases in DNA. ... You can describe blood vessels as pipes. ... that genes cause the expression of certain molecular building blocks, ...
    (talk.origins)
  • See the future of biotechnology
    ... genes inside the bean are deleted and medicinal gene are inserted in it ... genome was made compatible to photosynthesis as Plants in sun light. ... There is no such industry which was looking in the past. ... Any living cell can be made totipotent now. ...
    (sci.bio.ecology)