I'm looking for kind but detailed criticism of the following proposal. 
I'm not a biologist, so please bear with whatever elementary mistakes 
I may make along the way. This isn't homework: I'm not in school.

A number of researchers are studying the origin of life. Some are 
taking a bottom-up approach, trying to explain how life could have 
come from chemicals, while others are embracing a top-down approach, 
taking a living organism and stripping it down to its bare essentials.

Craig Venter is taking the top-down approach, starting with 
Mycoplasma genitalium, trying to rip out as much as possible and 
still have a living organism. This really seems quite laborious. 
Why not let life itself provide the answer? Let me explain.

My central proposal is the following: start with biologically 
diverse microbial life in a growth medium. Pass it all through a 
filter which keeps out all organisms larger than a certain size. 
What comes through the filter is placed in a growth medium 
and allowed to grow back to a healthy population. The idea is 
to keep repeating this process with smaller and smaller filters, 
each filter passing smaller and smaller life forms into the
next iteration [1]. At the end of this process we must arrive at a 
minimal life form (or a set of collaborating forms [2]).

There are several details that should be explained further: the
start condition, the goal condition, and the growth medium.

Start condition: While it's natural for a manipulation-based 
approach like Venter's to focus on a single organism, I think such 
a focus in my proposal would significantly reduce the chances of 
success. Biodiversity is key, since different forms may have to 
"collaborate" to come up with something small enough to make it 
through some of the later filtration steps. 

Goal condition: Remember, I'm not a biologist, so I may be way off 
here; I would welcome your corrections. I seem to recall seeing one 
set of goal conditions like the following: the life form must be 
(i) reproducing, (ii) metabolizing, and (iii) bounded by a cell wall. 
While I think the discovery of the minimal, simplest such form will 
have scientific value, I don't think it should be our end goal. I 
think it's reasonable to expect only one of (i), (ii), or (iii) to 
arise at a time, not all at once. Furthermore, (iii) isn't very 
compelling because lipids can do it already [3]. I find option (i) 
the most compelling, because evolutionary processes can then take 
over the discovery of (ii) and (iii) later. Note that even if 
(i) is our goal, we may have to accept at least two cases: first, 
a single self-replicating form, or second, a collaboration, for 
example, A and B collaborate to catalyze the formation of new 
copies of A and B.

Growth medium: I don't know enough about this to constrain it very 
well. While standard growth media might serve just fine at early 
stages of the filtration process, one wonders what to provide at 
later stages as the organisms are less and less able to synthesize 
what they need. So I would assume we would want a rich organic broth 
which would include a variety of short protein sequences, as well as 
short RNA and DNA sequences. Another whole question is the temperature:
what temperature should be maintained during this process? Or should 
it change? You don't have to answer this question precisely because 
it may not be known to science, but I would welcome whatever light 
you can shed on it.

---------------------------

Payability conditions: In order for your answer to be satisfactory 
and payable, you have to meet the following payability conditions: 

Case 1: Somebody has already made this proposal. If there are indeed 
researchers doing this already, I will consider the question answered 
and payable if you can provide references to their work as well as 
criticism of their work from distinct references, some positive and 
others negative from the scientific community. It's okay if your 
references are online, but they must be from scholarly journals. 
You're welcome to add your own, if you like, which need not be 
scholarly. But the references to the work equivalent to my proposal 
as well as the criticism must be from scholarly journals.

Case 2: No one has proposed this yet and you think the proposal
outlined above is sound. If so, say so, cite five of the most
closely related scholarly references, and describe what you think 
the likely outcomes of my proposal would be. 

Case 3: No one has proposed this yet and you think the proposal is 
unsound. If so, please say so and describe in detail why not. Provide
five scholarly references to back up your argument.

In all cases, anyone meeting the qualifications listed in the next 
paragraph may submit a payable answer at any time. However, if no 
one meeting these qualifications has answered within the first 
ten days of the question period, and you believe you can nonetheless 
answer the question adequately, you may submit a Comment containing 
your qualifications and stating your desire to answer the Question. 
If I reply affirmatively to your Comment, you may then proceed to 
answer the question.

Qualifications: You should have at least a Master's degree in 
biochemistry, molecular biology, microbiology, or a related field. 
Preferred qualifications: a Ph.D. in any of these areas as well as 
publications. In any case, you must declare your qualifications 
in order for your answer to be payable.



[1]: The use of filters is hardly new to biology. They were used on 
viruses:
http://en.wikipedia.org/wiki/Foot_and_mouth

"Virus (life science)," Section VI, Discovery. Microsoft® Encarta® 
Online Encyclopedia 2005 http://encarta.msn.com 
© 1997-2005 Microsoft Corporation. All Rights Reserved.

[2]: http://www.santafe.edu/sfi/People/kauffman/sak-peptides.html

[3] http://en.wikipedia.org/wiki/Origin_of_life

---

Request for Question Clarification by pafalafa-ga on 29 Nov 2005 15:42 PST

anova12-ga,

Hello.  I am a microbiologist, and I found your question full of
interesting speculation and information.

But I'm not clear on the experiment you are suggesting.  Experiments
are usually designed to test a hypothesis of some sort, with the aim
of either falsifying the hypothesis, or generating information that
will add to its credibility.

Can you give us a succinct statement of what your hypothesis is?  And
also, a bit more information as to how your experiment would shed
light on the hypothesis?

Or...if I'm missing the point of your proposed filtering effort,
perhaps you can restate it for us, so I can understand it more
clearly.

Thanks a lot,

pafalafa-ga

---

Clarification of Question by anova12-ga on 29 Nov 2005 22:46 PST

Hello pafalafa-ga,

   Thanks for writing. My reply may have some elementary 
mistakes in it due to the quick turn-around time, but
here goes anyway.

   Mind if I take two passes at it?

Attempt 1: Hypothesis: Life arose from a very simple 
           self-replicating molecule (or simple collaboration
           of molecules), not a single cell.

Clearly, if the experiment succeeds by yielding a self-replicating
molecule (or collaboration of molecules) the hypothesis will have
been confirmed. However, if the experiment terminates by arriving
at some minimal cell which can't be further minimized, the
hypothesis wouldn't be strictly falsified but we'd be given 
circumstantial evidence against it.

Attempt 2: May I turn the tables by asking what hypothesis Craig
           Venter is testing with his Mycoplasma experiments? I 
           may be able to phrase something analogous based on his 
           hypothesis.

Many thanks,

anova12-ga

u can refer this www.kasamba.com/ViewExpert. asp?CatID=10250&conMemID=107440

I am not sure whether your goal is to isolate an organism that would
have similarities to the earliest forms of life, or one that has the
absolute minimum genetic information to still be a free-living
organism.

The filtering bit seems like it would just select for small size, sort
of the runts of the litters.

As markvmd has pointed out, your process would simply select for the
smallest viable organism(s) in a sample.  Smaller does not necessarily
mean "simpler" or more "primitive".

For instance, viruses are much smaller than bacteria, so they would
pass through filters that would retain bacteria.  However, they are
definitely not more "primitive" (in the evolutionary sense) than
bacteria.  Viruses rely on other cells for replication, and are
adapted for specific interactions with various types of cells, so they
must have evolved later than cellular organisms.  (One can actually
argue that viruses are not really alive, so this might not be the
greatest example.)

Case 3 : You are confusing physical size (which will be determind by
the dimensions of the filter) with the magnitude of the genome.

While the two may be correlated; this is far from a close relationship. 

For example http://en.wikipedia.org/wiki/Genome includes a table of genomic sizes. 

The plant cited is significantly smaller than the mammal cited, and
significantly larger than the insect; although it has the largest
genome of all.

A related wiki article also has a discussion of the
conditions/definition of life that you might be interested in:
http://en.wikipedia.org/wiki/Life . For example, that all the
conditions should be meet at least once in the 'life' rather than all
occuring at the same point of time. Your suggestion of evolution falls
would thus fall outside the 'definition'. Interestingly, some
scientists suggest that evolution should be one of the 'defining
features' of life.

mikewa-ga:  My hope is to create the latter. This may shed light on
            the former.

markvmd-ga: If the experiment just yields runts, it's clearly a 
            failure. The hope is that mutations would arise which
            would yield smaller, simpler forms. That is, if no
            evolution (or should I say devolution?) occurs during 
            the repeated rounds of the experiment, it's a definite 
            failure.

hfshaw-ga:  I guess my statement of the experiment was a bit vague.
            My statement "What comes through the filter is placed in 
            a growth medium and allowed to grow back to a healthy 
            population" should exclude viruses since they can't 
            reproduce independently. That is, if we just filtered
            down to viruses, we could put them on no non-living
            growth medium which would allow them to reproduce.
            More specifically, we should be able to confirm that
            there is more DNA/RNA/protein/whatever after the 
            "grow-back" phase than what could possibly have 
            originally came through the filter.

contemplations-ga: 
            Of course, the plant genome must have diverged due to
            later evolutionary pressures: other things being equal,
            it takes more energy to maintain a larger genome, so
            there is a bit of selection pressure to minimize the
            genome. Furthermore, I seem to recall (though I can't
            name the source) that these "out-of-whack" overly-large
            genomes have a huge number of repeated sequences.

            As for your second paragraph, I'm unsure of its meaning,
            but I can sidestep the issue by simply starting with
            organisms we can agree are alive and then forcing the
            evolution-by-filtration technique of my experiment to
            come up with minimal molecules. In fact, the whole goal
            is to show how clearly living things came from clearly
            non-living things, so we must encounter the gray zones
            you mention at some point.

20 And God went on to say: ?Let the waters swarm forth a swarm of
living souls and let flying creatures fly over the earth upon the face
of the expanse of the heavens.? 21 And God proceeded to create the
great sea monsters and every living soul that moves about, which the
waters swarmed forth according to their kinds, and every winged flying
creature according to its kind. And God got to see that [it was] good.
22 With that God blessed them, saying: ?Be fruitful and become many
and fill the waters in the sea basins, and let the flying creatures
become many in the earth".
26 And God went on to say: ?Let us make man in our image, according to
our likeness, and let them have in subjection the fish of the sea and
the flying creatures of the heavens and the domestic animals and all
the earth and every moving animal that is moving upon the earth.? 27
And God proceeded to create the man in his image, in God?s image he
created him; male and female he created them. 28 Further, God blessed
them and God said to them: ?Be fruitful and become many and fill the
earth and subdue it, and have in subjection the fish of the sea and
the flying creatures of the heavens and every living creature that is
moving upon the earth.?
From these scriptures, it is possible to deduce that the chicken came first.
And the eye cannot evolve. It has to be complete to work. Q.E.D.

If you allow the growth medium to supply all of the needs, then the
extreme case is an intracellular parasite. There is a bacterium,
Nanoarchaeum equitans, that has just 552 genes in 490,000 bp of DNA.
You could use this as a possible starting point for selecting an even
smaller genome

Your comments above "My hope is to create the latter" and "If the
experiment just yields runts, it's clearly a failure" indicate
experimenter bias. If you conduct an experiment to get a desired
result, the experiment is flawed. Please familiarize yourself with the
Scientific Method and rethink the setup.

1] Observe and describe a phenomenon or several phenomena.
2] Formulate a hypothesis to explain the phenomenon.
3] Use the hypothesis to predict other phenomena, or to predict the
results of new observations.
4] Perform experimental tests of the predictions.

Ideally, an experimenter is open to the possibility that the
hypothesis is correct or incorrect. Sometimes an experimenter may have
a belief that a hypothesis is true or false, or is pressured to get a
specific result. In these cases there may be a tendency to find
something "wrong" with data which do not support expectations, while
those data which agree with expectations may not be validated
carefully.

Oh, sheesh, I just noticed Pafalafa's clarification request, so I'm
pretty much repeating that.

As for Venter, he says, "We now have a team that's been working to
knock out each one of the M. genitalium genes to find out which ones
are really essential for life. We found out that we can get rid of
maybe 100 of those and still have something that's a living organism.
To test that, we're trying to make an artificial chromosome with just
those 370 genes in it to see if we can actually get life from it. And
if we can do that at this minimalist level, then we can work forward
and understand something like Haemophilus influenzae, which has about
2,000 genes."

This odd experiment is akin to surgically sawing off bits of a person
to find out when they die. The information received from the
experiment may not be perfect-- if you remove an arm, a hand, part of
a leg, one eye, the hair, and pieces from the earlobes from a person,
they would survive quite nicely in an experimental environment (look
at Michael Jackson)-- but it is part of a larger investigation.

That proto-life began as molecules that replicated is called the RNA
World hypothesis. It's not a very good hypothesis, but then neither
are most of the other ones.

Now the Flying Spaghetti Monster hypothesis, on the other hand...