Monday, July 18, 2005

The Minimal Cell: A Problem of Evolution 1/2

Human genomics pioneer Craig Venter has revived his
project of artificially constructing a bacterium. Venter's
company Synthetic Genomics will take the bacterium with
the simplest known genome, Mycoplasma genitalium, a
parasite that lives in the human urogenital tract, and remove
each of its 517 genes one-by-one until the minimum gene
set is reached for the organism to survive in a controlled

Earlier theoretical studies by Mushegian and Koonin
predicted that the minimum bacterial genome would be 256
genes. Gene knockout experiments on M. genitalium by
Venter's The Institute for Genomic Research found
that the minimum genome for a bacterium was 265 to 350

However, the Mycoplasmas are parasites and cannot live
outside their host or the laboratory, lacking the genes to
synthesise all their metabolic requirements.1 Indeed, of all
bacterial genomes sequenced to date those that fall below
1,500 gene products (proteins and RNAs) belong to
parasites. Free-living organisms (those capable of
permanent independent existence) seem to require a
minimum of between 1,500 and 1,900 gene products.2

A gene is made of nucleic acids (DNA or RNA), and as Michael
Behe explains, "Imagining a realistic scenario whereby natural
processes may have made proteins on a prebiotic earth-
although extremely difficult-is a walk in the park compared to
imagining the formation of nucleic acids such as RNA. The
big problem is that each nucleotide `building block' is itself
built up from several components, and the processes that
form the components are chemically incompatible."3 Atheist
origin of life theorist Robert Shapiro regards the chance origin
of a ribozyme (a self-replicating strand of RNA) to be equivalent
to the idea that a golf ball could play its own way around a
difficult golf course, at well-under par, without the golfer!4

Another atheist origin of life researcher, Cairns-Smith, based
on the 14 steps, each comprising an average of 10 sub-steps,
that a chemist would take to synthesise a nucleotide, estimates
that the probability of the spontaneous generation of even
one nucleotide to be of the order of 10-109, which is 1 chance
in 1 followed by 109 zeros!5 By comparison the number of
elementary particles in the universe are estimated to be 1080.

Yet M. genitalium has 580,070 nucleotide base pairs with
each gene being an average of 1,040 base pairs.5 Even
assuming the lower minimum of 256 genes necessary for life,
and an average of 1,000 base pairs per gene, that is a
requirement that no less than 256,000 nucleotide base pairs
would have to spontaneously self-assemble.

But as we shall see in part 2/2, that is just the start of
evolution's problem with the minimal cell!

1. Morowitz H.J., "Beginnings of Cellular Life: Metabolism
Recapitulates Biogenesis," Yale University Press: New Haven
CT, 1992, p.67.
2. Rana, F.R. & Ross H.N., "Origins of Life: Biblical and
Evolutionary Models Face Off," Navpress: Colorado Springs CO,
2004 pp.162-163.
3. Behe, M.J., "Darwin's Black Box: The Biochemical
Challenge to Evolution," Free Press: New York NY, p.171.
4. Shapiro R., "Planetary Dreams: The Quest to Discover
Life beyond Earth," John Wiley & Sons: New York NY, 1999,
5. Cairns-Smith A.G., "Seven Clues to the Origin of Life: A
Scientific Detective Story," [1985], Cambridge University
Press: Cambridge UK, 1993, reprint, pp.46-47.
6. Fraser, C.M., t al., "The minimal gene complement
of Mycoplasma genitalium," Science, Vol. 270, October 20,
1995, pp.397-403.

Stephen E. Jones
"Problems of Evolution"


Anonymous said...

I was reading your comment with interest. I would like to note two things to your assay:

1) the genome of the minimal cells are the genomes they have now.

compare this to looking at the cupola in the sistine chapel and saying: I cannot remove a single stone from this dome without it falling down - therefore it must have arisen in one piece.

this is obviously not true since there were wooden pillars and scaffolding there that held it in place until it was finished.
since those are not needed any more (the dome can carry it's own weight) they were removed.

the same principle applies for these "minimal-genome" cells.

other genes that enabled the cell to reach this state have been there before. now, at its current complexity, you can't remove a part any more since the system depends on it.

2) nucleotides do not spontaneously fall together and form the complete genome of an organism. that is what the theory of evolution by natural selection is all about.

the fact that we don't yet know how it happened exactly (even though we have a pretty good idea) does not mean that "god did it" is automatically in order.

we didn't know a lot of things 2000 years before, but history has told us that these gaps are being closed.

a scientist

Stephen E. Jones said...

a scientist

>I was reading your comment with interest. I would like to note two things to your assay:

Thanks for your comments.

But rather than respond to them `down here' in comments under a 3 year-old-post, where few would ever see it, I will answer your points in a separate blog post.

But it may not be until after Christmas.

Stephen E. Jones