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Irresistible Complexity


I just couldn’t resist including these two quotes from a new posting on PhysOrg. It has to do with lateral gene transfer, and the study as to what kind of information is swapped between microbes.

The bottom line, apparently, is that “lone” genes—rather than metabolic apparatus or interacting genes—are what is swapped most commonly between bacteria.

But as the scientists describe their work, it’s really a wonder to listen to the imagery they invoke.

Sit back and enjoy!

Genes whose protein products rely on many partners to do their job are less likely to work properly in a new host, Gophna said. Transferring a highly connected gene into a new host is like importing a fax machine into a remote village, he explained. “While the machine itself is potentially useful, it needs a number of additional connections to work – electricity, a phone line, a supply of paper, possibly a technician. If one of these is missing the machine becomes useless and ends up as junk.

I’m sorry. Doesn’t this sound like irreducible complexity?

Bacteria are more likely to adopt ‘loner’ genes than genes that are well-connected, the authors added. “If you think of the cell like a machine, it’s much more difficult to exchange the hub of a machine than some of its accessories,” Pupko said.

Indeed, I do think of a cell as a machine.

If it looks like a rose, and smells like a rose, and feels like a rose . . .

Pav, in this paper, Estimating the size of the bacterial pan-genome http://www.paulyu.org/wp-content/uploads/2010/02/Estimating-the-size-of-the-bacterial-pan-genome.pdf on page 108, figure 2, they break down the pan genome of bacteria and find, 8% genes shared by all bacteria (essential genes) 64% character genes 28% accessory genes and they describe the 'gene pool' this way; Figure 2. The bacterial pan-genome. Each gene found in the bacterial genome represents one of three pools: genes found in all but a few bacterial genomes comprise the extended core of essential genes (250 gene families that encode proteins involved in translation, replication and energy homeostasis); the character genes (7900 gene families) represent genes essential for colonization and survival in particular environmental niches (e.g. symbiosis and photosynthesis); and finally, the accessory genes, a pool of apparently infinite size, contains genes that can be used to distinguish strains and serotypes; the function of most genes in this category is unknown. At the genomic level, a typical bacterial genome is composed of 8% of core genes, 64% of character genes and 28% of accessory genes. Although the character genes contain only 7900 gene families, they are the most abundant at the genomic level. Expanding the gene centered approach to 573 bacterial genomes or sampling of 508 genomes, excluding highly reduced genomes, yields similar results (Table S2), except that the total number of families in the accessory pool is increased as expected for an open pan-genome. 21 28% totally unique ORFan genes are of course the biggest surprise from sequencing bacterial genomes, as Dr. Nelson illustrates in this video; ORFan Genes Challenge Common Descent - Paul Nelson http://www.vimeo.com/17135166 Moreover these completely unique ORFan genes are just as likely to be 'essential' as 'older' genes with homologies to other genes; Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." http://www.sciencedaily.com/releases/2010/12/101216142523.htm Moreover they predict that this pattern for finding completely unique ORFan genes will continue for each new genome sequenced: Estimating the size of the bacterial pan-genome - Pascal Lapierre and J. Peter Gogarten - 2008 Excerpt: We have found >139 000 rare (ORFan) gene families scattered throughout the bacterial genomes included in this study. The finding that the fitted exponential function approaches a plateau indicates an open pan-genome (i.e. the bacterial protein universe is of infinite size); a finding supported through extrapolation using a Kezdy-Swinbourne plot (Figure S3). This does not exclude the possibility that, with many more sampled genomes, the number of novel genes per additional genome might ultimately decline; however, our analyses and those presented in Ref. [11] do not provide any indication for such a decline and confirm earlier observations that many new protein families with few members remain to be discovered. http://www.paulyu.org/wp-content/uploads/2010/02/Estimating-the-size-of-the-bacterial-pan-genome.pdf ----------- it is interesting to note the extreme level of integrated complexity for the 'essential genes for life' First-Ever Blueprint of 'Minimal Cell' Is More Complex Than Expected - Nov. 2009 Excerpt: A network of research groups,, approached the bacterium at three different levels. One team of scientists described M. pneumoniae's transcriptome, identifying all the RNA molecules, or transcripts, produced from its DNA, under various environmental conditions. Another defined all the metabolic reactions that occurred in it, collectively known as its metabolome, under the same conditions. A third team identified every multi-protein complex the bacterium produced, thus characterising its proteome organisation. "At all three levels, we found M. pneumoniae was more complex than we expected," http://www.sciencedaily.com/releases/2009/11/091126173027.htm bornagain77

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