I very rarely have a genuine "ohmigawd!" moment when reading, but this article did it for me.
I studied Genetics at university, and while whatever knowledge I had is now more than twenty years out of date, I still find the subject as interesting as I ever did.
The article talks about the views of a very good evolutionary microbiologist Carl Woese, working with physicist Nigel Goldenfeld have postulated, that most evolution was not vertical, in the sense that it passed from parent to offspring, with genetic variations between generations, but horizontally, with organisms swapping DNA sequences with other, even completely unrelated organisms.
The latter idea might sound a bit daft to the layman, but microbes are perfectly willing to swap DNA sequences with each other, what no-one had really understood was how important this might be. (Me included I know all the basic facts in the article, and I had never even remotely considered what the true implications might be.) From the article:
"At the root of this idea is overwhelming recent evidence for horizontal
gene transfer - in which organisms acquire genetic material
"horizontally" from other organisms around them, rather than vertically
from their parents or ancestors. The donor organisms may not even be
the same species. This mechanism is already known to play a huge role
in the evolution of microbial genomes, but its consequences have hardly
been explored. According to Woese and Goldenfeld, they are profound,
and horizontal gene transfer alters the evolutionary process itself.
Since micro-organisms represented most of life on Earth for most of the
time that life has existed - billions of years, in fact - the most
ancient and prevalent form of evolution probably wasn't Darwinian at
all, Woese and Goldenfeld say."
In support of this they talk about the efficiency of the DNA coding for the proteins that it produces, and how exceptionally good it is at dealing with transcription and other errors. Basically, to make a protein, which is used to regulate all the chemical interactions in the body, the DNA in the chromosome of a cell, is unzipped, a messenger RNA matches up with its opposite DNA, to make a sequence of three sign codes for the amino acids that make up the protein. The final assembly is achieved by the fact that each amino acid is linked to a transfer RNA specific for that protein, which makes a kind of assembly line of the amino acids that then are bound together in the ribosomes of the cell, and the protein chain goes off and gets involved in the highly complex, and as yet not fully understood process of protein folding.
Even just this high level description lets you see there is room for error, like zipping up a jacket wrongly. However, the way the system works, it is very resistant to errors in the transcription. This is a fact that we never really discussed, how come we have one DNA process for all living organisms, and how come it is so efficient?
"In 1991, geneticists David Haig and Lawrence Hurst at the University of
Oxford went further, showing that the code's level of error tolerance
is truly remarkable. They studied the error tolerance of an enormous
number of hypothetical genetic codes, all built from the same base
pairs but with codons associated randomly with amino acids. They found
that the actual code is around one in a million in terms of how good it
is at error mitigation. "The actual genetic code," says Goldenfeld,
"stands out like a sore thumb as being the best possible." That would
seem to demand some evolutionary explanation. Yet, until now, no one
has found one. The reason, say Woese and Goldenfeld, is that everyone
has been thinking in terms of the wrong kind of evolution."
This is where it all gets madly brilliant. They modelled random DNA assignments for the codons, and then tried to evolve a single efficient system using vertical inheritance. They could not get it to work.
"While the ability of the code to withstand errors improves with time,
they found that the results were inconsistent with the pattern we
actually see in two ways. First, the code never became shared among all
organisms - a number of distinct codes remained in use no matter how
long the team ran their simulations. Second, in none of their runs did
any of the codes evolve to reach the optimal structure of the actual
code. "With vertical, Darwinian evolution," says Goldenfeld, "we found
that the code evolution gets stuck and does not find the true optimum."
Then they tried it using the horizontal approach, and they found that this worked well.
"The results were very different when they allowed horizontal gene
transfer between different organisms. Now, with advantageous genetic
innovations able to flow horizontally across the entire system the code
readily discovered the overall optimal structure and came to be
universal among all organisms. "In some sense," says Woese, "the
genetic code is a fossil or perhaps an echo of the origin of life, just
as the cosmic microwave background is a sort of echo of the big bang.
And its form points to a process very different from today's Darwinian
evolution." For the researchers the conclusion is inescapable: the
genetic code must have arisen in an earlier evolutionary phase
dominated by horizontal gene transfer."
This is quite simply some of the most important biological thinking that I have seen in decades, if not ever. Amazing.
