Gene Expression

It’s about inevitability….

Laelaps has an excellent post up, Evolution’s Arrow, which you should read. Set some time aside, it is long. I don’t know enough about paleontology to comment with great insight on the many of the topics which Laelaps alludes to, and some of them get a bit philosophical for my own taste (that is, issues turn on the interpretation of words), but there is one point which I might assert is somewhat muddy:

…Looking at the hominid evolutionary bush pictured below [see here, it’s clear that we are but a single surviving twig of a group that once had a much greater diversity, australopithecines (including the “robust” forms in Paranthropus) seeming to be a much more successful type of hominid even if they are presently extinct. Given that our own species has only been in its modern form for little more than 200,000 years and we are daily poisoning our own well in terms of the global environment, I don’t know if we can rightly say that we are any better or worse than any of the related forms that came before. The extinction of so many different hominids begs the question of why they are no longer around to join us if their forms were so good. If so many hominids so close to us could go extinct, doesn’t that reflect that evolution is more contingent than directed towards a certain number of forms?

First, regarding the other hominid groups. Certainly some of them had some longevity on their side, but, it is important to note we are considerably more numerous. One could integrate across the time period that these species flourished and sum up total numbers to compare a raw count and use this as an estimator of “success.” But as I said, much hinges on words such as successful. But the second point is that I think there is a strong likelihood that other hominids no longer exist because we marginalized them (or absorbed them) through direct competition or destruction of their habitat. Look at what we are doing the other extant homonoids. We are co-opting their ecosystems for our own use, and on occasion we even hunt and consume them. It seems likely that they have been saved so far because they tend to inhabit biomes which our species has exploited to a lesser degree until recently. This emphasizes the fact that adaptation and response to other organisms, evolution’s arms race, is a critical parameter which expands the scope of the discussion beyond the interface of the environment and the phenotype of a given species.


  1. #1 AG
    December 30, 2007

    Agree. The degree humans shape their earth is credible. Homosapience modifies the landshape, montains, plants, animal, even microorganism through antibiotics or genetic engineering. It is possible that, in future, every things on this earth will be modified or eliminated to fit human needs. Then every things on earth seems designed for human.

    I always wonder about why DNA code for each amino acid is same for all living creature on the earth. It might that be our ancestor creature (a viral like creature) wipe out all other competitive living beings with different code in the very early evolution.

  2. #2 Caledonian
    December 30, 2007

    I have heard it said that the system of codon-to-amino-acid association we have maximizes the chances that a mutation will have no effect on what the genetic sequence encodes. The system would likely have dominated because it was the best at encoding and transmitting the relevant data.

  3. #3 Fly
    December 31, 2007

    AG: “I always wonder about why DNA code for each amino acid is same for all living creature on the earth.”

    While the gist of your statement is right, it isn’t literally correct. Biology is full of exceptions.

    “While slight variations on the standard code had been predicted earlier,[44] none were discovered until 1979 when researchers studying human mitochondrial genes discovered they used an alternative code.[45] Many slight variants have been discovered since,[46] including various alternative mitochondrial codes.[47] ”

    Also some life forms use more than the standard 20 amino acids.

    “In certain proteins, non-standard amino acids are substituted for standard stop codons, depending upon associated signal sequences in the messenger RNA: UGA can code for selenocysteine and UAG can code for pyrrolysine as discussed in the relevant articles. Selenocysteine is now viewed as the 21st amino acid, and pyrrolysine is viewed as the 22nd. A detailed description of variations in the genetic code can be found at the NCBI web site.”

    “Despite the variations that exist, the genetic codes used by all known forms of life on Earth are very similar. Since there are many possible genetic codes that are thought to have similar utility to the one used by Earth life, the theory of evolution suggests that the genetic code was established very early in the history of life and meta-analysis of transfer RNA suggest it was established soon after the formation of earth.

    One can ask the question: is the genetic code completely random, just one set of codon-amino acid correspondences that happened to establish itself and be “frozen in” early in evolution, although functionally any of the many other possible transcription tables would have done just as well? Already a cursory look at the table shows patterns that suggest that this is not the case.

    There are three themes running through the many theories that seek to explain the evolution of the genetic code (and hence the origin of these patterns).[7] One is illustrated by recent aptamer experiments which show that some amino acids have a selective chemical affinity for the base triplets that code for them.[8] This suggests that the current, complex translation mechanism involving tRNA and associated enzymes may be a later development, and that originally, protein sequences were directly templated on base sequences. Another is that the standard genetic code that we see today grew from a simpler, earlier code through a process of “biosynthetic expansion”. Here the idea is that primordial life ‘discovered’ new amino acids (e.g. as by-products of metabolism) and later back-incorporated some of these into the machinery of genetic coding. Although much circumstantial evidence has been found to suggest that fewer different amino acids were used in the past than today,[9] precise and detailed hypotheses about exactly which amino acids entered the code in exactly what order has proved far more controversial.[10][11] A third theory is that natural selection has led to codon assignments of the genetic code that minimize the effects of mutations.[12].”

    I think all three themes played a role in reducing the number of genetic codes. In addition, gene-swapping may have been important. Lifeforms that could share genes gained an edge. As with the VHS vs. Betamax format wars, the market would support only one winner.