The Archaean Expansion

[Edit added 4/27/11.

PZ Myers, the atheist activist who recently helped organize a smear campaign against Nick Matzke, has offered some opinions about this blog entry. He writes:

One of the creationist summaries is by an intelligent design creationist. He looks at the paper and claims it supports this silly idea called front-loading: the Designer seeded the Earth with creatures that carried a teleological evolutionary program, loading them up with genes at the beginning that would only find utility later. The unsurprising fact that many gene families are of ancient origin seems to him to confirm his weird idea of a designed source, when of course it does nothing of the kind, and fits quite well in an evolutionary history with no supernatural interventions at all.

I’ll ignore the use of stereotype in calling me a “creationist,” as Myers also calls Ken Miller a creationist. That should clue you in to the level of intellectual rigor that is involved in his labeling. The main problem is that his description is a total misrepresentation of my position.

First, front-loading has nothing to do with “loading them up with genes at the beginning that would only find utility later.” I explained the error of this interpretation two years ago. Secondly, no where do I argue for a supernatural intervention in evolutionary history. I agree there is no evidence of supernatural intervention in evolutionary history.

Myers characterization of my views are rooted in a form of ignorance that is sustained by stereotype. In fact, what is ironic is that the conclusions from the summary figure he cites are the very ones I picked out before he got around to the paper.

Myers: If you draw any conclusions from the graph, it’s that life on earth was essentially done generating new genes about one billion years ago…but we know that all the multicellular diversity visible to our eyes arose after that period. What gives?

Me (from below): Note that gene births, shown in red, explode on to the scene and then become insignificant about a billion years ago, long before the Cambrian explosion.

Myers: That’s what the blue and green areas tell us. We live in a world now rich in genetic diversity, most of it in the bacterial genomes, and our morphological diversity isn’t a product so much of creating completely new genes, but of taking existing, well-tested and functional genes and duplicating them (blue) or shuffling them around to new lineages via horizontal gene transfer (green). This makes evolutionary sense. What will produce a quicker response to changing conditions, taking an existing circuit module off the shelf and repurposing it, or shaping a whole new module from scratch through random change and selection?

Me (from below): This is a visual pattern that maps nicely to the dynamics of front-loading that I have been discussing for years, as gene duplication is an excellent strategy of forwarding designs into the future and allowing them to function as feelers.

And from the linked essay:

So while most are content to view gene duplication and pseudogenes merely as a sign of common descent, there is a deeper perspective available that will help you to begin to appreciate the logic of evolution.

You don’t refute the hypothesis of front-loaded evolution by agreeing with me. So, as it stands, nothing Myers offers leads me to think there is anything wrong in thinking this new research strengthens the case for the design of evolution.]

Check this out:

MIT scientists have created a sort of genomic fossil that shows that the collective genome of all life underwent an enormous expansion about 3 billion years ago, which they’re calling the Archean Expansion.

[…]

The scientists traced thousands of genes from 100 modern genomes back to those genes’ first appearance on Earth to create a genomic fossil telling not only when genes came into being but also which ancient microbes possessed those genes. The work suggests that the collective genome of all life underwent an expansion between 3.3 and 2.8 billion years ago, during which time 27 percent of all presently existing gene families came into being.

So one out of four gene families that are known to exist came into existence about 3 billion years ago.Actually, it would be higher than this, as the researcher’s excluded genes that we already present at the Last Universal Common Ancestor.  So if we are to add in the universal genes, it’s probably closer to one out of three or two gene families originating near the origin of life.  Thus, it is important to remember that all subsequent evolution took place in the context of this ancient genetic information.

This new research strengthens the case for the design of evolution:

So if we posit that the original life forms were designed, instead of viewing the composition and architecture of life as something that natural forces cannot possibly account for, consider the more tantalizing possibility that the composition and architecture of the first cells as representing a choice architecture designed to influence/nudge the “choices” made during subsequent evolution. The manner in which the various pieces and parts of life were hooked up would represent the architecture of life and this, in turn, would amount to a logic that would help guide and facilitate subsequent evolution. The actual pieces and parts of life would represent the composition of life and this, in turn, would amount to various preadaptations that would favor certain evolutionary trajectories over others.

This recent research has helped to show more clearly that a huge chunk of the composition and architecture of life is very ancient and could thus serve the objective of nudging subsequent evolution.  In fact, consider one figure from the study:

 

Whoa!  Note that gene births, shown in red, explode on to the scene and then become insignificant about a billion years ago, long before the Cambrian explosion. And in its place gene duplication, shown in blue, has progressively become more significant.  This is a visual pattern that maps nicely to the dynamics of front-loading that I have been discussing for years, as gene duplication is an excellent strategy of forwarding designs into the future and allowing them to function as feelers.

HT:  Brig Klyce

 

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20 responses to “The Archaean Expansion

  1. I can’t find the original publication, but it looks to me like this result is entirely due to the fact that their particular dated phylogeny puts the divergence of the bacterial phyla into the period 3.3-2.8 billion years ago. The fact that gene losses and gene gains spike at similar times is evidence for this — basically any retrospective phylogenetic method works by inferring events backwards down the phylogeny. The only place any action can take place is at the nodes. Is that particular cluster of nodes a real signal, or just what happened to survive and get sequenced? The deepest branches are the hardest ones to get the length correct on, and the resolution of the relationships of the bacterial phyla is the deepest, toughest phylogenetic problem except for the divergence of bacteria/archaea/eukaryotes itself.

  2. There’s definitely something compelling there, though I’m guessing the response by critics will be along the lines of, “This must be proof evolutionary mechanisms work faster than we thought…” Popper would be proud at such a defense don’t you think?

    Admire the fact that you almost single-handedly put front-loading on the discussion table. You’re bound to get your place in history for that alone. Glad to see a maverick voice in the debate over origins is still active! You’ve given me hope that doing work under a pen name can wield just as
    much influence as going public altogether; I suspect whatever role I might take will work out the same way.

  3. What supports front-loading is not the spike and whether it resists flattening or extension back into time by further phylogenetic analysis. What supports front-loading is the finding that so many genes are so old and what happens subsequent to the spike (in other words, the two themes I raised in the OP).

  4. Mike,

    More novice questions, as usual. So with this data, it seems that 1/4 to 1/2 of the currently existing genes are ancient. In modern eukaryotes, do we have any good estimations of the “high end” and “low end” of the number of genes in given organisms that are ancient versus recent?

    Does the green on that chart represent HGT?

    And ‘gene births’ seem to come to an end or near-end roundabout a billion years ago. This doesn’t really mean that there have been (compared to the past) hardly any ‘new genes’ for a billion years, does it? I’m getting the impression from this illustration that most of the ‘ingredients’ for many (far, far later) organisms were present billions of years ago, and evolution over hundreds of millions of years has been more a matter of ‘assembly’ at the gene level rather than anything else.

  5. I’m not quite following the argument. The graph shows an initial explosion of new genes, with some transfer and some duplication. That would fit in with an initial design event of the origin of life. Then it shows a spike in new genes. This fits in with…what exactly? Then it shows a spike in gene loss, which fits in with…? Then a steady, large amount of gene loss and transfer, a diminishing amount of new genes and growing amount of duplication. Which fits in with…?

  6. Hi Null,

    I have not read the paper yet, so I’ll probably post a more lengthy blog entry once that is done. I don’t know off hand if anyone has done the estimates you mention, but that is a good idea to look into. Yes, the green shows HGT which, as we can see, has been a rather constant feature of evolution since the expansion.

    If I understand the study correctly, new genes have arisen since a billion years ago, but not new gene families. For example, gene duplication generates new genes, but they are members of a pre-existing family.

    The impression you get is, I think, the correct one.

    Hi Bilbo,

    “The graph shows an initial explosion of new genes, with some transfer and some duplication. That would fit in with an initial design event of the origin of life. Then it shows a spike in new genes. This fits in with…what exactly? Then it shows a spike in gene loss, which fits in with…?”

    I could be an artifact as Nick describes above, where a lot of these events extend backward in time but we don’t have the modern day descendants of these intermediate states. Also, I think it could be a residue of the bacterial-superorganism “learning” from the ancient earth’s environment as it adapted to the planet. Y’know – terraforming.

    “Then a steady, large amount of gene loss and transfer, a diminishing amount of new genes and growing amount of duplication. Which fits in with…?”

    That’s easier – it fits with my book:

    So evolution has been working with basically the same set of components within the same basic system architecture. The work it does has been primarily reshuffling and tweaking the original toolkit.

    Front-loading is plausible because, across all forms of life, cells share the same basic architecture and components. A designer with an eye to the future will know that this architecture and these embedded components are likely to remain intact. And even if a specific component were to be lost in one lineage, it may very well remain in many or most of the other lineages.

    Even though evolution is supposed to be inherently unpredictable, as we can see, it has occurred within a very predictable biological matrix.

  7. There seems to be an issue concerning the physical evidence for the arrival of living organisms on this planet:

    Tiny filaments thought to be ancient fossils are shown to be inorganic

    Know what else is cool? When I look at the graph I can see a profile of a face (right side)- the nose is between 1-15GY then the lips and it has a collar pulled up covering the chin. Above the nose we have the eye socket area, a little forehead and then a hat.

  8. Pingback: Archaios - Telic Thoughts

  9. Rapid evolutionary innovation during an Archaean genetic expansion

    Lawrence A. David & Eric J. Alm
    AffiliationsContributionsCorresponding author

    Nature 469, 93–96 (06 January 2011) doi:10.1038/nature09649
    Received 15 July 2010 Accepted 27 October 2010 Published online 19 December 2010

    The natural history of Precambrian life is still unknown because of the rarity of microbial fossils and biomarkers1, 2. However, the composition of modern-day genomes may bear imprints of ancient biogeochemical events3, 4, 5, 6. Here we use an explicit model of macroevolution including gene birth, transfer, duplication and loss events to map the evolutionary history of 3,983 gene families across the three domains of life onto a geological timeline. Surprisingly, we find that a brief period of genetic innovation during the Archaean eon, which coincides with a rapid diversification of bacterial lineages, gave rise to 27% of major modern gene families. A functional analysis of genes born during this Archaean expansion reveals that they are likely to be involved in electron-transport and respiratory pathways. Genes arising after this expansion show increasing use of molecular oxygen (P = 3.4 × 10−8) and redox-sensitive transition metals and compounds, which is consistent with an increasingly oxygenating biosphere.

    http://www.nature.com/nature/journal/v469/n7328/abs/nature09649.html

    Subscription or payment needed.

  10. Valery Anisimov

    On my view this paper is not especially serious. Per example the authors use for the molecular clock calibration traces of the eukaryotes biomarkers from the Pilbara craton which was reassessed already more than 2 years ago (see http://www.nature.com/nature/journal/v455/n7216/abs/nature07381.html )! What they named as “Archaean Expansion” most probably is just consequence of the defect in the evolutionary tree which they used, where first bifurcation is between archaea and eubacteria branches. On the more (according to my opinion) realistic trees where archaea deviated later, this “Archaean Expansion” effect practically totally disappear and new genes birth play very modest role during all history of life on the our planet.

  11. Hi Valery,

    That’s actually the second reference in their paper, they don’t use that. The biomarker-based evidence that is consistent with their result is here:

    Waldbauer, J. R., Sherman, L. S., Sumner, D. Y. & Summons, R. E. Late Archean molecular fossils fromthe Transvaal Supergroup record the antiquity of microbial diversity and aerobiosis. Precambr. Res. 169, 28–47 (2009).

  12. Valery Anisimov

    Hi Guts,

    OK, let’s have a look on the table 1 in the SUPPLEMENTARY INFORMATION of this paper. There we have event number 3 – “Eukaryotes diverge from Archaea” with indicated age > 2670 Ma. In the last column (Evidence) for this event you can see “Preserved sterane biomarkers [8,20]“.
    Than if you will check the list of the sources it will give you:
    8. Brocks, J. J., Logan, G. A., Buick, R.&Summons, R. E. Archeanmolecular fossils and the early rise of eukaryotes. Science 285, 1033–1036 (1999).
    20. Waldbauer, J. R., Sherman, L. S., Sumner, D. Y. & Summons, R. E. Late Archean molecular fossils fromthe Transvaal Supergroup record the antiquity of microbial diversity and aerobiosis. Precambr. Res. 169, 28–47 (2009).

    But inside paper [20] you can find again only reference on the [8] and one later paper of the same authors about the same evidence. So as far as I see on the moment we have only direct or indirect references on the same evidence which was reassessed by authors themselves more than two years ago! It means that one of the key molecular clock calibration point is certainly wrong and so all other authors conclusions in big questions.

  13. Valery, reference [20] concerns the findings in the Agouron Griqualand Drilling Project in South Africa, not Australia. It’s not the same evidence.

  14. Valery Anisimov

    Guts, sorry you are right they actually claims about some steranes existence in the bitumens in the drill which is located in Transvaal region. But what is strange for me is that C13/C12 ratio in kerogen (delta C13 >= -40 ) looks not typical for the late Archean. Also huge (nearly 1 billion years) gap between the age of this stratum with possible steranes biomarkers and the age of first widely accepted fossils of eukaryotes looks too large. There is no evidence that oxygen was presented in the atmosphere already 2.7 billions years ago. So for me this is the only possible evidence which suppose that eukaryotes appear nearly 2.7 billions years ago. And much more safe will be wait for the additional evidences than use this one for the molecular clock calibration.

  15. I don’t think delta C13 in and of themselves are indicative of any particular age, and there does seem to be evidence of oxygenic photosynthesis by the late Archaean (see for example here http://rstb.royalsocietypublishing.org/content/363/1504/2731.full.pdf+html), but I agree overall with your point about the controversial nature of this type of evidence and more evidence is always a good thing.

  16. Valery Anisimov

    Concerning delta C13 you are right in general. But specifically for the late Archean some scholars believe that delta C13 is really like a fingerprint of this epoch. Per example for the nearly the same age kerogen in the Pilbara Craton shales delta C13 <= –40. This is probably because of the large methanotroph bacteria activity on that time which produce superlight carbon.

  17. According to figure 2 , it looks like there are values that are < -40, this more high resolution study seems to confirm this:

    The most striking feature is the occurrence of organic C values <−40‰, a feature that appears to be commonplace in Late Archean successions. Framed in the context of carbon cycle isotopic mass balance, both organic and carbonate carbon isotopic data suggest that the proportion of carbon buried as organic matter was not radically different before the appearance
    of free environmental oxygen.

    http://schraglab.unix.fas.harvard.edu/publications/CV96.pdf

  18. Valery Anisimov

    Lines on figure 2 indicated delta C13 values for total organic carbon, not specifically for the kerogen. For delta C13 in kerogen you should look on circles on figure 2 or on the last column of the table 1.

  19. Yes I saw that. I just thought you’d find it interesting, the ultralight kerogens is suggestive of another possible process that can explain the pattern of C13 enriched kerogens that are associated with limestone and dolomite, and ultralight kerogens with shale. That there might be another process at play, carboxidotrophy using the reductive acetyle CoA pathway, could
    actually be responsible for the ultralight kerogens of Late Archean age.

  20. Valery Anisimov

    Yes I agree it may be also an interesting option.

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