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Graaarh, physicists BIOLOGISTS

Graaarh, physicists

I thought physics was the most hubristic scientific discipline of them all, but I may have to revise that assessment. Last week I was sent another of those papers published in archiv, the physics repository, making grand pronouncements about evolution, and I made the mistake of simply dismissing it on twitter — it was simply too ridiculous to post about. But now io9 has picked it up, and more people are clamoring at me to explain it.

Jebus, it’s terrible.

Here’s what Sharov and Gordon claim:

An extrapolation of the genetic complexity of organisms to earlier times suggests that life began before the Earth was formed. Life may have started from systems with single heritable elements that are functionally equivalent to a nucleotide. The genetic complexity, roughly measured by the number of non-redundant functional nucleotides, is expected to have grown exponentially due to several positive feedback factors: gene cooperation, duplication of genes with their subsequent specialization, and emergence of novel functional niches associated with existing genes. Linear regression of genetic complexity on a log scale extrapolated back to just one base pair suggests the time of the origin of life 9.7 billion years ago. This cosmic time scale for the evolution of life has important consequences: life took ca. 5 billion years to reach the complexity of bacteria; the environments in which life originated and evolved to the prokaryote stage may have been quite different from those envisaged on Earth; there was no intelligent life in our universe prior to the origin of Earth, thus Earth could not have been deliberately seeded with life by intelligent aliens; Earth was seeded by panspermia; experimental replication of the origin of life from scratch may have to emulate many cumulative rare events; and the Drake equation for guesstimating the number of civilizations in the universe is likely wrong, as intelligent life has just begun appearing in our universe. Evolution of advanced organisms has accelerated via development of additional information-processing systems: epigenetic memory, primitive mind, multicellular brain, language, books, computers, and Internet. As a result the doubling time of complexity has reached ca. 20 years. Finally, we discuss the issue of the predicted technological singularity and give a biosemiotics perspective on the increase of complexity.

Life originated 9.7 billion years ago, huh? Maybe 13 billion plus years ago? I didn’t even have to read the paper: I predicted that there would be a certain graph in it, opened it up, scanned to Figure 1, and there it was.

dumbassgraph

We’re done. Anyone else see the problem?

They cherrypicked their data points. They didn’t include lungfish, ferns, onions, or some protists because that would totally undermine their premise; those are contemporary organisms with much larger genomes than mammals’, and their shallow, stupid exercise in curve-fitting would have flopped miserably. It’s a great example of garbage in, garbage out.

There’s another figure, in which they slap their ‘origin of life’ numbers on a diagram of the history of the universe. Very convincing. I could also stick a label on such an image and show the ‘origin of clowns’ at the time of the Big Bang. It wouldn’t make it scientific, though.

sillyorg

Do they have any other evidence to support their claim? No, not one bit. Most of the paper is a handwavey summary of various models of abiogenesis, with no effort to be quantitative…except for their quantitative claim on the basis of one fudged graph that life originated over 9 billion years ago. There’s also some weird stuff about biosemiotics, which they use to argue for goals and meaning in evolution. It seems to be a popular term among creationists, and what little I’ve read on it from marginally more credible sources makes it look like nonsense.

That graph, though, just kills it. At least try to respect the larger data set, will ya, guys?

This was published in archiv, probably to escape the restrictions of peer review (i.e., slip some bullshit under the door), and really, I read that and thought, “physicists, again?” But then I looked closer at the authors. I am so ashamed.

Alexei A. Sharov, Ph.D.
Staff Scientist, Laboratory of Genetics
National Institute on Aging (NIA/NIH)

Richard Gordon, Ph.D.
Theoretical Biologist, Embryogenesis Center
Gulf Specimen Marine Laboratory

They’re biologists of some sort. Now I have to crawl off in embarrassment for my discipline.

Comments

  1. #1 Richard Bellingham
    England
    April 18, 2013

    Isn’t there a problem with the assumption that the origin of life was two base pairs, as well?

  2. #2 Richard Bellingham
    England
    April 18, 2013

    Sorry, one base pair!

  3. #3 Nick Theodorakis
    April 18, 2013

    If you get to choose your data points, you can fit them to almost anything you want to!

  4. #4 Jim Galasyn
    April 18, 2013

    The planets circle a star that is 7 billion years old—about 2.5 billion years older than our sun. Kepler spots the planets as they go between Earth and their star ever so slightly, reducing the light from the star.

    “If there’s life at all on those planets, it must be very advanced” evolutionarily because the planets are so old,” said Borucki.

    http://www.mercurynews.com/breaking-news/ci_23054409/nasa-sees-distant-planets-that-seem-ideal-life

    I assume that the denizens of these worlds have hit Kurzweil’s Singularity by now…

  5. #5 Nick Theodorakis
    April 19, 2013

    I don’ t think “evolutionarily advanced” is going to mean what he thinks it means, if it means anything. They may just have some really nifty bacteria (or bacteria-like organisms).

  6. #6 Cashier
    April 19, 2013

    At least one of them isn´t a biologist. Stay relaxed :-)

    “He (Richard Gordon) was educated at University of Chicago where he did an undergraduate degree in Mathematics and then completed a PhD at University of Oregon in Chemical Physics”

  7. #7 bobh
    April 19, 2013

    Hmmm…as a physicist by training, and without all of the detailed knowledge on lungfish, onions, etc, even I could tell the graph was BS. On what possible basis would one expect the evolution of life to be linear in time? My minimal understanding is that evolution of life builds on itself just like science – invent tools to solve one problem and then use those tools again to solve another one. Could we do a graph of progress in physics, or biology and with the linear in time assumption show that either predates humans? Probably if you pick the right data and assume linear growth of scientific knowledge

  8. #8 Eric Lund
    April 19, 2013

    @Cashler: Gordon’s degrees may be in other areas, but he calls himself a “theoretical biologist.” Whatever that means.

    The Gulf Specimen Marine Laboratory apparently exists, and their web site indicates that they do some research and education/public outreach there. IOW, it’s not one of those “research institutes” run out of somebody’s home. But Dr. Gordon doesn’t seem to be a co-author on any of the papers they list there. Either he’s a recent hire, or he’s employed in something other than a scientific capacity, or he’s lying about being affiliated with this institution. That he uses a gmail address rather than an institutional e-mail address is also a bad sign.

    @bobh: That’s a log scale on the Y axis, but an exponential model is hardly better than a linear model here. “Progress”, however one defines it, is not even monotonic.

    There are supposed to be some minimal kook filters on the arXiv, but they clearly have failed here. A physicist, Wolfgang Pauli, did come up with the appropriate description for stuff like this: not even wrong.

  9. #9 Cashier
    April 19, 2013

    @Eric Lund

    I remember a “Journal of Theoretical Biology”. Most of the authors were mathematicians, modelling the population development of algae blooms and stuff like that.

  10. #10 Nick Theodorakis
    April 19, 2013

    Mark Twain on linear extrapolation:

    “In the space of one hundred and seventy-six years the Lower Mississippi has shortened itself two hundred and forty-two miles. That is an average of a trifle over one mile and a third per year. Therefore, any calm person, who is not blind or idiotic, can see that in the Old Oolitic Silurian Period, just a million years ago next November, the Lower Mississippi River was upwards of one million three hundred thousand miles long, and stuck out over the Gulf of Mexico like a fishing-rod. And by the same token any person can see that seven hundred and forty-two years from now the Lower Mississippi will be only a mile and three-quarters long, and Cairo and New Orleans will have joined their streets together, and be plodding comfortably along under a single mayor and a mutual board of aldermen. There is something fascinating about science. One gets such wholesale returns of conjecture out of such a trifling investment of fact.”

    - from “Life on the Mississippi”

  11. #11 Adrian Lanser
    Iowa
    April 19, 2013

    Let me see if I understand the gist. You scoff at idiotic extrapolation in an effort to blunt an agrument against your proposition that aliens brought life to the Earth? Aliens? Really? Morons chasing dimwits proves nothing.
    Mr. Myers, your worship at the foot of some Mayan temple is shameful. Bring evidence or go home.

  12. #12 mikel
    April 19, 2013

    Errr…. Adrian, where did you get the idea that PZ believes that aliens brought life to Earth?

  13. #13 Mick
    Ireland
    April 19, 2013

    I think the point of the paper in totality (without taking specific parts of in in isolation) was that life is a result of complex adaptivity. Other things are also a result of complex adaptivity….

    Now life is a fortress of the science of biology, often times chemistry and on the outside or fringes at a stretch physics…

    But complex adaptivity theory has no home (perhaps mathematics).

    So what they are hypothesising here is the timeline, the mathematical timeline that would be required to generate X amount of complexity. Given how little we know about all the variables operating in this soup of chaos it’d be a stretch to hammer it down to 9.5 billion years or 1 billion years (assuming we hadn’t any evidence except the current complexity of living things and a knowledge of chaos theory).

    But the paper was not saying life evolved elsewhere and was seeded to earth, its saying that in the system we call ‘universe’ that the result of X amount of time (perhaps 4 billion years) is all the time required to start a complex process we define as life. and after that period it will begin all over the place… because the conditions to do so are met.

  14. #14 Mick
    April 19, 2013

    To add to this though I will agree with PZ that these biologists are well out of their depth and really need to have a very long talk with a few guys and gals from the Santa Fe institute before they start blathering on about complexity again.

    It really wouldn’t hurt them to read Melanie Mitchells excellent book on genetic programming or The Quark and the Jaguar by Gell Mann. This at least would give them a basic understanding of how complex adaptivity manifests in the real world.

  15. #15 Alan D McIntire
    April 19, 2013

    Sharov and Gordon’s linear extrapolation of life originating 9.7 billion years ago may be dubious, but there’s nothing unreasonable in suspecting life may have originated in space.
    See
    http://zeenews.india.com/news/space/seeds-of-life-may-have-originated-in-space_833304.html

    Washington: A new experiment simulating conditions in deep space has suggested that the complex building blocks of life on Earth could have been created on icy interplanetary dust and then carried to Earth, jump-starting life.

    Chemists from the University of California, Berkeley, and the University of Hawaii, Manoa, showed that conditions in space are capable of creating complex dipeptides-linked pairs of amino acids-that are essential building blocks shared by all living things.

    http://www.sciencedaily.com/releases/2007/08/070814093819.htm

    Aug. 14, 2007 — Recent probes inside comets show it is overwhelmingly likely that life began in space, according to a new paper by Cardiff University scientists.
    Professor Chandra Wickramasinghe and colleagues at the University’s Centre for Astrobiology have long argued the case for panspermia – the theory that life began inside comets and then spread to habitable planets across the galaxy.

  16. #16 Nick Theodorakis
    April 19, 2013

    Re: “…Professor Chandra Wickramasinghe …”

    That’s pretty much all you need to read right there.

  17. #17 Sascha Vongehr
    http://www.science20.com/alpha_meme/power_grab_science_vs_critical_theory-109492
    April 20, 2013

    Gordon is on an editorial board here:
    http://www.tbiomed.com/about/edboard
    and for example on Science2.0 here:
    http://www.science20.com/profile/richard_dick_gordon
    where he is my “friend”, as one nowadays has “friends” on such sites, but yes, he is not a serious scientist if he ever was one, but so are most scientists nowadays – just surviving in that social structure. Certainly has jumped the shark now with this crap.

  18. #18 Arthur, Art
    April 20, 2013

    Awesome story! Thanks so much for sharing!!

  19. #19 Kevin
    Tempe,AZ
    April 20, 2013

    Making shit up is easy.
    Science is hard.
    Keep up the good work.

  20. #20 David Marjanović
    Museum für Naturkunde, Berlin
    April 20, 2013

    Isn’t there a problem with the assumption that the origin of life was [one] base pair[...], as well?

    Of course: the problem is that it’s utter nonsense.

    there’s nothing unreasonable in suspecting life may have originated in space.

    It’s not outright unreasonable, it’s just an unnecessary hypothesis.

    (And look up Wickramasinghe.)

  21. #21 Richard
    Brooklyn
    April 21, 2013

    (1) I fail to see any way to justify their assumption to use the complexity of existent members of a clade as a proxy for the genomic complexity of the earliest members of that clade, not when they are comparing worm with eukaryotes (where do you draw the line, anyways?).
    (2) Sharov does spend some words defending excluding plants in his earlier paper (cited as Sharov 2006 here) in Biology Direct. He suggests that plant genomes are not as complex as animals because of a high amount of redundant genomic information in plants, referring specifically to polyploidy. That of course ignores the fact that copies of redundant genes often undergo mutations and acquire new functions (which is viable since there is another copy of the gene floating around). Sharov’s argument is especially unconvincing because he cited [i]Arabidopsis thalia[/i] genome complexity to demonstrate the supposed lesser complexity of flowering plants, when [i]A. thalia[/i] is used for genetics research for their small genome size.
    (3) The extrapolation wholly fails to account for the difference in mechanisms of inheritance in prokaryotes versus, say, fish: to wit, polyploidy and sexual reproduction. It makes no sense to do an extrapolation of any sort when there are two major discrete mechanism changes that you can’t really adjust for.

  22. #22 Dean
    Vancouver Island
    April 21, 2013

    @bobh

    It’s a log graph. They’re proposing that complexity is exponentially related to time and provide some reasons as to why they think that. The reasons sound reasonable to an unqualified layman (i.e. me), so I think PZ’s comment about cherry-picking data points is more pertinent.

  23. #23 David Marjanović
    Museum für Naturkunde, Berlin
    April 21, 2013

    Besides, “worm” isn’t a clade.

    They’re talking specifically about Caenorhabditis elegans and seem to be unaware of biodiversity or phylogeny in general.

  24. [...] span-time to devote to consideration of a trail begun by the biologist blogger P. Z. Myers. [Link] He is rather critical of some work [Link] that advances, based on the “genome size” [...]

  25. #25 Gelgamark
    April 23, 2013

    Cherry-picked, non-peer reviewed data? Well, not the data that’s in the graph he’s referring to. The data used in that graph is taken directly from a 2006 peer reviewed paper, Genome increase as a clock for the origin and evolution of life.

    If Myers wants to go public with his criticism, he needs to spend the time it takes to form an honest opinion. Absolute moron.

  26. #26 Erik
    April 24, 2013

    Things don’t get ‘published’ on the arXiv…You sometimes put it there if the review process is slow and you want to have your results in the open. It is ‘expected’ that you add the reference to the published paper later. It is more an open access repository than a non peer reviewed journal club. I can tell you from personal experience that your paper will not be cited more than a few times and mostly ignored unless 1. it is published or 2. you are a famous/ respected /accomplished author with many high impact papers already on your name.
    If you really think that a paper is bad or a hit piece on some other work, you are always free to post a comment or rebuttal on the arXiv.

  27. #27 David Marjanović
    Museum für Naturkunde, Berlin
    April 24, 2013

    Cherry-picked, non-peer reviewed data? Well, not the data that’s in the graph he’s referring to. The data used in that graph is taken directly from a 2006 peer reviewed paper, Genome increase as a clock for the origin and evolution of life.

    That paper does sound like a failure of peer review, though.

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