May 15, 2007 | David F. Coppedge

OOL Study Substitutes Computer for Chemistry

Upon reading a recent origin-of-life paper in PNAS,1 you might think the authors ran experiments with real chemicals and real deep-sea rocks.  A more careful look, however, reveals that their model only worked in cyberspace.  This raises interesting questions about the ability of simulations to substitute for empirical evidence.
    Their claims were dramatic – accumulation of the building blocks of life by factors of 100 million and more.  The paper makes optimistic, if not enthusiastic, claims that “nucleotides” and other important biochemicals can be highly concentrated in micropores in deep-sea geological formations: “We find that interlinked mineral pores in a thermal gradient provide a compelling high-concentration starting point for the molecular evolution of life.”  This, they advertised, can overcome the “concentration problem” that has plagued other models: how does one get a significant number of prebiotic chemicals close enough together to interact?
    From the first-sentence reference to Miller and Urey, who used real lab apparatus and real chemicals, the paper appeared to follow the experimental tradition.  It focused on the problem of concentrating chemicals in a plausible environment.  By positing convection currents inside microscopic pores of rocks around deep-sea vents, the model overcame – by at least two orders of magnitude – a minimum set by the Second Law of Thermodynamics on how many molecules are needed for interaction to be considered probable.
    True, the authors used the word “simulated” in the title and 14 times in the paper.  Their references to nucleotides and other “real” chemicals were qualified with indirect references.  Nevertheless, until the “Materials and Methods” section at the end of the paper, it seemed they were talking about real chemicals and physical pores in real rocks.  One of the figures showed photographs from real hydrothermal vents.  They mentioned nucleotides 37 times – including the title.  The body of the paper was filled with references to temperatures, pressures, volumes, and concentrations that looked real.  Actually, the entire model was done within two software programs, Comsol and Femlab.  The nucleotides, pores, and thermometers were virtual, not physical.
    They tried to plug in real-world values into the programs and use realistic boundary conditions.  They input known properties of real molecules.  Putative pore sizes were based on photographs of real hydrothermal vents.  The bottom line, though, is that none of the concentration results were observed or measured in the wild.2  The model revolved around simplified geometries of pores as programmed into a computer – and that, of pores in only two dimensions.
    Here was their concluding paragraph.  Note the lack of reference to a computer simulation.  Is it real, or is it memo tricks?

In conclusion, we propose a type of mechanism, driven solely by a temperature gradient, which strongly accumulates even small protobiological molecules in semiclosed hydrothermal pore systems.  This setting provides a compelling, dissipative microenvironment to promote the first steps in the molecular evolution of life.

The line between real and virtual was blurred in another passing thought near the end of the paper:

Equally, freshly precipitated mesoscopic mineral grains are subjected to thermal cycling by the convection.  Their catalytic surfaces might generate nucleic acid multimers by thermally triggered periodic condensation and unbinding reactions.  In this context, we note that, in a comparable thermal convection setting, DNA was shown to replicate exponentially by using the, albeit protein-catalyzed, PCR.

Critics of origin-of-life studies might be stunned at this line.  PCR, or polymerase chain reaction, is an intelligently-guided reaction, performed by machines in laboratories by scientists with PhDs.  PCR depends on protein catalysts – highly complex molecules from living systems, whose specificity enables them to react with DNA.  By associating a guided process that uses complex biological parts with a theoretical process that is unguided and uses simple abiological parts, can the one be properly compared to the other without assuming what needs to be proved – the origin of complex biological processes?
    This paper was presented as part of a colloquium by the National Academy of Sciences last December on “In the Light of Evolution I: Adaptation and Complex Design” (see 05/10/2007 entry), published May 9 on the Proceedings website.


1Baaske, Weinert, Duhr, Lemke, Russell and Braun, “Extreme accumulation of nucleotides in simulated hydrothermal pore systems,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0609592104, published online before print May 9, 2007.
2In addition, they did not test complications, such as whether pores might become clogged with tar and sediments – they just speculated and dismissed the possibilities, viz: “One may ask whether the strong accumulation of solvated organic molecules would lead to the tarring of the pore.  This is not expected because thermophoretic coefficients become small for concentrations in the molar range.”

Models are OK, and have a long history in science, but the bluffing-to-proof ratio in this paper was beyond the pale.  These authors might be able to defend it by claiming they “said” it was just a simulation in a computer, but nobody scanning the contents would think so.  Few readers are going to look at the Materials and Methods section (usually boring, unless you’re trying to replicate the results).  This paper gave every appearance of being an empirical, laboratory experiment in the real world.  It was all done with software smoke and model mirrors.
    As we saw 12/03/2004, one of the conspirators (Russell) is a master bluffer.  He has a propensity to gloss over major problems and swap out experimental facts for cartoon pictures on a screen.  In his 2004 lecture, he made everything look so simple, so problem-free, life should just pop out of the pore.  If life by the yard is hard, and life by the inch is a cinch, wouldn’t life by the micron be right on?  It’s a foregone conclusion.  The hard part over, little Poregum would just gloriously evolve into us.  Some unbiased, objective scientist he is.  He should read Shapiro’s devastating critique (02/15/2007) of such notions.
    Observational facts have a way of tarring up computer models.  Let us ask a simple question: where are these nucleotides supposed to get their ribose?  Doesn’t Russell and gang know that deep-sea vents are the last place one would expect to find ribose?  It is so difficult to imagine it forming by chance, in fact, that Steven Benner (11/05/2004) had to envision it forming in a desert in the presence of borate.  (Not Borat, mind you – no humans allowed, no matter how perverse.  It’s borate.)  Now, since Benner’s surface model falsifies Russell’s deep-sea model, and vice versa (Russell thinks the surface environment is “disastrous” for life), this one little “problem” we raised is enough to gum up the software and send their little computer instantly into BSOD (blue screen of death, pun intended).  We would continue with more real-world pressure, but as Windows users know, one BSOD is enough to ruin your whole day.

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