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ID at the AAAS Annual Meeting, Part 2: David Deamer on the origin of life

This post is the second in a series reviewing the February 15, 2009 session at the AAAS annual meeting, Why Evolution Makes Sense of Biology. The first post is here.

David Deamer: Why Evolution Makes Sense of Biochemistry

...so-called prebiotic chemistry, which is of course falsely named, because we have no reason to believe that what they're doing would ever lead to life -- I just call it 'investigator influenced abiotic organic chemistry'...

-- Robert Shapiro, Chemistry (NYU), at the roundtable "Life, What A Concept!" (p. 92), August 2007

First to the podium following Joshua Rosenau of the NCSE was David Deamer, a biochemist and leading origin of life researcher from UC-Santa Cruz. After outlining the Darwinian historical context -- the famous "warm little pond" of Darwin's 1871 letter to Hooker -- and probable early Earth geochemistry, Deamer asked his motivating question: "What is needed for evolution itself to begin?"

What follows directly below is a summary, with links, of Deamer's talk, as he answers his motivating question. I then offer some critical reflections.

"We're Just About There"

Processes such as natural selection, Deamer said, require discrete entities that

-- are cell-like, existing in populations
-- take in nutrients and synthesize polymers
-- replicate information (i.e., direct their formation of polymers) by 'genetic' molecules
-- vary, that is, allow some errors in the replication of their informational molecules, which provides the raw materials for selection and hence, evolution
This list of structural and functional properties, he noted, seems "to a certain mind-set impossible without intelligent design."

But "five milestones" in origin-of-life research, he argued, show that the goal of demonstrating a fully natural (undirected) pathway from prebiotic chemistry to the living state is within reach. These milestones are experiments and data showing the formation or appearance of

1. the monomers (building blocks) of proteins and nucleic acids
2. self-assembling stable membranes
3. protocells (vesicles)
4. the non-enzymatic synthesis of RNA molecules
5. genetic information, "from scratch," without any intelligent design
Sources for (1), the building blocks, include geochemical processes (modelled for instance in the Miller-Urey experiment), but especially the infall of meteorites and comets: it's estimated, Deamer noted, "that 10 percent of ocean water came from comets." For (2) and (3), amphiphiles will self-assemble into sheets and bilayer vesicles; much of Deamer's own work has been focused on this. As to (4), the non-enzymatic formation of RNA, the work of James Ferris and others has shown how activated mononucleotides will assemble, on a clay template, into polymers up to 50 nucleotides (50-mers) long.

Lastly, milestone 5: Bartel and Szostak (1993) have answered a "bugaboo of those people of a creationist persuasion," Deamer said, by showing how "genetic information can appear out of nowhere" as "order emerging from chaos." Although their experiment of evolving ligase activity with engineered ribozymes (RNA catalysts) was not, Deamer cautioned, "meant to be a simulation" of early Earth processes, nevertheless Bartel and Szostak "proved the principle" that selection can generate information without the need for intelligent design.

"We're just about there," Deamer concluded. A demonstration of the natural pathway from chemicals to cells lies just at the horizon of current research, closer now than ever before.

The Frowning Face in the Notepad Margin

Would Deamer have given this same talk at an ISSOL meeting, or to a group of his colleagues?

Or let's imagine, rather than the overflow audience with hundreds of eager AAAS conferees (many of them high school students, sitting right behind me), a much smaller audience -- with the late Stanley Miller himself, or the late Leslie Orgel, or the very much alive Robert Shapiro, sitting in the room. As Deamer reached his description of milestones 4 and 5, I sketched a frowning face in the margin of my notepad. A tiny disgruntled biochemistry professor, holding up a skeptical hand questioning Deamer.

Miller, Orgel, Shapiro, and nearly all other origin-of-life researchers are (by definition, one might say) persuaded that a discoverable natural pathway from chemistry to life exists, awaiting elucidation. But these scientists, when alert, are also conscious of the role they play in affecting experimental outcomes.

This self-awareness matters, of course, when one claims (as Deamer did) that "no intelligent design" is needed to explain the origin of biological complexity. Consider Deamer's discussion, for instance, of his "milestone number 4," the work of Ferris et al., on the clay-templated assembly of RNA

The AAAS audience might have gone away thinking, 'wow -- RNA forms naturally given a pool of activated mononucleotides and a clay surface.' But that conclusion would be deeply misleading, with respect to Deamer's main thesis, namely, that intelligence is not required for real biochemistry to arise from non-living starting materials. For several decades, origin-of-life researchers have known that running abiogenesis simulations under plausible early Earth conditions yields "intractable mixtures" -- tar, or what 1999 Urey Medalist Alan Schwartz (2007, 656) calls "gunk":

For prebiotic chemistry, where the goal is often the simulation of conditions on the prebiotic Earth and the modeling of a spontaneous reaction, it is not surprising -- but nevertheless frustrating -- that the unwanted products may consume most of the starting material and lead to nothing more than an intractable mixture, or 'gunk'.
How to avoid gunk? Rig the conditions -- i.e., specify, via intelligent intervention, the circumstances that will yield a desired product. Now, self-aware origin-of-life researchers know when they are doing this, and see it in the results of others:
Prebiotic syntheses conducted in the laboratory often involve multistep procedures, with purified reagents and very different conditions permitted at each step (Zubay 2000). The extensive purification procedures and changes of locale that would be needed to produce comparable results on the early Earth are seldom discussed, but must be taken into account when attempting to judge the plausibility of the entire sequence. (Shapiro 2006, 107)
Take the clay used in the Ferris et al. experiments, for instance. Montmorillonite (often used in cat litter) is a layered clay "rich in silicate and aluminum oxide bonds" (Shapiro 2006, 108). But the montmorillonite employed in the Ferris et al. experiments is not a naturally-occuring material, as Ertem (2004) explains in detail. Natural or native clays don't work, because they contain metal cations that interfere with phosphorylation reactions:
This handicap was overcome in the synthetic experiments by titrating the clays to a monoionic form, generally sodium, before they were used. Even after this step, the activity of the montmorillionite depended strongly on its physical source, with samples from Wyoming yielding the best results....Eventually the experimenters settled on Volclay, a commercially processed Wyoming montmorillonite provided by the American Colloid Company. Further purification steps were applied to obtain the catalyst used for the "prebiotic" formation of RNA. (Shapiro 2006, 108)
Several years ago, a prominent origin of life researcher complained to me in private correspondence that 'you ID guys won't be satisfied until we put a spark through elemental gases, and a cell crawls out of the reaction vessel.'

But this is not an unreasonable demand that ID theorists make of the abiogenesis research community. It is, rather, what that community claims to be able to show -- namely, that functional complexity arises without intelligent intervention, strictly from physical precursors via natural regularities and chance events.

Thus, pointing out where intelligent intervention (design) is required for any product is hardly unfair sniping. It is simply realism: similar criticisms apply to the other steps in the Ferris et al. RNA experiments, such as the source of the activated mononucleotides employed, a point Ferris himself acknowledges:

A problem with the RNA world scenario is the absence of a plausible prebiotic synthesis of the requisite activated mononucleotides. (Huang and Ferris 2006, 8918)
Deamer didn't mention this. But when No ID Needed is the bottom line the audience takes home -- it's relevant. One can be sure that Orgel, or Miller, or Shapiro would have raised their hands about the problem in the Q & A.

Deamer did sound a note of caution about his milestone 5, the origin of genetic information. The ribozyme engineering of Bartel and Szostak 1993, he said, was "not meant to be a simulation" of plausible early Earth conditions. Indeed, since key steps in any RNA engineering experiment presuppose the intelligent intervention of clever biochemists, it is hard to see what relevance such experiments have to Deamer's No ID Needed thesis.

The experiments actually support the opposing thesis. That's why there's a little frowning chemistry professor in my AAAS notepad margin.

Milestones 2 and 3 have problems of their own, as Thomas and Rana (2007) argue.

Up next: Ken Miller on evolution, ID, and cell biology


References
Ertem, Gözen. 2004. Montmorillonite, oligonucleotides, RNA, and origin of life. Origins of Life and Evolution of the Biosphere 34: 549--570.

Huang, Wenhua and James P. Ferris. One-Step, Regioselective Synthesis of up to 50-mers of RNA Oligomers by Montmorillonite Catalysis. Journal of the American Chemical Society 128:8914-8.

Shapiro, Robert. 2006. Small molecule interactions were central to the origin of life. Quarterly Review of Biology 81:105-125.

Schwartz, Alan. 2007. Intractable Mixtures and the Origin of Life. Chemistry & Biodiversity 4:656-664.

Thomas, Jacquelyn A. and F. R. Rana. 2007. The Influence of Environmental Conditions, Lipid Composition, and Phase Behavior on the Origin of Cell Membranes. Origins of Life and Evolution of Biospheres 37:267-285.