Arsenic DNA was back in the headlines in May [1], as Science published eight critical comments, one editorial, and a reply from the authors of a report from last December [2] that concluded that a microbe (GFAJ-1) had DNA with some of its backbone phosphorus atoms replaced by arsenic atoms. But that report had already entered the curriculum of science education, where courses on the philosophy and history of science at schools as diverse as the University of Chicago and East Side High School in Gainesville, Florida, pondered what the report of arsenic DNA showed about how science works.

The technical details will be lost on most students. However, even high school students can perceive the form of the arguments being made in this collection of pieces. They center on where “burdens of proof” lie in science and what “standards of proof” should be.

This sounds like law, but even this point may convey something important about how science works. Different from “proof” in math, “proof” in experimental science is much like proof in law. Like in law, it relates to a set of evidence that is sufficient for a community to declare that a problem is “solved” or that a criminal is “guilty beyond a reasonable doubt” [3,4]. What standards that collection must meet are not determined by logic; it is more of a cultural thing.

And different branches of science have different cultures. For this reason, a set of data sufficient to force one community to accept a conclusion might cause another community to reject the very same conclusion entirely.

We can see this clash of cultures within the discussion of arsenic DNA. Those who suggested that GFAJ-1 had arsenic atoms substituting for phosphorus atoms in its DNA were mostly geologists. The geologist included one physicist, from a community also represented by Michio Kaku, who published an editorial in the Wall Street Journal that accepted arsenic DNA without question [5]. However, biologists found the same data inadequate to conclude the presence of arsenic-substituted DNA [6]. Chemists went further, seeing disproof of arsenic DNA in the very same data [7].

This interdisciplinary conflict is obvious in the latest exchange. The geologists continue to argue that their data show arsenic DNA to be “viable” based on “multiple congruent lines of evidence” [8]. The biologists continue to find the data “unconvincing” [9]. The chemists continue to insist that arsenic DNA is an “extraordinary claim” [10].

Let us return to an old observation by Carl Sagan, who said that “extraordinary claims require extraordinary evidence” [11]. But what is extraordinary? This it turns out, depends on your culture.

Why do chemists find a claim for arsenic DNA to be extraordinary? Well, over the past two centuries, chemists have made and studied millions and millions of compounds. Each of these is associated with a molecular structure, a model that describes the arrangement of atoms in the molecule, together with measurements of how that molecule behaves.

These collections support “Structure Theory” in chemistry. Structure Theory explains the properties and reactivities of all chemicals in terms of these molecular structures. More than this, the structures in the chemist’s databases are tightly and logically interconnected, making Structure Theory very highly cross-validated. Water is H₂O, not H₃O. Any claim that water is H₃O, therefore, is a claim that all of the structures in the entire collection must be revisited. Indeed, an enormous amount of data commonly viewed as true must be false if water turns out to be H₃O. This makes this particular claim extraordinary.

Cross-validation in chemistry includes reactivity. For example, modern databases of molecular structures contain many arsenate esters, molecules containing an arsenic atom surrounded by four oxygen atoms, two of which are attached to carbon chains (the C-O-As-O-C linkage). The chains are different in different arsenate esters, but the species react analogously. In particular, all known arsenate esters fall apart (hydrolyze) rapidly in water, leading chemists to expect that all arsenate esters will hydrolyze rapidly in water, even those not yet known.

But chemists have done more. They have measured the difference in the rates of hydrolysis of different arsenate esters having differences in what is attached to the carbon atoms. Thus, if the C atoms are attached to three hydrogen atoms (to give a -CH₃ “methyl” group), the esters fall apart faster than if the C atoms are attached to two hydrogen atoms and another -CH₃ group (to give a -CH₂CH₃ “ethyl” group). The ester falls apart a bit slower if the C atoms are attached to one hydrogen atom and two -CH₃ groups (to give a –CH(CH₃)₂ “isopropyl” group). And the pattern seen with arsenate esters is rationalized with respect to patterns seen in phosphate esters, carbonate esters, and thousands of other compounds.

As a result, if one draws out a structure of a new arsenate ester, a chemist will anticipate how fast it will hydrolyze by analogy to structures of arsenate esters whose hydrolysis rates have already been measured. For the arsenic DNA proposed for GFAJ-1, one of the carbons is like an “ethyl” group and the other is like an “isopropyl” group. So Structure Theory allows the chemist to interpolate, not extrapolate, the rate of hydrolysis of the proposed arsenate DNA linkage. It will be slower than the “diethyl ester” and faster than the “diisopropyl ester”. Since the range of measured rates in this series is not large, and since this is an interpolation between two measured rates, chemists do not expect the error in the prediction to be large. And certainly not off by factors of millions needed to make arsenate esters into molecules able to support genetics.

Chemists are so sure of the power of such analogies that they now routinely reverse the logic. They often do not look at molecular structure to predict molecular properties. Rather, they look at the properties of a molecule to infer its structure. Here, arsenate esters are the novel molecular structures proposed for the DNA in GFAJ-1. The specific structure is not in the database of known arsenate esters, so its instability in water has never been specifically measured. However, the hypothesized arsenate-DNA was reported to be stable in water. Chemists, confident in the power of inference-by-analogy arising from the interconnectedness of their database, conclude from evidence that the geologists presented in their report that the DNA in GFAJ-1 is not arsenate-linked.

Chemists therefore find any claim to the contrary extraordinary. Perhaps not to the extent as a claim that water is H₃O. But if the band on the gel in Wolfe-Simon et al. (2010) [2] is in fact arsenate-DNA from GFAJ-1, then all of the reactivities reported for all of the arsenate esters in the chemist’s database collection must be revisited. Further, due to the interconnectedness of those data, an enormous body of data commonly held to be true must be false about esters in general. This, to the chemist, hands the burden of proof over to the geologists. Until the geologists generate some “extraordinary” evidence, the chemist dismisses their claim.

How did the geologists in Science manage this criticism? In a fascinating example of cross-cultural confusion, the geologists simply decline to accept the burden of proof [2]. After all, the specific arsenic DNA structure proposed for GFAJ-1 is not found in the database of the chemists. The geologists can therefore truthfully write: “There is little literature on the stability of arsenate bound in long chain polyesters or nucleotide di- or triesters, which are more relevant to our studies”. Therefore, the geologists write, “it is conceivable” [italics added] that arsenic DNA is “more resistant to hydrolysis than generally assumed” [2].

The logic of the argument is to refuse the burden. The geologists are saying: “Well, we may not have produced any ‘proof’ that arsenate DNA could survive long enough to be isolated as we reported on our gel, let alone long enough to support genetics. But you have not provided any ‘proof’ that it would not survive.” Like in the courtroom, GFAJ-1 is guilty of having arsenate DNA until the chemists prove it is innocent.

“Not so fast”, says the chemist. “We have provided the ‘proof’.” The geologists, the chemists repeat, are not just attacking the specific interpolation, claiming that their particular proposed structure is millions of times more stable “than generally assumed”. They are attacking the interpolation process, and the century of work on many compounds that support it. If the interpolation process fails for arsenate esters, why not for phosphate esters (which include long chain polyesters and nucleotide di- or trimesters)? And carbonate esters. If GFAJ-1 has the arsenate DNA that the geologists suggest, the entire edifice of Structure Theory must be flawed throughout, for many molecules; the entire thing needs to be revisited.

And so it might. But as discussed in the book Life, the Universe, and the Scientific Method, this makes the claim “extraordinary”. And so, “dammit” say the chemists, the geologists had better put forth some extraordinary evidence, or at least some arguments worthy of the title “extraordinary”.

What do the geologists offer? Well, they write that “arsenate esters of large biomolecules are likely to be more sterically hindered leading to slower rates of hydrolysis than occurs in small compounds, which are relatively flexible and can adopt a geometry that allows water to attack the arseno-ester bond.” Um. No. Steric hindrance was already considered in the interpolation. And what geometry are we talking about? This is “technobabble”, some technical terms strung together without any deeper semantic content.

Then the geologists write: “Geraldes et al. (27) showed by nuclear magnetic resonance that arsenate esters with glucose have surprisingly slow hydrolysis rates”. Well, we got the paper. The rate of hydrolysis mentioned is 9.5 x 10^-5 per second, that is, a half-life of about two hours. Surprisingly slow? That judgment was not expressed in the paper, and depends on what one expects. But in any case, a half-life of about two hours is far too short for the band reported by the geologist to contain even one arsenate link, let alone large amounts of arsenate-for-phosphate substitution. And, of course, it is not far outside the expectations based on Structure Theory.

But the chemists are not yet in a position to walk away muttering about uneducated babbling geologists. As I have written elsewhere, when challenged with theory-altering claims, a correct response does not dismiss them, but rather to say: “Hmmm. Among what we think is true, what must be wrong if the challenge is correct?”

Often, pursuit of this question leads one in long and futile chases through the literature. And so we turn to the paper that the geologists offer from Kay [12], who reported the “incorporation of radioarsenate into proteins and nucleic acids” in a study of mammal cells. This, the geologists suggest, is one of many congruent lines of evidence supporting their hypothesis of arsenic DNA.

The details of Kay’s paper will be understood by only the chemist. Briefly, Kay fed some radioactive arsenate to some cells, recovered the RNA from those cells, and decomposed the RNA down to its building blocks of RNA. Kay then reports that those building blocks were radioactive.

This paper is frustratingly short of details. It is impossible from the paper to understand how the author inferred the structure of species that he isolated. For example, he says that he isolated “adenylic acid” into which arsenic had been incorporated, without (evidently) realizing that if arsenic had been incorporated, it would no longer be adenylic acid. No source is provided for the radioactive arsenate. Consistent with the technology available to him in 1965, he did not do isotope identification and chemical analyses that would be routine today. A subsequent paper was promised to discuss “the implications” of this research; it never seems to have appeared.

But the paper did immediately attract the attention of two chemists [13] who were interested in “the possible formation of nucleoside arsenates in certain biological systems.” Just four years later, they reported their attempt to prepare the arsenate nucleosides hypothesized by Kay. They failed, writing that their “[a]ttempts at the synthesis of nucleoside 5′-arsenate 5 indicated that these compounds may be too unstable to be isolated.”

To the chemist, nothing here meets the standards of “extraordinary”.

The chemists, however, offered yet another line of reasoning to doubt the existence of arsenate DNA. They pointed out that any bacterium that uses arsenic DNA must also be able to make arsenic DNA. The path by which bacteria make phosphorus DNA is well known. It proceeds via many intermediates that would be quite unstable if their phosphates were replaced by arsenate. Many of these intermediates are quite close in structure to arsenate esters that have been made and studied.

Here, the geologists have no opportunity to retreat to a claim that the known molecules are not “relevant” to the arsenic DNA proposal, or that they are “large biomolecules …likely to be more sterically hindered”. These metabolic intermediates certainly can “adopt a geometry that allows water to attack the arseno-ester bond”.

And what do the geologists have to say about this? Nothing.

This back-and-forth shows (at least) that geologists have different ways of deciding what is “exceptional”. To geologists, the controlling analogy comes from the Periodic Table. Analogies based on the Table have worked well for them for a century. Hafnium, for example, stands below zirconium in the Table; unexceptionally, hafnium is found in zircons. Arsenic stands below phosphorus, making it therefore entirely expected that phosphate is a common contaminant of arsenate in rocks, and vice versa.

From this controlling analogy, arsenate esters are expected to be analogs of phosphate esters, with its C-O-P-O-C linkage. To geologists unfamiliar with the chemists’ databases, an analogy based on the Periodic Table drives their view that arsenic DNA is not an extraordinary claim demanding extraordinary evidence, just some congruent lines of argumentation.

Thus, to the geological community, extraordinary evidence is not required to accept the arsenate-DNA conclusion. To geologists, an “Occam’s razor” argument is sufficient based on “multiple congruent lines of evidence” [2] that they themselves collected. Never mind the chemists’ databases. Arsenate-DNA is, in this view, the simplest explanation for the data extracted from GFAJ-1. So why not propose this structure? And get it published by Science, if you can?

The shifting of the burden of proof based on their perception of what is “extraordinary” extends throughout the reply. For example, the geologists write that it is possible that GFAJ-1 “evolved specific strategies to cope” with the instability of arsenate esters [2]. Indeed, it is possible. But under the argument, the burden lies on those who doubt the hypothesis to show that GFAJ-1 did not evolve “specific strategies to cope”, rather than on those who make the proposal to show that it did.

As a clear example of a discussion of burdens in scientific argument, the analysis of the analysis (the meta-analysis?) of GFAJ-1 is likely to be more interesting than the analysis itself. In much of science education, science is “a thing” that has “a method”; conflicts between the sciences in how they meet burdens of proof are not discussed. If we are going to develop a multidisciplinary science, these conflicts must be recognized. To teach cross-disciplinary science, they must be managed. GFAJ-1 offers a marvelous example.

References

[1] Alberts, B. (2011) Science, DOI: 10.1126/science.1208877
[2] Wolfe-Simon, F. et al. (2010) Science, DOI: 10.1126/science.1197258
[3] Galison, P. L. (1987) How Experiments End, Chicago, University of Chicago Press
[4] Benner, S. A. (2009) The Life, the Universe and the Scientific Method. Gainesville, FfAME Press.
[5] Kaku, M. (Dec. 3, 2010) Life as we don’t know it: NASA’s discovery of an ‘exotic’ DNA changes everything. Wall Street Journal
[6] Redfield, R. (Dec. 4, 2010) Arsenic associated bacteria.
[7] Drahl, C. (Dec. 8, 2010) Arsenic bacteria breed backlash. Chem. Engineering News
[8] Wolfe-Simon iet al., Response to Comments on “A Bacterium That Can Grow Using Arsenic Instead of Phosphorus”
[9] Redfield, R. J., Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”
[10] Csabai. I., Szathmáry, E. Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”
[11] Sagan, C. (1990) Encyclopedia Galactica. Cosmos: A Personal Voyage. Episode 12, 1 min 10 sec.
[12] Kay, E. R. M. (1965) Nature 206, 371-373
[13] Dods, R. F., Roth, J. S. (1969) J. Org. Chem. 34, 1627-1630.