My bad. And to think of it, more correct for such folks would be the word “chemist”. After all, the Periodic Table is at the core of chemistry. Further, those whose work in geology departments centers on the Table might call themselves “geochemists”, to distinguish themselves from those whose work centers on hiking landscapes to plot strata.

Now, anyone who finds the string c-h-e-m-i-s-t somewhere in their CV does not a priori find it absurd to propose that an element below another element in the Table might substitute for an element above. Especially organic chemists. Indeed, the “halogen series” of compounds (fluorine replaced by chlorine replaced by bromine replaced by iodine) is a staple of physical organic chemistry; the changing reactivity of one set of compounds along that series is used to calibrate changing reactivity for many other sets.

This is even true for elements in the middle of the Table. People who base expectations using the Periodic Table (shall we call them X-chemists?) do not discard generally as absurd the notion that silicon might substitute for carbon in some contexts, or arsenic might substitute for phosphorus, with “trend-like” changes in behavior.

But Sagan’s aphorism (“extraordinary claims require extraordinary evidence”) was the focus of my comment, not the naming of fields. It is not easily applied, as “extraordinary” depends on context. If all that you know about chemistry is the Periodic Table, the claim of arsenate DNA might not strike you as requiring extraordinary evidence. Only if you know much more chemistry does this change.

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.

“Synthetic biology” is a contranym. In a version popular today in some engineering communities, “synthetic biology” seeks to use natural parts of biological systems (like DNA fragments or protein “biobricks”) to create assemblies that do things that are not done by natural biology (such as digital computation or specialty chemical manufacture). Here, engineers hope that the performance of the molecular parts drawn from living systems can be standardized, allowing them to be mixed and matched to give predictable outcomes, just as an electrical engineer can assemble standardized transistors to give integrated circuits with predictable performance.

Among chemists, “synthetic biology” means the opposite. Chemist’s “synthetic biology” seeks to use unnatural molecular parts to do things that are done by natural biology. Chemists believe that if they can reproduce biological behavior without making an exact molecular replica of a natural living system, then they have demonstrated an understanding of the intimate connection between molecular structure and biological behavior. This would provide a chemical understanding of life. Although central to chemistry, this research paradigm was perhaps best expressed by a physicist, Richard Feynman, in the phrase: “What I cannot create, I do not understand” (quoted in [1]).

Waclaw Szybalski had yet a different meaning in mind when he coined the term “synthetic biology” in 1974 [2]. Szybalski noted that recombinant DNA technology would soon allow the construction of new cells with rearranged genetic material. He realized that this deliberate “synthesis” of new forms of life provided a way to test hypotheses about how that material contributed to the function of natural cells. More commonly, this came to be known as “genetic engineering”.

Szybalski had the experience of chemistry in mind when he coined the term. In 1974, Structure Theory in chemistry was the most powerful theory in science. It became that way largely because chemistry possessed technology that allowed chemists to synthesize new chemical matter to study. This allows a powerful process for testing hypotheses and models, a power that Szybalski was hoping to gain for biology. These tests were (and remain) unavailable to (for example), astronomy, planetary science, and the social sciences.

By 1974, “synthetic organic chemistry” had already encroached deep within biological territory. For example, in the previous decade, “biomimetic chemists” had created small designed molecules that reproduced the elementary behaviors of single biomolecules, such as their ability to bind to ligands or to catalyze reactions. Jean-Marie Lehn in Strasbourg shared a Nobel Prize for his work developing molecules in the 1960′s to do exactly this.

Today, the chemist’s vision for synthetic biology goes further. The grand hope is that molecular design supported by Structure Theory will yield unnatural molecular species able to mimic not just binding and catalysis, but also the highest kinds of biological behavior, including macroscopic self-assembly, replication, adaptation, and evolution. Any theory that enables such a design will have demonstrated its ability to account for “life”. It will also thereby demonstrate an understanding of life, by making a synthetic version of it.

Given these nearly opposite uses of the same term, spectators are naturally puzzled. I am repeatedly asked about the emerging use of “synthetic biology” in the engineering sense: “What’s the fuss?” I am asked. “Isn’t synthetic biology just more ‘Flavr Savr’^® tomatoes?” The question is raised in analogous form by molecular biologists who see in synthetic biology “contests”, which attract student participation worldwide, nothing more (and nothing less) than the cloning that has been done since the 1970′s.

Nor do molecular biologists entirely understand the hullabaloo over the (difficult to repeat) use of DNA hybridization and ligation to compute a solution to the “traveling salesman problem” [3] or create “smiley faces”. There is no obvious reason to do this kind of digital computation with DNA. After all, the rate at which DNA molecules hybridize in solution is limited by the rate constant for molecular diffusion, about 10⁸ M^-1sec^-1. In layman’s language, this means that the half-life with which a DNA molecule finds its complement cannot be faster than a few hundredths of a second under typical laboratory conditions. Contrast this with the limit on the rate at which semiconductors compute: the speed of light. Even with the possibility of improved parallelism with DNA computation, there is no contest.

Francis Collins, director of the National Institutes of Health, captured a similar sentiment as applied to virus synthesis as a “synthetic biology” challenge. “This was completely a no-brainer,” he mused. “I think a lot of people thought, ‘Well, what’s the big deal? Why is that so exciting?” (quoted in [4])

The salesmanship that accompanies some discussions today of “synthetic biology” has engendered a degree of cynicism. Those whose professional lives started before the age of the internet remember more than one time where biology, it was claimed, had at last entered the realm of engineering.

For example, a quarter century ago, Science published an article entitled “Protein Engineering” by Kevin Ulmer, Director of Exploratory Research at GeneX, a biotechnology company [5]. His 1983 paper declared that the new engineering biology would “control in a predictable fashion” the properties of proteins to be building blocks in industrial processes. This new engineering would set aside “random mutagenesis techniques” in favor of a “direct approach to protein modification”. Ulmer referred to protein domains encoded by exons and the use of repressors with altered enzymes to assemble new regulatory pathways in cells. The language was in 1983 no so different from the breathless reports in the media today on the advent of “synthetic biology”.

Ulmer’s 1983 vision failed. GeneX is no longer in business. And 25 years later, we are still struggling to engineer the behavior of individual proteins.

The 1980′s engineering vision failed for reasons discussed in a 1987 review by Jeremy Knowles, then Dean of Harvard College. The review was entitled Tinkering with Enzymes [6]. Knowles, a chemist, understood that “scale” matters in the physical world. Molecules, which exist at the one to one-tenth nanometer scale, behave differently from transistors, even transistors existing at the one to one-tenth micrometer scale. This creates difficulties in transferring engineering concepts to molecular engineering.

Knowles’ “Tinkering ” comments are applicable today for those who say that biology is now engineerable. Referencing Ulmer’s paper, Knowles dryly wondered whether the engineering vision was not, perhaps, a bit “starry-eyed”. He acknowledged that “gee-whiz” experiments that put things together to “see-what-happens” could aid in understanding. But he made the point that is still true: Nothing of value comes unless the tinkering is followed by studies of what happened. Especially if the experiment fails. Absent that, modern synthetic biology, at the molecular, DNA, protein, or cell level, will be “tinkering” without consequence.

We understand much more now about the behavior of molecules, biological and otherwise, than we understood a quarter century ago because tinkers of yore studied their failures. Accordingly, the ball has been moved, from small molecules to proteins and now, to synthetic genes, protein assemblies, and cells and their assemblies. We are still doing what might be best called “Tinkering Biology”; we are just doing it farther down the field. This term will be appropriate until failures in synthetic biology are commonly examined to understand what went wrong.

However, the contranymic views of “synthetic biology” have one thing in common. Synthesis is a research strategy, not a field [7][8]. Synthesis sets forth a grand challenge: “Create an artificial chemical system capable of Darwinian evolution.” Or: “Create a set of DNA bricks that can be assembled to form an adding machine.” Or: “Rearrange a set of regulatory elements to make a cell that detects nerve gas.” Or: “Assemble enzyme catalysts from a variety of organisms to generate a pathway to make an unnatural chemical that is part of an anti-malarial drug.” Attempting to meet this challenge, synthesis drags scientists and engineers across uncharted territory, where they must encounter and solve unscripted problems. If their guiding theory is wrong, the synthesis fails, and fails in a way that cannot be ignored.

Synthesis, as a research strategy, has a value different from observation, analysis, and probing, other strategies used in science. Here, as often as not, observations are often either discarded or rationalized away when they contradict a (treasured) theory. Experiments are reported only if they get the “right” answer.

Selection of data to get the “right” answer has a long tradition in biology. A well-known example is Gregor Mendel, who evidently stopped counting round and wrinkled peas when the “correct” ratio (which is 3:1) was reached. Objective observations have an uncanny ability to confirm a desired theory, even if the theory is wrong.

Self-deception is far more difficult when doing synthesis. If, as happened with the Mars Climate Orbiter, the guidance software is metric and the guidance hardware is English, one can ignore the incongruent observations (which was done) arising from a false theory in transit all of the way to Mars. But when the rocket gets to Mars, if the theory is wrong (and it was), the rocket crashes (and it did).

For this reason, synthesis as a research strategy drives discovery and paradigm shift in ways that observation and analysis cannot. Science is, after all, a human intellectual activity that incorporates a mechanism to avoid self-deception [8]. Synthesis provides such a mechanism. And for those who do not capture this, the benefit of this mechanism will be largely lost.

References

[1] S. Hawking, The Universe in a Nutshell, Bantam Spectra, New York, 2009.
[2] W. Szybalski, in: A. Kohn, A. Shatkay (Eds.), Control of Gene Expression, Plenum Press, New York, 1974, pp. 23-24, 404-405, 411-412, 415-417.
[3] L. M. Adleman, Science 266 (1994) 1021-1024.
[4] E. Regis, What is Life? Investigating the Nature of Life in the Age of Synthetic Biology, Oxford University Press, Oxford, UK, 2009.
[5] K. M. Ulmer, Science 219 (1983) 666-671.
[6] J. R. Knowles, Science 236 (1987) 1252-1258.
[7] S. A. Benner, A. M. Sismour, Nature Rev. Genetics 6 (2005) 533-543.
[8] S. A. Benner, Life, the Universe and the Scientific Method, FfAME Press, Gainesville FL, USA, 2009.