Can Craig Venter get Martian biology “at the speed of light”

Craig Venter was interviewed by Charlie Rose last week, repeating highlights from his recent book “Life at the Speed of Light”. As one of these, Craig told Charlie that if we were just to send a DNA sequencing instrument to Mars, sequence the DNA of Martians living there, radio that sequence back to Earth, and synthesize the Martian DNA here, then we could have Martian life on Earth without needing to do the rocket science needed to actually send a physical specimen of Martian life from Mars back to Earth.

Radio waves travel, of course, at the speed of light. Hence: life at the speed of light.

No one is a bigger fan of Craig than I am. However, Craig would be a better synthetic biologist if his enormous imaginative powers included imagination within organic chemistry.

Basically, Craig has caught himself in the “Earth-o-Centricity” trap. The trap catches those who assume that the chemical structures of the molecular parts of life throughout the universe are the same as the molecular parts of life on Earth.

Ask yourself a simple question: What makes us certain that Martian life has DNA? After all, the RNA-World hypothesis holds that life on Earth, at least for part of its early natural history, used RNA rather than DNA as its genetic material. If instead of going to Mars, we were to send Craig’s sequencer back in time to sample the life on early Earth expecting to find DNA, that hypothesis (if true) would imply a disappointment.

Nor is it beyond possibility that another biopolymer having a quite different backbone structure could support genetics. According to the “polyelectrolyte theory of the gene”, the only “universal” for a genetic biopolymer is a repeating backbone charge.

And even if Martians living today do have DNA, what makes us think that its building blocks have the same structure as the building blocks of terran DNA? Researchers in my laboratory have shown that alternative nucleobases can serve the roles of G, A, C, and T in natural DNA. What if Martian life used these?

If aliens have different biochemistries, Craig’s proposal is, well, problematic. The polymerase chain reaction (PCR) works only if it is done with enzymes and substrates appropriate for the genetic biopolymer being amplified. Considerable amount of work, some in our laboratories, shows that the enzymes that PCR amplify terran DNA do not work so well with structurally modified DNA, even if that structural modification is small. Likewise, the triphosphates included in a typical PCR kit (the terran G, A, C, and T) work only if Martian DNA is also built from G, A, C, and T).

If Martian genetics were based on a molecule whose structure differed even slightly (and certainly if that structure different dramatically) from the structure of DNA and RNA,  Craig’s mission would be a flop, perhaps not a cosmic flop but, at least, and interplanetary flop.

And unfortunately, the outcome could be considerably worse. Absent exceptional cleanliness, any sequencer that we send to Mars would carry with it a few terran microbes, microbes having exactly the DNA that Craig’s sequencer would most efficiently amplify and sequence. Unless Martian genetics had exactly the same biomolecules as terran, his sequencer would sequence these hitchhiking microbes. At the speed of light, we would recover the DNA of a terran organism that we ourselves had just sent to Mars. Bummer.

Earth-o-Centricity afflicts everyone. Like the screen writers for low budget science fiction movies, where all of the aliens appear to be Hollywood actors wearing prostheses.

The central challenge when setting out to discover alien life boils down to two simple chemical facts: It is easy to detect a molecule whose structure is known. It is difficult to detect a molecule whose structure is not known. And unless Martian biomolecules are like terran biomolecules, they will be difficult to detect. Even if we are sitting on a pile of them.

Alien Microbes in Comets? A Tempting Science

In middle school, we learned that scientists accept conclusions when they are supported by evidence. Were it only so simple.

Take Richard Hoover. Working at NASA in Alabama, Hoover sliced up a piece of a Murchison “carbonaceous chondrites”, a meteorite rich in tarry, carbon-rich material. Looking at the slices with an electron microscope, he saw features in the carbon-rich material that looked like bacteria and fungi.

These pictures were certainly evidence. Compare for yourself the images from the chondrites with electron micrographs of Earth bacteria and fungi. Both have round cell-like structures. Both have spirals, and other shapes familiar to microbiologist.

Which is the Earthling? Which is the alien?

Both have filaments. They look like microbes.

Let that sink in for a moment. Bacteria. In a rock. From outer space.

Hoover rejected the hypothesis that he was seeing bacteria from Earth that infected the rock after it had landed on Earth. The structures lacked the nitrogen that such bacteria would have brought with them. Instead, he concluded from his evidence that bacteria actually live in rocks in outer space.

This is Star Trek stuff. If alien life exists in rocks in outer space, even if only of the single-celled kind, then the likelihood of life on whole planets would seem to go up. Of the sophisticated kind. Vulcans, Klingons, Romulans. Considerably.

But his conclusion was not accepted by many in the community of people who call themselves “astrobiologists”. Why?

We might conjecture that astrobiologists rejected Hoover’s conclusion using the following reasoning: (a) We have never heard of microbes living in rocks in outer space. (b) Therefore, microbes cannot possibly be living in rocks in outer space. Accordingly, (c) Hoover must have been looking at something other than the remnants of outer space-bacteria.

Everyone would agree that this reasoning is not acceptable in science. Such reasoning would have caused scientists to miss most advances in the history of science. Continental drift (continents do not drift). Evolution (species are fixed). Relativity (space-time, what the heck is that?).

As it did indeed cause many “scientists” to miss these advances.

No. Scientists are supposed to consider novel ideas and evaluate them within the context of the question: “If this crazy idea were true what, among the things we think are true, must be false?”

Let us start with a fact: If a competent advocate has total control over what data to present (and what to ignore), (s)he can make a convincing argument that any proposition is correct. Lawyers can make a persuasive case that any client is innocent. Marketers, by mentioning only the good features of a product, can make any product seem to be a desirable purchase. Even Adolf Hitler might seem like a nice chap if you select the data carefully.

Awwww.

This fact is especially relevant when trying to recognize patterns in images. Percival Lowell spent hours with a telescope to see canals on the surface of Mars. They are not there. Indeed, if one looks at enough pictures of parts of Mars, you will eventually see a human face. It is not a human face. Ultramicroscopy produced images that looked like DNA, images in fact arising from defects in the surface on which the DNA was supposed to be supported.

Electron microscopes produce many, many images. A square centimeter of surface, if divided into pixels about the size of a bacterial cell, gives 100 million images. With tarry organic material, like found within carbonaceous chondrites, astrobiologists had a reasonable thought: Some of these are bound to look like bacteria, something filamentous, or round, or spirally. Take enough images, and you might even find Christ in your chondrite.

Humans naturally see familiar patterns in unpatterned data. Like a face on Mars.

Jesus in a pizza?

Unfortunately, Hoover released only a few of the many images that he collected as he looked closely at the Murchison chondrite. This does not mean that he was being dishonest. Scientists are allowed to select a subset of their data to present to the public; indeed, they must. Too much data are generated by a real laboratory to not pick.

But, as Richard Feynman says, people are easy to deceive, and the easiest person to deceive is yourself.

Which caused the scientific community to ask: Can we see the rest of Hoover’s images?

Hoover was invited to post his images, all of them, on the internet so that everyone could browse. To see how frequently the images showed something that looked like life. To see how many showed nothing. And, while we were at it, to see how many looked like a pizza. Dr. Hoover said that his institution did not provide such a hosting service. The Foundation for Applied Molecular Evolution offered to provide these services. Hoover declined.

Exceptional claims require exceptional evidence. What makes a claim exceptional is determined by the presumptions of the community, which place a burden of proof on the claimant. The astrobiology community, Hoover’s target audience, began with the presumption that life is not present in rocks living in outer space. They are willing to consider evidence to the contrary; indeed, most would love to be convinced of the contrary. But unless all of the evidence is available for inspection, the community will dismiss claims of such. The community might be wrong, but this is how science maintains reasonable expectations while seeking new knowledge.

 

Daniel Benner

Be Nice to Geologists

Well, I have been taken to the woodshed by my many geologist friends for using the word “geologist” to describe those who use the Periodic Table to guide their expectations, which in turn are key to deciding whether or not a result is viewed as “extraordinary”, in the Sagan sense.

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.

Arsenic DNA is not a “Heresy”

As a short follow up, lots of blogs are using the word “heresy” to describe the proposal that the DNA in GFAJ-1 contains arsenic at spots instead of phosphorus. It is not heresy; it is just a hypothesis, and can be tested like any other.

Does Arsenic Really Exist in the DNA from GFAJ-1?

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.

Continue reading ‘Does Arsenic Really Exist in the DNA from GFAJ-1?’ »

What is Synthetic Biology?

Kicking and screaming toward uncharted territoryMany languages have words and phrases, called contranyms, that have two nearly opposite meanings. For example, a “citation” from Harvard University is good, but a “citation” from the Harvard University police is bad. If you run “fast”, you are moving at great speed; if you hold “fast”, you are not moving at all.

“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.

Continue reading ‘What is Synthetic Biology?’ »

  • About "A Tempting Science"

    Steven BennerSteven Benner discusses recent events in science and how they force us to think about how science is done. For information about Steven Benner’s career, research goals, and publications, please view his biosketch.

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