Sequencing DNA on Mars – Science Far Out or Far Out Science?

There’s no shortage of clever “lab-on-chip” (LOC) devices for all sorts of interesting point-of-use applications; however, investigating the feasibility of an LOC for sequencing DNA on Mars seemed “far out” to me both extraterrestrially and scientifically. After some poking around in the literature to learn more about this research – which turns out not to be too far-fetched – I thought it would be worth sharing here some background about astrobiology and some experimental specifics.

What are Astrobiology and NASA’s Astrobiology Program?

According to the US National Aeronautics and Space Administration (NASA), “astrobiology is the study of the origin, evolution, distribution, and future of life in the universe. This multidisciplinary field encompasses the search for habitable environments in our Solar System and habitable planets outside our Solar System, the search for evidence of prebiotic chemistry and life on Mars and other bodies in our Solar System, laboratory and field research into the origins and early evolution of life on Earth, and studies of the potential for life to adapt to challenges on Earth and in space.”

Future astrobiologist in search of a sample for possible DNA detection? (Bing Images)

Future astrobiologist in search of a sample for possible DNA detection? (Bing Images)

NASA’s Astrobiology Program addresses three fundamental questions:

  • How does life begin and evolve?
  • Is there life beyond Earth and, if so, how can we detect it?
  • What is the future of life on Earth and in the universe?

Needless to say, these are truly profound questions requiring very long-term commitments by interdisciplinary teams supported by huge – dare I say astronomical – budgets. Readers interested in perusing a presentation detailing how NASA’s entire 2014 budget request of ~$18 billion will be spent can click here, while information about NASA funding opportunities can be found by clicking here. Incidentally, NIH’s budget request for FY 2014 is ~$31 billion.

Primordial Soup

Oparin

Alexander Ivanovich Oparin graduated from the Moscow State University in 1917 and became a Professor of Biochemistry there in 1927. Many of his early papers were on plant enzymes and their role in metabolism. In 1924 he put forward a theory of life on Earth developing through gradual chemical evolution of carbon-based molecules in primordial soup.

Theories and research on how life – as we know it – began and evolved has received considerable attention since 1924 when Soviet biologist Alexander Oparin proposed a theory of the origin of life on Earth through gradual chemical evolution of molecules that contain carbon in the “primordial soup.”

The research continued with Stanley L. Miller’s, now classic paper, “A Production of Amino Acids Under Possible Primitive Earth Conditions” in Science in 1953 – the same year as Watson & Crick’s discovery of the structure of DNA. Miller’s work involved paper chromatography after electrical discharges in a mixture of CH4, NH3, H2O and H2. Extensions of this line of experimentation to detect nucleobases formed under possible prebiotic conditions on Earth that led to evolution are now numerous (click here for more examples).

Possible contamination with terrestrial molecules has been a concern for detection of nucleobases in carbon-rich meteors. However, recent identification of nucleobase analogs 2,6-diaminopurine and 6,8-diaminopurine has been reported by Dworkin and coworkers to strongly support extraterrestrial origin. These investigators conclude that “[b]ecause meteorites may have provided a significant source of prebiotic organic material including purines, it is possible that alternative nucleobases such as 2,6-diaminopurine, 6,8-diaminopurine, xanthine, and hypoxanthine were available for constructing the first genetic molecules” involving an “expanded genetic alphabet,” as proposed in RNA World or all-purine primitive RNA.

According to a NY Times report on September 12th of this year, Dr. Steven Benner – founder of the Foundation for Applied Molecular Evolution – suggested that, if life started out as RNA, minerals containing borate could have been involved in the chemistry of its formation. Since boron has been recently found in a Martian meteorite, Mars might have been a favorable place for RNA to emerge, and for life to start. The report goes on to say that a giant impact could then have kicked up microbe-laden rocks, which latter fell to earth. I should note here that, while this Mars-to-Earth scenario is opposite an Earth-to-Mars pathway discussed below, these “interplanetary nucleic acid-exchange schemes” are, in principle, not mutually exclusive.

Incentive to continue work in this area has been provided in the form of The Origin-of-Life Prize® that is intended to “encourage the pursuit of natural-process explanations and mechanisms of initial ‘gene’ emergence within nature.” Interestingly, this one-time prize worth $1,000,000 that will be paid to the winner(s) as a twenty-year annuity of $50,000 per year “in hopes of discouraging theorists’ immediate retirement from productive careers.”

What is the Possible Origin of Martian Genomes?

One answer to this question is provided by the “common ancestry hypothesis” that involves natural transfer of viable microbes in space, such as from Earth to Mars and Mars to Earth. An international team of scientists, including some from NASA, have published supporting data for the possibility and probability of such transfer of microbes from traveling in meteoroids billions of years ago following the Big Bang development of the universe. Factors taken into account include radiation protection, vacuum, temperatures, acceleration pressures, and spontaneous DNA decay. They conclude that “if microbes existed or exist on Mars, viable transfer to Earth is not only possible but also highly probable, due to microbes’ impressive resistance to the dangers of space transfer and to the dense traffic of billions of Martian meteorites which have fallen on Earth since the dawn of our planetary system. Earth-to-Mars transfer is also possible but at a much lower frequency.” I encourage those of you interested in more information about this possibility, (depicted below), to click here to read Scientific Logic for Life on Mars by Gilbert V. Levin, who was the Principal Investigator of the 1976 Viking mission Mars Lander Labeled Release (LR) experiment.

According to a 2012 article in National Geographic, the LR experiment involved scooping up Martian soil and mixing it with a drop of water containing nutrients from a source of radioactive carbon. The hypothesis was, if the soil contained microbes, metabolism of the nutrients would release either radioactive CO2 or CH4 that could be measured by a radiation detector in the probe. A number of control experiments were also performed. The LR experiment came out positive for life, and the control experiments came out negative.  Unfortunately, two other experiments did not confirm these results and NASA dismissed the possibility of life having been detected. Levin and others have reanalyzed the results and stuck by the claim.

Taken from “Scientific Logic for Life on Mars” by Gilbert V. Levin at www.gillevin.com via Bing Images.

Taken from “Scientific Logic for Life on Mars” by Gilbert V. Levin at www.gillevin.com via Bing Images.

Developing the Search for Extra-Terrestrial Genomes (SETG) Instruments

Feasibility studies aimed at development of instrumentation for SETG have been published in a series of reports by a team of researchers including Christopher E. Carr [MIT & Massachusetts General Hospital (MGH)], Holli Rowedder (MGH), Clarissa S. Lui (MIT), Maria T. Zuber (MIT), and Gary Ruvkun (MGH & Harvard Medical School) – click here for photos and bios of the SETG Team.

In a 2011 report, they addressed various aspects of isolating, extracting, and sequencing nucleic acids in situ on Mars – particularly 16S and 23S ribosomal RNA genes. These genes are used for phylogenic analysis to address whether sequences found on Mars are similar to those on Earth and likely contamination, or indicative of extant Martian life isolated from that on Earth for the past 3+ billion years.

These investigators note that investigating DNA extraction and amplification from Martian soil of unknown composition is a significant issue; however, “Martian soil simulants” have been developed based on spectral characterization of soild matter on Mars from the Viking and Pathfinder landing sites. Among various LOC-compatible DNA purification and concentration methods, synchronous coefficient of drag alteration (SCODA) was said to be a promising new technique—click here for a poster on SCODA applied to a Martian soil analog presented at the Astrobiology Science Conference 2012. Challenges facing all of the other steps in sample-to-answer for a SETG instrument are addressed in the aforementioned 2011 report, which correctly – in my opinion – emphasizes that library preparation will be especially difficult to solve due to there being numerous steps and reagents.

setg

The current SETG instrument contains a 2 cm x 2 cm microfluidic chip module containing tiny nanoliter wells where the real-time polymerase chain reactions occur. Tiny tubes feed in chemicals and blue light illuminates fluorescent dyes that help identify and analyze DNA molecules (picture and caption taken from MIT website).

In addition to the SETG reports, two follow-on reports have been published in Astrobiology this year. In the first of these, Carr et al. demonstrated that Ion Torrent’s semiconductor proton-sensing, optics-free (“no fluorescence”) sequencing chips survive several analogs of space radiation at doses consistent with a 2-year Mars mission, including protons with solar particle event–distributed energy levels and 1 GeV oxygen and iron ions. There was no measurable impact of irradiation at 1 and 5 Gy doses on either sequencing quality or low-level hardware characteristics. The second report by Carr et al. demonstrated that biological and chemical components, such as polymerase, dNTPs, and fluorescent dye molecules survived several analogs of the radiation expected during a 2-year mission to Mars, including proton (H-1), heavy ion (Fe-56, O-18), and neutron bombardment. Other reagents had reduced performance or failed at higher doses. It was concluded that, overall, the findings suggest it is feasible to utilize space instruments with biological components for mission durations up to several years in environments without large accumulations of charged particles, such as the surface of Mars.

After reading these SEGT-related publications, I contacted Prof. Carr to ask if a SEGT instrument was part of NASA’s Mars 2020 Mission that I had read about in a July 27th blog post by Van Kane on The Planetary Society website. The detailed blog was entitled The Mars 2020 Rover In-Depth, which said that NASA’s next major mission to the Red Planet will store samples for eventual return to the Earth. Prof. Carr’s reply to me was that “[w]e are not currently slated for a mission. The Mars 2020 rover mission is likely to include the best package of instruments possible based on the submitted proposals and the priorities outlined in the recent Science Definition Team report….[T]he strawman set of instruments is somewhat similar to those on Curiosity. But there will almost assuredly be some new instrumentation. Sample return caching certainly would be completely new.”

In closing this post, I welcome comments, especially opinions on whether sequencing DNA on Mars is “science far out” or “far out science”?

Postscript

Doubts about Martian methane: On September 19th the Wall Street Journal reported in an online video that NASA scientists say they cannot find any traces (less than one part per billion) of methane in the thin Martian air, dimming hopes that microbes might lurk under the protective blanket of soil on the cold arid world. Also reported were long-range data to the contrary, and mention of upcoming Martian methane-detection missions by India and the European Space Agency.

Soil samples taken and analyzed from this site have been found to contain Martian water. The left dimension of each scoop is 4 cm (~1.5 in)! Courtesy NASA/JPL-Caltech/MSSS via Bing Images.

Soil samples taken and analyzed from this site have been found to contain Martian water. The left dimension of each scoop is 4 cm (~1.5 in)! Courtesy NASA/JPL-Caltech/MSSS via Bing Images.

Mars has a surprising amount of water! One week later on September 27, Curiosity researcher Laurie Leshin and colleagues told Science Magazine that Mars’ dusty red covering holds about 2% water by weight. This could be a useful resource for future astronauts, they say. “If you think about a cubic foot of this dirt and you just heat it a little bit – a few hundred degrees – you’ll actually get off about two pints of water – like two water bottles you’d take to the gym,” Dr Leshin explained. Aside from drinking or farming, water could also be a source of H2 and O2 for fuel and breathing, respectively.

Do you want a one-way ticket to Mars? Mars One is a non-profit organization that plans to establish a permanent human colony on Mars by 2023. The private spaceflight project is led by Dutch entrepreneur Bas Lansdorp, who announced official plans for the Mars One mission in May 2012. In 2022, four carefully selected applicants will be launched in a Mars-bound spaceflight to become the first residents on Mars. Every step of the crew’s journey will be documented for a reality television program that will broadcast 24/7/365. On August 9th, CNN reported that more than 100,000 people have applied for this one-way trip to Mars, hoping to be chosen to spend the rest of their lives on uncharted territory. Who knows, maybe they will be able to extract Martian soil samples in attempts to detect and sequence DNA.

Coincidentally, it was reported in the September 12th, 2013 issue of Nature that NASA is launching a research program to investigate how human and other tissue reacts to time spent in space. Grant applications for up to $500,000 for a 5-year period will be accepted in Fall of 2014.

Artist rendition of the Mars One colony (taken from oditycentral.com via Bing Images)

Artist rendition of the Mars One colony (taken from oditycentral.com via Bing Images)