Autocatalytic Sets Center Stage - Princeton Origins of Life

Earlier Reports in this series:
Conference Preview
Conference Report #1
Conference Report #2
Conference Report #3

Wednesday, 23 January 2013:

As British chemist John Sutherland et al. exited following their conference presentations and other invited guests were no-shows, the Princeton Origins of Life event further opened up to the public, which invigorated proceedings.

One of the morning presenters was Loren Williams, who heads NASA's Georgia Tech team and addressed the "ironing out of ancient biochemistry," noting that early Earth was rich in iron and "collaborated" with RNA, but that magnesium also entered the picture as a co-factor in the origin of life, important in autocatalysis.

Nilesh Vaidya, a researcher at Princeton University and rising star, agreed with Williams about magnesium's importance in autocatalysis. Vaidya gave the next talk: "Spontaneous network formation among cooperative RNA replicators." He has succeeded in creating spontaneously emerging self-reproducing autocatalytic sets from RNA fragments, making them replicate -- "at least three times."

Vaidya said that recombination could have been the earliest replication tool.

In a followup conversation with me and Dutch computer scientist Wim Hordijk, who also presented on autocatalytic sets, Vaidya said this:

"Fragments of RNA and lots of magnesium, as you heard from Loren Williams' talk. For RNA catalysis to happen and to bring the RNA fragments together. And some water. Buffer. That's it. RNA starts making one another. That's the unique thing about that system. You don't need to add anything."

Vaidya's and Hordijk's presentations were a departure from the general conference proceedings. Vaidya explained that his experimental system is dependent on recombination events whereas the other systems are template-directed polymerization processes, requiring "high-energy molecules for a polymerized system to take over."

Vaidya said further that in his experiment there was direct competition between selfish and cooperative systems, with cooperativity increasing with complexity.

McMaster University's Paul Higgs, one of the Lonsdale Origin of Life award winners who spoke Tuesday about the origin of the RNA world, cautioned regarding selfish and cooperative conclusions, saying what he, Higgs has in his model is already cooperative.

Hordijk, now at the University of Lausanne, noted that the concept of autocatalytic sets is 40 years old. Hordjik said he has taken Stuart Kauffman's 1971 concept of Collectively Autocatalytic Sets (CAS) and developed it further in collaboration with New Zealand mathematician Mike Steel from the University of Canterbury. Hordijk and Steel call their model RAFs. Hordijk (hopefully Vaidya, as well) will be presenting again in a few weeks at the Origin of Life conference at CERN -- COOL EDGE 2013.

Former ISSOL president Antonio Lazcano, now at Universidad Nacional Autonoma de Mexico, commented following Hordijk's presentation that there was actually a conversation that took place between Einstein and another scientist about autocatalysis, which is referenced in an obscure paper. No one else I spoke with at the conference seemed to be aware of the paper Lazcano had in mind.

Synthetic biologist Steve Benner "not to pile on" said that increasing complexity can also be an inhibiting factor, something Stu Kauffman acknowledged to me in a post-conference conversation.

NASA's senior-most scientist on Origin of Life, Andrew Pohorille, discussed the puzzle of functionality of the protein, describing its flexibility and robustness and compared it to a scifi character you just cannot kill. He then showed a picture of Tom Cruise dangling from a cliff and quipped that unlike Tom Cruise he does his own stunts.

Loren Williams in a comment from the floor said his observations were that "functional promiscuity went along with structural flexibility" in early proteins. Williams said proteins at first multitask and later become specialized and rigid.

A freeze set in over Princeton on Wednesday. Participants shook off the chill over a group dinner following the afternoon session, which ended with a lecture by University of Connecticut's Peter Gogarten ( one of the "Lonsdale 8") on "coalescence, gene transfer, and the study of pre-LUCA molecular evolution.

Thursday, 24 January 2013:

As various speakers remembered the late Carl Woese in relation to their work, I was reminded of my conversation with him in October in what was probably his last feature interview . Laura Landweber, principal organizer of the Princeton event, who is to be applauded for seeing to it that one-third of the presenters were women, was also one of those to honor Woese's contribution to the field, putting his photo over the Three Domains of Life. Landweber also cited the work of Lamarck in her presentation on the ciliated protozoa, Oxytricha trifallax.

As Darwin Day approaches, I am further reminded of something Woese told me in our interview about both Lamarck and Darwin:

"I've maintained for a long time up until the end of the 20th century that the problem of the evolutionary process is a problem before its time. Darwin was trying to get personal credit by barging in. Conceptual thought about evolution was laid down first by people like Buffon and Darwin's own grandfather, Erasmus Darwin -- whom Darwin never mentions in the Origin of Species, except in a footnote when he was forced in the third edition to add it to the footer of the preface.

He named him in a dismissive way. He basically said, oh yes, a lot of people thought of that and named people like Buffon and Lamarck. But he didn't name his own grandfather, Erasmus Darwin, except to say his grandfather had the same wrong ideas as Lamarck and Goethe. And he didn't say what they were or what his objection to them was. He wanted to distance himself from his grandfather as much as he could."

The Landweber presentation was exacting. At one point she explained how the microorganism's genes scramble and "how RNA-guided eipigenetic mechanisms orchestrate" events leading to remodeling of the genome.

I was looking forward to Dave Deamer's update on his experiment funded by Harry Lonsdale. Deamer did not disappoint. In a carefully documented slide presentation with animation, Deamer discussed how his team formed polymers from monomers. He went from phospholipids to wet - dry cycles. Drying vesicles became multilayered and then the multilayered structures following rehydration reformed into vesicles, capturing inside some of the material that was originally present on the outside.

Said Deamer:

"What we're going to do in just a few minutes is send xray beams into this kind of a matrix and we're going to see what it looks like when a monomer is organized within the matrix. . . . This is just ordinary decanoic acid, we tried it now with a double-stranded DNA just to demonstrate the power of this. All of these fluorescent vesicles have fluorescent-stained DNA inside the vesicles. So this is what you call a protocell and a potentially replicating molecule captured in membrane survivors. . . ."

Deamer then broke for a commercial message about the machine he invented and it's usefulness in pulling RNA through a nanopore. He said it had a 4% rate of error and that the device would be availabe this year at $900@, joking that everyone in the room should buy one.

I managed to get a question in about how much he was making per machine. Deamer responded that his cut was just a small piece of the action and that the University of California was taking the lion's share.

Andrew Pohorille countered that "a 4% error is terrible, absolutely horrible."

Deamer advised that the company was trying to get the error rate down to 1%.

Pohorille was not satisfied, telling Deamer that was "still terrible."

Pohorille also wanted to know if Deamer was making peptides, saying that if both peptides and nucleic acids could be made using the same general mechanism, that would be significant progress and might be a way around problems origin of life investigators have been "fighting over for years."

Deamer said, he's tried a few simple experiments to get peptides but never attempted to activate a peptide.

The Origin of Life caravan moves on to CERN in Geneva end of February, as mentioned, where the focus will indeed be autocatalytic sets.

Useful Link: Princeton Conference Schedule

Suzan Mazur is the author of The Altenberg 16: An Exposé of the Evolution Industry. Her interest in evolution began with a flight from Nairobi into Olduvai Gorge to interview the late paleoanthropologist Mary Leakey. Because of ideological struggles, the Kenyan-Tanzanian border was closed, and Leakey was the only reason authorities in Dar es Salaam agreed to give landing clearance. The meeting followed discovery by Leakey and her team of the 3.6 million-year-old hominid footprints at Laetoli. Suzan Mazur's reports have since appeared in the Financial Times, The Economist, Forbes, Newsday, Philadelphia Inquirer, Archaeology, Connoisseur, Omni and others, as well as on PBS, CBC and MBC. She has been a guest on McLaughlin, Charlie Rose and various Fox Television News programs. Email: sznmzr@aol.com

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