The Origin of Life discussed at Cern.

Biology as a foundation for theoretical physics has taken a step forward.

CERN Colloquium

"The current status of work on the origin of life" by Stuart Kauffman (FRSC, U Vermont, Santa Fe Institute, Tampere U. Technology) Thursday 19 May 2011 from 16:30 to 17:30 (Europe/Zurich) at CERN

A miniconference, but still a step in the right direction. “The aim of this research group is to create theory and experiments to produce at least one, or several, candidate evolving protocells in the next decade.”

While physicists at CERN currently study the origin of the universe and the origin of matter, in the future they may be asked to help crack the origin of life too. On May 20, a small group of chemists and biologists gathered at CERN for a brainstorming workshop discussing ideas about the origin of life, and to hear from CERN experts about how to organize a scientific community from disparate research groups and how to access powerful computational resources.

“There is a serious risk that the answer to the question ‘How on Earth has life appeared on Earth?’ will mainly remain in the realm of philosophy for the years to come unless we can take definitive scientific approaches,” said Stuart Kauffman, an American molecular biologist and complexity theorist who co-organized the workshop with Markus Nordberg, resources coordinator at ATLAS, one of the largest experiments at CERN.

Kauffman and his colleagues believe that the crucial step towards life was the formation of autocatalytic sets. An autocatalytic set is a group of molecules which undergo chemical reactions in which some of the molecules catalyze - that is, significantly increase the rate at which the reaction takes place - other reactions in the set. Importantly, though, all molecules mutually catalyze each other’s creation, meaning that autocatalytic sets are ‘self-sustaining’. It’s thought that molecular reproduction and protocells then emerge from such a system.

The text in Cern: called together by Ignatios Antoniadis/PH-TH & Markus Nordberg/PH-ADO.

Work on the Origin of Life is poised to converge onto a fourth phase and, many of us hope, success.

The first phase concerned prebiotic synthesis of the small molecules, amino acids, nucleotides, lipids and others, essential for life and spanned some forty years.

The second overlapping phase was inspired by the symmetric of the DNA or RNA double helix, presumed that life must necessarily be based on some form of template replication of one strand by ligation of free nucleotides to create the second strand, melting of the two strands and cycling again. Spearheaded by L. Orgel, but with many others, this effort has, to date, failed.

The third phase begins with the discovery that RNA molecules can act as enzymes, and posited the RNA world, in which RNA molecules dominated. This has led to slightly successful efforts to evolve an RNA sequence able to template replicate itself. Current success is an evolved ribozyme able to do so for 14 nucleotides.

The forth phase is converging around four ideas: 1) liposomes, hollow bilipid spheres obtainable from lipids in water, can grow and divide. We now widely hope that these can serve as “containers” bounding proto-cells. 2) Sources of free energy, from pyrophosphate to proton pumps. 3) A minimal metabolism in a “messy” systems chemistry which supplies the small amino acids, nucleotides and lipids for proto -life. 4) Collectively autocatalytic sets of polymers, peptides, RNA, or other, which achieve molecular reproduction in dividing liposome containers, hence also open ended evolution. At present, a 9 peptide collectively autocatalytic set has been constructend, achieving catalytic closure, and demonstrated beyond doubt that the DNA or RNA double helix is not needed for molecular reproduction. In addition a two membered DNA autocatalytic set has been constructed and two two membered RNA ribozyme autocatalytic sets have been selected from a large RNA library.

The author, in 1971 and 1986 proposed a theory in which the emergence of collectively autocatalytic sets is a first order phase transition as the diversity of polymers that are also candidates to catalyse the reactions they undergo, increases in diversity. Recent theorems have improved upon this initial model, simulations have shown that small collectively autocatalytic sets can emerge in this process and grow together, and also that, in the presence of inhibition of catalysis and if contained in duplicating containers, can indeed serve as plausible protocells able to evolve indefinitely.

The author has gathered some 17 scientists from around the world to collaborate and compete with one another, CERN/LHC experiments style, in a generative scientific environment.
http://indico.cern.ch/event/137302

Kauffmans talk (bad quality, webcam only):
"The current status of work on the origin of life"

“For a long time, it has been debated how likely it is that such autocatalytic sets exist in arbitrary chemical reaction systems,” said Wim Hordijk, a computational and bioinformatics specialist at the University of Lausanne in Switzerland.

“If I randomly throw a bunch of molecules together, and let them react according to the possible reactions between them, can I expect to see one or more of these autocatalytic sets? Some researchers believe they are very likely to occur. Others believe that it is almost impossible that they appear in a random chemistry – similar, they sometimes argue, to the question of what the probability is that a whirlwind blowing through a scrap yard will put together a Boeing 747,” Hordijk said.

Analyzing autocatalytic sets

Until now, little mathematical analysis has been done on this question. But recently, Hordijk developed computer models to explore possibilities and scenarios for autocatalytic sets, in the hope that it could help others figure out how to set up laboratory experiments that would otherwise be too expensive and time-consuming without this prior knowledge.

“So far we have used our own personal computers or relatively small computer cluster to run our simulations on. However, we have already run into limitations in terms of available computing power,” Hordijk said.

Hordijk and his colleague Mike Steel have developed a model of a chemical reaction system where the probability of an arbitrary molecule being a catalyst for an arbitrary reaction was two in a million, a probability that is “chemically plausible” he said. Running this model on the LHC computing grid, he found that, with this level of catalysis, a set of about 65,000 different molecule types or more will have a high probability of forming an autocatalytic set. This is actually reasonable for a chemist in a laboratory to test, he said.

“We are hoping to use the computing grid to perform [future] simulations and analyses, which would enable us to go much further and deeper than we have been able to do so far. We have already done some small test runs just to make sure our software runs on the LHC grid [facilitated by the ATLAS experiment], which seems to be the case,” Hordijk happily reported.

Other areas being explored include self-reproducing RNA, ‘metabolism first’ theories and self-reproducing liposomes - small vesicles formed when lipid molecules, like fats and oils, align to make a membrane. Almost all the theoretical work is underpinned by complex models that would need large-scale computing power.

There are several options for computing power available out there, Bob Jones, project director of CERN’s openlab told the group, including other grid infrastructures, supercomputers, clouds and volunteer computing.

“New science can arise in unexpected ways”

"Our group of seven origin of life workers, representing an initial group of 22 of the top researchers in the field, were truly thrilled by our CERN meeting,” said Kauffman. “If CERN wishes it, we hope to become a small part of the CERN world, for the origin of life is itself a problem in physics. New science can arise in unexpected ways."

First, however, the Origin of Life group needs to make a formal proposal for such a project, and CERN must agree formally to support the work. “We hope this occurs. Such approval will help drive an international effort in origin of life research,” Kauffman said.

So, no results from here in several years.

Quantum biology - DNA

The Relevance Of Continuous Variable Entanglement In DNA June 28, 2010. ArXive blog.

Quantum entanglement helps prevent the molecules of life from breaking apart? Earlier I wrote of quantum photosynthesis, now the DNA-bondings. I quote:

There was a time, not so long ago, when biologists swore black and blue that quantum mechanics could play no role in the hot, wet systems of life. Since then, the discipline of quantum biology has emerged as one of the most exciting new fields in science. It's beginning to look as if quantum effects are crucial in a number of biological processes, such as photosynthesis and avian navigation which we've looked at here and here.

Now a group of physicists say that the weird laws of quantum mechanics may be more important for life than biologists could ever have imagined. Their new idea is that DNA is held together by quantum entanglement.

Entanglement is the weird quantum process in which a single wavefunction describes two separate objects. When this happens, these objects effectively share the same existence, no matter how far apart they might be.

The question that Elisabeth Rieper at the National University of Singapore and a couple of buddies have asked is what role might entanglement play in DNA. To find out, they've constructed a simplified theoretical model of DNA in which each nucleotide consists of a cloud of electrons around a central positive nucleus. This negative cloud can move relative to the nucleus, creating a dipole. And the movement of the cloud back and forth is a harmonic oscillator.

When the nucleotides bond to form a base, these clouds must oscillate in opposite directions to ensure the stability of the structure.

Rieper and co ask what happens to these oscillations, or phonons as physicists call them, when the base pairs are stacked in a double helix. Phonons are quantum objects, meaning they can exist in a superposition of states and become entangled.

To start with, Rieper and co imagine the helix without any effect from outside heat. "Clearly the chain of coupled harmonic oscillators is entangled at zero temperature," they say (T=0K). They then go on to show that the entanglement can also exist at room temperature.

That's possible because phonons have a wavelength which is similar in size to a DNA helix and this allows standing waves to form, a phenomenon known as phonon trapping. When this happens, the phonons cannot easily escape. A similar kind of phonon trapping is known to cause problems in silicon structures of the same size.

That would be of little significance if it had no overall effect on the helix. But the model developed by Rieper and co suggests that the effect is profound.

Although each nucleotide in a base pair is oscillating in opposite directions, this occurs as a superposition of states, so that the overall movement of the helix is zero. In a purely classical model, however, this cannot happen, in which case the helix would vibrate and shake itself apart.

So in this sense, these quantum effects are responsible for holding DNA together.

The question of course is how to prove this. They say that one line of evidence is that a purely classical analysis of the energy required to hold DNA together does not add up. However, their quantum model plugs the gap. That's interesting but they'll need to come up with something experimentally convincing to persuade biologists of these ideas.

One tantalising suggestion at the end of their paper is that the entanglement may have an influence on the way that information is read off a strand of DNA and that it may be possible to exploit this experimentally.

Speculative but potentially explosive work. Maybe the experimental proofs comes from things discussed at Gibbs and Keas bloggs? Keas hexagons are also interesting as a minute synapse model and receptor model in biology. I have long looked for something like that. Also TGD has much on DNA and quantum biology.