Later On

A blog written for those whose interests more or less match mine.

Seeing Emergent Physics Behind Evolution

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Jordana Cepelewicz interviews Nigel Goldenfeld, director of the NASA Astrobiology Institute for Universal Biology.

The physicist Nigel Goldenfeld hates biology — “at least the way it was presented to me” when he was in school, he said. “It seemed to be a disconnected collection of facts. There was very little quantitation.” That sentiment may come as a surprise to anyone who glances over the myriad projects Goldenfeld’s lab is working on. He and his colleagues monitor the individual and swarm behaviors of honeybees, analyze biofilms, watch genes jump, assess diversity in ecosystems and probe the ecology of microbiomes. Goldenfeld himself is director of the NASA Astrobiology Institute for Universal Biology, and he spends most of his time not in the physics department at the University of Illinois but in his biology lab on the Urbana-Champaign campus.

Goldenfeld is one in a long list of physicists who have sought to make headway on questions in biology: In the 1930s Max Delbrück transformed the understanding of viruses; later, Erwin Schrödinger published What is Life? The Physical Aspect of the Living Cell; Francis Crick, a pioneer of X-ray crystallography, helped discover the structure of DNA. Goldenfeld wants to make use of his expertise in condensed matter theory, in which he models how patterns in dynamic physical systems evolve over time, to better understand diverse phenomena including turbulence, phase transitions, geological formations and financial markets. His interest in emergent states of matter has compelled him to explore one of biology’s greatest mysteries: the origins of life itself. And he’s only branched out from there. “Physicists can ask questions in a different way,” Goldenfeld said. “My motivation has always been to look for areas in biology where that kind of approach would be valued. But to be successful, you have to work with biologists and essentially become one yourself. You need both physics and biology.”

Quanta Magazine recently spoke with Goldenfeld about collective phenomena, expanding the Modern Synthesis model of evolution, and using quantitative and theoretical tools from physics to gain insights into mysteries surrounding early life on Earth and the interactions between cyanobacteria and predatory viruses. A condensed and edited version of that conversation follows.

Physics has an underlying conceptual framework, while biology does not. Are you trying to get at a universal theory of biology?

God, no. There’s no unified theory of biology. Evolution is the nearest thing you’re going to get to that. Biology is a product of evolution; there aren’t exceptions to the fact that life and its diversity came from evolution. You really have to understand evolution as a process to understand biology.

So how can collective effects in physics inform our understanding of evolution?

When you think about evolution, you typically tend to think about population genetics, the frequency of genes in a population. But if you look to the Last Universal Common Ancestor — the organism ancestral to all others, which we can trace through phylogenetics [the study of evolutionary relationships] — that’s not the beginning of life. There was definitely simpler life before that — life that didn’t even have genes, when there were no species. So we know that evolution is a much broader phenomenon than just population genetics.

The Last Universal Common Ancestor is dated to be about 3.8 billion years ago. The earth is 4.6 billion years old. Life went from zero to essentially the complexity of the modern cell in less than a billion years. In fact, probably a lot less: Since then, relatively little has happened in terms of the evolution of cellular architecture. So evolution was slow for the last 3.5 billion years, but very fast initially. Why did life evolve so fast?

[The late biophysicist] Carl Woese and I felt that it was because it evolved in a different way. The way life evolves in the present era is through vertical descent: You give your genes to your children, they give their genes to your grandchildren, and so on. Horizontal gene transfer gives genes to an organism that’s not related to you. It happens today in bacteria and other organisms, with genes that aren’t really so essential to the structure of the cell. Genes that give you resistance to antibiotics, for example — that’s why bacteria evolve defenses against drugs so quickly. But in the earlier phase of life, even the core machinery of the cell was transmitted horizontally. Life early on would have been a collective state, more of a community held together by gene exchange than simply the sum of a collection of individuals. There are many other well-known examples of collective states: for example, a bee colony or a flock of birds, where the collective seems to have its own identity and behavior, arising from the constituents and the ways that they communicate and respond to each other. Early life communicated through gene transfer.

How do you know?

Life could only have evolved as rapidly and optimally as it did if we assume this early network effect, rather than a [family] tree. We discovered about 10 years ago that this was the case with the genetic code, the rules that tell the cell which amino acids to use to make protein. Every organism on the planet has the same genetic code, with very minor perturbations. In the 1960s Carl was the first to have the idea that the genetic code we have is about as good as it could possibly be for minimizing errors. Even if you get the wrong amino acid — through a mutation, or because the cell’s translational machinery made a mistake — the genetic code specifies an amino acid that’s probably similar to the one you should have gotten. In that way, you’ve still got a chance that the protein you make will function, so the organism won’t die. David Haig [at Harvard University] and Laurence Hurst [at the University of Bath] were the first to show that this idea could be made quantitative through Monte Carlo simulation — they looked for which genetic code is most resilient against these kinds of errors. And the answer is: the one that we have. It’s really amazing, and not as well known as it should be.

Later, Carl and I, together with Kalin Vetsigian [at the University of Wisconsin-Madison], did a digital life simulation of communities of organisms with many synthetic, hypothetical genetic codes. We made computer virus models that mimicked living systems: They had a genome, expressed proteins, could replicate, experienced selection, and their fitness was a function of the proteins that they had. We found that it was not just their genomes that evolved. Their genetic code evolved, too. If you just have vertical evolution [between generations], the genetic code never becomes unique or optimal. But if you have this collective network effect, then the genetic code evolves rapidly and to a unique, optimal state, as we observe today.

So those findings, and the questions about how life could get this error-minimizing genetic code so quickly, suggest that we should see signatures of horizontal gene transfer earlier than the Last Universal Common Ancestor, for example. Sure enough, some of the enzymes that are associated with the cell’s translation machineries and gene expression show strong evidence of early horizontal gene transfers.

How have you been able to build on those findings?

Tommaso Biancalani [now at the Massachusetts Institute of Technology] and I discovered in the last year or so — and our paper on this has been accepted for publication — that life automatically shuts off the horizontal gene transfer once it has evolved enough complexity. When we simulate it, it basically shuts itself off on its own. . .

Continue reading.

I am coming to the conclusions that everything in biology happens the way it does because it has to happen that way, given the principle of least effort. Obviously, there are outside forces impinging on the biological world—for example, the asteroid impact near Yucatan some 64 million years ago—but life’s response to such events still follows the least-effort principle.

That may also apply to human culture and our daily lives.

Written by Leisureguy

4 September 2017 at 3:00 pm

Posted in Evolution, Science

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