Comments on a cultural reality between past and future.

This blog describes Metatime in the Posthuman experience, drawn from Sir Isaac Newton's secret work on the future end of times, a tract in which he described Histories of Things to Come. His hidden papers on the occult were auctioned to two private buyers in 1936 at Sotheby's, but were not available for public research until the 1990s.

Friday, January 24, 2014

Evolutionary Babylon

"A rainbow-colored beast from the margins of a fifteenth-century text." Image Source: Public Domain Review via Paris Review.

The Justin Bieber mugshot is already an Internet meme (do not click here or here and don't don't don't click here (told you not to)). Fortunately, there are other things to think about, like the origins of life. Jeremy England, a 31-year-old physicist at MIT, thinks that he has identified the physics that underlies the difference between inanimate and animate matter. The thermodynamic theory, which complements Darwin's theory of evolution, is outlined in Quanta Magazine, and summarized below the jump.

The Hanging Gardens of Babylon, with the Tower of Babel in the background ("probably 19th century after the first excavations in the Assyrian capitals"). Image Source: Wiki.

Already, critics are queueing to attack England's ideas. But is this simply because his concept has appeared in many guises, to researchers working in various fields, each of which has a field-specific language and set of research precedents? Is the theory of the origin of life a modern Tower of Babel?

Quanta Magazine summarizes England's work:
From the standpoint of physics, there is one essential difference between living things and inanimate clumps of carbon atoms: The former tend to be much better at capturing energy from their environment and dissipating that energy as heat. Jeremy England, a 31-year-old assistant professor at the Massachusetts Institute of Technology, has derived a mathematical formula that he believes explains this capacity. The formula, based on established physics, indicates that when a group of atoms is driven by an external source of energy (like the sun or chemical fuel) and surrounded by a heat bath (like the ocean or atmosphere), it will often gradually restructure itself in order to dissipate increasingly more energy. This could mean that under certain conditions, matter inexorably acquires the key physical attribute associated with life.

“You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant,” England said.

England’s theory is meant to underlie, rather than replace, Darwin’s theory of evolution by natural selection, which provides a powerful description of life at the level of genes and populations. “I am certainly not saying that Darwinian ideas are wrong,” he explained. “On the contrary, I am just saying that from the perspective of the physics, you might call Darwinian evolution a special case of a more general phenomenon.”

His idea, detailed in a recent paper and further elaborated in a talk he is delivering at universities around the world, has sparked controversy among his colleagues, who see it as either tenuous or a potential breakthrough, or both. ...

At the heart of England’s idea is the second law of thermodynamics, also known as the law of increasing entropy or the “arrow of time.” Hot things cool down, gas diffuses through air, eggs scramble but never spontaneously unscramble; in short, energy tends to disperse or spread out as time progresses. Entropy is a measure of this tendency, quantifying how dispersed the energy is among the particles in a system, and how diffuse those particles are throughout space. It increases as a simple matter of probability: There are more ways for energy to be spread out than for it to be concentrated. Thus, as particles in a system move around and interact, they will, through sheer chance, tend to adopt configurations in which the energy is spread out. Eventually, the system arrives at a state of maximum entropy called “thermodynamic equilibrium,” in which energy is uniformly distributed. A cup of coffee and the room it sits in become the same temperature, for example. As long as the cup and the room are left alone, this process is irreversible. The coffee never spontaneously heats up again because the odds are overwhelmingly stacked against so much of the room’s energy randomly concentrating in its atoms.

Although entropy must increase over time in an isolated or “closed” system, an “open” system can keep its entropy low — that is, divide energy unevenly among its atoms — by greatly increasing the entropy of its surroundings. In his influential 1944 monograph “What Is Life?” the eminent quantum physicist Erwin Schrödinger argued that this is what living things must do. ...

Using Jarzynski and Crooks’ formulation ... [England] derived a generalization of the second law of thermodynamics that holds for systems of particles with certain characteristics: The systems are strongly driven by an external energy source such as an electromagnetic wave, and they can dump heat into a surrounding bath. This class of systems includes all living things. England then determined how such systems tend to evolve over time as they increase their irreversibility. “We can show very simply from the formula that the more likely evolutionary outcomes are going to be the ones that absorbed and dissipated more energy from the environment’s external drives on the way to getting there,” he said. The finding makes intuitive sense: Particles tend to dissipate more energy when they resonate with a driving force, or move in the direction it is pushing them, and they are more likely to move in that direction than any other at any given moment.

“This means clumps of atoms surrounded by a bath at some temperature, like the atmosphere or the ocean, should tend over time to arrange themselves to resonate better and better with the sources of mechanical, electromagnetic or chemical work in their environments,” England explained.

Self-replication (or reproduction, in biological terms), the process that drives the evolution of life on Earth, is one such mechanism by which a system might dissipate an increasing amount of energy over time. As England put it, “A great way of dissipating more is to make more copies of yourself.” ...

The chemistry of the primordial soup, random mutations, geography, catastrophic events and countless other factors have contributed to the fine details of Earth’s diverse flora and fauna. But according to England’s theory, the underlying principle driving the whole process is dissipation-driven adaptation of matter. ...

Scientists have already observed self-replication in nonliving systems. According to new research led by Philip Marcus of the University of California, Berkeley, and reported in Physical Review Letters in August, vortices in turbulent fluids spontaneously replicate themselves by drawing energy from shear in the surrounding fluid. ...

Besides self-replication, greater structural organization is another means by which strongly driven systems ramp up their ability to dissipate energy. A plant, for example, is much better at capturing and routing solar energy through itself than an unstructured heap of carbon atoms. Thus, England argues that under certain conditions, matter will spontaneously self-organize. This tendency could account for the internal order of living things and of many inanimate structures as well. “Snowflakes, sand dunes and turbulent vortices all have in common that they are strikingly patterned structures that emerge in many-particle systems driven by some dissipative process,” he said. Condensation, wind and viscous drag are the relevant processes in these particular cases.

“He is making me think that the distinction between living and nonliving matter is not sharp,” said Carl Franck, a biological physicist at Cornell University, in an email. “I’m particularly impressed by this notion when one considers systems as small as chemical circuits involving a few biomolecules.” ...

If England’s approach stands up to more testing, it could further liberate biologists from seeking a Darwinian explanation for every adaptation and allow them to think more generally in terms of dissipation-driven organization. They might find, for example, that “the reason that an organism shows characteristic X rather than Y may not be because X is more fit than Y, but because physical constraints make it easier for X to evolve than for Y to evolve,” Louis said.
One commenter on this article, Karo Michaelian, notes prior discoveries on this "Thermodynamic Origin of Life":
The theory for the origin and evolution of life as presented above and accredited to Jeremy England is not new. It was published by myself in 2009, K. Michaelian, arXiv:0907.0042 [physics.gen-ph] http://arxiv.org/abs/0907.0042 and again in 2011, K. Michaelian Earth Syst. Dynam., 2, 37-51, 2011 http://www.earth-syst-dynam.net/2/37/2011/doi:10.5194/esd-2-37-2011[.] The observation that under a generalized chemical potential material self-organizes into systems which augment the dissipation of that potential should be accredited to Ilya Prigogine, “Introduction to Thermodynamics of Irreversible Processes”, John Wiley Sons Inc., 1968. I have written a number of other papers on the thermodynamic dissipation theory for the origin of life, including an explanation of homochirality. These papers are freely available by searching for my name “Karo Michaelian” on ResearchGate. I welcome Jeremy’s contribution to the effort to understand life from a thermodynamic perspective. A more direct access to the ... article is[:] http://www.earth-syst-dynam.net/2/37/2011/esd-2-37-2011.html Best regards, K. Michaelian.
Other commenters are highly critical and regard England as a "latecomer" to already established fields of investigation into the relationship between energy, matter, entropy and the origin of life. One writes: "[England is] just restating thermodynamics, with different words[. B]iologists & system theorists have said this for decades; is ... [England's] math equation different from a logical or linguistic equation?"

One sympathetic remark came from the physics camp:
I am a Ph.D. student in physics. I just wanted to say that what he proposes does not run into any conflict with the existing law of thermodynamics. The existing law of thermodynamics only applies to systems in equilibrium that many people are familiar with (increases in disorder (entropy) etc). They all have one fundamental assumption: that the system is already in equilibrium. Non-equilibrium systems are not very understood at all. Non-equilibrium statistical mechanics is a huge open question in physics. Its why we don’t understand every day things such as underwater bubble formation. Because such [a] phenomenon can only happen under non-equilibrium conditions.
The Earth is certainly not an equilibrium system, we take in energy from the sun the day and emit our entropy at night to the emptiness of space. If this proves to be correct it will be a huge in the step of understanding non-equilibrium systems.
A critical remark came from Charles Hall:
I agree with the many responders that these ideas are not new at all (such as I can tell), including to this systems ecologist. Indeed Ecologist(s) Ramon Margalef discussed this and so did Howard Odum ... . Life does not dissipate energy just to do that; it is a necessary requirement for building structure, capturing more energy than that required for maintaining that energy and for energy acquisition, and propelling one’s genes into the future. (“Evolution is an existential game, the object of which is to keep playing”: Ecologist L. B. Slobodkin).
Finally, Mark Mahin takes issue at his blog, Future and Cosmos, with how England ignores the genetic code, a "semantic framework," of life that well beyond the interactions of energy and matter:
Explaining the origin of all of this ends up being an incredibly difficult problem, and England's work does very little to help solve this problem. England claims to have found reasons why certain molecular systems might tend to reach a more organized state because of thermodynamic reasons. So what? You can explain how water becomes more self-organized when it freezes, but that is not relevant to the origin of life.

One of the key issues in the origin of life is whether or not there would have existed the building blocks needed for the appearance of the first RNA molecules. As explained here, there are reasons for doubting that there would have existed the ribose sugars, nucleotides, and nucleosides needed for RNA molecules to originate. Does England discuss the issue? No, he apparently says nothing about the chemical state of the Earth at the time of the origin of life.

Another difficult thing to explain is the origin of the genetic code. How did mere chemicals turn into the semantic representation system needed for the origin of life, before Darwinian evolution began? England gives us zero insight on this issue, which he completely ignores. England's paper doesn't even mention the genetic code.
These commenters all hail from different fields; their remarks suggest that they have all been dealing with similar ideas around a thermodynamic theory of evolution - but from various angles and with diverse terminology - for decades. If only they spoke one language, they might find a complete answer.