Thursday, 4 January 2018

The Origin of Life: Correcting Common Mistakes on Thermodynamics

Vincent Torley is a philosopher who contributes posts to The Skeptical Zone. In the past year, he wrote an article critiquing my writings on the origin of life in which he presented several counterarguments based on a variety of popular and academic articles. He erred in his description of thermodynamics and the state of the literature, but his mistakes were completely understandable. He has not extensively studied non-equilibrium thermodynamics, and the ideas can be quite subtle. In addition, he took at face value claims from origins puff pieces that greatly exaggerated experimental results. And he attempted to discuss concepts such as complexity that are often poorly defined and not used consistently even in technical articles. However, he has assembled a fairly complete sampling of common mistakes related to the origins conversation, so his efforts were of great value. Today, I will correct the mistakes related to thermodynamics.

The core thermodynamic problem for the origin of life is that nature always tends to move towards states of higher entropy or states of lower energy or both. More specifically, the entropy and energy (or enthalpy at constant pressure) is commonly combined into the measure of the free energy, and all spontaneous processes without outside assistance move toward lower free energy. As an analogy, imagine a library with some portion of the books on book shelves and many on the floor. The higher shelves correspond to higher energy states. Also imagine a small percentage of the books have been arranged according to the Library of Congress Classification (LCC) system, but most are distributed randomly. Books more randomly arranged correspond to higher entropy. Any state of life would then correspond to the majority of books on the top shelves (high energy) with a large percentage arranged in LCC order (low entropy).

The driving tendencies in nature on the early Earth would have been analogous to seismic tremors rearranging the books in the library. During the tremors, some of the books on the floor would jump to the shelves, and some of the books on the shelves would jump to other shelves or onto the floor. The natural tendency over time would be for books on the higher shelves to fall to lower shelves, and the largest number would ultimately reside on the floor. In addition, books that were to some extent sequenced in a specific order would tend to randomly shuffle around. The books would never end up highly ordered on the top shelf. In the same way, any arrangement of chemicals at nearly any stage of coalescing into the first cell would move away from that target and towards simple randomly arranged molecules. Adding more energy would not help, since any natural energy source would act like a more intense earthquake impacting the library. The system would move in the opposite direction of life even faster.

As a technical digression, the library books analogy works best for those who are comfortable with the formalism of configurational entropy. However, the principle still holds true even for those who wish to think only in terms of traditional thermodynamic entropy. The bottom line is that life has higher energy and lower entropy by any definition than the molecules from which it sprang. Therefore, nature would always resist its spontaneous formation. The fact that the building blocks have to be arranged in a highly specific order could simply be added to the entropy as a configurational part. Alternatively, the probability of them coming together properly could be thought of as a separate probabilistic challenge in addition to the entropy challenge. Either way, the entropy/configurational barrier is insurmountable.

In relation to energy, a common belief is that adding energy strongly biases molecules toward higher energy states. This assumption is completely wrong. Systems will tend to configure into states with a probability that drops off exponentially with increasing energy as crudely illustrated in the books analogy. In other words, lower energy states are always more likely than higher energy states unless the higher energy states are considerably more numerous. At equilibrium, any system would move towards the Boltzmann Distribution. If energy were added, the net effect would be to raise the temperature which would cause the distribution of higher energy states to drop off more slowly. In other words, adding energy does not cause a large percentage of the lower energy states to jump to significantly higher energy. The lower energy states still dominate, just less so than before.

In addition, adding energy always causes the entropy to increase. As an example, imagine some environment that contains many individual amino acids and some amino acid chains of varying length. A challenge is for the amino acids to combine with the chains to lengthen them since that reaction is thermodynamically unfavorable. Adding energy would increase the rate at which amino acids combine into longer chains since they would on average have more kinetic energy to overcome reaction barriers. However, the added energy would to a much greater extent cause the existing chains to break apart since the breaking of a peptide bond only has to overcome the activation energy barrier which is smaller. Similarly, dehydrating a pond could help amino acids to combine into chains, but the process would more likely destroy existing chains. The net effect would always be to move away from large numbers of longer chains that would be essential for life.

The only solution is for some engine to process an energy source and then redirect that energy to perform useful work. Also, information would be required, so the work could be directed properly to assemble and operate the cell. In life, the processing of energy requires cellular structures coupled to chemical cycles which use sunlight or the breakdown of fuel (e.g., glucose) to produce high-energy molecules such as ATP. And information is embedded in the highly specific sequences of chains of amino acids in proteins. The sequencing causes the chains to fold into the correct structures (enzymes) which drive the needed reactions to build the right cellular components and maintain the metabolism. The enzymes also link the breakdown of the high-energy molecules to reactions and other processes that move energetically uphill, so the net change in free energy is negative. The energy from the former reaction is used to drive the uphill ones, thus overcoming the free energy barrier.

Torley writes that the work of Jeremy England has overcome all of these challenges by demonstrating that natural processes could move a system toward higher free energy. This claim represents a complete misunderstanding of his research. England’s simulations study how energy could be absorbed from some source and then released (dissipated) into the environment. His models presuppose that energy is readily available, and it can be directly accessed to drive specific reactions of interest. In other words, if his models did relate to the origin of life, he would have assumed that the central problem of processing and redirecting an available energy source would have already been solved.

However, in none of his technical papers does he directly relate any of his work to concrete origin-of-life research. He simply states that his models might offer possible analogies, and he identifies minimum heat dissipation in self-replication. Popular-level articles have strongly made the connection to the origin of life but without any justification. To the contrary, England’s work is based on fluctuation theorems which demonstrate that systems driven from equilibrium tend towards states of higher entropy and greater energy dissipation — the opposite direction of what is needed for the first cell. For perspective on the problem: combining basic molecules into a bacterium requires energy being absorbed (opposite of dissipated) from the environment in the amount of roughly 0.27 ev/atom. This value, if scaled, would parallel a bathtub of room-temperature water absorbing enough heat from the environment to start boiling. A clear impossibility.

Torley also references a paper by David Ruelle which attempts to explain how the free energy challenges to the origin of life could be overcome based on statistical mechanics. The paper is quite technical and abstract, so the underlying arguments are not easily accessible. In addition, Ruelle primarily references other highly theoretical research, and he makes no attempt to ground his arguments in physical reality. However, the key point is fairly straightforward. He first fully acknowledges that physical processes tend toward lower free energy. He then describes how a set of stable reactions could form that draw free energy from outside “nutrients” which act as fuel. In other words, Ruelle presupposes the existence of an engine which can process fuel and mechanisms which then redirect the energy toward specific chemical reactions.

All other papers that propose solutions to the thermodynamic challenges use the same approach. They ignore nearly all practical challenges and completely disassociate their work from realistic experiments. And they assume the existence of an unlimited source of energy, an efficient energy converter (engine), and information. However, the converter and the required information must already exist before the converter could be created. The only explanation for the sudden appearance of such molecular machinery and the information is intelligence.

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