Brian Miller: Thermodynamics and the Origin of Life

Hmmmm…

Maybe there is a participant here who has published research on membranes and membrane transport?

2 Likes

I found the original source for the claim. It comes from
Introduction to Molecular Biophysics by ­­­Jack A. Tuszynski Michal Kurzynski, p. 413

They may have simply made a mistake, or they may be including all of the other structures in the membrane as part of the “order”.

I heard back from the lipid expert, and he commented that any lipids produced on the early earth which could have been candidates for a viable cell membrane would have been in very small quantities. As a consequence, their concentration and purification would have corresponded to a significant drop in entropy before they reached a concentration where the formation of a membrane would have been thermodynamically favorable.

2 Likes

I was asked about my views on common ancestry and whether I believed cells just popped into existence. The questions can be summarized into what would I expect to see if I traveled back in time to watch the appearance of life. The answer is that I do not know. I am open to many possibilities. In terms of origin of life my scientific sensibilities would lean toward the most parsimonious infusion of information into the system as possible. In other words, I would expect that everyday physical processes would be allowed to act as much as possible, and infusions of information would be a strategic points.

In the case of OOL, the formation of a cell would have to be in dramatic jumps since each stage represents increasing the free energy of the system. And, nature would push back toward equilibrium more forcefully as the system moved away from it. Imagine pushing a bolder up a hill. If one stopped pushing, it would immediately roll back down the hill. The same is true in any OOL scenario. At any stage, if the next miraculous set of conditions and chemical modifications did not take place, the entire system would move back toward simple, low-energy molecules.

You have highlighted why I believe an ID perspective is essential for the advancement of biology. Materialist scientists have constantly fallen into the imperfection-of-the-gaps fallacy:

In the case of the importance of proton gradients, Nick Lane explained their advantage of accessing energy from reactions in fractional proportions.

But one glaring problem with aerobic respiration is that it doesn’t balance. Exactly how much ATP is produced per oxygen molecule consumed? The amount varies, but it’s somewhere around 2.5 ATP molecules. That works out to 28–38 ATPs per glucose — again, a variable number, and never an integer (Silverstein 2005). Aerobic respiration is not stoichiometric, so it’s really not chemistry. And that’s why the long search for a high-energy chemical intermediate (a molecule able to transfer the energy from the oxidation of glucose to form ATP) was doomed to failure.

In place of such an intermediate, Mitchell proposed a proton gradient across a membrane: the proton motive force (Mitchell 1961). It works much like a hydroelectric dam. The energy released by the oxidation of food (via a series of steps) is used to pump protons across a membrane — the dam — creating, in effect, a proton reservoir on one side of the membrane. The flow of protons through amazing protein turbines embedded in this membrane powers the synthesis of ATP in much the same way that the flow of water through mechanized turbines generates electricity. This explains why respiration is not stoichiometric: a gradient, by its very nature, is composed of gradations.

Speaking theologically, can the claim that living systems look poorly designed possibly fit within any traditional theistic framework? Does not such a claim imply that a Creator played no meaningful part in Creation, but we are simply an accident of nature?

In addition, the positive evidence for design has constantly increased as biology and technology have advanced. The correspondence of the two keeps increasing, and engineering presupposes direct intelligent agency. Imagine a spaceship crashed on earth. What approach would yield more useful insights, assuming the vessel was purely a product of natural processes or the product of advanced engineering. A minimally complex cell looks more much more like a spaceship than a glob of tar.

Moreover, a self-replicating autonomous system demands exacting constraints. It is combining a machine, its manufacturing facility, and its operator into a single entity. It demonstrates teleology (purpose) at a level beyond human engineering since it possesses closure to efficient causation. If you really wish to learn how deep the rabbit hole goes, study Rosen’s work on life:
http://panmere.com/?p=22

1 Like

Hi Brian,

I appreciate your insights into OoL research and hope that we have many future discussions on it. Besides the difference in your ID vs my hypernaturalistic approach is that 1) you presuppose information, whereas I focus on energy dissipation, 2) you focus on past improbabilities whereas I look at the existing commonalities of archaea, bacteria and eukaryotes to alkaline vent processes and 3) I hold to Big Bang ((BB) cosmology which I suspect you do not.

The BB was a high energy, far from equilibrium and low entropy event. It is the relentless increase in entropy of the universe that defines the arrow of time, so there are deep philosophical, theological and scientific possibilities to explore. My bias, as stated previously, is strongly toward a chain of energy from the BB to stars to mantle convection on Earth to alkaline vents to life to humanity relying on low entropy energy from the sun for our physical lives. It is powerful to me that even as we increase the entropy of the universe we act on a local scale to bring order from disorder for 6 days then spend one day reflecting on the absurdity of it in light of the relentless passage of time which is God’s domain. This ties back to my fascination with the Lane-Russell-Carroll trifecta and my rejection of projecting biology on to OoL.

2 Likes

Thank you.

1 Like

I agree with you on this.

I also agree that this is in error. We noted this article from you here: Denis Lamoureux on the God-of-the-Gaps Fallacy.

I’m very confused by this. Poorly designed is not the issue; it’s that if any design is less than perfect how does that imply direct divine agency? I guess I part with “any traditional theistic framework” since I find no logical, or scriptural, necessity to expect perfection in any aspect of physical creation. The purpose of this world is not as a stage for demonstration of God’s perfection outside of Christ. This world has been designed not just for the origin of physical life which just needs to be good enough to accomplish God’s plan of redemption, but Eternal Life which is by definition knowing True Perfection. You seem to conflate this creation at any point in time with the New Creation. I find this scripturally indefensible, but may be wrong. Very interesting, especially since our disagreements on the origin of physical life are inconsequential compared to our agreement on the origin of Eternal Life in Christ by nothing we can earn, or even deserve!

I actually do hold to a BB cosmology. Although, I am skeptical of inflation and more exotic models such as string landscapes.

2 Likes

This statement is very striking to me. A lot of the discussion have been centered on the entropy of the production of cell membranes. Suppose that production of cell membranes do produce a large amount of entropy. @Art, what about the rest of the cell? Do the same principles apply and their production also generate a large amount of entropy?

1 Like

The problem here is that Brian’s sources ignore - completely ignore - the fact that cells have water, and that this constituent must be accounted for. This is true when we consider the formation of membranes, folded proteins (that entails increases in entropy owing to changes in the ways water interact with unfolded and folded proteins), and various macromolecular complexes that also form (at least in part) due to hydrophobic forces. Once all constituents are accounted for (including water), it is apparent that my initial assertions are in fact accurate.

We have seen above that one of Brian’s sources - the paper by Davies et al. - has this flaw. Another source that Brian favorably mentions above as describing a reduction in entropy due to compartmentalization - the paper by Marin et al. (2009) - is even more badly flawed (and that is being very, very generous). The authors of this paper basically invent from out of thin air molar quantities and concentrations for some constituents of bacterial, yeast, and algal cells, and use these fabricated numbers to perform a calculation that defies comprehension. (I am not joking, the values provided in Table 1 of the paper do not match those from the citation they provide, at all.) On top of this, when conducting an inventory of the constituents of these cells, they neglect to take into account the water contents of the cells and compartments. In other words, they ignore 99+% of the molecules in the cell! They plug their imaginary molar values into an equation derived from a model is analogous to, say, dividing a liter of pure water in a beaker into two compartments (by inserting a divider). In fact, if you use their model and equations (equation 19 in the paper, to be specific), one can calculate that dividing a beaker of water thusly leads to a decrease in entropy of the “system” of some 300 J/K. I will let the physicists here tell us what the scope of such a change would be. But it sounds preposterous to me.

Why this rant? It is difficult to move a discussion forward in any productive manner when one first has to wade through a comedy of errors, in a manner of speaking. Brian may think I am confused, but I would assert that any confusion in this discussion arises from the poor quality of some of the sources that Brian leans on in framing his arguments and ideas.

2 Likes

I see! Thank you for this answer, it clarifies a lot of things for me.

Thanks for the kind words. And for putting up with my rant.

What would be good sources which claim that the formation of a cell from the chemicals on the early earth would not be an entropy decreasing process?

In reality, the key issue is not entropy but free energy since that quantity determines whether changes are favorable. Do you know of any sources which claim the formation of a cell would not correspond to an increase in free energy? Do you feel Morowitz made serious errors in his calculations?

A particularly serious challenge is that the macromolecules form through condensation, so the reactions are unfavorable in water. And, those reactions are not helped by other disconnected processes being energetically favorable.

Bioenergetics and Life’s Origins

A central problem therefore concerns mechanisms by which prebiotic monomers could have been activated to assemble into polymers. Most biopolymers of life are synthesized when the equivalent of a water molecule is removed to form the ester bonds of nucleic acids, glycoside bonds of polysaccharides, and peptide bonds in proteins.

Just so I can follow here, we are talking about delta free energy, a change in energy between two systems: (1) a protocell and (2) what? What is the base state we are using against which to measure the delta free energy?

I’m pretty sure he is just talking about the difference between free energy of a protocell and its constituents. The ratio of probabilities of forming living vs non-living things are given by (sub in protocell for living and constituents for nonliving in the subscripts if you prefer those terms)

Free energy is just a way to talk about g*Exp(-E/kT) under constant pressure, i.e. it’s a way to talk about both the entropy and energy (enthalpy in constant pressure) together at once.

Mathematically, the entropy, S is given by

S = k ln(g),
so
g*Exp(-E/kT) = Exp[- (E - S * T)/kT ]

Under constant pressure, E~H the enthalpy, and the free energy is defined as G = H - TS, so

g*Exp(-E/kT) = Exp[-G/kT]

Therefore,

P(living)/P(nonliving) = Exp[-(G_living - G_nonliving)/kT)]

This (G_living - G_nonliving) is the Delta Free Energy that you mention in your comment, and is just a proxy of talking whether living/nonliving (or rather protocell/constituents) are thermodynamically favorable or not.

1 Like

From here:

Another analogy will illustrate how this question should be understood. Imagine a large pond of water sitting on top of a hill. We know that there are any number of other states—any in which the water is lower than it is at the top—which have lower energy and are therefore states toward which the system will tend to evolve over time. In terms of our question, the ”problem” faced by the system is how to get water from its initial state to any state of lower energy—how to get the water down the hill. We need not think of the laws of physics as being endpoint directed; rather, they simply adjudicate between states of higher or lower energy, with a preference for lower. Can we apply the same reasoning to the chemistry of life?

For real hills, we understand not only that the water will flow downward but also many things about how it will do so. Molecules of water will not each flow down a random path. Instead the flowing water will cut a channel in the hillside. In fact, the flow of water is at once constructing a channel and contributing to the collapse of the energy imbalance that drives the entire process. In addition, if we look at this process in detail, we see that what really matters is the configuration of the earth near the top of the hill, for it is there that the channeling process starts. This part of the analogy turns out to be particularly appropriate when we consider early chemical reactions.

In the analogy, the “problem” is the fact that the water begins in a state of high energy; the creation of the channel ”solves” this problem by allowing the water to move to a lower energy state. Furthermore, the dynamics of the system are such that once the channel is established, subsequent flow will reinforce and strengthen it. There are many such systems of channels in nature—the lightning bolt is an example, although in that case the forces at work are electrical, not gravitational. (When lightning occurs, positive and negative charges become separated between clouds and the ground. The charge separation ionizes atoms in the air, creating a conducting channel through which the charges flow—the lightning bolt—much as water flows down a hill).

We argue that the appearance of life on our planet followed the creation of just such a channel, except that it was a channel in a chemical rather than a geological landscape. In the abiotic world of the early Earth, likely in a chemically excited environment, reservoirs of energy accumulated. In effect, electrons (along with certain key ions) were pumped up chemical hills. Like the water in our analogy, those electrons possessed stored energy. The “problem” was how to release it. In the words of Albert Szent-Gyorgi: “Life is nothing but an electron looking for a place to rest.”

For example, carbon dioxide and hydrogen molecules are produced copiously in ordinary geochemical environments such as deep sea vents, creating a situation analogous to the water on the hill. The energy of this system can be lowered if the electrons in the hydrogen ”roll down the hill” by combining with the atoms of carbon dioxide in a chemical reaction that produces water and acetate (a molecule with two carbon atoms). In the abiotic world, however, this particular reaction takes place so slowly that the electrons in the hydrogen molecles find themselves effectively stranded at the top of the energy hill.

In this example, the problem that is solved by the presence of life is getting energized electrons back down the chemical hill. This is accomplished by the establishment of a sequence of biochemical channels, each contributing to the whole. (Think of the water cutting multiple channels in the hill). The reactions that create those channels would involve simple chemical transactions between small organic molecules.

Are you suggesting that Morowitz was arguing against himself in the American Scientist article?

I must say that Dr. Hunt’s reference to this article is quite intriguing. He suggests that it supports his claim that the formation of a cell does not represent an increase in free energy and a corresponding decrease in entropy. Yet, the article states the following, which I previously referenced:

On the theoretical side, we have to start with the realization that if we apply standard equilibrium thermodynamics to living systems, we arrive at something of a paradox. Living systems possess low entropy, which makes them very improbable from the equilibrium thermodynamic viewpoint.

Morowitz writes in depth about precisely why life represents an increase in free energy from that of its starting chemicals in any OOL scenario. His estimates for the required increase were the basis for his calculations on the improbability of life forming near equilibrium:

Morowitz in EFB (p. 66) calculates the probability for a cell forming at roughly 1 in 10 to the power of 100 billion. Later he calculates the probability for monomers in the ocean forming into a cell (p. 99) at roughly 1 in 10 to the power of 10 billion.

The article Dr. Hunt references reaffirms that life represents an increase in free energy when it states that it needed an engine to convert one form of energy into another which is useful to construct and drive cellular metabolism:

Pumping electrons up chemical hills into reservoirs requires a complex engine, for unaided natural processes tend to drive reservoirs of electrons toward lower energy. Life accomplishes this task through sophisticated machinery such as photosynthesis. It moves electrons to higher energy states in the form of glucose through an exceedingly complex process. The breakdown of glucose into water and carbon dioxide results in the electrons moving back to lower energy which can be tapped to drive metabolism. Cells use other processes to access energy from chemicals, but they also require multiple steps directed by enzymes.

In a previous post, I outlined the challenges to Morowitz’s completely hypothetical scenario. Morowitz fully acknowledged some of them. First, any natural source of energy which could potentially help produce the electron reservoir or generate some desired chemical pathway would break apart complex molecules and rip apart a cell membrane.

For driven non-equilibrium systems, the situation is far worse. In addition to the constant thermal disruption of microscopic order, the same random reactions by which order is assembled stands ready to degrade it away. Unless a driven system is continually self-amplifying, it cannot even persist. It is as if, in addition to handling the customers, the watchmakers were bedeviled continually by gremlins that disassembled any module not kept in hand.

Second, any natural process would produce chemical reactions which would undermine any useful metabolism.

Networks of synthetic pathways that are recursive and self-catalyzing are widely known in organic chemistry, but they are notorious for generating a mass of side products, which may disrupt the reaction system or simply dilute the reactants, preventing them from accumulating within a pathway.

To summarize, all theoretical, experimental, and observational evidence affirm that OOL requires complex machinery to act as an engine to produce high energy molecules. And, enzymes are required to drive the correct set of reactions and to couple the breakdown of the high-energy molecules to targeted energetically unfavorable reactions. Only meeting these requirements would allow the free-energy barriers to be overcome.

A simple answer would be that the base state is the collection of molecules in some realistic environment on the early earth. However, the challenge is that no environment would be suitable, for individual steps in the formation of a cell’s building blocks require multiple mutually exclusive environments:

Origins of building blocks of life: A review

It is indicated from the overviews that completion of the chemical evolution requires at least eight reaction conditions of (1) reductive gas phase, (2) alkaline pH, (3) freezing temperature, (4) fresh water, (5) dry/dry-wet cycle, (6) coupling with high energy reactions, (7) heating-cooling cycle in water, and (8) extraterrestrial input of life’s building blocks and reactive nutrients. The necessity of these mutually exclusive conditions clearly indicates that life’s origin did not occur at a single setting; rather, it required highly diverse and dynamic environments that were connected with each other to allow intra-transportation of reaction products and reactants through fluid circulation.

OOL requires that the building blocks form in different environments. And, the more complex molecules require a highly orchestrated transport of chemicals through the right environments at the right times. Then, they must all converge in the same microenvironment such as a cell membrane or a micropore in a thermal vent. The problem is that the molecules in any realistic scenario have to search an enormous volume of water before they have any chance of finding the developing protocell. Remember that multiple streams must converge in the same area. The required timescales would be vastly greater than the lifespan of a protein or ribozyme.

In addition, byproducts of the reactions which created the building blocks and other contaminants already in the environment would have eliminated many of the essential molecules. This conclusion is confirmed by all realistic OOL experiments and honest theoretical analyses. Therefore, the localization problem is unavoidable and intractable. Calculating the timescales demonstrates that extreme skepticism for all OOL theories is not based on personal incredulity but on mathematical certainty.

I used to be highly caustic toward the YEC community because I felt they were not honestly addressing key scientific challenges to their framework. However, I later realized that they embraced their framework for several quite understandable reasons. And, I met top YEC scientists who were honest about the challenges they faced and about their driving assumptions. I find the same situation exists for scientists who insist that some purely materialistic explanation must exist for OOL. The challenges they face are just as great as those faced by the YEC community. I can respect why many scientists feel the naturalist approach is needed, but they should be cautious criticizing YEC scientists since doing so might come accross as a tad hypocritical.

I don’t know if this is a fair comparison.

First of all, I have no problem with honest YECs who acknowledge these problems. Many do. The issue is that many are not honest, claiming the evidence indicates a young earth. This is just false. I’m not caustic towards them, but I do not think that God needs false witness.

Second, the challenges YECs face are different than in OOL. We have strong evidence of a deep history in an ancient earth. This is different than lack of knowledge about abiogenesis. We do not know how the first life arose. We do not have a detailed history of how the first cell arose established with evidence for several lines of scientific evidence. Even Genesis is silent on the origin of life because it knows nothing about cells.

Third, most scientists will agree that we do not yet know how the first life arose. That appears to be wildly agreed upon, even though it is misreported all the time in the media. This contrasts with a common YEC trope of claiming the evidence shows the earth is young.

What is at question here is whether there is sufficient reason to think it is impossible for the first life to arise. Very reasonably scientists will find this an equivocal question. We do not know how the first life arose, and we may never know. Even Jim Tour argues that it could have been by natural process we might one day figure out. He just insists, rightly, that we have not yet figured it out.

So this is just not the same situation as YEC. Are you really seriously arguing this @bjmiller? Or are you just taking a rhetorical swipe to be quickly retracted?

4 Likes

(note: this is responding to a post a few weeks ago earlier in the thread, @bjmiller’s response to my question regarding if he a priori rejects all research done on the OOL)

Got you. If the laws of nature were sufficient (which you argue they are not and cannot be in our universe) then this is evidence of your idea being correct (which is that the Intelligent Designer just popped the first replicating life together from scratch or at least got some materials together that were already produced by billions of years of cosmic evolution? feel free to correct me what you think happened). However if it were the other way around and the laws of nature were sufficient to produce life, then that too would be evidence of your model and the Intelligent Designer just made the conditions even better in the 2nd universe than in the real one. I’m obviously confused as to what your main point actually is and it seems as if you have done a lovely combination of building a strawman and potentially moving the goalposts. But if your model gets to be true regardless of what we find then it really is no scientific explanation at all. It seems its only prediction is that we will never find an explanation of the OOL, but if we did, then that too is evidence of ID.