Brian Miller: Thermodynamics and the Origin of Life

Design

(Arthur Hunt) #97

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.


#98

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


(Arthur Hunt) #99

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


(Brian Miller) #100

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.


(S. Joshua Swamidass) #101

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?


#102

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.


(Arthur Hunt) #103

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?


(Brian Miller) #104

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.


(Brian Miller) #105

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.


(S. Joshua Swamidass) #106

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?


(Matthew Pevarnik) #107

(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.


(Brian Miller) #108

An analogy might be helpful. Imagine someone sees a fully functional car sitting in a junkyard and argues that the car was the product of some natural process such as a tornado moving through the junkyard and assembling it from scrap parts. You naturally argue that no physical process could possibly accomplish such a feat since a car represents such a highly improbable arrangement of parts clearly put together to accomplish a purposeful goal. You then imagine a universe where a set of laws existed which would, under the right circumstances, cause a tornado moving through a junkyard to assemble a functional car. That set of laws would clearly have been designed for the purpose of assembling cars. The same principle holds true for life. A highly improbable arrangement of parts assembled to achieve a complex goal always points to design by its very nature.

This point can be further illustrated by Conway’s Game of Life. Several programmers have created self-replicating patterns such as Gemini. The game functions as an artificial universe with its own laws. Self-replicators can be generated using the standard rules of the game, or special rules can be designed to help the processes. For instance, if the rules are sufficiently complex, constructors can self-organize. The key point is that a minimum amount of information needs to be present at the beginning. That information can be split between the information embedded in the laws and/or in the initial conditions. The minimum amount is around 4 or 5 Kbytes if memory serves. The game represents an idealized universe which can be tailored to generate life, yet a large amount of information in the initial conditions is still always required at the beginning. Our universe is far less conducive to generating life, so a far greater amount of required information would be expected.


(Brian Miller) #109

The similarities are quite striking between YEC and materialist arguments when examined in detail. I do not mention this fact to demean either position, but the comparison is important to recognize. The amount of data related to the age of the earth is certainly greater, but the technical challenges faced by YEC and materialist OOL accounts for specific pieces of data are comparable. Let me give a few specific examples.

Radiometric Dating/Design Inference for Minimally Complex Cell (MCC)
A large amount of radiometric dating indicates that the universe and earth are billions of years old. The YEC response is that anomalies exist in certain dates, so these examples justify for some of them that all dating examples can be rejecting.

Similarly, the positive evidence in a MCC seems quite clear to anyone who is not viewing it through a materialist lens. Those who reject the appearance of design often point to some features in life whose design logic is not immediately obvious, and such examples justify in their minds the rejection of all appearances of foresight, coordination, top-down engineering, and goal direction.

Green River Formation/Protein Formation
The Green River Formation consists of millions of alternating layers of sediment which points to a very long process of formation. The YEC response is to propose some peculiar event, such as a perfectly orchestrated series of water movements, generated the layers. I have not actually studied the details of their theories.

Similarly, the formation of proteins requires that some miraculous set of conditions generated large quantities of a variety of homochiral amino acids. Then, some other miraculous process concentrated and purified them. Then, they arrived in some lagoon or another environment
which went through countless perfectly orchestrated dry/wet cycles
which caused the amino acids to combine in just the right way into long chains
which just happened to have the right sequences to fold into the needed proteins.
This set of circumstances repeated for each required protein. Then, they all migrated long distances to the same microenvironment of a developing protocell with a membrane with the right properties.

Dating of Ocean Floor/DNA Encoding-Decoding
The ocean floor can be dated at various distances from the point of formation. The radiometric dates coincide with the dates inferred from the time required to move from the point of the formation based on the plate velocity. This correlation is difficult to explain in a YEC framework. However, a YEC proponent would argue that some other mechanism correlated the levels of radiometric isotopes with the distance.

Similarly, the encoding of amino acid sequences in proteins into nucleotide sequences in DNA is difficult to imagine since no chemical connection exists between an amino acid and a coding triplet. One has to imagine something along the lines of a protocell filled with proteins filling with nucleotide triplets. Then, the proteins unfolded and somehow caused the right codons to bind together in the right order into DNA. Then, all of the translation machinery appeared. Eventually, full cellular replication emerged. The last two steps involve the acquisition of dozens of new complex proteins, tRNAs, and mitochondria.

The OOL scenarios proposed to overcome these hurdles are no more plausible than the YEC scenarios. When both groups encounter technical challenges, they simply state that future studies may resolve them. And, they both greatly downplay evidence which challenges their positions.

Someone like a James Tour has chosen to play by the rules of the secular academy, so he must always state that some materialist explanation may eventually be discovered. I fully support his decision to play by those rules since not doing so would prevent him from accomplishing his work. The vast majority of design proponents also play by those rules, so they never mention intelligent design but simply let that perspective guide their research. For instance, ID proponents were the first to argue that most of human DNA was not junk and orphan genes would be prevalent throughout life. They also were early adopters of applying engineering in biology and Shapiro’s ideas of natural genetic engineering.

The challenge is that scientists are trained to see the world through a very powerful materialistic philosophical lens, so recognizing the evidence for design becomes impossible. For instance, when paleontologist Gunter Bechly encountered ID literature, he first mocked it. He then decided to read through it, but he had to carefully examine every argument and analyze the philosophical assumptions for many years. He needed much time and reflection to detoxify from being marinated in philosophical materialism for decades. Once he broke free from that lens, the evidence for design became crystal clear. Do not be surprised if Jim Tour also fully endorses ID after he retires. He would then have the time to carefully study the arguments.


(Matthew Pevarnik) #110

Oh dear. The probability argument? Is that somewhere worth going for the origins of life- as if anyone can calculate the probability of anything. Maybe if we had infinite knowledge of all possible interactions and conditions could one even put a number on it.

And the intelligent designer is inept. The maker of the finely tuned laws apparently didn’t have the foresight to build any rules into place that could assemble any kind of life. What do you imagine actually happened at the OOL? Natural processes make all of the parts that make up a cell and the Designer is wondering why they don’t just snap together. After sending the Late Heavy Bombardment to power up hydrothermal vents, it’s still not working so he decides to go down and snap the first one together himself- maybe some 3.77 billion years ago. But then after a few billion years of adding random hints like wiggling motors to the flagellum these prokaryotic cells aren’t doing much of anything interesting so he goes down and shoves one inside another one and that really gets the whole thing going with endosymbiosis. All the while he wonders what went wrong when he was first making the laws that are so exquisite to fine tune aspects of fundamental particles yet they utterly fail to make anything beyond atoms.


(S. Joshua Swamidass) #111

@bjmiller, I read this and was very concerned.

If James Tour endorses ID privately, but chooses to keep it private, you have absolutely no right to out him this way in a public forum. Such claims could have a real impact on him. If they are true, you sharing private information about him that you believe can impact him very negatively.

In this case, I know James Tour well, and have discussed this at length with him. He is not an ID advocate. He genuinely seems to believe that scientists will one day figure out how the first cell arose without appealing to Intelligent Design. He stresses that he puts this directly or indirectly in just about every talk he gives. I have heard from other people that he says this to them. I do not know why he would be duplicitous with me.

So I would ask you to clarify what you are saying about James Tour. If you are saying you think he might move to a new position that is fine. However you are saying here that he is not being honest about where he really stands. That is a serious accusation in this context.

This is wonderful example of pseudohistory. Thanks.


(Timothy Horton) #112

Several problems:

  1. You have no idea of the actual probability when it comes to biological life.
  2. You have no evidence living creatures were assembled from the constituent parts.
  3. You have no evidence there was any preconceived complex goal for biological life.

Some day ID-Creationists will learn that analogies aren’t considered evidence in science, but not today it seems. :slightly_smiling_face:


(T J Runyon) #113

Most ID proponents make both arguments without realizing they are in tension. Trent Dougherty (a Christian.) points that out in this paper:
http://tedposton.org/Documents/usersguide.pdf
I also struggle with the thought God made his creation incapable of accomplishing his goals and had to intervene. I don’t know.


The Fine-Tuning and Design Catch-22
(Arthur Hunt) #114

It’s not (explicitly) thermodynamics, but seeing as Brian has broached the subject …

His statement quoted here is yet another in a list or erroneous claims he has made in this discussion. Consider the following, from this review:

(The first paragraph) " In all likelihood, construction of the genetic code required specific interactions between amino acids and RNAs, acting alone, before peptides could be encoded. Close study of this molecular interaction, therefore, is one of the most promising routes we possess to the origin of the code and translation itself. Here we test for unexpectedly frequent cognate coding triplets within, taking an essential role in, a specific set of RNA-amino acid binding sites."

(The first part of the conclusion) “We decisively confirm the hypothesis in this review’s first paragraph. The RNA-amino acid interface does contain the logic of (some of) the genetic code, relating triplets to amino acid side chains. Cognate triplets, though their functions may vary, are unexpectedly close to their amino acids. The conclusion is unequivocal—the probability that the contrary is true hovers in negative exponential triple digits (Figures 2–5). These data together strongly confirm intuitions of Crick [65], Orgel [66], and Woese [62], who thought that such a connection would exist.”

In other words, there are known and relevant chemical interactions between amino acids and RNAs bearing cognate codons and anticodons.

As an aside, any discussion of the OOL that presumes that 'tis DNA and not RNA that is the essential and original information-bearing molecule cannot be taken seriously. I encourage Brian to update his thinking on this matter. An introduction to one of the more interesting aspects of this may be found here. Enjoy!


(T J Runyon) #115

Work from Bojan Zagrovic is also compelling:


(Brian Miller) #116

Thank you for your comment. I am not saying that James Tour privately endorses ID. I have actually never spoke with him on that topic. He is fallowing the rules of the academy in his disposition toward the topic as expressed in everything he has ever publicly stated. Although, all of his research invokes intelligent design to force molecules to form into target complex interactions.