Brian Miller: Thermodynamics and the Origin of Life

Design

(Brian Miller) #42

This article was not mentioned at the top, but it relates to England’s research:
https://evolutionnews.org/2017/08/hailed-as-the-next-darwin-mits-jeremy-england-sheds-little-light-on-lifes-origins/


(Matthew Pevarnik) #43

Thanks for sharing… I suppose I would ask are you (@bjmiller) committed to debunking/dismissing all research on the OOL or would you be open to changing your mind? I almost hate to ask such a question, but for example, Answers in Genesis explicitly says they reject the Big Bang Theory because “from the Bible we can already know the big bang idea is wrong: the Word of God in Genesis 1 says the earth was created before the stars.” Now I understand that as a writer at EN, you are not obligated to any particular holy text or whatnot. But I wanted to just ask before discussing your article whether or not you are committed to always rejecting all aspects of OOL research from the start- since a major talking point (at least from my limited perspective) of EN is that since abiogenesis is ‘so unlikely’ therefore some intelligent being (who just so happens to have the characteristics of the God of the Bible) intervened.


(S. Joshua Swamidass) #44

That is a fair question.

A corollary question: What parts of OOL research do you think is helpful and valid?


(S. Joshua Swamidass) #45

15 posts were split to a new topic: A Better Approach to Abiogenesis


(Brian Miller) #47

I would have no problem if science demonstrated that life could form through the laws of nature. In such a universe those laws would be so obviously engineered for that result that the argument for design in life would simply move to the argument for fine tuning. In such a universe we could easily demonstrate simple chemicals turning into the building blocks of life, and we would observe those building blocks combine into long chains. And, we could use randomized libraries of amino acids to form complex enzymes which could interconnect two chemical reactions or form complex molecular machines. We could also put cells into a blender and then watch them coalesce back into functional cells. However, we see no such evidence. Instead, we see a universe where practically every natural process breaks apart complex biological chemicals into simple biologically inert ones. Such observations have led many OOL researchers to describe life as a freak accident.

A corollary question: What parts of OOL research do you think is helpful and valid?

I would say most OOL research is very helpful for several reasons related to each type of experiment:

  • Realistic Experiments: Experiments which attempt to realistically model the conditions on the early earth demonstrate that natural processes lead primarily to simple low-energy molecules, and they break apart the complex, high-energy molecules needed for life.
  • Synthesis Experiments: Experiments which recreate life’s complex building blocks require enormous investigator interference involving several highly controlled steps which involve purification and concentration of desire intermediate products, constantly changing conditions, added catalysts, and the like. These experiments provide insights which chemical companies could use to better manufacture such molecules as nucleotides and lipids. They also demonstrate the absolute need for intelligent agency in most steps leading to OOL.
  • Simulations and Mathematical Models: Such research always involves the models including the equivalent of energy production machinery and enzymes to couple the produced energy to desired reactions. They thus demonstrate to need for both.

To summarize the main issues concerning OOL:

  1. Nearly all OOL researchers would acknowledge that the chances of a cell forming are too small to occur unless physical processes helped to beat the odds.
  2. The driving tendencies toward greater entropy and lower energy both work against OOL, so it is far less likely for a cell to form than by pure chance if all configurations of atoms were equally likely.
  3. The minimally complex cell demonstrates high levels of coordination, foresight, and goal direction which are unmistakable signs of intelligent design.

One would naturally ignore all of these points if one assumed that life must be purely a product of the blind laws of nature. This position would be nonoptional for an atheist, agnostic, or even a deist. However, for those who believe in a Creator, they must consider the natural drive for creators to create. Allowing for that possibility, the conclusion for design in OOL is most natural.


(S. Joshua Swamidass) #48

This seems like a false choice @bjmiller. Have you considered other options?

This also seems like a false choice. Are you open to other options?


(Joseph Akins) #53

IMO point 1 is irrelevant to OoL, as is biochemistry itself. The complexity we see in cells today is the result of cosmochemistry to geochemistry then biochemistry. Biochemistry is NOT just improved geochemistry and OoL was necessarily organized geochemistry, and therefore low entropy, or it would not have been able to get a foothold. The most promising OoL research IMO is that of Nick Lane and Michael Russell. The low entropy conditions of early life, resulting from strong disequilibrium, even has an analogy with the Big Bang as pointed out by Sean Carroll in a series of short videos culminating with “What is the purpose of life?”: http://www.preposterousuniverse.com/blog/2016/11/03/entropy-and-complexity-cause-and-effect-life-and-time/

A nice article by Russell et al. (2013): http://rstb.royalsocietypublishing.org/content/368/1622/20120254

And a brief Nature Scitable review of chemiosmosis by Nick Lane: https://www.nature.com/scitable/topicpage/why-are-cells-powered-by-proton-gradients-14373960

A different approach to @bjmiller would be why are there so many similarties between cellular chemistry and alkaline vents?
How is pumping protons upstream first an “intelligent” design for ATP production? It seems to be more a result of Archea and Bacteria developing in the background geochemistry of alkaline vents.

Yes, I am a Christian. Yes, I am a creationist. Yes, I see God working in all of this. I just also believe He left a record for us that He might be glorified.


(Brian Miller) #60

My article on natural engines addresses the Russell/Lane model:
https://evolutionnews.org/2017/06/free-energy-and-the-origin-of-life-natural-engines-to-the-rescue/

Russel and Lane were very insightful in recognizing the need for machinery to convert one form of energy into another which could be used to drive the metabolism. The challenge is creating a mechanism sufficiently efficient to provide the needed energy output and developing a way to couple that energy to the specific reactions needed for a viable metabolism.

Even the simplest cells which draw power from proton flows have multiple ATP synthases which are highly efficient. The chances of some membrane or some macromolecule lodged in the membrane being able to produce the needed energy is minuscule. And, the proper coupling would require information-rich enzymes or the equivalent. Paul Davies has written quite a bit about information being central to life. For these and many other reasons, the OOL research community has not largely embraced the model as plausible.

The key issue in OOL research is whether the investigator interference is moderate enough to solely accelerate reactions which would realistically occur on the early earth, or is it dramatic enough to force reactions to move in directions which would not have occurred and to force final products which would not have been produced in significant quantities. Nearly all OOL research protocols fall into the latter category, so they demonstrate the need for intelligent agency.

In addition, the conditions required for the different building blocks are mutually exclusive, so they had to be produced in different locations. The challenge is then for all of the needed pieces to culminate in the same microenvironment. The time required for a protein to make contact with a cell membrane in even a relatively small pond could be millions of years. However, a protein would have broken apart in a matter of years in most cases. Therefore, millions of copies of that same protein would have been needed for one to have a chance to reach the target. In a large body of water, far more than trillions of copies could have been needed.

Compounding the problem, the chance of generating one amino acid or nucleotide chain long enough to create something useful is exceedingly small. And, the chance of that chain stumbling upon the right sequence as something like a topoisomerase or a polymerase is also quite small. No plausible mechanism could have existed to yield such enormous quantities of long-chained molecules to have any realistic chance of hitting the target.

A counter question to ask is to what extent different people are open to ever considering the possibility of design. Or alternatively, in what other context would encountering an artifact which could perform the functions of a minimally complex cell not immediately be recognized without question as designed? If SETI picked up a transmission from a distant star containing the encoded information for the schematics of a spaceship, should those scientists be allowed to claim that the signal came from an intelligent agent? Is that inference scientific? Or, should they be forced to only consider theories of how self-replicating quasars could have been selected for signals resembling spaceship schematics?

That analogy might sound absurd, but the chance of the ancient earth containing oceans filled with self-replicating RNAs or long-chained proteins which just happened to stumble accross all of the needed enzymes and other machinery needed for life and then ending up inside the same cell membrane is equally as absurd.


(S. Joshua Swamidass) #61

This easy. I already affirm that God created us, and in that sense he designed us all. Perhaps he directly created the first cell. Why not? Even if not, he designed a process to create the first cell. So of course, I am open to considering design. I’ve considered it and agree God designed us all.

Human designed artifacts are nothing like cells. Animal designed artifacts are nothing like cells. So we should conclude that cells do not look like they are designed. Life fits into a different category. It does not look like a creaturely design. It does, correctly in my opinion, give us the correct impression that it is divinely designed. We need to be honest however that cells do not look anything like any human created design.

Non-sequitor. This is almost nothing like abiogenesis.

It is hard to even imagine how this would be possible on several levels. I cannot imagine deciphering a message that complex without knowing the intelligent aliens by other means first, to understand how they encoded it.

Of course not. They would start looking for the intelligent aliens, to confirm they weren’t being hoodwinked by a prank or a reflected message, etc. This, however, is not allowed for divine design inferences. So ID is just nothing like SETI.

Incredulity is not an argument, especially when based on a false analogy. You have basically answered @pevaquark’s questions it seems:

It seems that you are committed to debunking/dismissing all research in OOL and are not open to changing your mind. Is that a correct interpretation of your response?


(Joseph Akins) #64

Brian,

Much thanks for your thoughtful response. We agree on most every point, but are approaching it from different angles. My perspective is from within Naturalistic science and yours is the ID perspective. As such you hone in on the intricacy of the the proton motors, but have not addressed the overall design of the system. Why would a Designer basically create a hydroelectric dam for energy so that people can grow crops and build houses just to have the energy to carry buckets of water upstream to supply energy to the dam? Not an exact analogy, but highlights why I struggle to see Intelligent Design in it.

This short talk (~ 30 minutes) by Nick Lane summarizes why I favor hypernaturalistic vs supernaturalistic design: https://youtu.be/gb7pZyks_HE

The difference being that I believe in low probability, yet reproducible, events and not poofing (to be descriptive not perjorative).

Much thanks for considering my perspective.


Brian Miller: Thoughts on ID and Good Theological Questions
(Joseph Akins) #65

Nick lane responded to the paper by Baz Jackson which I had posted earlier:
“Unfortunately, Jackson mainly criticized his own interpretations of the theory, not what the literature says. This counterpoint is intended to set the record straight.”

http://nick-lane.net/wp-content/uploads/2017/05/Lane-BioEssays-proton-gradients-2017.pdf

I should clarify that much of the way I think about OOL predated by many years my awareness of the work of Lane and Russell. My support of their work is because it coherently presents how I tend to view OOL as a geologist.


(Brian Miller) #67

One of the forefronts in biology is the robust conversations taking place between biologists and engineers. The similarities between human design and biological systems are becoming more clear as both fields advance. They are typically at levels in the biological hierarchy where functional relationships are identified. This effort is advancing most in the fields of systems biology, synthetic biology, and biomimetics.

Here is a small sampling of resources:

Survey of Engineering Models for Systems Biology

As a discipline, systems biology shares many characteristics with engineering. However, before the benefits of engineering-based modeling formalisms and analysis tools can be applied to systems biology, the engineering discipline(s) most related to systems biology must be identified. In this paper, we identify the cell as an embedded computing system and, as such, demonstrate that systems biology shares many aspects in common with computer systems engineering, electrical engineering, and chemical engineering.

Control Theory and Systems Biology Laboratory

The logic of the heat shock response is implemented through a hierarchy of feedback and feedforward control architectures that regulate both the amount of sigma-32 and its functionality. We have developed a dynamic model that captures known aspects of the heat shock system and are using it to exploring the logic of the heat shock response from a control theory perspective, drawing comparisons to control systems in engineering.

Systems Biology and the Quest for Design Principles

Some approaches compare living systems to well-functioning engineered systems to identify so-called optimality principles. Examples are the discovery of the general ‘optimal’ branching angle in vascular systems inspired by the designs of pipe systems that minimize the flow of resistance (Rashevsky 1961, Rosen 1967), and Savageau’s demand theory for optimal gene regulation (Savageau 1989). Engineering approaches have recently had a renaissance with the application of graph theoretical tools to biological datasets. In systems biology such principles are typically referred to as design principles. These need not focus on optimal performance but are organizational rules “that underlie what networks can achieve particular biological functions” (Ma et al. 2009, 260).

Engineering and control of biological systems: A new way to tackle complex diseases

It is worth briefly considering the relationship between systems biology and synthetic biology: systems biology can be thought of as the other side of the coin, in that it aims at developing a formal understanding of biological systems through the application of engineering and physics principles. …The drive in merging engineering and biology has begun and shows no sign of slowing down.

An Introduction to Feedback Control in Systems Biology

Although many of these researchers have recently become interested in control-theoretic ideas such as feedback, stability, noise and disturbance attenuation, and robustness, it is still unfortunately the case that only researchers with an engineering background will usually have received any formal training in control theory. Indeed, our initial motivation to write this book arose from the difficulty we found in recommending an introductory text on feedback control to colleagues who were not from an engineering background, but who needed to understand control engineering methods to analyse complex biological systems.

Biomimetics: forecasting the future of science, engineering, and medicine

Leonardo da Vinci’s (1452–1519) work is a fundamental example of biomimicry. He designed a “flying machine” inspired by a bird. In the Far East, General Yi Sun-sin built the turtleship, a warship modeled after a turtle, to fight Japanese raiders during invasions. The Wright brothers (1867–1948) took note of the wings of eagles and made a powered airplane that succeeded in human flight for the first time in 1903. Over the next century, the airplane became faster, more stable, and more aerodynamic. Schmitt was the first to coin the term biomimetics in 1957, and he announced a turning point for biology and technology.

Lecture on Applying Engineering to Life:

Obviously, many differences exist between human engineering and biological systems, but the nature of those differences demonstrates that biological systems are the product of a much higher intelligence. The latter demonstrate greater levels of efficiency (e.g. ATP synthase) and greater levels of ingenuity (e.g. capacities of birds to navigate and control their flight).


Brian Miller: Complexity in Biology as Incremental Addition
(S. Joshua Swamidass) #68

I understand you have to think this way, but this is a very selective reading. There is an exchange between engineering and biology, but a large amount of the complexity in biology is best explained by incremental addition of parts, more like a goldberg machine than a fresh de novo design. This is an immensely difficult way to design things for human designers, which is why we have such difficulty engineering biological systems. This complexity, however, actually improves the odds of biological evolution. What biology shows us is that life is not designed at all how a human designer would design it, and it cannot be understood with out engaging its deep history.

I know you are not talking about common descent here, but it is worth asking. Do you affirm common descent? If not, why did not God make it more clear that common descent is false?


Brian Miller: Complexity in Biology as Incremental Addition
(Arthur Hunt) #69

Sorry to jump back a few days, but there are some errors that need to be pointed out. As before, these pertain to Brian’s claims about the entropy status of cells.

Davie’s article makes no such calculation. Moreover, as I have shown here, the paper by Davies et al. is, to be kind, a very unreliable source when it comes to this subject.

This is also mistaken.

And I have never, until our discussion, encountered a serious scientist who would deny the roles that hydrophobic interactions play in the assembly of macromolecular structures, or that hydrophobic interactions are entropy-driven.

The fact remains - cells, today or at the inception of life, are high-entropy entities.

The OOL requires no such thing, and Morowitz’ calculation had nothing to do with such a preposterous claim.

This is a misrepresentation of Morowitz. He “hoped” for no such thing, but rather presented a coherent and entirely reasonable explanation for why life is not (in physical chemical terms) an equilibrium proposition. Moreover, the “order” mentioned here is quite akin to that seen in cells.

To understand the scope of what we are speaking about - recalling that chemical reactions are accelerated by 1000-1,000,000 fold or more in cells, if we equate a 1 mph breeze with uncatalyzed reactions, then we can see that cells are veritable maelstroms, comparable to storms with windspeed of tens of thousands of mph or more. This is quite far in excess of the pitiable storms Brian’s graduate group studied, and it is quite reasonable to suppose that this much-accelerated state of chemistry is going to be quite amenable to the sorts of spontaneous self-assembly and order we see in living cells.

Since cells are high-entropy entities, I believe Morowitz’ book is spot on.

I have to wonder - Brian continues to cling to thermodynamic considerations that completely ignore the fact that water interacts with solutes and macromolecules and makes very significant contributions to the entropy of living cells. It is almost as if Brian (and, by extension, the Discovery Institute) is proposing a new and different status for water - maybe that it is inert aether of sorts. While I haven’t read it, maybe Denton’s recent book about water had some similar ideas. Perhaps Brian can elaborate on this, or at least explain why he continues to completely ignore the principal chemical constituent of all living things.


(Arthur Hunt) #70

Seriously?

If one is going to use this sort of logic, then I believe the reasoning is more like:

Human engineering (intelligent design) cannot come close to accomplishing what we see in living systems. It thus stands to reason that life is beyond the capabilities of intelligent design.

(If one is going to use the logic that Brian is deploying here …)


Brian Miller: Complexity in Biology as Incremental Addition
(Brian Miller) #71

What would be the best examples and related research articles which demonstrate your point? You might desire to add some additional commentary to emphasize the salient points.


Brian Miller: Complexity in Biology as Incremental Addition
(Timothy Horton) #72

No it doesn’t. It merely shows humans in a few hundred years of engineering design haven’t achieved the results natural processes working over 3.5 billion years have achieved.

Why ID-Creationists still think arguments from personal incredulity count as scientific evidence is a real mystery.


Brian Miller: Complexity in Biology as Incremental Addition
(Brian Miller) #73

OOL researchers have known for almost a century that cells represent low entropy configurations of matter. Here are a few representative descriptions:

On the Free Energy That Drove Primordial Anabolism

In 1944 Schrödinger published his famous book “ What is Life ”, in which he points out that life is avoiding the rapid decay into the inert state of equilibrium and that it is continually drawing negative entropy from its environment. Although the term negative entropy or negentropy created some confusion and his description is far from being a definition of life, Schrödinger already recognizes a very important basic principle that, with only a few exceptions, is unique to all things that are alive. Life is capable to create order and complexity, the opposite of entropy, by feeding on a suitable kind of free energy. In terms of biochemistry, the continuous supply of free energy is essential for anabolism, which is defined as the processes in metabolism that result in the synthesis of cellular components from precursors of low molecular weight. Reactions that build up complex molecules from smaller building blocks are fundamental to every living being. As a consequence, the utilization of free energy, vitally important for every anabolic reaction, is essential for the origin of life as well.

The Origin of Life

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.

Very few have actually attempted to calculate the precise drop in entropy since doing so is likely very difficult. However, Morowitz in Energy Flow in Biology (EFB) estimates the entropy drop due to the formation of macromolecules (p. 97). A few others have also made attempts.

Dr. Hunt’s confusion is due to his apparently assuming the entropy increase due to the formation of a cell membrane could help compensate for the entropy reduction for the rest of the cell, which is not accurate. The rest of the cellular structures have just as much difficulty going to a lower entropy state. A good book to better understand entropy at a more intuitive level is Entropy and the Second Law by Arieh Ben-Naim. He may also be confusing the entropy change due to the folding of a protein and the creation of a protein.

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. He was clearly taking into consideration the effect of water.

He also states (p. 68)

Again, we stress in a very firm quantitative way, the impossibility of considering life organizing as a fluctuation in an equilibrium ensemble.


(Arthur Hunt) #74

I think this discussion has run its course. What I have learned from this exchange is that:

  1. Brian doesn’t believe hydrophobic interactions are important for protein folding and assembly, or in other macromolecular associations. (There is bit of irony here since he cites an author who disagrees quite completely with this view. But I do not know the behind the scenes here, so…)

  2. Brian apparently doesn’t believe that water interacts with macromolecules. (Again, this is something that Ben-Naim has published on.)

  3. Since Brian repeatedly cites a calculation by Mrorowitz (“Morowitz in EFB (p. 66) calculates the probability for a cell forming at roughly 1 in 10 to the power of 100 billion” etc.) as support for his position, he obviously believes that living cells are in chemical and thermodynamic equilibrium. (This is the context for Morowitz’ calculations.)

Brian has dug in his heels and doubled down on this erroneous ideas, and it is clear that more discussion will not accomplish anything. While not likely, I would be interested in knowing if the DI brain trust (Behe, Axe, and Gauger, to name three biologists) holds to these views of the chemistry of living things.


(S. Joshua Swamidass) #75

A post was split to a new topic: Does Peaceful Science Misrepresent ID?