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Thermodynamics and the Molecules of Life

Making biology's important molecules requires energy.


Questions:

Short Answer:

Thermodynamics 101 (albeit watered down a bit!): Simple chemicals with a bit of energy alone—absent of biological systems—may contribute to making a few but not all of the complex molecules required for life. And how is energy applied in wide open space—the great out-of-doors—on a primitive planet? Also, if some energy flows into an area where some chemicals have collected, does that assure us of a start to life?

Energy requirements are a critical barrier that must to be bridged in order for a reaction to go forward.

A + B + energy = C

Without energy A and B won't combine. That's a typical case for atoms and simple molecules that might combine to produce biologically significant compounds. Certainly, some of what chemistry offers includes examples of chemicals that will spontaneously make products—even give off energy instead of consuming energy—but these aren't the key biological substances that count in this discussion.

Energy pushes the reaction to make product C. You can't roll a stone down the hill until you have used energy to get to the top of the hill in the first place! This is one way to think of thermodynamics in simple terms. The equals sign is like getting to the top of the hill and making the last little push ... this requires energy that once added makes production of C look easy.

So, everyday principles of chemistry tell us that unless the barrier is surpassed, life's molecular building blocks would be rare to nonexistent on a primitive planet. Not to mention that one would need to put all the required chemical products in just the right place—and in sufficient quantities—to make a plausible scenario. And the expansive land and water surface of the planet might cause diffusion rather than concentrating key components. Even with some spontaneous reactions that might be assisted by energy from heat, lightening, or other naturally occurring source, the total package—in thermodynamic terms—still needs to be assembled. Something or someone has to put all the ingredients in one place to make the first cell. Where did that help come from? So maybe, at best, all this describes a low probability proposition.

The short answer tells us that the principle of thermodynamics is a potential show stopper. Even if basic ingredients are present, the energy requirements pose a significant hurdle. Further, there is a complexity to putting together molecules such that life will work properly. So, energy plus information need to be actively coupled somehow. And there seems no scenario to explain this in a simple physical system such as the primitive earth. In fact, there is no such evidence for spontaneous assembly of these molecules on the planet today. Remember, in the previous discussion it appears that the primitive conditions may be sufficiently similar to today's. If molecules and life itself had an inherent spontaneous property of self-assembly, then we'd find clues to this even now. But without the clues we are left with a mystery—and thermodynamics helps to provide reasons why life's appearance cannot be readily explained by science alone. Why don't more people just know this is true? Again, so much is assumed. We get the "standard story" in place of this information and thus to avoid the simple truth of the matter in question!

figure 1

Consider This :

In simplest terms, the laws of thermodynamics tell us something about how chemistry—and even the universe—works. From the perspective of making biological compounds, one cannot merely dump simple chemicals into a bowl and expect complex products. There needs to be some form of help to make reactions go forward.

Applying energy does the trick. But biological systems use enzymes and cofactors to reduce the energy requirements, to speed up reactions, that otherwise would take forever or never happen spontaneously. That is, energy free in the environment might come from heat, lightening, static electricity, or light, but there is still an element of randomness to the application of these sources. To coordinate a real production of significant amounts of chemical compounds requires a directed flow of information and energy.

The key concept is that biological function is integrally connected to highly specific arrangements of the molecular building blocks in the biopolymers. It has been demonstrated that this molecular complexity can be quantified using information theory. Thus the enigma of the origin of life can ultimately be reduced to a question whether information-intensive molecules can be produced from simple building blocks with only the flow of energy through the system and, possibly, the intervention of molecular selection of some sort. Bradley and Thaxton (CH) Page 179



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The previous consideration of chemical origins reveals how the primitive earth was not conducive to either forming or maintaining the products of chemical reactions in a presumed primordial soup. Even laboratory conditions where a scientist controls conditions to favor chemical reactions—such as those initiated by Miller and Urey—yields limited results. And the more complex chemistry of life is also found to be difficult to reproduce under the best of laboratory conditions. Bradley and Thaxton (CH, Page 182) note how Robert Shapiro, a Harvard-educated DNA chemist from New York University, revealed (in discussion at a 1986 meeting of the International Society for the Study of the Origin of Life (ISSOL) meeting in Berkeley) that prebiotic conditions are not favorable (i.e., impossible) for production of the all important ribose sugar. This is a molecule critical to life function. Is this the only such example of a key molecule that's difficult to synthesize?

... Dose, who includes ribose, deoxyribose and replicable oligo or polynucleotides in his list of hard-to- synthesize molecular building blocks. Horgan also notes that RNA and its building blocks are difficult to synthesize in a laboratory under the best of conditions, much less under plausible prebiotic ones. Bradley and Thaxton (CH) Page 182

Again, thermodynamics dictates that an energy requirement must be met before any chemical reaction can come about. So, even under the guidance of human intelligence there is no spontaneous appearance of chemical components that then fall into place leading to a functioning precursor of biological life. Certainly there is much intrigue and wonder that can be ascribed to the chemical roots that must have grown into life's appearance. But we are face with the chicken or the egg dilemma. Without macromolecules that are necessary components of any living cell one cannot have a functioning cell. But how did these form and how did they first get to a place that allowed them to compose the cell in the first place. More than simple free energy is required. On the other hand, given the mastery of cellular systems—coordinated by complex information—the manufacturing of complex biomolecules is facilitated by enzymes and cofactors that reduce all thermodynamic barriers and allow rapid production of every molecule needed—even those that are hard to make in a laboratory under the best of conditions.

The cell performs thousands of different chemical reactions. Each reaction consists of changing a molecule into one or more others. All the chemical reactions in a cell are mediated by catalysts. A catalyst always comes out of a reaction unchanged, and it can be reused indefinitely. Spetner (NBC) Page 31

No matter how life achieved its biochemical mastery of cellular chemistry, there is a remarkable trick in all this. As in the simple example at the top of this page, once energy is used to "operate" a reaction, it is consumed and tied up in the product. Energy use is a one shot option. But cells use enzymes as catalysts that can be repeatedly used over and over ... and very rapidly recycle to product several to hundreds of molecules in minutes. Now that's really cool! Seems engineered!

Note that enzymes are proteins that make reactions go ... and these are reactions by any other standard, under any ordinary set of conditions, that would go nowhere. This is a tailor made process with a specific enzyme engineered especially for a specific reaction!

And enzymes speed up a reaction rate by a factor of at least a million [Darnell et al. 1986]. An increase in rate by factors of ten billion to a hundred trillion are not uncommon [Kraut 1988]. A factor of a hundred trillion means that what takes a thousandth of a second with the enzyme would take about 3000 years without it. Most biochemical reactions would take so long without their enzyme that, in effect, they wouldn't go at all. Because enzymes controlled nearly all chemical reactions in the cell, we can say that, to a large extent, proteins control the chemistry of life [Stryer 1988]. Spetner (NBC) Page 32

The catalysts persist whereas more and more energy would be required if energy alone were to drive chemical synthesis. Why didn't chance and random evolutionary processes produce something less efficient? How did something so well designed become the cornerstone to cell chemistry? Yes, it might have been 'selected' naturally, but then how did it arise in the first place?

To be clear, energy can be sort of a two-way street. Some reactions release energy while others require it be added. We previously considered the composition of the earth's early atmosphere. If Miller and Urey were correct by their assumptions, maybe energy could be less a requirement. But if the recent evidence is for a primitive earth wrapped in nitrogen, carbon dioxide and water vapor, then energy would certainly be a critical requirement ...

... making amino acids out of ammonia, methane and hydrogen is an exothermic reaction (energy released) with an enthalpy decrease of approximately 200 Kcal / mole. By contrast, making amino acids out of nitrogen, carbon dioxide and water vapor is an endothermic reaction (energy must be added) with an enthalpy increase of +50 Kcal / mole. Small wonder that chemists prefer Oparin's hypothetical, but incorrect, atmosphere of ammonia, methane in and hydrogen. Bradley and Thaxton (CH) Page 184

In a chapter on thermodynamics and chemical origins, Bradley and Thaxton review energy requirements in relation to the production of functional proteins and DNA. Might energy flow through a simple system to create these complex molecules! The Natural History Museum in Washington, D.C., features an exhibit with a video that suggests that alternating cycles of heat and thus drying followed by wet conditions imparts energy and potentially explains how chemicals formed on earth. Is this cycling sufficient to explain the flow of energy through a primitive system? To be clear, the museum exhibit can only suggest a possibility because no clear explanation can be given. So, the analysis by Bradley and Thaxton serves to give a much needed critical look at this topic.

The analysis sounds a bit technical. But making the macromolecules of life (DNA, RNA and proteins) needs energy:

... energy flow available in the early earth might have been suitable to make the biopolymers of life. ... In terms of classical thermodynamics, polymerization will proceed spontaneously if the Gibbs free energy (G) associated with polymerization, or the joining of the building blocks, decreases ([delta]G is smaller than 0). However, if the assembly of the building blocks results in an increase in the Gibbs free energy in the system ([delta]G is greater than 0), then work is required to cause of this chemical reaction to go forward. Bradley and Thaxton (CH) Page 185

... Thus energy flow through the system must be able to provide enough work to raise the system to the higher energy level associated with the polymerized building blocks. If a typical protein contained approximately one hundred amino acids, then the total work required would be three hundred kilocalories per mole of protein formed to get a "random" assembly of the amino acids. Bradley and Thaxton (CH) Page 186

The last quotation above is part of the discussion that looks at calculations for what is really needed to make the chemical products for life.

Research shows that amino acids can link to form polymers by driving off water. In such cases heat becomes an energy flow moving through a system. This is perhaps the source for the National Natural History Museum's video presentation concerning chemical origins. But Bradley and Thaxton remind us that the order or arrangement of the amino acids is vital, ordered, and specific to a protein's function. And as we noted previously, the L-amino acids are the biological choice. So, a random assembly of L- and R-amino acids does not work. Something beyond the principles of thermodynamics applies to this selective factor.

Other factors to consider include the type of bond formed between amino acids:

... the peptide bond ... represents only one of several possible ways that amino acids may be joined together. Analysis of the bonds formed when the amino acids are joined in prebiotic simulation experiments indicate that no more than half of the bonds are peptide bonds. Yet functional protein requires 100 percent peptide bonds to be able to fold into the particular three-dimensional structures that give biological function. Bradley and Thaxton (CH) Page 186

Function is related to structure and shape ... and to get the specific molecule requires energy:

The three-dimensional topography that determines biological function depends on the sequencing of these amino acids. ... The additional work required to get this degree of specificity can be calculated to be 18.2 Cal / gm for one hundred active sites or 9.1 cal / gm for fifty active sites in a protein molecule consisting of one hundred amino acids. Bradley and Thaxton (CH) Page 187

In simple terms, the bigger and more specific a protein, the more energy is required to make this biospecific-molecule. And remember, the larger and more complex molecules need more information applied (somehow!) to direct the construction of the specific molecule!

Furthermore, once a specific molecule is produced—say in that primordial soup—there needs to be the specific molecule that fits the protein's enzymatic active site. There is no economy in making a protein whose function is of no use! And this somehow has to relate to all the other molecules that would have arisen in the primitive chemical scenario:

... possibly the most difficult problem in assembling amino acids into chains that fold into three-dimensional structures that give biological function is to react the amino acids only with each other and not with the many other chemical substances that would be present in a prebiotic soup. The fact that one has to do work (30 cal /gm) to chemically react amino acids with each other indicates that amino acids do not readily react chemically. ... So it is difficult to imagine how amino acids could be either concentrated in solution or selectively absorbed on surfaces such as clays before they were consumed in a chemical reactions with other substances in the prebiotic soup. Bradley and Thaxton (CH) Page 187

The latter comment addresses one of the many alternative ideas for chemical evolution—but an idea like the rest that encounter impracticalities. In spite of the complexities cited above, Bradley and Thaxton made calculations for the energy required for the random assembly of amino acids:

We have calculated the work required to provide the necessary specified complexity in a protein of one hundred amino acids and found it to be similar in magnitude (18.2 + 4.2 + 4.2 cal/gm) to the required work to get our random assembly of the building block (30 cal /gm), if we neglected the major problem of amino acids' tendency to react with other molecular species in the prebiotic soup. Bradley and Thaxton (CH) Page 188

Energy is required and what specifically keeps the amino acids available for only the right reactions? So now we arrive at problems:

While energy flow is clearly able to do the required work to get assembly, it is doubtful that energy flow is ever coupled to, or capable of, the generation of information. ... Biological information ... has no physical connection whatsoever. Bradley and Thaxton (CH) Page 188

These points may sound familiar to statements made in our prior feature article, but here we are adding the perspective of thermodynamics as it relates to energy requirements to get the work done. But as before we seem to run into the issue of information and the gap between the mere physical world and the leap into the biological framework of life itself.

Bradley and Thaxton note that many prebiotic simulation experiments concern making proteins following some Miller-Urey type scenario. Much of the selective process favoring production of products like amino acids comes from the laboratory setup and the design created by the scientist. We think this introduces an element of intelligence and design, but even with this effort ...

The net result is that even "contrived prebiotic" simulation experiments have produced chains of amino acids whose catalytic activity is trivial at best. Bradley and Thaxton (CH) Page 188

The work the simulations are capable of accomplishing is nothing like that within cells.

In sum total the calculations and approaches to solving the questions posed by thermodynamics come down to the scientists statement:

... we conclude that energy flow through the system is capable of joining molecular building blocks but appears to be incapable of joining them in the very specific ways necessary to have biological function. Bradley and Thaxton (CH) Page 188

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Added Perspective:

We may err on the side of presenting numerous examples of what could not have happened. But that's where we find ourselves, because no one is able to provide the explanation of how it could have happened. We looked previously at fine-tuned conditions required to make the universe and our solar system—the earth too—favorable to supporting life. Yet the energy necessary to set the physical stage of life was there from the beginning. The physics and physical chemistry that stem from the big bang is easily comprehended by comparison to the biophysics and biochemistry that is built into the puzzle of assembling life. Formation of stars by condensing gases in outer space if favorable, building biomolecules of just the right kind and necessary concentration, along with assembly into functioning life systems is not a thermodynamically favorable proposition.

The perspective we glean here is that life is quite unique. Energy requirements for the chemistry of life raise the bar once more. Explanations go wanting. The most knowledgeable of the world's scientists are still thinking about possibilities, but without resolution or clear results. And science's knowledge base has never been greater than today.

Again, we are adding perspective to perspective—looking at all the angles. Here, we have one more element of the WindowView that along with other perspectives guides us to a conclusion that is very different from simply natural, material, and evolutionary scenarios. If this were the only complication we might just excuse it for a time. But if not excused out of hand, there is good reason to see that life did not arise by simple chemicals or by self assembly—not of its own accord and not simply by chance reactions over eons of time. In fact, life appeared too quickly on the primitive earth to give eons of time as an option.


Quotations from "The Creation Hypothesis" (CH) edited by J. P. Moreland are used by permission of InterVarsity Press, P.O. Box 1400, Downers Grove, IL 60515. www.ivpress.com All rights reserved. No portion of this material may be used without permission from InterVarsity Press.

Quotations from "Not By Chance" (NBC) written by L. Spetner, are used by permission granted by Dr. Lee Spetner.


The WindowView drops many of the typical presumptions to take another look. What does scientific data tell us if we start without assumptions? And ... how contiguous is science information if examined along with scriptural perspectives provided by the Bible? The Bible is the only religious or holy book we know of that is in fact consistent with science. While not a textbook, the Scriptures are either contradictory or complementary to scientific perspectives. Have you looked at these perspectives? To see 'Science and Scripture in Harmony' is to reveal life, reality, and your future.


Download the free PDF version of this book:
Mystery of Lifes Origin

Writer / Editor: Dr. T. Peterson, Director, WindowView.org
(040408)


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Creation Hypothesis Not By Chance Evolution Theory in Crisis Mystery of Lifes Origin Origins Mere Creation
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