The Origin of Life - Chemical Evolution & Naturalism

This is one of my four pages (scientific, thermodynamic,
methodological, and philosophical) about the origin of life.

Theories about the origin of life on earth are usually evaluated in a context of methodological naturalism by assuming that "everything (throughout the entire history of nature) happened by natural process." Is this assumption true, and is it always useful in our search for truth?

1. The Science of Chemical Evolution (Part 1)

An Origin of Life by Chemical Evolution?
In an attempt to explain the origin of life, scientists propose a two-stage process of natural chemical evolution:
1) formation of organic molecules, which combine to make larger biomolecules;
2) self-organization of these molecules into a living organism.
For each stage, scientists are learning that what is required for life seems much greater than what is possible by natural process. The huge difference has motivated scientists to creatively construct new theories for reducing requirements and enhancing possibilities, but none of these ideas has progressed from speculation to plausibility.

Later, we'll return to scientific evidence-and-evaluation in The Science of Chemical Evolution: Part 2 and Part 3. Before then, let's look at how scientific evaluation is affected by philosophy.

2. A Test-Case for Naturalism
Confusion is caused by the common use of "naturalism" with two meanings: in a narrow meaning, naturalism is a specific claim — which is compatible with Christianity — of "only natural process" for a particular event, series of events, or period of history; in a broad meaning, NATURALISM (or naturism) is a general claim — not compatible with Christianity — that "only nature exists" with matter/energy but with no God and thus no divine action.
In this page, "naturalism" has the narrow meaning. But a wider range of people, including both theists and non-theists, affirm this narrow meaning. But non-theists, who hope the general meaning is also true, provide much of the emotional intensity and sociological pressure (in the scientific and educational communities) for opposing non-naturalistic theories.

For judging the depth of commitment to naturalism — an assumption that everything in the history of nature happened by natural process — the origin of life makes a fascinating test-case. To see why, let's compare three characteristics of chemical evolution and biological evolution.
• Scientific Support? Current theories about chemical evolution seem highly implausible, so the scientific support is very weak. But support is much stronger (*) for biological evolution, for a neo-Darwinian development of biocomplexity and biodiversity. * the scientific support is stronger, but is usually overestimated due to a shifting of support
• Unifying Function? Most scientists and educators think biological evolution — but not chemical evolution — plays an important unifying role in biology.
• Worldview Function? Both types of evolution are necessary for a worldview of naturalism, for a universe with a natural total evolution (astronomical, chemical, and biological), with only normal-appearing natural process throughout the entire history of nature.
Worldview Asymmetry: If a natural origin of life (of any type, anywhere in the universe) is impossible, this would be devastating for the worldview of an atheist, deist, or rigid agnostic. But either way — with or without a natural origin of life — is fine for Christians, including me, as explained in my FAQ for Creation, Evolution, and Intelligent Design (conclusion of 5B, plus 5C) and No Proof for the Existence and Activities of God? Why isn't God more obvious?

When we look at the origin of life, interesting questions arise from an interesting combination, because chemical evolution
• is not supported by a logical evaluation of evidence,
• and is not important for unifying biological science,
• but is essential for a "no miracles" naturalism.
This is an opportunity for scientific humility about naturalism. Is the response a humble acknowledgment that maybe life did not begin by natural process, so maybe naturalism is wrong? No, instead there are confident statements (by individuals and organizations, in textbooks and websites) claiming that chemical evolution definitely did produce life, even though we don't yet know the details of how this happened.

This transition between Sections 2 and 3 is a story about scientists — who are speaking "in the name of science" for a prestigious organization — making a claim that is confident but is not scientifically justifiable:
Although a natural origin of life by chemical evolution seems implausible, the National Academy of Sciences confidently asserts (in Science and Creationism, 1999) that "For those who are studying the origin of life, the question is no longer whether life could have originated by chemical processes involving nonbiological components. The question instead has become which of many pathways might have been followed to produce the first cells." This confidence in the power of natural process doesn't seem consistent with the scientific evidence, so why does the NAS make the claim? Maybe they are influenced by an assumption, which is not based on science, that everything in the history of nature happened due to natural causes.

comments about Sections 3-8:
Originally, this page was a "sampler" that combined a variety of ideas about science and philosophy. Then I split it into several pages that are more specialized, that focus on each major idea. In the current page, some sections (6 & 7) are unchanged, some (4 & 8) are omitted, and others (3 & 5) include selected excerpts. { Or you can see the entire original page. }

3. Closed Science and Open Science
This section was moved into Methodological Naturalism but the main ideas (in quoted excerpts, with some minor revisions) are below:

Methodological Naturalism and Closed Science
Currently, most scientific inquiry is closed by methodological naturalism (MN), a proposal to restrict the freedom of scientists by requiring that they include only natural causes in their scientific theories. In a closed science (restricted by MN), evidence and logic are not the determining factors because the inevitable conclusion — no matter what is being studied, or what is the evidence — must be that "it happened by natural process."

Can we avoid the possibility of unavoidable error?
Imagine two possible worlds: one has a history of nature with all events caused by natural process, while the other has a history that includes both natural and non-natural events. In one of the two possible worlds, a closed science (restricted by MN) must inevitably reach some wrong conclusions. (*) By contrast, in either world a non-MN science will allow, although it cannot guarantee, reaching correct conclusions.
* Logically, MN should be accompanied by MN-Humility that acknowledges the possibility of unavoidable error: If the origin of a feature actually involved a non-natural cause, then any explanation by MN-Science (in terms of only natural causes) will be incomplete or incorrect.

The Freedom of Open Science
Imagine that we're beginning our search for truth with a logically justifiable attitude of humility, by refusing to decide that we already know — with certainty, beyond any doubt — what kind of world we live in. If we don't know whether history has been all-natural, our best scientific strategy for finding truth is an open science, with scientists humbly asking a question instead of arrogantly assuming an answer.
In open science... a scientist begins with an MN-assumption, but does not insist that — no matter what the evidence indicates — it is necessary to end with an MN-conclusion. An open scientist adopts testable-MN instead of rigid-MN, because the assumption of MN is treated as an assumption, as a theory to be tested rather than a conclusion to be accepted. There is flexible open-minded inquiry, with freedom of thought for the individual and community, and scientists are free to follow the evidence-and-logic wherever it leads. ...

Should science be logical?
Should we let methodological naturalism force us to accept a "scientific" conclusion that is less logical ... simply because it is natural?

Is evidence irrelevant? MN-Science can
bypass the process & claim the support.
The Conclusion of MN-Science — that no matter what is being studied, or what is the evidence, it happened by natural process — is actually The Assumption of MN. The circular logic of MN, which converts a naturalistic assumption into a naturalistic conclusion, is illogical (because circular logic is bad logic) yet is unavoidable, and it requires no science.
To see the irrelevance of evidence when MN determines the conclusion, compare the evidence-based implausibility (earned by current theories for a "chemical evolution" origin of life) with the naturalism-based confidence of the NAS in claiming that "the question is no longer whether life could have originated by chemical processes. ... the question instead has become which of many pathways might have been followed to produce the first cells." Yes, with MN the evidence is irrelevant. Even though each of the "many pathways" is implausible, one pathway must have produced life (because according to MN this is the only possibility) so confidence does not require evidence. { Words are carefully chosen by NAS to avoid technical falsity, since they say "could have originated" and "might have been followed." But the words are also chosen to clearly express the claim that "the question is no longer" whether it did occur naturally, the only question is how it occurred naturally. }
Of course, the irrelevance of evidence does not mean there is no evidence, or that MN is leading to the wrong conclusion. But it does illustrate a logical weakness of MN, since MN requires that we must reach a scientific conclusion before doing any science. But instead of acknowledging this logical weakness, usually MN-Humility is ignored and there is an implication that the assumption made by MN (that it happened by natural process) is a conclusion reached by science (and is therefore probably true). MN provides a way to bypass the process of science and then claim the authority of science as support.
For example, there is an implication that the declaration by NAS (speaking with authority "in the name of science") is based on scientific evidence and logic. But the main reason for believing that life had a natural origin is not science, it's a naturalistic assumption that everything had a natural origin.

Is a closed science theologically acceptable?
For a Christian who believes that God can do miracles, as claimed in the Bible, is a closed science (with MN forcing scientists to assume that no miracles have occurred in the entire history of nature) theologically acceptable? { "yes" is my answer, as explained in Methodological Naturalism }

4. What is a theory of design?
This is now in Four Types of Design which describes design (in general, broadly defined so it includes all four types) and Design (specific, with a narrow definition that includes only two types).

5. Can a theory of design be scientific?
Most of this section is now in Intelligent Design: Is it scientific? and Methodological Naturalism and some (re: design and religion) is in Four Types of Design.
• Design is Testable in Science
Design can be tested using scientific logic. How? When we use the definitions above, design [narrowly defined] and non-design are mutually exclusive (it was one or the other) so we can use eliminative logic: if non-design is highly improbable, then design is highly probable. Thus, evidence against non-design (against production of a feature by undirected natural process) is evidence for design. And vice versa. The evaluative status of non-design (and thus design) can be decreased or increased by observable empirical evidence, so a theory of design is empirically responsive and is testable. Based on a logical evaluation of evidence, we can conclude that a design theory is probably true (if all non-design theories seem highly implausible) or is probably false (if any non-design theory seems highly plausible). { But can design be proved? What about future developments in science? }
• Observable Signs of Design
• Can historical science be scientific?
• Design is Common in Science
• What difference will it make?
• Will it be scientifically productive?
• Does it violate The Rules of Science?
• When is critical thinking unscientific?
• Why is it controversial?
• Should you examine it more carefully?
The arguments for Closed Science seem less logical when we look more closely ... so the closer we examine Open Science the better it looks.

The main part of this page ends by looking at current science & future science, in Sections 6 & 7.

6. The Science of Chemical Evolution (Part 2)
In an attempt to explain the origin of carbon-based life on earth, conventional naturalistic theories of chemical evolution propose two stages in the transformation of lifeless chemicals into life: 1) the formation of small organic molecules, which then combine to form larger biomolecules; 2) the self-organization of these molecules into a primitive living organism.
Despite initial optimism following the famous Miller-Urey experiments in 1953, closer investigations have revealed major problems that have not been solved (and perhaps cannot be solved) in both stages of the proposed scenario:
In the first stage, chemical equilibria are usually unfavorable (they are "energetically uphill") for the formation of small biomolecules and also for their synthesis into larger biomolecules. During experiments in which there is a realistic simulation of the atmosphere on an early earth — using the probable starting molecules (H2O, plus N2 and CO2 which are stable and unreactive) instead of the improbable starting materials (H2O, plus reactive NH3 and "explosive" H2 and CH4) in the reducing atmosphere used for the Miller-Urey experiments — the yields of essential biomolecules are extremely low.
Even if biomolecules could form in Stage 1, these lifeless chemicals would have reached only the starting point for the most challenging part of their journey toward life in Stage 2. The simplest "living system" we can imagine, involving hundreds of components interacting in an organized way to achieve energy production and self-replication, would be extremely difficult to assemble by undirected natural process. And all of this self-organization would have to occur before Darwinian natural selection (which depends on self-replication) was available.

Basically, what scientists are learning is that the complexity required for life (in terms of biomolecule formation and self-organization) seems to be much greater than the complexity available by natural process (beginning with lifeless matter). This huge difference has motivated scientists to stretch their imaginations, to creatively construct new theories for reducing requirements and enhancing possibilities.
For example, in an effort to avoid a "chicken and egg" problem — in modern cells, DNA is required for protein synthesis, but protein is required for DNA synthesis — scientists have proposed that RNA (which combines the replicating ability of DNA and the catalytic activity of proteins) was the key life-producing molecule in the earliest cells. But this "RNA World" theory now seems implausible due to the apparent impossibility of pre-biological RNA synthesis, and because the catalytic activities of RNA have not matched initial optimistic hopes. In response, scientists are now proposing "pre-RNA World" theories with key functional roles played by other molecules, and with metabolic energy sources that would be easier to use.
Other alternatives include variations on the classic "soup" scenario, with new environments such as a semi-evaporated pond, a seafloor hydrothermal vent, the surface of a clay-like mineral, or even another planet. Or the first life in the universe might have been different than familiar carbon-based life on earth.
Scientists are trying to develop principles for a prebiological selection of molecules, analogous to the biological selection of genes in living organisms. And they are continuing to explore the self-organizing properties of complex chemical systems, and to search for ways of reducing the minimal complexity required for a living system.
What is the status of these alternative theories? So far, none has progressed from speculation to plausibility. But they do stimulate experimental and theoretical research, and offer the hope that eventually scientists may discover new principles to serve as the basis for new theories, and may develop a plausible explanation. But the major reasons to question chemical evolution come from what we do know about chemistry and life, not from our lack of knowledge.

There is also a more detailed version of this section.

Irreducible Complexity and Minimal Complexity
In Darwin's Black Box: The Biochemical Challenge to Evolution (1996), Michael Behe illustrates the principle of irreducible complexity with a mousetrap that has five interacting parts: a base, hammer, spring, catch, and holding bar. Each part is necessary, and there is no function unless all parts are present. A trap with only four parts has no practical function. It doesn't just catch mice poorly, it doesn't catch them at all.
What are the evolutionary implications? Behe says, "An irreducibly complex system cannot be produced directly... by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution." (Darwin's Black Box, page 39)
For a nonliving system, the implications are even more challenging, because natural selection — which is the main mechanism of Darwinian evolution — cannot exist until a system can reproduce. For the origin of life, we can think about the minimal complexity that would be required for reproduction and other basic life-functions. Most scientists think this would require hundreds of biomolecular parts, not just the five parts in a simple mousetrap.

7. Can design be proved?

Although "design and non-design are mutually exclusive" a design theory does not claim that non-design is impossible and design is certain, it only claims that design seems more probable, based on scientific evidence and logic. This type of probability-based conclusion is consistent with the logic of science in which proof is always impossible, even though scientists can develop a logically justified confidence in the truth or falsity of a theory. In science, a high level of confidence (not proof) is the goal when scientists evaluate a theory to determine whether it is worthy of acceptance.
If a design theory claims only to be "more probable" or to warrant "a high level of confidence" this is the standard by which it should be judged. It seems unreasonable for critics of design to demand — along with radical postmodern critics who challenge the credibility of all science — that if scientists cannot claim the certainty of proof, they should claim nothing. {a continuum of theory status}

Is it rational to consider all possibilities?
All current theories for a natural origin of carbon-based life seem highly implausible. Is it rational for scientists to consider the possibility that life on earth did not originate by undirected natural process, but was the result of design-directed action? The certainty of "proof" is impossible because we can never propose and test all possibilities for non-design. But we could develop a logically justified confidence that our search has been thorough yet futile, and no promising approaches remain unexplored.
Logic requires that, during any intellectually rigorous attempt to explain the origin of an observed feature, scientists should consider all possibilities. Perhaps a feature, such as the first carbon-based life in the universe, was produced by undirected natural process that: 1w) did occur even though it was extremely improbable (and therefore it should be rejected as a scientifically plausible explanation, *); or maybe the natural process was reasonably probable (so we could reasonably expect it to occur in the available times-and-places *) and it can be described in a satisfactory way by a naturalistic theory that 1x) is currently known (whether or not this theory currently seems adequate) or 1y) could be known in the future, or 1z) could never be known because the natural process was too complex or cognitively unfamiliar for humans to propose. Or maybe the feature was produced by design-directed action, by 2A) natural design and construction, or 2B) supernatural design and creation.
* In any scientific evaluation the "probabilistic recources" must be considered. For example, in one five-card deal the odds of getting a royal flush are low, 1 in 649,740. If 9 hands are dealt, the odds of getting a royal flush (in any of the hands) is still low, about 1 in 72,000. But the probabilities are very different if there are 9 million deals, with the odds becoming a million-to-one in favor of getting at least one royal flush.
1w* One speculative theory, which is designed to neutralize all types of DESIGN-claims (for either a design of nature or design-action during history), proposes that if an immense number of universes exist, then even the extremely improbable — such as a universe with properties of nature that naturally allow life and also produce life — will become highly probable.

Due to possibilities for a future theory (1y) or no theory (1w, 1w*, or 1z), the implausibility of current non-design theories doesn't prove the truth of design. And if scientists want to deny design (as a possibility to seriously consider) they can do it forever, no matter how advanced their science becomes. For example, imagine a scientific community with trillions of super-intelligent space aliens (IQ = 20,000) each having a life span of a billion years, devoted to science (and using high-speed travel to explore a variety of environments throughout the universe) for the past 5 billion years, who have not yet constructed a plausible theory for a natural origin of life. Even in this situation a denial of design would be possible, but would it be rational?
In the near future, however, the actual state of human knowledge will remain much less advanced than in this imaginary super-science. And critics of design will point out, with some justification, the reasons for cautious humility when making claims for design. Regarding the implausibility of current theories, defenders of non-design say, "please be patient and eventually our improved scientific knowledge will make non-design seem more plausible." But is this assumption necessarily true? Compared with fifty two years ago (when the Miller-Urey experiments were "hot news" that inspired optimism about naturalistic theories) now we know more about "origin of life" science, and what we've learned has made a natural origin of life seem less plausible, not more plausible.

What might happen in the future of science?
Even though advocates of non-design imply that future science will support their claims, the change in support could go either way, up or down. Will non-design seem more plausible because we have discovered how a feature could have been produced by undirected natural process? Or will it seem less plausible because we have learned more about the limits of natural process? Either of these results could occur.
In fact, both changes have occurred in the history of research about chemical evolution. Compared with 1952, in 1953 our plausibility estimates for a natural origin of life were higher because the Miller-Urey experiments had converted inorganic chemicals into small biomolecules. Many scientists optimistically assumed that we would soon discover a natural production of large biomolecules that would transform themselves into a simple reproducing cell which could then evolve and increase in complexity. Since then, however, the warm glow of optimism has been cooled by the harsh reality of improved scientific knowledge. The distance between what is naturally possible (before life) and what is necessary (for life) seems much greater now than in 1953. An increase in knowledge has made a natural origin of life seem less plausible, and this has strengthened the scientific support for a theory of design. In the future, if our knowledge continues to improve, and if a natural origin of life continues to seem highly implausible, a claim for design will become even more strongly supported.
In the future, what will happen in science, and how will this affect the status of non-design and design? When thinking about this, we can use our imaginations to predict improvements in current theories and inventions of new theories. And we can use current knowledge to guide our questions. Most of the skepticism about current theories of chemical evolution is based on what we know, and this knowledge can help us ask specific questions. We can look at each obstacle to a natural origin of life — such as the unfavorable equilibria for the chemical reactions needed to make biomolecules, the high degree of biocomplexity needed for metabolism and reproduction,... — and try to imagine ways in which future knowledge might change our views about each obstacle. We can ask, "How likely is each change?" and "How would it affect our evaluations for a natural origin of life?"
To make good predictions about future scientific developments, we need creativity (to imagine what could be) plus criticality (to make realistic predictions about what is probable in reality, not just possible in our imaginations) so we can avoid the extremes of insisting that in this area of science "nothing new will happen" or "anything could happen."

Should we ask the question?
Design cannot be proved, but in science the goal is logically justified confidence, not certainty. In the near future, scientists will disagree about the plausibility of design. But this is not a cause for concern, because disagreement is healthy for science when it stimulates productive thinking and research by advocates for different points of view. And the points of view should include design. When we ask, "Was design-action involved in producing this feature?", it will be impossible to answer with certainty. But it should be easy to decide, "Should we ask the question?" A curious, open-minded community will say "YES, we want our science to be flexible and open to inquiry."

8. Questions and Freedom

• 8A. Scientific Questions (but not Proof)
This has been moved (in condensed form but with some new ideas added) into Intelligent Design: Can it be scientific?
Scientific Evaluation of a theory: . . .
Philosophical Evaluation of a theory: . . .

• 8B. Scientific Freedom (instead of Necessity)
This has been moved (in expanded form) into Methodological Naturalism: Is it theologically acceptable?