Chemical Evolution (for Origin of Life)

Originally, this was a "sampler" page with condensed versions of ideas
about scientific studies of origins questions. It was the first part of a
three-part overview. Together, this page and Logical Evaluation of
Neo-Darwinian Theories and Logical Evaluation in Origins Education
provided an overview for many of my ideas (but not all) about origins.
This introduction is in past tense (was,...) because the page has been
condensed — mainly by omitting entire sections — and I suggest that
you first read The Origin of Life: Is it a test-case for naturalism?
to get an overview of the main themes.

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, we'll look at how scientific evaluation is affected by philosophy.

2. A Test-Case for Naturalism
For judging the depth of commitment to naturalism — a belief 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 (although it is usually overestimated due to a shifting of support) for biological evolution, for a neo-Darwinian development of biocomplexity and biodiversity.
• 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.

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 naturalistic worldview of "a universe without miracles."
This is an opportunity for scientific humility about naturalism. But instead of humbly acknowledging that maybe life did not begin by natural process, so maybe a naturalistic worldview is wrong, there are confident statements (by individuals and organizations, in textbooks and websites) that chemical evolution definitely did produce life, even though we don't yet know the details of how this happened.

3. Closed Science and Open Science
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?
Is MN the best way to do science? Maybe not. It depends on what actually happened in history. We should ask, "Does the assumption match the reality?" because a rigidly enforced MN will probably be scientifically useful IF there is a match between "what MN assumes about the world" and "how the world really is."
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. When we ask, "Which type of world do we live in?", we hope our science will help us, not hinder us, in our search for truth. But in one of the two possible worlds, a closed science (restricted by MN) must inevitably reach the wrong conclusion. By contrast, in either world a non-MN science will allow, although it cannot guarantee, reaching a correct conclusion.

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 MN by assuming, consistent with MN, that "it happened by natural process." But an open-thinking scientist is free to use both MN and non-MN modes of thinking while logically evaluating the evidence, to consider a wider range of possibilities. 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. Each theory is evaluated based on its merit, and if a non-MN conclusion is justified by the evidence, this is allowed.

Should science be logical?
If we want science to be a search for truth, should we define science as a search for NATURAL explanations, or a search for LOGICAL explanations? Of course, when we ask "Should science be logical?", everyone agrees that YES is the answer. But disagreements occur when we ask "If there is a conflict between logical and natural, which criterion should have higher priority?" If we want to be logically rational, should we let methodological naturalism force us to accept a "scientific" conclusion that is less logical — and less likely to be true? — simply because it is natural? For example,...

Is evidence irrelevant?
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.

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. But instead of acknowledging this logical weakness of MN-Science, 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 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 (the National Academy of Sciences, 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. Instead, it is 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? This question is examined in Section 8B.

If you receive a radio signal — 2, 3, 5, 7, 11, 13, 17,... — and you think "this long string of prime numbers probably was not produced by undirected natural process," you are proposing a theory of intelligent design.

To explain the origin of a feature (an object, organism, system, situation,...) the only two possibilities are non-Design and Design:
A. non-Design, with undirected natural process producing the feature (*);
B. Design (and production) by an agent using design-directed action that converts a design-idea into the reality of a designed feature; more specifically, origin by design-action can be due to
Dn. design (and construction) by a natural agent (a human,...) using design-directed action.
Ds. design (and creation) by a supernatural agent (God,...) using design-directed action, or

* Production of a feature by what appears to be undirected natural process (by what is commonly called non-design) could be due to:
Ni) design-directed action occurring at the beginning of history (in a design of nature at the "initial instant of time") that eventually results in production of a feature by undirected natural process,
Ns) a gentle guiding of natural process by a supernatural agent, in design-directed action that occurs during history but is not empirically detectable (*), or
Nu) a process that actually is undesigned, undirected, and unguided.
Therefore, of the five possibilities (Ds, Dn, Ni, Ns, Nu), four are DESIGN, and only one (Nu) is non-DESIGN.
* An undirected process (in Ni, Ns, or Nu) is not directed by agent-action. But an undirected natural process, with no agent-action, is not necessarily totally random with no direction. For example, natural selection that is undirected can cause populations to change in directions that are beneficial for survival, thus producing what Daniel Dennett calls "good tricks" (for improved survival and reproduction) that can be similar in different historical situations. / In 1B, with a "gentle guiding of natural process," everything appears normal and natural because the guidance blends smoothly with the usual workings of nature. Can a guiding of natural process be detected? NO and YES

Design (specific, narrowly defined) and design (general, broadly defined)
For improved precision, I'll use words that are Capitalized and regular to distinguish between Intelligent Design (defined narrowly) and intelligent design (defined broadly).
In this page, and in most other contexts, a Design theory is a claim that a feature was produced by empirically detectable Design-directed action during history (by Dn-or-Ds, with Design-action by a natural agent or supernatural agent) rather than Ni (design of nature, which is not during history), Ns (design-directed guidance of natural process, which is not empirically detectable), or Nu (which is not by design-directed action).
My definition of design is broader; it includes Ds-or-Dn (Design) and also Ni and Ns (which are not Design but are design). Therefore, of the five possibilities — Natural-initial design (Ni), Natural-supernatural design (Ns), Detectable-supernatural Design (Ds), Detectable-natural Design (Dn), and Natural-undesigned (Nu) — four are design and only one (Nu) is non-design.

The table below shows the four types of DESIGN (in the three columns with a white YES) and the three questions that are used to define DESIGN (Does the production of a feature involve design-directed action?) and design (Does the design-action occur during history and is it empirically detectable?).

testing for Design and design: Using my definitions, a feature was produced by either Design (Dn-or-Ds) or non-Design (Ni, Ns, or Nu), so Design and non-Design are mutually exclusive, and evidence for one is evidence against the other. But design includes Design and more, so evidence against Design (during history and detectable, Dn-or-Ds) is not evidence against the other two types of DESIGN, by design before history (Ni) or by undetectable design-action (Ns).

Design is Testable in Science
Design can be tested using scientific logic. How? When we use the definitions above, design 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. {more about testing and the logic of mutual exclusion} 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
How do scientists detect design? By using eliminative logic, as explained above. This logic can also be described in terms of the characteristics (including complex specified information) that typically are produced by design-directed action, but not by undirected natural process. Scientists have developed, and are continuing to develop, ways to recognize these signs of design, which seem to occur only when a design-idea has been actualized by design-action.
If we observe strong signs of design — such as a long string of prime numbers, or circumstantial evidence for a murder — we can infer that design-directed action did occur, even if the agent and action were not observed. Scientists can infer the existence of an unobservable cause (an electron, a thought, a volcano acting in the past, a person acting in the past,...) from the observable effects it produces, in studies of current events or historical events, with or without agent-action.

Can historical science be scientific?
The methods used in design are similar to methods used in historical sciences like geology, archaeology, evolutionary biology, and astronomy. Many arguments against design are also arguments against every historical science. But scientists have developed methods for coping with the limitations of historical data, and historical science can be authentically scientific. The same principles of scientific logic are used in both operations science (to study the current operation of nature, what is happening now) and historical science (to study the previous operation of nature, what happened in the past).
A historical theory can include proposals for agent-action in history. In some historical situations, only undirected natural process was involved, so a mechanistic explanatory theory (which usually is related to mechanistic theories in operations science) is adequate. In other historical situations, what happened was affected by the decisions and actions of an agent. This introduces an element of unpredictability when making predictions, but this is acceptable because in a descriptive theory a historical scientist (in anthropology, archaeology, history, sociology, psychology, or forensics; or in geology, biology, paleontology, or astronomy) only has to determine what did occur, not predict what will occur. And in an agency explanatory theory, proposing that "agent action was involved" is part of the scientific explanation.

Design is Common in Science
In science, theories of design are common. In every design investigation, scientists ask the same question: If we assume a uniformity of natural process, was undirected natural process sufficient to produce what we observe? Sometimes the answer is "probably not," and design-action is proposed to explain a wide variety of features such as bird nests, ant hills, predator-prey events, paintings on a cave wall, metal satellites in orbit, and faces on Mount Rushmore. A design theory is proposed — for example, when a crime detective concludes that "this death occurred by murder, not natural causes" — when an inference that "design-directed action did occur" can be justified based on a logical evaluation of evidence.
Design is common in science, and most design theories are judged on their scientific merit. But some are controversial, as explained later.

What difference will it make?
Although design might significantly affect philosophy of science, probably it will have little impact on the overall productivity of science, because most areas of science are not affected by controversial claims for design. But in several historical areas — including origins of the universe, first life, and complex life — scientific analysis shows that design deserves to be accepted, not as the only possible explanation, but as a potentially plausible explanation that is worthy of serious consideration and further development. The potential of design theories to make valuable scientific contributions should be recognized and welcomed.

Will it be scientifically productive?
Perhaps the search by Closed Science (restricted by a rigid methodological naturalism) is occasionally futile, like trying to explain how the faces on Mt Rushmore were produced by undirected natural processes such as erosion. If scientists are restricted by an assumption that is wrong (that does not correspond with historical reality) the finest creativity and logic will fail to find the true origin of the faces.
Occasionally, perhaps MN is forcing scientists into a futile search, like a man who is diligently looking for missing keys in the kitchen when the keys are sitting on a table on the front porch. No matter how hard he searches the kitchen, he won't find the keys because they aren't there! On the other hand, if the keys really are in the kitchen, they probably will be found by someone who believes "the keys are in the kitchen" and is diligently searching there, not by a skeptic.
Perseverance and Flexibility: How is scientific productivity affected by attitude? In the complex blend that generates productive thinking, "There can be a tension between contrasting virtues, such as persevering by tenacious hard work, or flexibly deciding to explore new theories that may be more productive in a search for truth. A problem solver may need to dig deeper, so perseverance is needed; but sometimes the key to a solution is to dig in a new location, and flexibility will pay off." {from Productive Thinking: Creative and Critical }

Should scientists dig deeper in the same location, or dig in a new location? Should they search the kitchen or porch? The answer is YES if we notice that one word is wrong, if we replace "or" with "and" because we refuse to remain trapped in narrow thinking. Instead of thinking that we must make an either-or choice, we should search both kitchen and porch, we should dig deeper and in new locations, as suggested in open science. We can adopt a humble attitude "by refusing to decide that we already know with certainty... what kind of world we live in."
Is a claim for design a science-stopper? No, this simplistic "slippery slope" argument is based on restrictive either-or thinking, and is unrealistic because most scientists will continue their non-design research — probably with renewed vigor because they are responding to a challenge — when they hear a claim that "maybe a non-design explanation doesn't exist." And proponents of design want non-design research to continue so we can learn more, so we can more accurately evaluate the merits of non-design and design, because the goal is to find truth. They want to supplement non-design research, not replace it. They want to stimulate productive action and critical thinking, with invigorating debates between critics of a theory and its loyal defenders. And this type of scientific stimulation did occur due to Michael Behe's claims for irreducible complexity in 1996.

Will design theories be productive in helping us achieve the goals of science? Most scholars who have examined the issues in detail think this question, which is discussed in the subsections above and below, is the most important question. {an example of scholarly consensus}

Does it violate The Rules?
A basic design theory does not propose supernatural action, but does acknowledge this as a possibility, so a design theory violates a rigid methodological naturalism and thus, according to some people, it violates "the rules of science."
Is science a game with rules? This is an interesting perspective. In terms of sociology, regarding interpersonal dynamics and institutional structures, it is an idea with merit. But it seems less impressive and less appealing when we think about functional logic and the cognitive goals of science. It seems more logical to view science as an activity with goals (which include searching for truth) rather than a game with rules (which include the restrictions imposed by rigid-MN).
Let's compare "cheating" in sports, business, and science. In a Strong Man Contest, if other contestants carry a refrigerator on their backs, one man should not be allowed to move it using a two-wheel cart because this is not useful for achieving the goal of the game, for determining who is the strongest man. But if the goal of a business is to move refrigerators quickly, many times during the day, a two-wheeler is useful.
Although it isn't the only goal, for most scientists the main goal of science is finding truth about nature. But a rigid-MN might lead to unavoidable false conclusions. When some scientists recognize this and they decide to reject the dogma of rigid-MN by adopting testable-MN, is it cheating or wisdom? Is a rigid-MN always useful in our search for truth? {more about Science as a Game}

When is critical thinking unscientific?
Scientists have proposed many theories about chemical evolution. When supporters of one theory point out the weakness in other theories, their critical thinking is welcomed and is published in scientific journals. What would make this critical thinking unscientific? a claim that a natural formation of life is extremely improbable, and maybe impossible? a perception (by others) that this claim implies a non-natural cause? an explicit proposal for a non-natural cause? Is there any limit to the severity of criticism before it becomes unscientific? If all non-design theories are criticized and there is a proposal for design-directed action, is this unscientific? If severe criticism is accompanied by a proposal for a naturalistic theory, does this make it scientific?
In closed science, a scientist can admit that "we are far from finding the answer," but cannot suggest that "maybe there is no natural answer." Is this wise? In a scientific search for truth, is it useful to insist — consistent with the restrictions of a rigid Closed Science — that we must control the thinking of scientists by removing their freedom to think that "maybe..."? Or should we allow open inquiry, with individual and communal freedom of thought, with scientists being free to follow the evidence and logic wherever it leads? { Is it easy to have critical thinking in closed science? }

Why is it controversial? (Is it because of science or religion?)
Since design theories, which are common in science, can be evaluated using the logical methods of science, why are there any doubts about whether a design theory can be scientific? Usually there are no doubts, and most design theories are judged on their scientific merit. But some people claim that some design theories should be excluded from science. Why?
Concerns about design occur when design-action seems unfamiliar. In some situations the action and agent are familiar (as when a beaver builds a dam, or humans make faces on Mount Rushmore) but in other cases the design-action is unfamiliar and it could be either natural (for example, if space aliens produced designed features by using their unfamiliar advanced technologies) or supernatural (as in Biblical miracles). For most opponents of design, questions occur when design-action is unfamiliar and it could be supernatural. In these situations the main concerns are religious, and a common claim is that a design theory is a creation theory. Is this claim justified?
For any question about design, in any area (radioastronomy, homicide, origins,...), we can view the scientific inquiry as a two-stage process: first we ask "Was there design-directed action?", and then we investigate the details. A basic design theory claims only that design-directed action did occur (the first stage) but does not try to explain the details (who, why, how,...) of design-and-production. Of course, we should evaluate a design theory based on what it does claim (that design occurred) instead of what it does not claim (that it can explain the details).
In origins, a design theory is not a creation theory. A basic design theory can be supplemented with details (about the designer's identity and actions, about who, why, how,...) to form a variety of theories about supernatural creation (by God or...) or natural non-creation (as in a theory proposing that evolution on earth was intelligently designed and directed by space aliens who evolved before us). A design theory — which does not propose divine action, but does acknowledge it as a possibility — does not try to distinguish between creation and non-creation. Instead, a design theory just claims that "design-directed action did occur."
A basic (non-supplemented) design theory is limited to claims that can be scientifically evaluated. In a Response to Critics, Michael Behe explains: "Most people (including myself) will attribute the design to God, based in part on other, non-scientific judgments they have made. ... From a scientific point of view, the question [who is the designer?] remains open. ... The biochemical evidence strongly indicates design, but does not show who the designer was." As a person, Behe says "I think the designer was God." But as a scientist, he says "the evidence doesn't show who the designer was."

analogy and consistency (in design and non-design)
analogy: We can view a naturalistic theory of non-design (such as chemical evolution or neo-Darwinian biological evolution) as being mainly religious — because it supports deism or theism (if a clever design of nature seems to be necessary for it to happen) or atheism (if it seems to make God unnecessary) — or as mainly scientific even though it can have some religious implications. Similarly, we can view a design theory as being mainly religious or mainly scientific. In open-minded science, a scientist uses evidence and logic to evaluate "mere science" theories (such as mere evolution or mere design) that are considered, during a process of objective evaluation, to be mainly scientific with minimal religious implications.
consistency: Supporters of non-design and design should ask themselves, "Are we being objective and logically consistent in our views of their theory and our theory, or are we trying to make ourselves look more scientifically rational by claiming that their theory is mainly religious, and our theory is mainly scientific?"

Should you examine it more carefully?
Although arguments for excluding design from science make good cartoons and one-line slogans, the arguments seem less logical when you look more closely. Can design be scientific? If you want to explore this question in more depth, another page describes the arguments, analyzes them logically, and concludes that "the closer we examine Open Science, the better it looks."

The main part of this page ends by looking at current science and future science.

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 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.

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. {one reason we cannot be certain} 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. Earlier, the DESIGN-and-design Table included a "?" to indicate that, when we're trying to explain our "just right" universe, currently we cannot scientifically distinguish between two theories: an immense number of universes with no design, and a design of the universe(s).

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 chemical reactions needed for making 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)
Here are some ideas, both old (from earlier in this page) and new, about evaluating theories of design and non-design:

In a closed science that is restricted by methodological naturalism, the inevitable conclusion — no matter what is being studied, or what is the evidence — must be that "it happened by natural process." .....
But in one of two possible worlds [totally natural, or mostly natural] a closed science (restricted by MN) must inevitably reach the wrong conclusion about some questions. By contrast, in either world a non-MN science will allow, although it cannot guarantee, reaching correct conclusions. ...
If we don't know whether history has been all-natural, our best scientific strategy for finding truth is an open science... [in which] a scientist begins with an MN-assumption [that "it happened by natural process"] 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, with the assumption of MN 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. .....
Because design and non-design are mutually exclusive (it was one or the other) 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,... so a theory of design is empirically responsive and is testable.
In closed science, a scientist can admit that "we are far from finding the answer," but cannot suggest that "maybe there is no natural answer."... But in a scientific search for truth, is it useful to insist that we must control the thinking of scientists by removing their freedom to think that "maybe..."?

In Section 7, I ask you to "imagine a scientific community with trillions of super-intelligent space aliens... who have not yet constructed a plausible theory for a natural origin of life." And I ask, "Even in this situation a denial of design would be possible, but would it be rational?"
Maybe. In a rational open science, a design theory is evaluated in two ways, in terms of scientific evidence and theory interpretation.
• Scientific Evaluation of a theory: First, we use evidence-and-logic to evaluate each current non-design theory for plausibility, and we use creativity (to imagine what could be) plus criticality (to make realistic predictions about what is probable in reality, not just possible in our imaginations) in an effort to predict improvements in current theories and inventions of new theories.
• Philosophical Interpretation of a theory: Second, based on a wide range of scientific and nonscientific criteria (including worldviews) we think about the possibilities for how a feature was produced: 1w (an event of low probability), 1w* (if events with apparently low probability are in reality highly probable because there are so many universes), 1x (a current naturalistic theory is approximately true), 1y (a future naturalistic theory will be approximately true), 1z (a naturalistic theory is true, but we will never propose and accept it), 2A (natural design and construction), or 2B (supernatural design and creation). All of these are logically possible, but — based on our interpretations (which are based on scientific and nonscientific logic, plus personal experience and values) — do we think they are equally probable?
In both evaluation and interpretation, we should recognize that "proof is always impossible, even though scientists can develop a logically justified confidence in the truth or falsity of a theory. ... 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." We should want to be appropriately humble by avoiding the extremes of arrogant overconfidence (in claiming too much) or timidly overcautious relativism (in claiming too little) and not descending into aggressive postmodern skepticism about the futility of logic and the illusion of reliable conclusions in science.
Should we ask the question? Design cannot be proved, but in science the goal is logically justified confidence and a high degree of plausibility, not certainty. ... 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."

Section 8A was motivated by a similar suggestion for "science plus interpretation" by Loren Haarsma in Science and Miracles.

8B. Scientific Freedom (instead of Necessity)
necessity: An atheist (or an agnostic who wants to remain agnostic) has no options and no scientific freedom, since only one conclusion is acceptable: some type of natural total evolution somewhere in the universe, with no action by God.
freedom: By contrast, a Judeo-Christian theist has a wide range of options — in the many variations of theistic evolution (chemical and/or biological), old-earth creation (this is my view), or young-earth creation — and is free to follow the evidence and logic of science wherever it leads.

Does it matter? (Part 1)
Theologically, does it matter whether the first life began by natural process or miracle? Not much, as far as I'm concerned, because I think that:
• a devout Christian with sound theology can believe that God designed the universe so life would naturally arise (in chemical evolution) and then evolve (in biological evolution), with this natural formative history followed by a salvation history (as recorded in the Bible) in which God used a combination of natural process and miracles.
• criticizing theistic evolution by implying that "since atheists must be evolutionists, evolutionists must be atheists" is not logical, for the same reason that "all dogs are animals" cannot be reversed to show that "all animals are dogs."
• the evaluation of a design theory for the origin of life is an interesting scientific question that has some theological implications, but concluding that "detectable design-action did occur" is not necessary for sound theology. But I think that some DESIGN-action was theologically necessary. { What is the difference between design and DESIGN? } What human characteristics (physical, mental, emotional, and spiritual) did God want us to have, and how flexible were His goals? I think a creation of humans by unguided natural process would not be theologically adequate to achieve the goals of God, but a creation by natural process that was divinely guided (but was not directed in a detectable way) could be adequate.

Nonscientific Motivations and Scientific Evaluations: Even if a theory of design (or non-design) is motivated by a desire to show that "God did it" (or "God didn't do it"), our recognition of this motivation should not influence our theory evaluations. We should recognize the religious (or anti-religious) beliefs that may be motivating scientists to propose a theory, persuade other scientists about its plausibility and utility, and hope it is true, but these nonscientific motivations don't indicate that the theory is false or is nonscientific.
Recognize and Minimize: Scientists are influenced by cultural-personal factors that include personal desires, group pressures, philosophical or religious views, and cultural thinking habits. In my opinion, we should recognize the influence of cultural-personal factors, and — in an effort to make science more effective in a search for truth — we should try to minimize the influence of these factors. One way to minimize nonscientific influences is to make science more open, allowing theory evaluation to be based on evidence and logic, not rules that can bypass the process of science and make evidence irrelevant.

Does it matter? (Part 2)
My views are explained more thoroughly in a page about Theistic Evolution (Evolutionary Creation) & Theology that includes these topics:

A natural process is just a normal-appearing process. A theist believes that God designed and created nature, and constantly sustains nature, so natural does not mean "without God." And natural does not mean "without control" because God can guide nature so one natural result occurs instead of another natural result.
When scientists discover that natural properties are "just right" for important natural processes, a theist proposes that God is responsible for this clever design of nature. But this does not "prove" that God designed the universe, and to explain a universe that is "just right" for life there are two currently plausible theories: a single universe (that was designed), or an immense number of universes (that may or may not be designed).
"Why isn't God more obvious? Why is there any evidence... that might lead some rational people to propose "atheistic evolution" as an explanation? Perhaps..... Or maybe..... Or maybe a "veiling of miracles" during the creation process is one aspect of a state of uncertainty intended by God, who seems to prefer a balance of evidence, with enough logical reasons to either believe or disbelieve, so... we have freedom to choose what we really want, and an opportunity to develop the "living by faith" character that is highly valued by God, with a trust in God serving as the foundation for all thoughts and actions in daily living."

A methodological naturalism (assuming that "it happened by natural process" while doing science) differs from philosophical naturism (claiming that only nature exists) in two ways: methodological is not philosophical, and naturalism is not naturism. Therefore, I think MN is theologically acceptable, and can be viewed in two rational ways by Christians:
In one view, described in Section 8A, a Christian begins a scientific investigation with MN (by assuming it happened by natural process) but considers this naturalistic assumption to be a theory that can be tested instead of a conclusion that must be accepted. In another view, a Christian accepts MN (and also MN-humility by acknowledging the possibility of unavoidable error) but considers MN-science to be only one aspect of a broader "search for truth" that considers all possibilities, including miracles.
In both views, a Christian believes that natural process was designed by God, is sustained by God, and can be guided by God, so "natural" does not mean "without God", and a naturalistic explanation does not increase the plausibility of atheistic naturism.
With either view a controversial design theory (involving unfamiliar design-action) can be evaluated using the methods of science (using reality-checks based on evidence and logic) but the views disagree about whether this scientific logic occurs inside or outside science, because a design theory — which does not propose that a supernatural miracle has occurred, but does not deny that this may have occurred — may violate MN.

What does "God of the gaps" mean? When current naturalistic theories seem implausible, is this science gap due to the inadequacy of current science, or does it indicate a nature gap (a break in the continuous chain of natural process) that was bridged by miraculous-appearing theistic action? Sometimes, a theory proposing a nature gap is ridiculed by calling it a "God of the gaps" theory. I think this term should be eliminated from our vocabulary because it is imprecise and confusing, since it could refer to four different views: biblically justifiable criticisms (of an "always in the gaps" or "only in the gaps" view) or a biblically unjustifiable criticism (of a "gaps are possible" view), or a theory (claiming "a gap did occur") that should be logically evaluated.

APPENDIX

Another Perspective on Two Worlds
The "two worlds" example is borrowed from Paul Nelson. Before hearing his "imaginary concrete illustration," I described the same ideas in terms of if-then logic: Probably MN will be useful if its assumptions are true, if there is a match between "what MN assumes about the world" and "how the world really is." IF the history of the universe really has included only natural process, then MN is correctly assuming an all-natural history, and MN will be useful because it helps scientists avoid being distracted by false theories about non-natural events. But IF non-natural events really did occur during history, the premise of MN is false, and MN will be harmful when it inevitably forces scientists to reach some false conclusions.

Biological Evolution
6C: Shifting of Support
evolution-shifting: Often, support is illogically shifted from a strongly supported meaning of evolution (such as basic "old earth" progressions in the fossil record, or micro-E changes that occur in drug-resistant bacteria and finch beaks) to a less strongly supported meaning (like Total Macro-E with a natural evolution, from bacteria to humans, of all biocomplexity).
creation-shifting: Often, scientific evidence against young-earth creation is illogically shifted onto old-earth creation, and the important scientific differences between two old-earth theories (independent creation and genetic modification) are ignored.
With an evolution-shift the implied support for evolution increases, and with a creation-shift the implied support for creation decreases. But in each case the shift (and associated implication) is not logically justified.
This section [from my Overview of Origins Questions] builds on the foundation of 6A (The Many Meanings of Evolution) and 6B (The Many Meanings of Creation). Principles for avoiding illogical shifts are examined in The Process of Logically Evaluating Origins Theories.
6E: Questions about Evolution
We should critically evaluate the plausibility of an extrapolation from micro-E through minor macro-E (such as a speciation that occurs due to an evolution of reproductive barriers between otherwise similar species) to Total Macro-E by asking "How many mutations and how much selection would be required, how long would this take, and how probable is it?"
Another important question is whether systems that seem irreducibly complex could be produced in a step-by-step process of neo-Darwinian evolution.

Testing for Design (by using the logic of Mutual Exclusion)
When theories of design and non-design are carefully defined they are mutually exclusive. Similarly, DESIGN and non-DESIGN are mutually exclusive. As shown below, two sets of categories — either non-design and design (this set is most important in science) or non-DESIGN and DESIGN (this set is theologically important) — will "cover everything."

Because non-design and design are mutually exclusive, either one or the other must occur, so together their probabilities add to 100 percent. The table below shows the relationship that allows design to be tested by testing for non-design. For example, if the estimated probability of a non-design cause decreases from 20% to 10%, the estimated probability of design increases from 80% to 90%.

%-probability of non-design	100	99.99	95	90	70	50	30	10	5	.01	0
%-probability of design	0	.01	5	10	30	50	70	90	95	99.99	100
sum of %-probabilities	100	100	100	100	100	100	100	100	100	100	100

The two shaded regions are a reminder that the 100%-certainty of "proof" or "disproof" are impossible in science, and are not the goal in science.

Can we observe a guiding of natural process? (no and yes)
For various reasons, sometimes an agent wants design-action to be undetectable, as with the design-directed action of an illusionist (entertainment magician) who "directs" things in a way that is difficult to detect, or a criminal, plastic surgeon, or the special effects of a movie-maker, or when God "guides" natural process. Why isn't God more obvious?
In my definitions: a directing of natural process can be detected, in principle and usually in practice, IF the observational data is adequate and our logic is skillful; "natural" is "normal appearing", so (by definition) the guiding of a natural-appearing event cannot be detected. But...
Sometimes a series of undetectable events can become detectable, as in this example: If you pick the winning number for a roulette wheel once, it looks natural. But what if the wheel is guided by God so you win 20 times in a row? Each event appears natural, but the overall process (with 20 events) does not appear to be undirected natural process, and most observers will think "the wheel was rigged."
Perhaps some biological complexity was created when God combined many individually undetectable "guided natural events" to produce a desired-and-designed overall result that can be scientifically detected — if the data is sufficient and is skillfully analyzed — when we observe an increase of genetic information (and biological complexity) that could not be produced, with a reasonable probability, by undirected natural process. If this occurred, would we categorize the design-action as 1B (undetectable) or 2B (detectable)?
This type of doubt — when we wonder "is it detectable? have we detected it?" — is one reason, among others, that scientists cannot prove design or non-design.

Complex Specified Information
A prominent design theorist, William Dembski, suggests using the concept of complex specified information when thinking about signs of design. A short string of prime numbers (like "2 3 5") is not complex, so it could easily occur by chance. A long string of random numbers is complex, but is not "specified" because it has no pattern. But a long string of prime numbers is complex and (due to its conceptual functionality) is specified, and it contains functional information.
{ soon, I'll link to a more thorough explanation of specified complexity }

Is science a game with rules?
To answer this question, we'll compare "cheating" in sports and in science. Is it useful — as suggested by some critics of design — to view science as an intellectual game played with a set of rules, which include MN, that are established by tradition, approved by consensus in the scientific community, and enforced by funding agencies, journal editors, and hiring committees?
This is an interesting perspective. In terms of sociology, regarding interpersonal dynamics and institutional structures, it is an idea with merit. But it seems much less impressive and less appealing when we think about functional logic and the cognitive goals of science, when we acknowledge the distinction between games and reality.
The practical value of restrictive rules is different in a game and in reality. To illustrate, consider the Strong Man contests televised by ESPN. During these competitions, I've seen men tow a semi-truck, and carry a refrigerator on their backs.
For the game, if one competitor wanted to hook the semi to a tow truck or strap the refrigerator to a two-wheeler, this would be cheating. It would provide an unfair advantage and would not help in achieving the goal of the game: determining who is the strongest man. In this context, the rule about "no mechanical help" is useful.
But for reality, for accomplishing a practical goal, the same rule might not be useful. If the real-life goal of a business is to move vehicles or refrigerators quickly, over and over throughout the day, using tow trucks or two-wheelers is a more effective strategy than asking a person to do all the work.
It is obvious that a restrictive rule which is useful in the context of an artificial game — such as requiring that a heavy object must be moved by a human without mechanical help — may not be useful in real life for accomplishing practical goals. When this principle is applied to science, it seems more rational to view science as an activity with goals, rather than a game with rules. Then we can ask whether the restrictions imposed by MN will make scientists more effective in pursuing and achieving the goals of science. More specifically, we can ask "Is rigid-MN a useful strategy in our search for truth, in our development of increasingly accurate theories about nature?"

Among scholars who carefully study MN, most agree about Rules and Goals:

Dogma and Utility (used in defense of closed science)
Robert Koons wrote a summary of a major conference he organized in 1997:
The philosophers, scientists and scholars who met together at the Naturalism, Theism and the Scientific Enterprise conference made substantial progress on the very important question: Is methodological naturalism [MN] an essential part of science? .....
One important distinction that emerged... is between dogmatic or apriori methodological naturalism (DMN) and empirical or aposteriori methodological naturalism (EMN).
DMN involves the claim that the very definition or inherent logic of science demands that it accord with the rule of making use only of naturalistic explanations (that is, explanations in terms of events and processes located within space and time).
EMN, in contrast, is the claim that in the long run it will turn out that all successful scientific research programs are naturalistic ones, that science will converge upon methodological naturalism in the long run. EMN is based, not on the definition of science or on any supposed direct access to the essence of science, but upon the actual history of science. A defender of EMN... merely conjectures that such scientific enterprises [open to non-naturalistic theories] will not prove successful in the end.
I hope that, as a result of our conference, the thesis of DMN will be seen, once and for all, as definitively refuted. It is to my mind significant that no one defended DMN, not even those, like Michael Ruse, who have endorsed it in the past. I think we can only conclude that the DMN thesis is now in full and hasty retreat and will have no serious defenders in the very near future.

The Science of Chemical Evolution (Part 3: Another View)
Was the beginning of life simple or complex? Loren Haarsma and Terry Gray — in Chapter 13 (Complexity, Self-Organization, and Design) of Perspectives on an Evolving Creation — describe a theory proposing that a complex "interacting auto-catalytic system" was the beginning of life:
Is it possible that simple organic molecules could self-organize into a living, reproducing organism? Given our current scientific understanding, it is far too premature to definitely answer either yes or no. There are many hypotheses for how first life might self-assemble on the early earth. All of these hypotheses are still speculative. The most widely accepted hypothesis is a multistep process something like this: First, in the right environment (hypotheses include underwater thermal vents, shallow surface ponds, sandy beaches, volcanic craters, clay deposits, and weathered feldspar), simple organic molecules concentrated and self-assembled into strings of nucleic and amino acids (RNA and proteins). Second, when enough of these molecules were concentrated together, they formed an interacting auto-catalytic system that jointly catalyzed their mutual reproduction. Third, these RNA-and-protein catalytic systems evolved, with RNA and eventually DNA taking on the role of information storage, which we see in all living cells today. .....
Life is a complex web of interactions where proteins are required for nucleic acid synthesis and nucleic acids are required for protein synthesis. ... Origin of life investigators have had a difficult time envisioning a proteins-only solution. The RNA world scenario has fared somewhat better, but it is not clear how proteins get integrated. The replicating closed auto-catalytic system described by Stuart A. Kaufmann has the advantage that the complex web of interactions is built in from the outset. In essence this view acknowledges irreducible complexity, that is, the system has to be sufficiently complex in order for auto-catalytic behavior to emerge. There is no stepwise evolution of this emergent property; it suddenly appears (as with all emergent properties) once the polymer complexity has achieved the threshold level. Thus, the system is complex and whole from the start.

Critical Realism and Theory Status
In a page asking "Should science be eks-rated?" (where eks = x, to fool the filtering programs), Section 4 begins:
One response to the impossibility of proof is an instrumentalist perspective in which scientific theories are interpreted as making claims for usefulness, but not for probable truth. Instrumentalism and realism differ in their answer to the question: Does science try to find truth? Realism says yes, but instrumentalism says no. ... A realist places a high value on both plausibility (an estimate of whether a theory is likely to be true) and utility (an estimate of whether a theory seems to be useful); ... but an instrumentalist eliminates one of the two major criteria by focusing on plausibility and excluding a consideration of plausibility. .....
A critical realist (CR) distinguishes between goals and claims. A CR is a realist about goals, and a critic about claims. A CR combines realist goals (wanting to find the truth, to find theories that are true because they correspond to reality) with critical evaluation (willing to be skeptical about claims for the truth status of a particular theory). ...
For example, it is difficult to deny that scientists in the early 1950s who studied the structure of DNA were aiming for a theory that would describe the actual structure of DNA. They wanted to find the truth, so they were realists. Before 1953, however, their claims were modest, because all of their theories had a low truth-plausibility. They were evaluating critically, in an effort to achieve their realist goals. But after April 1953 the claims for truth became bold, and those who knew the most quickly decided that the double helix structure deserved to have a very high plausibility because it almost certainly was true.
Later in the section: "As a reminder that the outcome of theory evaluation is an educated estimate rather than a claim for certainty, my model of Integrated Scientific Method uses a continuum of theory status, ranging from very low to very high, to describe our degree of confidence in a theory. To allow a more precise description of theory status, it's useful to make eight additional distinctions" — each theory has six types of status (relative and intrinsic, for pursuit and acceptance, for truth and utility) and can be interpreted in two ways (realist or instrumentalist).

Two Explanations for a Just-Right Universe
An amazing discovery of scientists, in recent decades, is that many properties of the universe are "just right" for life. To understand why scientists think the universe is fine-tuned to allow life, imagine that you are sitting in front of a control panel with dozens of dials. To allow life, each dial — which controls one property of the universe — must be tuned to a specific setting within a very narrow range. You are alive, reading this web-page, because all dials are properly tuned, and this produces a wide variety of life-permitting natural phenomena that include stable atoms and molecules, the formation of stars which produce the energy and atoms needed for life, the amazing chemistry of DNA and water and enzymes, and much more.
Most scientists are convinced that the constraints on a life-allowing universe are very tight, that small changes would make it impossible to produce intelligent life of any kind we can imagine. Based on scientific evidence, there is little doubt about this conclusion. There are, however, two main theories claiming to explain how the universe became what it is:
• The simplest causal theory is Intelligent Design plus design-directed action, with our universe being designed and produced by an extremely intelligent and powerful designer/producer who cleverly designed the universe so it would support life.
• A universe able to support life is extremely improbable, but a theory of Many Universes (MU) proposes a way to beat these odds. Imagine that scientists have analyzed the probability of a universe capable of producing life-forms that are intelligent — so they can analyze the probability for their own existence! — and have estimated the odds to be very low, less than 1 in a thousand million billion trillion zillion. If there is only one universe, and it was not designed for life, we must conclude that we are very lucky. But if there were enough universes (as proposed in MU) and if all properties of these universes were distributed across a wide range, the odds would be highly in favor of having at least one universe with intelligent life. The basic principle of MU is simple: If there are enough universes, with properties randomly distributed, everything that can happen (even if it's extremely improbable) will happen, so MU can "explain away" all evidence for design, whether this evidence occurs at the level of the universe, the origin of life, or the development of life.
note: Perhaps we should just say "So what?" because if we are observing a universe, it obviously must have properties that allow our existence. This anthropic principle — which states that because humans exist, we will observe a universe consistent with our existence — is logically valid, and is compatible with either the presence or absence of a designer, so it doesn't favor either of the two theories.
{ This section contains excerpts, with minor revision, from a page about Anthropic Principle & Fine Tuning: Multiverse and/or Intelligent Design? }

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