What is Closed Science?
The most common type of closed science is produced by methodological naturalism (MN), a proposal to restrict the freedom of scientists by requiring that they include only natural causes in their theories.  The important difference between rigid-MN and testable-MN is explained in the right column.

A basic theory of intelligent design does not propose supernatural action, but — unless the "basic" theory of design is supplemented by explicitly claiming that the design-directed action was not supernatural — it does acknowledge this as a possibility, so it is potentially non-naturalistic and it does violate the rigid-MN of Closed Science.

If you're not familiar with the disadvantages of Closed Science — and the advantages of an Open Science that is willing to evaluate design theories based on their scientific merit — you can read an introduction.

In this half of the page, you can read about
The Freedom of Open Science
When is critical thinking unscientific?
Mike Behe's Adventures with Science Journals

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Of course, Section 7D below (quoted from a page that has been reorganized into other pages) is preceded by 7C, which concludes:
Some arguments against design are trivial, while others (especially those about the practical effects of methodology) are more worthy, if only because they stimulate productive thinking and discussion.  But even though some arguments for Closed Science may seem strong initially, I think the counter-arguments are stronger and more logical, and the closer we examine Open Science, the better it looks.

    7D. The Freedom of Open Science 
    This section, building on the foundation of Section 7C, examines the benefits of scientific freedom and conceptual diversity.

    The Benefits of Open Science
    The difference between science that is open and closed is the difference in responding to a question:  Has the history of the universe included both natural and non-natural causes?  In an open science (liberated from MN) this question can be evaluated based on scientific evidence.  In a closed science (restricted by MN) the process of science is irrelevant, since the inevitable conclusion — no matter what is being studied, or what is the evidence — is that "it happened by natural process."
    In open science, a scientist begins with MN but is free to use both MN and non-MN modes of thinking, to consider a wider range of possibilities that include both non-design and design.  There is metaphysical tolerance and open inquiry, with individual and communal freedom of thought, and scientists can follow the data 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.  An open science is consistent with scientists' preference for intellectual freedom.

    Critical Thinking in Closed Science
    Have the benefits of open science earned it a gracious welcome from the scientific community?  What has been the response to theories of design?  When Michael Behe submitted papers about irreducible complexity to science journals, individual editors were interested, but groups were intolerant.  One editorial board concluded its rejection letter, "Our journal... believes that evolutionary explanations of all structures and phenomena of life are possible and inevitable." {details about Behe-and-journals}
    In an open-minded free science, the response would be different.  Behe's thought-provoking questions would be welcomed as a constructive challenge, an opportunity to gain a more complete understanding of evolution at the molecular level.  The journals would be eager to communicate new ideas, to host invigorating debates between critics of a theory and its loyal defenders.
    Instead, critical questions are resented and rejected.  This response does offer a practical benefit.  It lets a community defend the reigning paradigm (*) by using its power to make important decisions:  which views will (and won't) be expressed in journals and textbooks, at conferences and in the media?  what types of research, by which scientists, will be funded?  who will be hired and promoted?  and who will determine the policies of scientific and educational organizations?  {* There are practical scientific reasons for defending a paradigm, as explained by Del Ratzsch in theories: maxi and mini.  But why should scientists defend a maxi-theory paradigm by preventing questions instead of answering them? }
    A "closed science" does not seem consistent with the lofty ideals of scientists, with their noble vision of science as an intellectually free, objective pursuit of truth.  Instead, in a community of scientists who are exploring freely, thinking flexibly, and dedicated to finding truth, Behe's tough questions would be used as a stimulus for critical analysis, creative thinking, and productive action.

    Should we ask the question?
    In the near future, scientists will disagree about the plausibility and utility of design, but conflicts are common in science, and can be productive.  Should journal editors wait until proponents of design have irrefutable proof?  As discussed in Section 7B, proof is impossible in science, and it can be difficult to confidently answer the question, "Was design-action involved in producing this feature?"  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, not rigid and closed by dogmatism.

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    When is critical thinking unscientific?
    To explain the origin of life, scientists have proposed many theories about chemical evolution, but — since what is required for life seems much greater than what is possible by natural process — each theory seems implausible.  Supporters of one theory point out the weakness in other theories, and their critical thinking is welcomed by the scientific community.
    What would make their 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?
    Can scientists admit that "we are far from finding the answer" but not that "maybe there is no natural answer"?  Consistent with the restrictions of Closed Science, should we control the thinking of scientists by removing their freedom to think that "maybe..."?

    What are the questions?
    If all questions about biological evolution have been answered, if the ideas of Mike Behe have no scientific merit and his claims already have been proved false, then his ideas should be excluded from science journals.  But if he asks questions that might raise doubts about current theories, there is a reason to include his ideas in journals.
    What are the questions?  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." (from Darwin's Black Box, page 39)

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    Mike Behe's Adventures in Non-Publishing

    Design of Biocomplexity?
    Design theorists have raised a variety of questions about the plausibility of neo-Darwinian evolution.  For example, in Darwin's Black Box: The Biochemical Challenge to Evolution (1996), Michael Behe claims that some biochemical systems are irreducibly complex and could not have been produced in the step-by-step process proposed in current neo-Darwinian theories.
    Consistent with the standards of modern molecular biology, Behe is encouraging a detailed examination of evolution, at a deeper level with higher standards.  As expected, his challenges have stimulated creative thinking and experimenting among individual scientists who read his book or heard about his ideas in subsequent reviews, lectures, or internet debates.  His critical questions have served as a catalyst for action by defenders of evolution who want to show he is wrong, and by proponents of design.

    Critical Thinking in Closed Science
    Section 7B concludes, "the potential of design theories to make valuable scientific contributions should be recognized and welcomed."  In reality, has there been a gracious "welcome to our house" reception, or is the door being jealously guarded by zealous gatekeepers?  When Mike Behe submitted papers about irreducible complexity to science journals, what was the response?  Behe summarizes: "While some science journal editors are individually tolerant and will entertain thoughts of publishing challenges to current views, when a group (such as the editorial board) gets together, orthodoxy prevails." { In this section, all quotations are from Correspondence with Science Journals: Response to Critics concerning Peer-Review by Michael Behe. }
    For example, one editor described a problem, "I am painfully aware of the close-mindedness of the scientific community to non-orthodoxy, and I think it is counterproductive."  Behe's submission was sent to a senior journal advisor, who responded to Behe's critical analysis with a generous proposal for delayed publication: "Having not yet understood all of biology is not a failure after just 200 years, given the amount of understanding already achieved.  Let us speak about it again in 1000 years."  The editor, in rejecting Behe's paper, said "I would like to encourage you to seek new evidence for your views, but of course, that evidence would likely fall outside of the scientific paradigm, or would basically be denials of conventional explanations.  You are in for some tough sledding."
    With another journal, after Behe submitted a tightly focused paper (a reply to specific criticisms) the editor made an excellent proposal for an expanded project that — consistent with the noble ideals of science — would have performed a valuable service by encouraging the open discussion of an exciting new idea:
    "The notion of intelligent design is one that may warrant further exploration, even though the topic has been dealt with extensively by both practicing scientists and philosophers of science.  Should this exploration take the form of contrasting viewpoints in articles by two persons, published in the same issue, on the more general aspects of the topic, then our editorial policy of presenting current issues of significance in the biological sciences might be satisfied.  /  Recast in more general terms, your article could present the "pro" side of the issue, and in that context it could address some of the criticisms that have appeared since your book was published, but it would have to provide a much broader perspective.  In particular, it would have to assume a readership that is not familiar with your book, at least not in any detailed way.  An accompanying article could present the "con" side of the issue, again taking a general perspective.  No doubt your book would figure prominently in both articles, but the theme would be modern concepts of intelligent design rather than a specific publication.  This approach would almost certainly reach a broader readership than a detailed response to specific criticisms.  It also has the added advantage of allowing you to present a synopsis of your entire case rather than just defending specific aspects of it.  Such a paired set of articles would imply that the topic is important, and therefore would attract additional readers."
    This is an excellent "open science" approach.  But the journal's editorial board was less enthusiastic.  They protested that "it is not possible to develop a meaningful discussion" between a design theory "based on intuitive, philosophical, or religious grounds" and an evolutionary theory "based on scientific fact and inference."  And they concluded, "Our journal... believes that evolutionary explanations of all structures and phenomena of life are possible and inevitable.  Hence a position such as yours, which opposes this view on other than scientific grounds, cannot be appropriate for our pages.  Although the editors feel that there has already been extensive response to your position from the academic community, we nevertheless encourage further informed discussion in appropriate forums.  Our journal cannot provide that forum, but we trust that other opportunities may become available to you."

    Comparing the Actual and Ideal
    The editors informally recognize that "there has already been extensive response to your position from the academic community," but official recognition (by publication in their journal) is denied.  Why?  They explain that, in contrast with Behe's intuitive religious philosophy, their journal contains pure science.  But the situation seems reversed.  Although Behe's ideas are based on observations and scientific logic, publishing them "cannot be appropriate" because "our journal... believes that evolutionary explanations... are possible and inevitable."  The rejection seems to be based on philosophical preference, not scientific merit.
    But according to a noble ideal of objective science — operating in a community of curious, open-minded scientists who are exploring freely, are thinking critically, creatively, and flexibly, and are dedicated to finding the truth — the response should be different.  Ideally, instead of ignoring the concept of design, pretending it doesn't exist and trying to exclude it from the mainstream of science, its tough questions would be carefully examined and used as a stimulus for productive action.
    Perhaps, when the evidence and arguments have been thoroughly examined and debated, when more experiments and analyses have been done, Behe's ideas will be shown to be wrong.  But critical thinking should be allowed in science, so there should at least be some recognition — by allowing publication in science journals — that his questions are important and are worthy of being asked.

Some possible reasons for rejection are examined in the appendix.

What is Open Science?
In open science, a scientist begins with an MN-assumption by assuming "it happened by natural process," but does not insist on ending with an MN-conclusion unless this is justified by the evidence.  An open scientist rejects rigid-MN (in which a naturalistic conclusion is required) and replaces it with testable-MN that treats the assumption of MN as an assumption, as a theory to be tested rather than a conclusion to be accepted.

    In the first half of this page, in the left column, I claim that "a closed science does not seem consistent with the lofty ideals of scientists, with their noble vision of science as an intellectually free, objective pursuit of truth."
    In this part of the page, I share my views about how — in a science that is open and is objectively pursuing truth — theories should be evaluated.

    Does biased evaluation produce false conclusions?
    In the current scientific community the conventional methodology, accepted by most scientists, includes methodological naturalism (MN), which is a proposal to restrict the freedom of scientists by requiring that they include only natural causes in their theories.
    How does MN affect the process and results of science?  The circular logic of MN converts a naturalistic assumption into a naturalistic conclusion by declaring that "no" is the only acceptable answer when we ask, "Has the history of the universe included both natural and non-natural events?"  With MN the inevitable conclusion — no matter what is being studied or what is the evidence — must be that "it happened by natural process."  In reaching this conclusion the process of science is irrelevant, yet the conclusion is considered scientific.  Thus, MN provides a way to bypass the process of science and then claim the authority of science.  But if some non-natural events did occur during history, MN will automatically force scientists to reach some false conclusions.  At the very least, methodological naturalism produces a significant decrease in the quality of critical thinking about naturalistic theories, which are unfalsifiable (since they're protected by MN) when they're being compared with non-naturalistic theories.
    But even though scientists (as individuals or in a group) may be motivated to reach a naturalistic conclusion, this does not necessarily mean that the process of scientific evaluation, or the conclusion reached, will be biased.  • process: Perhaps the scientists can overcome their "tendency toward bias" and make an objective evaluation.  • conclusion: Or a person (or group) might hope so strongly that the evidence will point to a certain conclusion, that they are incapable of an objective evaluation leading to another conclusion, but the reality is that an objectively neutral evaluation of the evidence actually would point to the desired conclusion, so the scientist's bias (during the process of evaluation) makes no difference in the conclusion.
    Therefore, we cannot say "If scientists have a motivation to be biased, their conclusion will be biased."  Instead, we must look at the evidence and ask, "If there was a neutral evaluation of the evidence, based on logic rather than desires, what would be the conclusion?"

    Scientific Objectivity: What is it?
    Here are two ways to think about objectivity in science:
    • One way to define objectivity, based on the premise that objectivity and flexibility are related, is to ask: "How strongly does a scientist hope that a theory evaluation will result in a particular conclusion?" or "To what extent has a scientist already decided, due to non-scientific criteria, that a particular theory must be correct?" or "Would a scientist be open-minded and willing to change views (if this is supported by the evidence and logic) and accept another theory?"
    • Another definition is based on the premise that a conclusion would be more objective if it was produced by pure scientific logic, if cultural-personal factors exerted no influence during the process of evaluation.  Just as Newton tried to imagine the characteristics of idealized motion without friction, we can try to imagine the characteristics of an idealized evaluation without cultural-personal influences, with only scientific logic.  {quoted from Tools for Analyzing Science: Idealizations and Range Diagrams}
    These definitions are examined in the next two sections.

    Objectivity and Flexibility
    The table below shows a range of nonscientific predispositions (in the purple column) about what five people hope is true, a range of scientific conclusions (in the green row), and a range of emotional responses (in the white cells) with shades of red showing levels of unpleasant cognitive dissonance.  Imagine that the five scientists are considering a theory claiming that design-directed action was involved in the production of a particular biological feature.
    The five imaginary people have decided, based on nonscientific criteria, that "design-directed action by God" certainly did not occur (at one extreme), or certainly did occur (at the other extreme), with three intermediate views.  Then imagine five different science-scenarios for the conclusion reached by an unbiased evaluation of the evidence.  Because proof is impossible in science, but strong confidence is possible, the conclusions range from almost-0% to almost-100%.  The responses (to each scenario, by each person) vary from +++ (Wow, am I happy!) to --- (This is worse than ants at a picnic!).

HOPE of scientist	idealized SCIENTIFIC LOGIC
	.1 %	25%	50%	75%	99.9%
A ( 0 %)	+ + +	+ +	-	- -	- - -
B (25%)	+	+	?	-	- -
C (50%)	OK	OK	OK	OK	OK
D (75%)	- -	-	?	+	+
E (100%)	- - -	- -	-	+ +	+ + +

    If objectivity is related to flexibility, a person who doesn't care about the outcome — whose predisposition is an indifferent "maybe or maybe not, either is OK, I don't care one way or the other" — will find it easier to be objective.  For this person, whatever the evidence indicates will be personally acceptable, so there is less motivation to evaluate the evidence in a non-objective way.
    By contrast, a person with an extreme view who wants a 0%-conclusion (that design certainly did not occur) will be highly motivated, in order to maintain personal consistency, to interpret the evidence in any way that is necessary to make it seem (to self and others) that "it certainly did not occur" is the most rational conclusion.  At the other extreme, a person with a 100%-view will feel a similar motivation to evaluate in a non-objective way.  Notice the steep gradient of emotions for A and E (the extreme views) from "+++" to "---", compared with the "all OK" plateau for the neutral unbiased C.  For A and E, an undesirable conclusion (labeled "---") would produce unpleasant cognitive dissonance that, if it isn't resolved by changing either the personal predisposition or personal conclusion, could lead to continuing mental distress due to a recognition of personal inconsistency.
    The "probably" positions (B and D) do care about the scientific outcome, but they have more flexibility, analogous to a weather forecaster who predicts "75% chance of rain" and, when it doesn't rain, says "Well, that was the 25% that I predicted."

    When a strong predisposition is supported by logic, as in a "+++" cell, process-bias is possible but its effects will be hidden because the conclusion will be the same whether or not the evaluation process is biased.  Questions of scientific integrity occur when there is a conflict between predisposition and logic, as in a "---" cell.  In this situation, how does a scientist (or a scientific community) respond?
    Is objectivity related to flexibility?  Yes, but only if a pre-disposition becomes a post-disposition that is retained after a scientist carefully examines the evidence and logic.  If a scientist begins the evaluation process with a predisposition (A or E, B or D) but is not deeply committed to maintaining this view, a flexible response could be: "Previously I hoped ____ would be the conclusion, but the evidence-and-logic indicates otherwise, so I'll change my view."  This temporal factor, regarding a willingness to change views if there is a scientific reason, is part of flexible objectivity.  Earlier, I said that "perhaps scientists can overcome their 'tendency toward bias' and make an objective evaluation."  If scientists are able to evaluate in an unbiased way despite their predispositions, they are being flexible and objective.
    Of course, scientific objectivity isn't the only goal in life.  A person may think that some benefits (scientific, intellectual, spiritual, social, professional, political,...) will arise from avoiding the noncommittal "maybe, maybe not" unbiased indifference of C, and these benefits are more important than a decrease in objectivity.  And if a non-scientific source of knowledge leads to a predisposition that is true (that corresponds to reality), this "bias" can be a scientific benefit in guiding a scientist's experimenting, theorizing, and evaluating.

    Objectivity and Scientific Logic
    It can be useful to think about evaluation factors (the criteria used by scientists when evaluating theories) as being in two general categories:  factors that are based on scientific logic, and are not based on scientific logic.
    Factors that I'm calling scientifically logical include:  • empirical reality-checks (made by comparing observations with theory-based predictions) and  • conceptual logic-checks (of a theory's internal consistency, and its external relationships with scientific theories that are well established). *
    The cultural-personal and conceptual factors that are not scientifically logical include:  • psychological motives and practical concerns that lead to asking, "If I evaluate this theory favorably, will it help me get publications, grant money, employment, and status?  Will I gain more by joining those who are arguing for this theory or against it?  Who has more power, and with whom should I form alliances?";  • metaphysical philosophy and ideological principles that exert an influence on science when theories are evaluated based on their external relationships with worldview theories (about metaphysics and ideology)*, and  • conceptual constraints on the types of entities and actions that should (and should not) be included in a theory;  to the extent that these methodological constraints are influenced by cultural-personal factors and worldviews, they are "not scientifically logical."
    * We should not allow naturalistic worldview theories to be defined as scientific theories.  (an example)
    Of course, factors that are "not scientifically logical" are part of the actual practice of science, so I'm asking "Is this factor a part of scientific logic?" rather than "Is this factor a part of science?"  I think we should recognize the existence of these factors in science, and try to minimize their influence if we want science to be more effective in helping us search for truth about nature.
    Calling a factor "not scientifically logical" does not imply an absence of logic, since non-scientific theories (about metaphysics and ideology) do have a basis in logic.  Also, an individual who is influenced by asking "Will I gain more by arguing for this theory or against it?" is behaving rationally on a professional and personal level.  And at the level of a community, factors that are not "scientific logic" can be effective "rhetorical logic" for persuasion within the community.  But these factors are not helpful if we want objective scientific evaluation that is based, as much as possible, on scientific logic.

The simplicity of basic science (with only empirical reality-checks) and the complexity of actual science (including conceptual and cultural-personal factors) are described in an introduction to scientific method.

    "In a rational open science, a design theory is evaluated in two ways, in terms of scientific evidence [using only scientific logic] and theory interpretation [based on a wide range of scientific and nonscientific criteria]."  { quoted from a page asking, Can a design theory be scientific? }
    The process of trying to imagine an idealized science (in which evaluations are made using only scientific logic) cannot be done using only scientific logic.  This process will include "theory interpretation" with subjective nonscientific judgments that are debatable and are debated, as discussed below.  There will be disagreement about the definition of an idealized pure-logic evaluation and also (because the scientific questions are complex and difficult) the idealized pure-logic conclusion.

    Is naturalism scientific?
    When we ask, "Is naturism (a belief that "nature is all that exists") scientific?", the answer is simple, and is NO.  But what are the relationships between naturism and naturalism, and between atheistic philosophical naturism and methodological naturalism?  And if you learn and use science, will this weaken your faith?  These questions are the focus of a page about The Non-Scientific Effects of Methodological Naturalism that builds on the foundation of another page that asks, "Are science and religion at war?", and looks at relationships between science and natural process, miracles, and scientism.
    When we ask, "Is methodological naturalism scientific?", the answer is complicated.  A principle of MN cannot be derived from science (so it is nonscientific) but it is compatible with science (so it is not unscientific).  A more important question is whether rigid-MN is useful in science, whether it makes science more effective in our search for truth about nature.  I think the answer is NO, for reasons that are summarized in a page about the origin of life.  But other scholars think there are reasons to say YES.  In the "foundation page" mentioned above, I briefly explain why "science does not claim that miracles are impossible,... and miracles are compatible with the logical methods of science," and I claim that "there are two rational ways [by either accepting or rejecting rigid-MN] to view historical science and miracles; among scientists and philosophers who are Christians, some support one approach and some think the other is better."
    Some scholars think that rigid-MN should not be required in science.  But others think rigid-MN is useful because, even though it is not based on scientific logic, it makes scientific logic more effective.  But if the history of nature has included some non-natural events, rigid-MN will lead to some unavoidable falsity.  Therefore, I think science will be more effective in a search for truth with testable-MN that lets scientists use scientific logic to consider all possibilities and decide which is the best explanation for the evidence.

APPENDIX
critical = evaluative   cultural influence
power and logic   defending a maxi-theory

Here are excerpts from other web-pages: