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A Response to Dr. Swamidass’s Questions, Pt. 2: Answering the Questions

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This is an ongoing discussion we are having with Dr. Swamidass over the question of Methodological Naturalism in science. For those who haven’t been keeping up, I posted Dr. Swamidass’s questions to critics of MN to UD a few weeks ago, then posted some of my questions for proponents of MN. Then, my first response to Swamidass’s questions is here, covering the nature of scientific inquiry, and this present post continues to answer Dr. Swamidass’s specific questions. You can find Dr. Swamidass’s original blog post here.

In my previous response to Dr. Swamidass, I pointed out that, even though he considers himself a methodological naturalist and I do not, our basic definition of science is the same.  Science develops models, or generalized schemata, with which we can better understand large swaths of the world.

Additionally, I used examples that I hoped we both thought of as science (the Big Bang, Pasteurization, and the Law of Biogenesis) to show that there is nothing wrong with science that is very close to someone’s theological preferences, and may even imply them in some way, and may even imply a miracle.  Whether or not God’s direct action can be included within science, if Swamidass includes the Big Bang as science, then we can agree that science can directly imply miracles, and can even get as close as 10^-43 seconds close to the miracle being implied.

I am going to respond to Dr. Swamidass’ questions not in the order that they are asked, but in an order that I think makes more sense to think about.  I will shorten the questions for space reasons, but if you go to the link above you will find the questions in full.  If someone thinks I didn’t answer the full question, leave me a note below.

6.1 Why is the label science so important?

I would answer that the label science is not important.  What is important is (a) even-handedness, (b) principled action, and (c) academic freedom for scientists.  A rule cannot be made such that it is only applied to certain groups, but other groups get a free pass.  If the term “science” has a specific definition that excludes ID, then so be it, but it should also be exclusive of other similar ideas.  As I showed before, if you aren’t too careful with your definition, you could easily exclude the Big Bang, Darwinism, and even evolution as a whole from science.

So, I guess I should ask, why is the label “science” so important to you?  If you develop a rule of science that excludes ID and excludes these other things, why not apply it evenhandedly?  What do you lose, exactly, if the Big Bang and Darwinism are no longer science but science-engaged philosophy?  ID proponents, at least generally, are on record saying that it is fine if someone wants to reclassify ID as science, provided that whatever rule is used is used across the board.  So, if there is nothing to be gained by being part of “science”, then why are some so eager to exclude ID without applying the same definitions to their own favored fields?

Then, there is academic freedom for scientists.  There have been numerous scientists that have been booted out of the academy for talking about Intelligent Design.  Now, professors, in the normal course of their work, are usually free to talk about all sorts of things – including philosophy.  So, if ID is really science-engaged philosophy, and professors are allowed to talk about philosophy, why would an ID proponent be kicked out of the University for doing what he should be allowed to do?  No, what is really happening is that the definition of science is being arbitrarily shrunk and used as a weapon instead of a tool in order to kick certain people out.  That is not a principled way of acting.  Normally, it wouldn’t matter so much if definitions are fuzzy and/or misapplied, but since there is a group of people actively weaponizing these definitions, we want to be sure they are based on principle and applied evenhandedly.

Is Theological and Philosophical Knowledge Real and/or Possible?

A whole series of questions of Dr. Swamidass seems to assume that theological and philosophical knowledge is either not real or not possible.  On the one hand, Swamidass seems to praise philosophy and theology as being able to find out more truth than science, but on the other side of the equation, several of his questions (especially 1.x-2.x and 6.1-3) seem to presume that theological and philosophical knowledge are simply not possible.

Many questions are of the form, “if we allow X, what about disputes between people who agree with X and people who disagree and think Y?”  To me, these questions are almost absurd.  The process of knowledge-building requires that there be people with different perspectives trying to hash out the truth. 

Take for instance question 6.3 – “There are longstanding and emotional debates between different types of creationists and atheists, which are not resolved with evidence or reason. What will keep these acrimonious debates (in which scientists usually have no interest) outside of science?”

Let’s reword the question and see if it still makes sense as a reason to exclude people from science:

“There are longstanding and emotional debates between those who are looking to quantum gravity and those who are looking to general relativity which are not resolved with evidence or reason.  What will keep these acrimonious debates outside of science?”


“There are longstanding and emotional debates between selectionists and neutral theory which are not resolved with evidence or reason.  What will keep these acrimonious debates outside of science?”


“There are longstanding and emotional debates between universe and multiverse proponents which are not resolved with evidence or reason.  What will keep these acrimonious debates (in which most scientists usually have no interest) outside of science?”

This could be applied to String Theory, or any number of things.

Now, someone will correctly say the following: “while these debates are heated, and there are presently more than one side, in the long run eventually reason and evidence should show the path to the correct answer, whether it is one of the current options or something entirely new.  It may take a short time or a long time, but by rigorously examining the evidence and having multiple perspectives on it, we will eventually find the truth.”

And my response will be, “yes, precisely!”  This is where Swamidass shows that he actually doesn’t hold theology and philosophy in the high esteem that he says he does.  If he did, then he would not use the classification of this debate as philosophy/theology as a reason for thinking it will not eventually resolve.  What is really happening is that we don’t have total knowledge, so there is in fact room for intelligent people to disagree.  People disagree all of the time within science, so why is the fact that intelligent people are disagreeing used by Swamidass to exclude them from science?  Additionally, he says that “scientists don’t care,” but that is precisely because Swamidass and others have thrown everyone who does care out of science!

Again, I want to really emphasize this point – if theological/philosophical knowledge is real, then we can’t blame our current inability to resolve an issue on the fact that it should be classified as theology/philosophy.  In fact, all of our tools for resolving issues come from philosophy and theology.  The two big ones that science uses – the identity of indiscernibles and the principle of sufficient reason, both came out of philosophy.  We look to philosophy and theology precisely because they provide the tools for resolving disputes. 

To me, it looks like Swamidass has confused philosophy with random people saying ignorant things about the state of the world, and theology with whatever the random people in his Sunday School class say about God.  This is no more philosophy and theology than asking random people on the street about the nature of the world is science.

I think that many of these things are science, and should be considered within science, precisely because I would like them resolved.  It is precisely because they are being excluded from the scientific effort that they cannot be resolved.  The people within science say, “I believe X.  I cannot even consider Y because it is not science.”  If this is the case, then it is obvious why the problem persists!  The people within science are not looking for truth, for causes, for answers – they are merely playing a game!  Only by opening up such questions to all possible causes can the answers possibly emerge.

So, again, I don’t really care how you classify these things.  However, you must be even-handed.  So, if evidence for a given cause is science, then so is evidence against it!  If the search for the cause of event A is science, then possible causes should be debated with science if the public should take anything at all from science at all.

Let me put it another way.  If science isn’t free to consider all possible causes of something, then the public has a responsibility to ignore the findings of science.  If science believes X not because it has reason to believe that it is true, but only because X is the allowed option by science, and science has no way of determining the truth value between X and other options because it is too limited, then the public should simply ignore everything that science says about X.  Period.  There is no possible reason that scientific views about X should have any bearing on public education, discussion, funding, or anything if X is simply the result of a game and not a result of a search for the truth.  If science wants to be relevant, it also has to be willing to evaluate other possibilities, or the public will have a responsibility to make it an irrelevant part of society.

Religious Texts (2.x)

While part of the question of “religious texts” is covered above in my statements about theology, I think it is worthwhile to address the question directly, because it has its own issues.

There are a few starting issues I want to get out of the way.  First of all, I object to the term “religious texts.”  It unnecessarily groups together all sorts of things that are objectively different.  The Bible is often what people mean when they say “religious texts”, but let’s look at that.  The Bible has stories about history, songs, proverbs, visions of the future, etc.  The fact that it is collected together and used by certain people for certain things actually has no bearing whatsoever on its epistemic validity. For instance, if a group of people collected together the writings of Motoo Kimura and decided to revere them and treat them as inspired, would neutral theory be required to be removed from science?  Obviously not.  As I said, the fact that some texts are used religiously by a group has no bearing whatsoever on their epistemic status.

Many parts of the Bible are used in science today.  For example, there is a paper in International Geology Review on Amos’ Earthquake (referred to in Amos 1:1).  The only place where this earthquake is known from is the book of Amos.  A geologist used the description and timing of the earthquake listed in the Bible to go and find/describe the results in ancient cities where it would be affected, and was able to estimate the magnitude of the earthquake from the evidence that was found.

The journal Cellular and Molecular Biology published a paper that included references to Genesis as well as a Biblical Exegesis of several passages, as well as references to the Egyptian Book of the Dead and Enuma Elish, as well as many others that would be classified as “religious texts.”  The author’s intention was to show that there is ancient wisdom that can help reconcile viewpoints in science.

So, what we have seen so far is that (a) classifying something as a religious text does nothing to its epistemic value, and (b) scientists do in fact use religious texts without breaking science.  I should also point out that what we know about mock modular forms in mathematics originally came from a self-taught mathematician who received his insights from the goddess Namagiri.  This did not break mathematics, either.

Now, a natural question is to ask, irrespective of whether a text is “religious”, is “what about scientists who use a text as authoritative when others do not hold the same viewpoint”?  That is a much better question, as it gets to the heart of the problem better than a bogus and/or useless classification of something as a “religious text”.  However, this already happens in science all the time.  Think about string theory.  String theory has not proven itself to be anything more than the dream of some physicists.  Therefore, some scientists engage in their work under the assumption of string theory, and others do not.  At some point in the future, we will hopefully have enough information to resolve the question.  Until then, those who operate under the assumption of string theory can still share results, theories, and opinions with those who don’t, but the utility of these will be limited by the degree that these results, theories, and opinions are based on their starting point of string theory, and those which are independent of it, or arise merely from inspiration of it.  So, for two people A and B, their results can be better shared and compared if their unproven assumptions match, and less so if they do not.  This already happens, so I don’t see how it changes anything at all from the normal practice of science.

What it seems to me is that it is difficult for some people to admit to how messy the search for knowledge already is, and many people want to pretend that the search for knowledge is simplistic and straightforward.  But the only way to really do that is to ignore what actually happens in science and replace that with a myth.  There are uses for myths in society, but more important is the ability to distinguish between myth and reality.  The view of the search for knowledge implied by many of these questions (i.e., that scientists all share the same assumptions except these crazy religious types, that all science would be peaceful if it weren’t for the creation/evolution question, etc.) is myth, not reality.

Is God’s Action on the Table for Discussion?

Short answer – yes, why wouldn’t it be?  Certainly some people will bring up evidence against God’s action, and some for it, and some will question the very notion of God.  Why not?  What is the risk?  That you might gain knowledge?  Christians are committed to the truth – that is why most of us came to Christianity – because we believe it to be true.  An examination of that truth should be welcomed by any Christian. 

The implication by Swamidass is that “science” will “conclude” something that is counter to the Christian faith – let’s call it X (where the Christian faith would say Y).  This can mean a variety of different things, each with different responses.  It can mean that certain, specific people within science (maybe even a plurality) conclude X, even though X is untrue.  If this is the case, so what?  If they are wrong, it doesn’t matter if it is one person or a thousand, they are wrong.

Another possibility would be that the evidence actually shows X (remember that X is counter to some Christian faith item).  If the evidence conclusively shows X, then I would say “thank you”.  I don’t want to believe untrue things.  If X is true then I shouldn’t believe Y.  Period.

So, certainly, science should discuss things, and the evidence for them should be out in the open.  Who thinks that this is a bad thing?  Why, especially, would a Christian who believes these things to be true?

What About Peace in Science?

Swamidass thinks that methodological naturalism keeps peace in science.  First of all, I would argue that there is not peace in science, and part of the problem is methodological naturalism.  A friend of mine is a creationist.  He built a research program that grew to receive millions of dollars in funding, and was even featured on a show on the BBC for his work.  He redesigned a lot of animal telemetry devices to cost much less.  He never mentioned creationism in his work at the school.  However, he did publish a few papers in the Creation Research Society Quarterly.  When people found out, they kicked him out of the school, and tried to retroactively take away his PhD.  He had to become a truck driver for the next two decades until retirement because no one would hire him in the academy anymore.  Is that peaceful?

It is not peaceful to say, “if we just get rid of the people we disagree with, we will be at peace”.  That is a false vision of peace.  That is like saying, “the way to stop bullying is to just give the bully everything he wants”.  If Swamidass thinks that methodological naturalism is what keeps the peace in science, then he should take a look at Lysenkoism.  It was fully methodologically naturalistic.  However, if you didn’t tow the state-imposed line on how biology should work, they threw you out.  Hey wait, that sounds like today! 

I think what keeps the peace is a common commitment to truth.  If two people have a common commitment to find the truth, that can establish peace between them.  Despite their differences, they can have respect for each other’s work to find truth.  However, if science moves from trying to find the truth to just playing a game (you can only have conclusions which match this form), then that is what will destroy peace in science.  There is no peace in gamesmanship, only winning.

Short Answers

So, my goal was to give well-thought-out answers, but I realize since I wasn’t hitting specific questions, some people may think I left something unanswered. If you are reading this, I hope you read the above first, as it is more fully answers the questions. These answers are just to make sure everybody is clear about my specific answers to the questions. So here are short answers to the questions, the bigger answer is above.

  • 1.1 – I would include all of the camps so we can find out the truth
  • 1.2 – (a) they will be resolved by evidence and reason (b) they are not resolved because there has been insufficient evidence and reason to resolve them to date to everyone’s satisfaction, which is not unusual either within science or outside of it.
  • 1.3 – see 1.1
  • 1.4 – see 1.1
  • 1.5 – see 1.1
  • 2.1 – the status “religious text” is invalid.  See “Religious Texts” above.
  • 2.2 – see 2.1
  • 2.3 – the same way we interpret any other document; why would theology be a sub-discipline and not just another discipline that has cross-disciplinary conversation?  Every other discipline encourages cross-discipline dialogue, why not science?  Why is it presumed that longstanding debates in theology are somehow different than longstanding debates in science?
  • 2.4 – there is no exclusion
  • 3.1 – “science” doesn’t conclude anything.  If “science” actually shows something false, then it is false whether or not anyone in science concludes it.  If it is just scientists that believe something to be false, then I don’t see how that has a lot of weight.
  • 3.2 – if by “would science” you mean “would individual scientists”, then sure, why not?
  • 3.3 – I am not interested in any “strategy” to install anything false anywhere.  My “strategy” is to actually find out answers to questions.
  • 4.1 – why not?  And, in fact, right now, it already is allowed within science.  Last time I checked, physiologists can conclude that someone is dead.  However, if MN is removed, then the converse also becomes open for examination.
  • 4.2 – so what?  If the evidence actually shows that the resurrection did not take place, I should thank people for showing me to be wrong.  If you are just talking about people, why should I care?
  • 4.3 – see 4.2
  • 5.1 – sure, why not?  If you have built the methodological tools to do so, go for it.  This is actually how many atheists have come to Christianity.  That’s where CS Lewis came from.
  • 5.2 – I’m not concerned about “science” “ruling” anything, because that’s not how science works.  That’s only how bullies work.  If science actually showed God didn’t exist, I would thank them for letting me know.
  • 5.3 – I am not interested in keeping anything outside of science’s domain
  • 6.1 – there is no cease-fire in effect.  Bullying people until they comply or are removed is not a cease-fire.  The answer to bullying is to remove the bullies, not to comply with them.
  • 6.2 – the ecumenical tradition in science is from the common search for the truth, not methodological naturalism.  See Lysenko.
  • 6.3 – there are all kinds of longstanding and emotional debates within science that have not been resolved.  Why is this one so different?
  • 6.4 – the label isn’t important.  Evenhandedness and principle is.
Excellent post Jonathan! Thanks for posting. Polanyi
For all events, some event is a miracle if it demands a cause whose causal powers are not possessed by anything in the physical world and in human intelligence (insofar as human intelligence is a non-physical entity). Not sure that works sufficiently to provide a good demarcation, Autodidaktos. Suppose, for the sake of argument, that ghosts were real, as some kind of impoverished non-physical entity. Wandering about its old haunt trying to get home, said ghost scares the kids (and the cat). But it hardly seems to qualify as a miracle. Of course, ghosts may not exist, but to state that upfront begs the question of scientific investigation. More theologically, classic Christianity believes that God is constantly active in and behind the causal powers inherent in the physical world, to the extent that he governs the world through them. Secondary causes, under that belief, are always incomplete, but what they lack, though it may be divine, is not miraculous - it is God doing nature, not supplementing nature. Jon Garvey
johhnyb, here's a definition of miracles that I've come up with: For all events, some event is a miracle if it demands a cause whose causal powers are not possessed by anything in the physical world and in human intelligence (insofar as human intelligence is a non-physical entity). Autodidaktos
Forgive me if I sound pedantic. But how do you define the word ‘miracle’?
Autodidaktos there are opinions that claim that if you touch the tip of your nose you touched a miracle. The presenter in the youtube video below argues in a rather convincing manner that all life and living organisms are genuine scientific miracles (go to minutes: 18-25) https://www.youtube.com/watch?v=bBtmOpPSYk0 If the smarter scientists had no clue how the human brain works (except some brain maps of electrical activity) even if billions have been invested in research for more than 50 years, doesn’t that qualify the brain (and humans) as scientific miracles? I am not even talking about how “mind” works or what is conscientiousness – which are even profounder scientific mysteries. Or maybe you can ponder if the human natural intelligence with its ability for abstract thinking, problem solving is a genuine scientific miracle – since the Artificial Intelligence scientists and engineers are far-away from being able to imitate the human mind workings. Autodidaktos, materialists should be the first to recognize these touchable and directly observable entities: living organisms as genuine miracles, because Matter (no intelligence allowed) has and never had any ability to create them. InVivoVeritas
Autodidaktos - Not necessarily. However, I'm not sure we have enough information to be certain. For instance, there is a lot of evidence that the laws of physics are "open". That is, state A might have a whole set of result states, not just one. In such a case, human agency may just be biasing the result state, not conflicting with some predetermined one. Under that definition, though, some miracles may be God doing the same thing, as well. However, if in fact physics has a single predetermined result state, then yes, human agency would be performing essentially miracles. However, what difference this makes to the present discussion I am not sure. johnnyb
johhnyb, Under your definition, aren't human interventions also miracles? Autodidaktos
Autodidaktos - I don't, really. Perhaps a simple definition would be some event X such that X was counter to what the physics of the situation would normally cause or be able to cause. I'm not really sure why it matters, though. johnnyb
johnnyb, Forgive me if I sound pedantic. But how do you define the word 'miracle'? Autodidaktos
johnnyb: Excellent thoughts and comments on methodological naturalism, science and ID. You may collect the questions and answers in a future presentation at AM-NAT conference: http://www.am-nat.org/site/ InVivoVeritas
Origenes - I agree completely. When I was referring to God and religious texts, I was not referring to ID, but rather the broader scope of possible human inquiry. My beef with MN is much deeper than just ID, or any facet of the origins debate. That's actually one of my criticisms of Swamidass - he is too focused on the specific question of whether to let these ID guys or those creationists into science. That quickly moves from principle to ad hominem to guilt by association. My goal is to take a more principled approach - figure out where the boundaries of science are... then we can decide whether or not ID is science, and whether or not anything else we are doing is science, too. Some of the most insightful biologists I know, for instance, are from the YEC camp - baraminology, specifically. Baraminologists actually *do* use the Bible as one of the sources of their inquiry. It sounds strange, but I have myself found some interesting things in doing so. However, as I said, if your theory is founded on an assumption that is not widely shared, your results will not be widely sharable. johnnyb
JohnnyB, While I agree with your analysis of methodological naturalism and the problems that it poses for science as a search for truth, I have to stress the simple fact that, in order to defend ID against Swamidass, it is neither necessary to argue that science should accept God(s) as possible causes nor that it should be open-minded about religious texts. ID is neither about the identity of the designer nor about religious texts.
Swamidass: ... ID seems to require a God-like being (i.e. God) to be the designer. This is why ID is held, by most scientists, to be ruled out from consideration with in science by MN.
So, "YES" MN is an stupid unevenhandedly applied rule imposed to defend materialism, but "NO" ID research is not a collection of religious texts about God, as Swamidass desperately wants it to be. Origenes
Gpuccio - All good points! Autodidaktos - I don't know, but if you know, you can be certain I'm not going to try to prevent your efforts! However, I think that what was specifically under discussion is something more limited than that. I.e., that a particular miracle actually occurred (whether or not it could be ascribed to a particular entity). Again, in many (maybe most) cases I don't know how that would be established or not established, but I am not going to a priori state that it can't be possible to do so. johnnyb
johnnyb: Very good work, as usual! :) I appreciate your patience in answering in detail so many questions. Some of them were probably interesting, but most of them, in particular all those dealing with religious specific views, seem really meaningless to me. I would say that a search for what is real is the ultimate purpose in cognition. I can accept some characterization of science as "different" from, say, philosophy and religion and art. But with great caution. All of those activities of human consciousness can contribute to our search for what is real. Probably, I can accept that the main character of science is that it depends less than other fields on personal experience, intuition and sensibility. That derives mainly from science being largely based on observed and shareable facts. But I would not go much further. I don't believe in any final "scientific method", or in any final "definition" of science and of what is science and what it is not. Those are only self-serving tricks of closed human minds. I do believe that, when we do science (and we don't need a final definition of it to do it, as we don't need a final definition of love to love), we should try to do it well, with respect for the reality we are investigating, and for the other people who are seriously investigating it. Many of the so called "rules of science" are, in the end, only rules of good reasoning, and good behaviour. The only important questions are, IMO: 1) Are we looking for what is real? 2) Are we doing that seriously, without self-deception (as much as it is possible), and without deceiving others (which is definitely possible) ? 3) Are we dealing, in our search for truth, with parts of cognition that can be based mainly in observed and shareable facts? And are we applying mainly shareable cognitive tools to understand and explain those facts? OK, if we can answer "yes" to those three questions, I would say that we are trying to do good science. The results will be different from person to person, but I would never exclude from a serious scientific community and debate anyone who can convincingly answer "yes" to those three questions. gpuccio
"Is God’s Action on the Table for Discussion?" How can one empirically show that the cause of a certain effect must be simple, necessarily existent and infinite? Autodidaktos

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