Wednesday, May 09, 2012

On the Difference Between "Evolutionary Theory" and Scientific Fact

There's been a lot of discussion about Elliott Sober's talk at the University of Chicago. You can watch the entire talk and the questions & answers at [The Problem with Philosophy: Elliott Sober].

Most of the debate is taking place on Jerry Coyne's site [Can God create mutations? Elliott Sober says we can’t rule that out.] and on Jason Rosenhouse's blog [The Reason For the Ambivalence Towards the Philosophy of Science]. Things aren't going well for Elliott Sober and, by implication, for the philosophy of science.

I want to discuss another troubling aspect of Sober's talk. Throughout the talk he refers frequently to "evolutionary theory" or "the theory of evolution." This is consistent with the introduction by Robert Richards where he says they are considering "... the application of evolutionary theory to the humanities and social sciences" (27 sec). The title of Sober's talk is "Naturalism and Evolutionary Theory."

What do they mean by "evolutionary theory"? To me, evolutionary theory means the kinds of things that are discussed in Stephen Jay Gould book "The Structure of Evolutionary Theory." It includes things like population genetics and the potential influence of genome size on the fixation of alleles. It includes things like species sorting and punctuated equilibria. It even includes speculation about selfish genes and the level of selection.

Evolutionary theory does NOT include whether birds and dinosaurs share a recent common ancestor, the age of the Earth, the amount of junk DNA in our genome, or the causes of mutation. Those are interesting questions that bear on evolution but the answers to those questions are not a fundamental part of evolutionary theory. The are questions of scientific fact, in my opinion.

Do philosophers like Elliott Sober agree with this distinction? I don't think so. The main point of Sober's talk is whether evolutionary theory can show that mutations are random. He concludes that evolutionary theory cannot conclusively prove that all mutations arose by chance; therefore, there's room for God-directed mutations as long as their frequency is indistinguishable from randomness.

Sober has a paper that discusses this issue [Evolution without Naturalism]. Here's the part that describes "evolutionary theory" (page 5).
What is this thing called “evolutionary theory,” which theistic evolutionism is able to encompass consistently? It includes the origin of life from nonliving materials by physical processes, the branching genealogical process whose upshot is that current organisms are connected to each other by relations of common ancestry, the random origin of new mutations, and the processes that govern trait evolution within lineages, such as selection and drift. Among these several propositions, the idea that mutations are “random” may seem to be a sticking point.
This is not what I think of when I use the term "evolutionary theory." I don't think the origin of life is a part of evolutionary theory. I don't think that the random origin of new mutations is part of evolutionary theory. As far as I'm concerned, the discovery that mutations occurred preferentially in hotspots or that there was a base composition bias—which there is—would not refute evolutionary theory. I think my understanding of evolutionary theory is closer to that of the majority of evolutionary biologists and it's troubling to me that philosophers seem to use a different definition.

Here's another example from that same paper (page 4) ...
Although evolutionary theory is silent on the question of whether there is a God, it is not neutral with respect to logically stronger hypotheses about God. Consider, for example, the statement
Life appeared on earth about 10,000 years ago due to divine intervention.
This statement is inconsistent with evolutionary theory.
The Young Earth Creationist statement is inconsistent with all available scientific evidence on the age of the Earth. This evidence is so overwhelming that it is a scientific fact (sensu Gould) that the Earth is billions of years old. Why does Sober think that "evolutionary theory" plays a role here?

This is not just a semantic quibble. By confusing "evolutionary theory" with scientific facts Sober makes it much more difficult to follow his line of reasoning.

Is it true that the majority of philosophers of science use "evolutionary theory" when they should frequently be referring to scientific facts? Is it true that most philosophers think that the age of the Earth is a "theory"? Do they also think that evolution is only a theory?


25 comments:

  1. It sounds like he is not using the correct definition of "random mutation". In Evolutionary Biology, a random mutation is one that occurs with out respect to the needs of the organism, i.e. selection. It is not a teleological statement.

    The existence of random mutations is a fact.

    And if it happens that magic is the force that causes mutations, it still does it in a way that is random with respect to selection.

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  2. Let's admit that philosophy is allowed to speculate more freely than science. The way Sober construes this speculative god, we could not possibly know it existed, even if it intervened. Hence it just drops out of scientific equations, observations, experiments, etc.

    What remains is a realm of belief or faith separate from knowledge. That describes the social primordial soup I grew up in.

    It seems as though believers (especially American creationists an ID-ologists) kept trespassing on the scientific turf by claiming some 'special kind of knowledge' for so long that gnus now strike back by denying faith as legitimate states of mind.

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  3. Concerning your conception of scientific fact vs. only a theory, I think that the received view is that a scientific theory (like relativity theory, or evolutionary theory) has a higher standing than a fact (like "look there's a fossil"). It's definitely what Dobzansky thought in his "Nothing in biology makes sense..." essay. If a hypothesis has made it up to the status of a theory, it will be supported by a great number of facts. You, however, then regard it as a fact in itself.

    Maybe philosophers of science have left a job for historians of science to be done: showing how things that have been regarded as theoretical once (e.g. atoms, gravity, mutations, genes, heliocentrism, tectonic plates) are now regarded as factual.

    It would be an important step in taking the rhetoric ploy of fact-vs-theory from creationists.

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  4. Ernst Mayr defined five elements to evolution.

    1. The earth is old. This is a result of physics and geology and is a fact.

    2. Extinction. This is an observable fact. Fortunately for us, Tyrannosaurs are no longer around, else we would not be here.

    3. Most existing animals not present in ancient strata. Haldane's no cat fossils in the pre-Cambrian. This is a fact.

    4. Common descent. This is the most parsimonious inference from the previous 3 facts which is backed up by genetic evidence. Thus, this is an inference from the facts.

    5. Natural Select/genetic drift are the mechanisms driving evolution. These constitute the theory part of evolution.

    The nearest analogy I can think of is the Kepler observation of the planets moving in ellipses equivalent to the first 4 elements above and the Newtonian inverse square law of gravity as the equivalent to the driving mechanisms of evolution.

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  5. While watching that boring video, Sober appeared to be confused between theory and hypothesis.

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  6. Sober:
    Life appeared on earth about 10,000 years ago due to divine intervention.

    This statement is inconsistent with evolutionary theory.


    Moran:
    The Young Earth Creationist statement is inconsistent with all available scientific evidence on the age of the Earth. This evidence is so overwhelming that it is a scientific fact (sensu Gould) that the Earth is billions of years old. Why does Sober think that "evolutionary theory" plays a role here?

    Perhaps because the statement involves more than just the age of the Earth - i.e. when life appeared? The statement that life appeared about 10,000 years ago sure isn't inconsistent with the Earth being billions of years old.

    Do they also think that evolution is only a theory?

    Are you saying that evolution is not a theory? Or are just trying to say that Sober lies with creationists? Or something else?

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    1. Good point.

      I was making the unwarranted assumption that the Earth was created 10,000 years ago. Sober could easily have been talking about an Earth that was 4.5 billion years old but life only appeared 10,000 years ago.

      If this is what Sober meant, then paleontologists would beg to differ. It still has nothing to do with "evolutionary theory."

      Are you saying that evolution is not a theory?

      I'm saying that Evolution Is a Fact and a Theory and that Sober doesn't seem to recognize the distinction between evolution facts and evolutionary theory.

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  7. I think that the Sober's point is that a lot of people say 'theistic evolution' is just as bad as the usual sort of creationism, and that it's one thing to push the wacko's who think jesus rode dinosaurs off-stage, but another to say that people who are religious can not be scientific (and so clearly there's a bit of a conflation between 'regligious' and 'theistic evolution'). Or, another way that people say this is that science should make a person an atheist, or some such.

    Having said that, Sober's argument is a pretty silly one, that an impossible to detect 'thing' is 'compatible' with a system that can not detect it. It's saying nothing, other than asking for an argument as to what 'compatible' means.

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  8. If this is what Sober meant, then paleontologists would beg to differ. It still has nothing to do with "evolutionary theory."

    Of course it does. You'd be hard pressed to squeeze in all evolutionary changes postulated in a 10,000 year time frame. And yes, the fossil record would not make sense under evolution if life started 10,000 years ago.

    I'm saying that Evolution Is a Fact and a Theory and that Sober doesn't seem to recognize the distinction between evolution facts and evolutionary theory.

    I can see no evidence that Sober doesn't know the difference. Although he might, of course, argue that there is no such thing as a non-theory-laden fact.

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  9. For a god to cause mutations such a god would have to exist in the first place. Sober is an imbecile.

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  10. This comment has been removed by the author.

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  11. Negative Entropy wrote two sentences:

    (1) For a god to cause mutations such a god would have to exist in the first place.

    (2) Sober is an imbecile.


    I would be interested how his conclusion in (2) follows from (1).

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    1. Rrrrriiight. An imbecile would probably be more likely to think that (2) follows from (1).

      But seriously, for those of us who aren't allowed to make our own rules of logic, there is something missing in your statement. Would you care to enlighten us?

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    2. I thought you read/heard the whole thing. Larry's post, Sober's talk, probably the stuff going on at Jerry's site, my comment. That should help you figure out how (2) follows from (1).

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    3. I have read it. I even understood some of it. What I can't understand is your silly conclusion that Sober is an imbecile. YOU have not justified this conclusion what-so-ever. And no, pointing out that there is stuff written on the subject is not a justification. That is just pure laziness. So, Negative Entropy, justify your conclusion. I bet you can't...

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    4. It is pure laziness, but not on my part. The conclusion is too obvious. I love the "I bet you can't ..." Reminds me of those old elementary school days. Are you by any chance a creationist?

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    5. The conclusion might be obvious to someone with a VERY simple mind. For those of us who understand a bit more about what Sober is saying, (1) and (2) seem utterly disconnected.

      What I've decided to do is to add this discussion to a forum that might be a bit more suitable. Old blog posts quickly get forgotten as new ones are added (Larry has already added seven new posts) and I also wanted to show your stupidity to a wider audience.

      So, you are welcome to add some arguments at http://www.skepticfriends.org/forum/topic.asp?TOPIC_ID=15048

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    6. This is sweet from you Hawks. Question, which is the "last sentence" that made you lose respect for me (not that you had much respect for me anyway)? The question about whether you are a creationist, or that your kinder-garden "I dare you" statement reminded me of those old school days? If the former, well, the latter is typical of creationist modus operandi. So, maybe you should rethink a bit about your self-respect.

      I could not register to the forum, might try another day. Traveling now. (Your link "explaining" what "should be understood by God" by Sober does not say anything about what should be understood by God. Maybe you linked the wrong paper. I am being serious, no sarcasm or anything about your mistake. Just an observation so that I can read the right paper and realize that Sober is not that much of an imbecile after all-provided the paper made sense of the apparent imbecility. But if the link is correct, I stand by my assessment.)

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    7. which is the "last sentence"

      The last sentence was the creationist one.

      "I dare you" statement reminded me of those old school days?

      That's your problem. I said that you can't do it because I can't see how you CAN do it.

      So, maybe you should rethink a bit about your self-respect.

      I fail to see why.

      Your link "explaining" what "should be understood by God" by Sober does not say anything about what should be understood by God.

      The link (and the quote) essentially states that god does not refer to any specific religious deity but rather religion in general.

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    8. ...any specific religious deity but rather religion in general.

      This is a minor point, but I should correct myself here and say that Sober is talking about theism and not deism.

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  12. Elliott Sober’s argument for the logical possibility of God-guided mutations has ignited a lot of ink and mental effort, both here and at other sites.

    I wonder if Environment-guided mutations, a more down-to-Earth presumption, can get a fraction of that attention. As a primer, I’m posting here as very shot paper I published two decades ago:

    Bandea, CI. A Mechanim for Adaptive Mutagenesis. Medical Hypotheses, 31:243, 1990

    Can organisms mutate adaptively in response to a selective agent? Four decades ago, Luria and Delbruck (1943) showed that in bacteria, and presumably in all organisms, mutations appear to be random. This notion is one of the basic principles of modern evolutionary theory.

    Recently, Cairns, Overbaugh and Miller (1988) challenged this notion by suggesting that “cells may have mechanisms for choosing which mutations will occur.”

    In this paper, I propose that transcription might be a mechanism by which organisms could discriminately increase the mutation rate of some of their genes in response to changes in the environment. An increase in the mutation rate would generate the genetic diversity necessary for rapid adaptation and evolution.

    Cells possess several repair mechanisms for reducing the mutation rate (3). A decrease in the repair efficiency would result in an increased rate of mutations. Transcription may interfere with the repair process by obstructing the activity of repair enzymes. Transcription interference has been reported in other cases (4, 5).

    During transcription, the DNA template becomes locally single stranded which makes it more susceptible to attack by some mutagenic agents. This is another way in which transcription may increase the rate of mutation.

    Therefore, the environment, by controlling the transcription rate of some genes, may influence their mutation rate and evolution.

    References
    1. Luria SE, Delbruck M. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28:491, 1943.
    2. Cairns J, Overbaugh J, Miller S. The origin of mutants. Nature 335:142, 1988.
    3. Sancar A, Sancar GB. DNA repair enzymes. Annula Reviews of Biochemistry 57:29, 1988.
    4. Bateman E, Paule MR. Promoter occlusion during ribosomal RNA transcription. Cell 54:985, 1988.
    5. Brewer B, Fangman WL. A replication fork barrier at the 3’ end of yeast ribosomal RNA genes. Cell 55:637, 1988.

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    1. You wonder wrongly because of course the adaptive mutations indeed ignited lots of "ink and mental effort." Curious that you published your work two decades ago and you did not notice. I attended a few conferences where evidences were exchanged. Read several papers pro and con to Cairn's initial results. It was quite the hot topic. Check out a few papers published by John Roth at PNAS. John showed that the apparent adaptive mutations were no such thing quite clearly and elegantly. I think it is a bit of a mistake to stop reading after publishing a paper two decades ago.

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    2. Hum, I was able to find even more papers on this up to 2010. So still somewhat ignited.

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    3. Thanks for your points and references. I did follow the literature on the subject for a while; Barry G. Hall published quite a few papers at that time and apparently John Roth has continued the work. I just scanned some of the more recent papers, but I’m not sure where the field (i.e. the experimental results) is on this topic.

      The problem with the research on this phenomenon was, and apparently still is, on trying to differentiate between the effects of the ‘selective agent’ on the process of generating the mutations versus the process of selecting the mutations. Ultimately, is all about the selection of mutations, but the hypothetical ‘directed mutations’ could increase the repertoire of mutations (i.e. genetic variation) on which the natural selection can act upon.

      Another relevant point is to differentiate between the mechanisms by which a selective agent, such as a stress or a specific metabolite, would increase the mutation rate of all genes, by repressing for example the production of DNA repair enzymes, or only of the specific gene(s) that are relevant for the selective agent.

      By the way, I posted my comment on some of the other sites, and you might wnat to take alook at this site (http://whyevolutionistrue.wordpress.com/2012/05/13/rosenhouse-on-god-guided-mutations-again/#comments), where JF Fortier(see comment #23) posted a video that might be relevant for Elliott Sober’s argument.

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