The Design Paradigm

An intriguing article in the Journal of Theoretical Biology I came across this afternoon.  The abstract:

The living cell exists by virtue of thousands of nonlinearly interacting processes. This complexity greatly impedes its understanding. The standard approach to the calculation of the behaviour of the living cell, or part thereof, integrates all the rate equations of the individual processes. If successful extremely intensive calculations often lead the calculation of coherent, apparently simple, cellular "decisions" taken in response to a signal: the complexity of the behavior of the cell is often smaller than it might have been. The "decisions" correspond to the activation of entire functional units of molecular processes, rather than individual ones. The limited complexity of signal and response suggests that there might be a simpler way to model at least some important aspects of cell function. In the field of Artificial Intelligence, such simpler modelling methods for complex systems have been developed. In this paper, it is shown how the Artificial Intelligence description method for deliberative agents functioning on the basis of beliefs, desires and intentions as known in Artificial Intelligence, can be used successfully to describe essential aspects of cellular regulation. This is demonstrated for catabolite repression and substrate induction phenomena in the bacterium Escherichia coli. The method becomes highly efficient when the computation is automated in a Prolog implementation. By defining in a qualitative way the food supply of the bacterium, the make-up of its catabolic pathways is readily calculated for cases that are sufficiently complex to make the traditional human reasoning tedious and error prone.

Shapiro seems to suggest that some application of this sort of thinking may be useful for analysis of IC systems.   I am only beginning to think about this, and will probably not be finished till at least next week.  So perhaps a disclaimer is in order:  This post does not imply, suggest or otherwise make any insidious claims about evolution, intelligent design, or any other theory of origins. 

But that needn’t thwart discussion– reach whichever conclusions you like on your own. 

Evidence is the most ubiquitous thing on our planet.  Sometimes, though, it has a doubtful releationship with our theories, and it is always tricky to bring it in quantity to support anything. 

Over at ID the Future Cornelius Hunter takes a look at one small piece of the mountains of evidence for evolution, a PNAS article on the highly fascinating electric fish (subscription required, so go through the Cornell library if you’re home for spring break).  The article itself, entitled Sodium channel genes and the evolution of diversity in communication signals of electric fishes:  Convergent molecular evolution is a look at "whether the evolution of electric organs and electric signal diversity of electric fishes was accompanied by convergent changes on the molecular level".  It appears to investigate this point very thoroughly, and the conclusion is that it does;  "changes in the expression and sequence of the same gene are associated with the independent evolution of signal complexity". 

Or almost; if you assume the (independent) evolution of signal complexity, the authors show it is accompanied by convergent, molecular level changes.  Hunter’s conclusion:

It turns out that there really isn’t any evidence, in particular, for the evolution of these electric organs or their sodium channels. …

The bulk of the paper reports empirical findings that do not hinge on, nor support, evolution. The force-fitting of the results into the evolution paradigm is gratuitous. Of course this assumption of evolution is no surprise. But this means that such papers do not help evolution as is claimed. Piles and piles of papers that presuppose evolution and force-fit results do little to rescue evolution from its many evidential problems.

It is important to note that there is nothing wrong with making assumptions; sometimes they are essential for any productivity.  But it’s also important to remember when we’re making them, and to be careful not to assume evolution in order to prove it.

If we want to avoid circular reasoning we need a high standard for papers called in to support any theory.  After all, if there is any contradiction in your premises, from them you can prove anything…

Suppose for a moment that Darwinian evolution was not consistent with reality.  What would it mean, then, to assume it?

• "Intelligent design holds that living organisms are so complex that they must have been created by a higher force - God."
• "Intelligent design says that life is so complex that God created it."

Atheists and those committed to antiteleological worldviews would like us to falsely believe that ID is a strictly religious idea, but even news sources that are constantly ridiculed for supposedly pumping the religious right agenda, like FoxNews, cannot get ID right.

   

In fact, I have developed a very keen sense of perceiving this error before even viewing the article. If I simply put the mouse pointer over the hyperlink of an article about ID, this new sense informs me of the error. This extraordinary sense has yet to be incorrect, because this misleading statement is in every media article I’ve read! I am kidding about the ESP, of course.

   

Any reporters reading this please note: the statements quoted above are not definitions of intelligent design. Some in the ID community call this Incredulous design. ID is based on observed physical effects of intelligent activity, not being amazed by nature. Here are some definitions of intelligent design, and here as well. Anyone knowledgeable about ID knows instantly that the reporter has an agenda, or does not know what ID is, if the quotes above are given.

Scientists in general have a rather rocky relationship with ‘philosophers of science’,  but since many opponents of intelligent design trot out bad philosophy to try to discredit it, it seems a field that can’t be ignored.

This past week I stumbled over a January post on methodological naturalism from Paul Newall at  Studi Galileiani.  He has a quarrel with the Kitzmiller decision and Judge Jones’ attempt to demarcate on ID out of science, for reasons that were all fundamentally flawed.

I’ll let the good judge speak for himself.  From the ruling:

    I[ntelligent] D[esign] violates the centuries-old ground rules of science by invoking and permitting supernatural causation.

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Steve Fuller makes an interesting side-note observation at another blog, that seems more important than he knows. Intelligent Design is conducting an open inquiry into the development of new scientific concepts that detect the effects of intelligent activity. In speaking of William Dembski, Fuller notes:

"…(unlike Newton) he’s exposing his ideas for public inspection and critique, rather than going underground for 10-20 years to work all the bugs out."

ID researchers are not hiding in closets developing hypotheses; it is an open process.

This approach, as is clear to anyone following ID, has certain drawbacks and advantages. Constant public scrutiny of work no doubt results in unnecessary stress, and in a lack of conceptual "breathing room" for the ideas of the theorist. This is a short-term drag on the research side of the concept.

To ID’s advantage, the pedagogical dimensions of the emerging study are being witnessed by a curious public. This allows a channel of information to new scientists, who can collaborate along side of, and with, other ID inquirers. Another positive result is the partial elimination of "retraining" in order to contribute to the dialogue, since many have followed ID’s development from the beginning.

The long-term payoff for the open approach is obviously worth the drawbacks, and will be necessary for further scientific development of Intelligent Design.

Over at Concerned Scientist Dan takes issue with my post from yesturday, "Minimal bacteria".  He has a graphic showing the proposed steps from simple chemicals to bacteria, juxtapositioned with what he considers to be the creationist paradigm.

The purpose of his post is to ‘correct pseudoscientific arguments’, but since we didn’t make any arguments of that nature he seems to have decided to make some rather bold assumptions about what we meant to say, and work from there:

The obvious implication is that, if the simplest known bacterium requires well over 200 genes to survive in modern laboratory conditions, with ample nutrients, etc., it’s inconceivable that it could have evolved from nothingness (a.k.a. that abiogenesis could have occurred without a Creator)?

The argument against this, of course, is that life–even such as the simplest bacteria– isn’t expected to arise in one magical step from a stewpot of simple chemicals, but slowly, via the steps outlined on his graphic above. 

But then– was it possible I was not implying anything about "arising from nothingness"?  The post in question was hardly more than a summary of the article, which was definitely not written by creationists.  Looking at minimum life forms is certainly relevant to abiogenesis, but from that does it necessarily follow that we posit the ‘minimal bacteria’ as the first step in life from simple chemicals?

We appreciate your clarifying this, Dan, and especially the collection of papers in your footnote– good spring break reading– but it isn’t quite fair to make up arguments for us just because Talk Origins has arguments against them.

Once upon a time, we thought there was such a thing as simple life. Now . . . well, we still talk about simple life, but our perception of it has changed drastically.

In the January issue of the Proceedings of the National Academy of Sciences there is an interesting article on “Essential genes of a minimal bacterium”. Mycoplasma genitalium was chosen for study because, according to the abstract, it has the smallest genome of any organism that can be grown in pure culture, minimal metabolism and little genomic redundancy, and so can be expected to be a good approximation to the minimal set of genes necessary for sustaining bacterial life. Researchers at the Venter Institute identified 382 of its 482 protein-coding genes as essential.

Why it matters? From their introduction:

One consequence of progress in the new field of synthetic biology is an emerging view of cells as assemblages of parts that can be put together to produce an organism with a desired phenotype. That perspective begs the question: “How few parts would it take to construct a cell?” In an environment that is free from stress and provides all necessary nutrients, what would constitute the simplest free-living organism?

The entire article is here; it’s somewhat technical reading, but includes nice graphics.

This is off-topic as regards the scientific issues, but on-topic as regards some objections that have been brought up against ID theory here at Cornell, and especially on the Evolutionlist (now online).  I always find it amusing when people go on about "ID is not only bad science, it is also bad religion!"   For one thing,  we ought to be willing to consider the truth value of a given theory whether or not it has uncomfortable religious or philosophical consequences, and then again . . . if I really wanted religious advice from them I would have asked :-).  There was probably a reason I didn’t.

The argument goes this way. "According to good theology, Christians are supposed to accept everything on faith.  Faith (and this is a Richard Dawkins definition) means blind trust, in the absence of evidence, even in the teeth of evidence.   If intelligent design is true you might perhaps not require  this sort of faith to believe in God.  Therefore all good Christians should flee from ID theory, and the perfidious slippery slope toward rationalism that it entails."

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Intentions, intentions.  Don’t let anyone have any cause for suspicion that you might have the slightest bit of sympathy for intelligent design or creationism, or you are not allowed to make critical remarks on anything.  To be portrayed as a sympathizer you don’t need to make any actual statements on either subject… if you raise questions on any topic which might possibly be construed as having possible creationist overtones, any subject they’ve ever considered supported their claims, you will be immediately suspect and your arguments are in danger of being perforce invalidated.

 At least, half of the establishement seems to be run that way.

There is an interesting exchange in this month’s Journal of Chemical Education.    Last July Wiliam Howard wrote an article on critical analysis in the chemistry classroom; entitled The Relationship between Balancing Reactions and Reaction Lifetimes: A Consideration of the Potassium–Argon Radiometric Method for Dating Minerals , it described how one might use an analysis of potassium-argon dating, a subject with the potential for generating a fair bit of student interest, to teach critical thinking in science and how to be good chemists. 

Science educators share a common objective: to familiarize students with critical thinking. An instructor may select a topic of current interest from the scientific literature or from the popular media and ask students to write critical essays concerning some aspect of this topic. For instance, students may criticize bond stretch isomerism (1), gallium–gallium triple bonds (2), the nature of carbon compounds in an alleged Martian meteorite found in Antarctica (3), or some other fun and controversial topic. Participation in such projects allows students to practice the scientific method firsthand. The students must gather facts concerning what is known, intelligently criticize published explanations of the facts, create imaginative and alternative explanations, and formulate experiments that could potentially falsify the explanations.  Such an experience is a very important part of a thorough education in science.

This was too much for Karen Bartlett of Eureka University, and she wrote an angry letter in response.  William Howard was trying to create confusion, clutter scientific thinking with red herrings, bring in nonsense criteria and false analogies .  Her scathing review finishes:  "The Journal of Chemical Education should pull this article from its Web site. You goofed."

The reviewers disagree. Richard Fireston, of Lawrence Berkeley National Laboratory, writes:

I may have been naïve about Howard’s intentions, and I agree with her concerns about intelligent design, but this paper must be considered on its merits, not on perceived intentions. The Howard paper should be credited for teaching students to be critical in their analysis of data . . . It is not the job of the Journal of Chemical Education to create a litmus test for what papers might or might not have hidden intelligent design meanings

Reed Howald of Montana State University writes along the same vein:

Karen Bartelt’s letter is not a fair evaluation of the William A. Howard paper. There are educational advantages of getting students involved in the scientific analysis of even controversial topics like the potassium–argon method of dating minerals.

And in Howard’s own response, he clarifies something that has been brought up  here: 

Radiometric dating is a well-established field of science, but this fact should not be used to intimidate someone from asking questions. Scientific knowledge advances only when well-established practices are questioned, and questioning radiometric dating is the responsibility of all professional scientists everywhere.

When teaching chemistry, I introduce my students to a number of theories, such as Atomic Theory, Quantum Theory, Valence Bond Theory, Molecular Orbital Theory, Crystal Field Theory, and more! These theories are well-established and supported by a great deal of experimental evidence. Nevertheless, I encourage my students to question the experimental support and to think of new experiments that could potentially falsify the theories. This activity is extremely important for producing first rate scientists. The students are well aware that these theories are not “controversial”, and that we question these ideas simply as an intellectual exercise.

I guess the crucial question… does the possiblity that something is not perhaps brute fact, that it may perhaps be questioned, have such a great probability of hopelessly confusing  our poor undeveloped brains that we shouldn’t be allowed to entertain the possiblity?  Is an attempt such as Howards to teach "skeptical chemists" too prone to produce students so muddleheaded we can’t think at all?  Is teaching us all science as "fact" really the only way to deal with such issues?  Note that the discussion here was college classes, not highschool. 

Here at Cornell we always take seriously whatever the establishment tells us.  If they tell us evolution is true, we can’t help but believe it.  If they tell us it is well supported by the evidence, we figure they must be right, even if it appears someone has gone and hidden that evidence in a top secret bunker in some undisclosed location, far away from where lowly undergrads like us could verify it.  And if they tell us that the fossil record is comprehensive enough to serve as a good, relatively complete record of evolutionary progress, that they can be reasonably sure about the life spans of various species, the proposed relationships between them, and the absolute dating involved–  well, they must be right.

That’s why new developments like the recent discovery of a member of the 11-million year extinct Diatomyidae– a small rodent like creature–  or the reptilian tuatara– extinct since the times of the dinosaurs– don’t make us stop and think.  It’s only creationists who might be inclined to go into uncomfortable questions, and wonder if perhaps some paleontologists have been a bit bold in their claims, are working too hard to fit things into an already-prepared paradigm.  We prefer to trust people who say they know better than us.

Still, if we were willing to question things, and thought that maybe new evidence might someday cause us to rethink our view of the world, perhaps articles such as this one from Science might catch our interest.  

 
As the search for extraterrestrial life continues in our solar system and beyond, NASA has made a rather remarkable discovery.
For long, we have been looking at the barren surface of Mars–sending brave Rover to transmit images of Mars back to Earth.
However, the history of extraterrestrial study is on the verge of being revolutionized.

Why? Scientists believe that water flows beneath the icy layers of Saturn’s moon- Enceladus.  The Miami Herald writes:

‘It seems, as far as we can tell, that these are geysers that are erupting out of pockets of liquid water under the subsurface of Enceladus,'’ Porco said in an interview published by NASA. “And this is just one of those smashing, surprising discoveries that we’ve just made, and we’re thrilled about.'’

She was careful, however, to stop short of declaring the definitive discovery of extraterrestrial water. As in all such cases, conclusions must be deduced from evidence gathered remotely at great distance. But she and other reputable space scientists called the evidence extremely persuasive.

‘’Our best models right now are those that suggest that there are pockets of water under the surface, and what we’re seeing in these jets are like the equivalent of Old Faithful in Yellowstone . . .,'’ said Porco, based at the Space Science Institute in Boulder, Colo. “It doesn’t seem to make sense that they are anything else.'’

What is so special about water? H2O ? - well for those of us who are not enthralled - scientist believe that water is essential for life (like ours) to form. 

James Webb, an astronomer and a physics professor at Florida International University notes "that several ingredients are required for life as we know it: water, a source of stable heat, and certain organic materials that now appear to be generously dispersed through the solar system."

So what does this all mean for intelligent design and evolution? Where do we go from here?

England is teaching the origins controversy in science classrooms, BBC reports:

The subject has been included in a new syllabus for biology produced by the OCR exam board, due out in September. . . .

The Qualifications and Curriculum Authority, which oversees the development of the national curriculum, in effect guiding exam boards, said discussions of "intelligent design" or "creationism" could take place in science classes.

The National Curriculum Online website says for science at Key Stage 4 (GCSE level): "Students should be taught how scientific controversies can arise from different ways of interpreting empirical evidence (for example Darwin’s theory of evolution)."

Classes should also cover "ways in which scientific work may be affected by the context in which it takes place (for example, social, historical, moral, spiritual), and how these contexts may affect whether or not ideas are accepted."

A spokesperson for the Department for Education and Skills said: "Neither creationism nor intelligent design are taught as a subject in schools and are not specified in the science curriculum".

Hat tip: Uncommon Descent

Update:  Andrew Rowell has an update on the political aftermath of this at ID in the UK.

I was brought up to believe that critical thinking was a good thing, and that idea affects much of my thinking today– if something is not to be questioned, I can’t help but be suspicious that it’s not on as firm footing as it pretends. 

The recent fuss over "critical analysis" has brought this issue up many times.  With people like Patricia Princenhouse in Ohio stating "Basically critical analysis is intelligent design relabeled" and Ken Miller adding "Everything is at stake" I’m made to wonder– is there something so wrong with evolutionary theory that it can’t survive anything less than blind acceptance as Fact?  If a given belief or theory is strongly supported by the evidence, critical analysis can do nothing but confirm it.  It’s only if the ground is shaky that teaching critical analysis can begin to undermine it, and only if the evidence really points the other way can it be equivalent to teaching a rival theory.

I should say though that not all evolutionists shy away from criticism, and Richard Sternberg of the Smithsonian Institute recently gave a refreshing testimony in South Carolina.

Perhaps there is no field of the biological sciences undergoing more rapid change than evolutionary research. Almost every day some new finding is reported that overturns— or seriously calls into question—long-standing assumptions and models. From the genome sequencing projects and studies of how genes operate to the discovery of new fossils, evolutionary biology is in a state of transition. Examples are simply too numerous to cover adequately. But here are a few. You have leaders in the field like W. Ford Doolittle presenting evidence that there is no “Tree of Life” but, instead, a complex web of gene sharing. Likewise, Carl Woese, one of the fathers of molecular phylogenetics, thinks the data support multiple, independent origins of organisms—that the notion of a Universal Common Ancestor is erroneous. Then again, evolutionary developmental biologists like Stuart Newman have performed experiments that suggest that animal body plans originated before genomes to “encode” them. I know it sounds radical, but he and other leaders in the field of “evo-devo” think that genes support development, but they don’t provide the blueprint. Embryos self-organize, and genes provide the building materials. Finally, even the specter of Lamarck has reappeared. Lamarck’s idea was, of course, that acquired traits can be passed on to offspring. None other than “Darwin Day” organizer Massimo Pigliucci is giving second thought to Lamarckism—after all, he notes, Darwin was a Lamarckian!

These are revolutionary times in evolutionary biology!

But we are not here this morning to discuss the latest in evolutionary thinking. We are here to discuss standards for teaching evolution in the state of South Carolina. Hence my reason for mentioning intellectual ferment in evolutionary research: we would be imprudent if we taught a particular theory as being the last word on the subject—as if all that remained is to place a few numbers after the Darwinian decimal point.

Now the subtext of the “teach evolution” controversy is usually “Darwinism: Right or Wrong?” I think this is a mistake. Darwinism is “right” in many respects. Mutations do occur and natural selection does operate. However, it is incomplete. Carefully study a textbook on evolutionary theory—not a popularization but an actual book on the mathematics of the theory—and you will notice several things. There are no equations for the development of organisms or even the cell. Nor is there any specification for how all the cellular molecules come together to shape a fly or a whale. Why the origin of new genes alone is a matter of differing views, models, and conjectures. By the way, this is not a trivial matter. It is a core issue of evolutionary biology. And this brings me to my major point:
While Darwinian theory should be taught in the science classroom, as rigorously and fully as is appropriate, to present the theory as complete and sufficient for understanding evolution is inaccurate—and thus misleading.

Not only that but I can think no better way to spark a student’s interest in evolution than to explore it in a critical way. Either evolution is an exciting, evolving field, or we are reciting passages from 1859; as though we know all there is to know. Such a stance is inimical to both the tentative nature of science and the intellectual process. This is why the suggested revised indicators can do much to improve science education—by stimulating a student’s interest in an open area.

I believe much of the future of evolutionary theory will depend on which of these internal factions wins out in the end.   A commitment to dogmatism and a refusal to allow questions can only lead to stagnation and failure as science.

HT: Scordova at Uncommon Descent

 At iDesign, a sister club at the University of California Irvine (partially responsible for inciting us to begin this website) Wedge has a post up about the falsifiability of intelligent design.  We’ve discussed this here at Cornell a good deal as well– while "God did it" is definitely not falsifiable, ID theory makes a far stronger claim than that; one that is– -theoretically anyway–  readily falsifiable.  In his words:  "Certain features of biological life as we understand it are best explained by the actions of an intelligent agent". (emphasis mine)  If evolution or any other theory comes up with a better explanation, there isn’t much more to be said for ID.

 He makes the point that it isn’t even an issue  if we can never rule out chance and necessity completely; while going for a best explanation, possible explanations we might have ten years down the road really don’t play any role.  

That notwithstanding I do think there are some aspects of our universe that by their very nature almost requre intelligence; things which no hypothetical natural law could cover. Almost by definition, no deterministic natural law can ever generate new information; at best they are functions preserving the original information content.  Non-deteministic laws, so long as they are non-telic, can generate information, but only by means of contingincy and so of a non-specified sort. 

Of course we can never rule out chance completely in any situation; especially when dealing with historical events; but too much reliance on it creates a strong inference against any theory.   

A question we ought to look at sometime soon:  is natural selection a "Maxwell’s demon" that will bring us out of the "no new information" rut?

Our puzzle for this semester:  what conclusions do you come to if you look at the data available now without extra presuppositions?

The basic presupposition of science is simple: a rational, ordered universe.  We have to accept, at least tentatively and for the sake of the argument, that the world is intelligible and that empirical evidence corresponds to reality.  But most of the time we bring in a great many other assumptions, gathered up over the years from various places.  Some may be valid, but if we can’t be sure they are true, they can clutter up our thinking and drastically increase our likelihood of reaching erroneous conclusions.

Without these extra assumptions, how  do you differentiate between intelligent design and evolution? Evolution explains divergence, but it leaves a huge, gaping hole at what may be the central problem in historical biology– the origin of new (complex specified) information.    Still, if the purpose is to determine what will happen in the future, is it better than ID, which most likely is limited to a one-time event?  Then again, what future predictions can evolutionary theory as it stands now really make?  Its track record shows it better at rationalizing the past then making sense of the what is to come.

These are difficult questions to answer, and it tempts us to go back to our old ideas of what a good theory ought to look like, what should have happened.  But if our worldview only admits of one answer to the question of origins, it is hardly fair to say that answer is "best-supported". Maybe intelligent design will be falsified… but not by those who rule it out a priori.  If we really want to decide honestly between the alternatives, we’ll have to work only with those presuppositions that are shared among both hypotheses.

Welcome to the weblog of the Intelligent Design Evolution Awareness Club (IDEA) at Cornell University!  This is an experiment, so we’ll see how the next month goes and may go offline at any time without notice. If we do and you’re annoyed, email us (idea@cornell.edu) and tell us why it matters.

We don’t promise anything– in particular, we don’t promise (or anticipate providing) any sort of continuous stream of articles and reading material.  We’re all busy students with more than enough to do keeping up with homeworks, lab reports, research and exams; and we don’t intend to write anything just for the sake of updating frequently. 

This blog is not a battle ground– come to our meetings for that! and not political in any way, shape or form.  Though at times we may discuss court cases or school board decisions related to the current controversies, the focus here is the science of intelligent design and evolution, and new research and insights into both.

Please feel free to leave comments and tell us what you think; we like to hear from both sides of the issue, and the only requirement is basic civility and no ad hominem attacks.  If you are a member of IDEA Cornell and would like to become a contributor, talk to one of the officers or email idea@cornell.edu and we’ll help you get started.