Educating an Intelligent Design Creationist: Introduction

Andyjones is a frequent contributor to Uncommon Descent, one of the main Intelligent Design Creationist websites. I don't know very much about him except that some people refer to him as a physicist and he seems to be based in the United Kingdom..

Andyjones and I debated the results of the ENCODE project in a series of posts ....

Function, the evolution-free gospel of ENCODE
ENCODE & Junk and Why We Call Them IDiots
(More) Function, the evolution-free gospel of ENCODE
ENCODE, Junk DNA, and Intelligent Design Creationism

He has now replied to my second post and I think I detect a real desire to learn about the issues [see (More and more) Function, the evolution-free gospel of ENCODE]. This could just be my imagination but please bear with me while I try to explain the facts to andyjones.

Andyjones begins with ...

Larry’s ‘reply’ (to my first post) appears to have replicated and evolved into a real reply (to my second post) with some real information. Well, a little information. When I say information, I don’t just mean grammatically correct and unambiguous English text, I mean things that offered ‘surprisal’ and improved my ability to understand the world and to function better in this debate. I learnt three things: firstly, some people have known since the mid 70s that most DNA is transcribed into RNA, but sat on it because apparently they didn’t realise its significance; secondly, where DNA is transcribed but a function is not known, it is generally transcribed only relatively rarely; and thirdly, that RNA polymerase (RNAP) binds at sites other than recognised promoters.

Later on he adds two other issues that he wants to learn about so that makes five in total. I'll devote a seperate post to each one.

1. Pervasive Transcription—especially the idea that this isn't new.
2. Most Transcripts Are Very Rare—what does this say about their possible function?
3. The Specificity of DNA-Binding Proteins—non-specific (i.e. nonfunctional) binding is an essential property of RNA polymerase and regulatory proteins.
4. The Meaning of Darwinism—why abuse of this term confuses creationists.
5. Evidence for Junk—there is plenty of data supporting the concept of junk DNA

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One Public School System in Ontario

I petition the Ontario Legislature to adopt legislation to establish a single, non-sectarian, publicly funded school system made up of English and French language school boards.

Sign the Petition.

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Monday's Molecule #201

The last Monday's Molecule was L-gulose and the winner was Bill Gunn. It was a special anniversary (#200) so I reposted my original Monday's Molecule from November 13, 2006 [Monday's Molecule #200]. I don't think it was any easier this year than it was seven years ago. That's a shame since biochemistry students should have had no problem getting the right answer if they understand the basic concept behind drawing structures of carbohydrates.

Let's see if you can do any better with the same molecule from November 20, 2006. It's a common molecule, although I think it's not taught in most introductory biochemistry courses. It's in most of the textbooks.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Zack Kopplin Defends Science

I watched Real Time with Bill Maher a few days ago and was delighted to see a young student named Zack Kopplin defending science. This clip has been making the rounds under various titles such a "snail logic" and "you are not a scientist." You know that it hit home when even the Intelligent Design Creationists are blogging about it [Non-Scientist Says, "You're Not a Scientist"].

The ignorant conservatives refer to a grant on snail sex as an example of waste. The grant, Genomic Consequences of Asexuality, has John Logsdon as one of the co-principle investigators. We know John through his blog, Sex, Genes, and Evolution, and because he was a post-doc with Ford Doolittle. We also know that the evolution of sex is a serious problem and that New Zealand snails are an excellent model organism for testing many theories.

The thing that puzzles me is why conservative pundits like Steve Moore have any credibility at all. None of their arguments many any sense. If even a young student like Zack Kopplin can shoot them down then why do these ideas keep coming up in the US Congress?

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Tweeting a Conference

Imagine that you are speaking at a conference. You spent a long time preparing your talk and you have wonderful slides to illustrate your most important points. Imagine that half your audience doesn't seem to be paying attention. Their heads are down and they seem to be messaging on their smart phones or tablets. How do you feel about that?

Now imagine that there's a second screen behind you. One of them shows your wonderful slides but the other shows a continuous stream of tweets about your talk. That's the situation that PZ Myers encountered at a recent meeting [Good ideas and bad ideas]. PZ thinks this is a good idea, he says ...

One particularly interesting technological development was that there were two screens at the front of the room: one big one for the presenter to use, and a smaller one on which a twitter wall was displayed — all the silent conversations using the “#skeptech” hashtag were continuously displayed, which meant there was a constant flow of commentary from the audience sharing the stage with the speaker. It was rather cool — I’d like to see more of it at more conferences. It certainly made that hashtag explode with content.

I think that's a very, very, bad idea. I'm not sure that I would agree to be a speaker if I knew that the audience was going to pay more attention to their own tweets than to anything I was saying.

I wonder if PZ will incorporate this technology into his course lectures?

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Not Everyone in the USA Hates Evolution!

I lived in New Jersey for six years. I've lived in North Carolina for several months and my daughter lived there for six years. She now lives in California. We visit and vacation in New York (state) quite often. All these states are different but North Carolina is more different than the others.

Jerry Coyne has posted a graph showing why (see below) [Acceptance of evolution vs. religiosity in the U.S.]. It reminds me that some parts of the USA are much more like Canada and Europe. It reminds me that I shouldn't assume that Texas (or North Carolina) represents the whole country.

It also reminds me of a conversation I once had with a well-known defender of evolution. That person expressed serious concerns about a possible second civil war if trends continue the way they are going. (It might not mean war, but the point is that the Union is fragile and there are many good reasons for splitting the country.)

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Alvin Plantinga Explains Why Naturalistic Evolution Is a Self-Defeating Proposition

Alvin Plantinga is a philosopher who is widely admired in the Intelligent Design Creationist community. They believe that his arguments offer strong support for theism and, more importantly, point out the logical inconsistencies of science and atheism. Yesterday (April 5, 2013) the main Intelligent Design Creationist website posted a short video of Alvin Plantinga giving a lecture where he shows that naturalistic evolution is logically inconsistent [In Two Minutes or Less: Plantinga on Naturalistic Evolution as a Self-Defeating Proposition]. They must think it's very important. They refer to the video as something that should "win a prize for elegant brevity." We should pay attention if we hope to counter these arguments.

Watch and learn. This is a philosopher who other philosophers seem to respect. It's the very best that the other side has to offer in the field of epistemology and philosophy of science.


Here's more stuff that I've written about Alvin Plantinga and his views. It's part of a larger discussion about the credibility of the entire field of philosophy of science.

What Do Philosophers Really Think About Arguments for the Existence of God(s)?
Boudry vs Plantinga
The Flying Spaghetti Monster Steals Meatballs (What's the Purpose of Philosophy?)
A Sophisticated Theologian Explains Why You Should Believe in God
Is Evolution Guided or Unguided?
Fideism

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Two Books on the Cambrian Explosion

I finished reading The Cambrian Explosion: The Construction of Animal Biodiversity by Douglas Erwin and James Valentine. It's a wonderful book. It brings you up to date on the fossil record, dating issues, evolutionary developmental biology, climate change, and molecular phylogeny. The book offers a reasonable evolutionary explanation for the apparent rapid diversification of animal groups during the Cambrian (about 530 million years ago).

The important point is covered in a paper by Erwin et al. (2011). It shows that the main animal groups probably split gradually over a period of tens of millions of years before the "explosion" became visible in the fossil record [see The Cambrian Conundrum: Fossils vs Genes]. The authors show that the molecular data indicates an earlier divergence and trace fossils are consistent with that data.

The other book is about to be published. It's called Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design and the author is an expert paleontologist and evolutionary biologist named Stephen Meyer.

It certainly sounds exciting if you read the announcement on Evolution News & Views (sic) [Coming in June, a Game-Changing New Book: Darwin's Doubt, by Stephen Meyer].

We've been keeping something from you, dear readers, but now it can be told. The evolution debate is about to undergo a paradigm shift....

Here is a sweeping account, stunningly illustrated with gorgeous color photos, of the frontiers of the scientific critique of Darwinism and the case for ID. Exacting and thorough, yet remarkably accessible to the thoughtful lay reader, Darwin's Doubt introduces us to the challenges to Darwinism based on the study of combinatorial inflation, protein science, population genetics, developmental biology, epigenetic information, and more.

Meyer explains how post-Darwinian alternatives and adaptions of Darwin's theory -- including self-organizational models, evo-devo, neutral or nonadaptive evolution, natural genetic engineering, and others -- fall short as well. He demonstrates that the weaknesses of orthodox evolutionary theory, when flipped over head-to-foot, are precisely the positive indications that point most persuasively to intelligent design.

Evolutionary biologists studying gene regulatory networks and fossil discontinuity, among other fields, have come tantalizingly close to reaching this conclusion themselves.

The Cambrian event, fundamentally, represents an information explosion, the first but not the last in the history of life. As no book has done before, Darwin's Doubt spells out the implications of this fact. Dr. Meyer stands on the verge of turning the evolution debate in an entirely new direction, compelling critics of the theory of intelligent design, at last, to respond substantively and in detail. The book will be a game-changer, for science and culture alike.

It would not be fair to criticize Meyer's book before we get a chance to read it. It will be fun to see how the science compares with that in the book by Erwin and Valentine. I'm really looking forward to reading about the Intelligent Design Theory that explains all of the scientific data. I'm especially curious about why the designer did the deed 530 million years ago and why everything since then looks so much like evolution. I'm sure that's going to be covered. We can be practically certain that a paradigm-shifting book like this isn't just going to be several hundred pages of evolution bashing.

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Erwin, D.H., Laflamme, M., Tweedt, S.M., Sperling, E.A., Pisani, D., and Peterson, K.J. (2011) The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 334:1091-1097. [PubMed] [doi: 10.1126/science.1206375]

Chris Hadfield and Barenaked Ladies: I.S.S. (Is Somebody Singing)

Ms. Sandwalk posted this on her blog and I just had to copy it. Here's Canadian astronaut Chris Hadfield, the current commander of the International Space Station, singing with Ed Robertson and the Barenaked Ladies band accompanied by the Scarborough Wexford Gleeks choir .

The song was written by Chris Hadfield and Ed Robertson.

You probably have to be Canadian to appreciate this but, what the heck, I'm posting it anyway. It combines science and the Barenaked Ladies. What more could you want?

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Can Science Test Supernatural Worldviews?

Jerry Coyne's recent post on methodological naturalism was based on a recent paper by Fishman and Boudry (2013). Previously Jerry had addressed a paper by Yonatan Fishman from 2009 (Fishman, 2009) [Can science test the supernatural? Yes!!] I think it's worth highlighting that 2009 paper because it makes a strong case against limiting science. I'm a bit confused by the stance taken by John Wilkins (and others) as I mentioned in the comments to my recent post [John Wilkins Revisits Methodological Naturalism]. Perhaps they could respond to this argument from the Fishman (2009) paper?

The recent court ruling in the United States against the teaching of ‘Intelligent Design’ (ID) as an alternative to evolution in biology classes (Kitzmiller v. Dover Area School District; Jones 2005) has sparked public interest and has been hailed as a victory by the scientific community. One of the reasons given for the verdict is the notion that science is limited strictly to the study of natural phenomena and therefore that ID and other claims involving supernatural phenomena are outside the proper domain of scientific investigation.

While the verdict is widely viewed as correct for other reasons cited in the court’s opinion, that particular rationale upon which it is based is questionable. Indeed, is science limited to the study of ‘natural’ phenomena? Does science presuppose Naturalism and thereby exclude supernatural explanations by definition? Are claims involving ‘supernatural’ phenomena inherently untestable and therefore outside the province of science? The present article argues that this is not the case. Science does not presuppose Naturalism and supernatural claims are amenable in principle to scientific evaluation [see Monton (2006) and Stenger (2006a) for a similar critique of Judge Jones’ verdict]. Indeed, science does have implications for the probable truth of supernatural worldviews (Gauch 2006, defends a similar thesis).

To exclude, a priori, the supernatural would validate the complaint voiced by some ID adherents and other creationists that science is dogmatically committed to Naturalism and thus opposed in principle to considering supernatural explanations (Johnson 1999; see Stenger 2006a). On the other hand, if there is no fundamental barrier preventing science from evaluating supernatural claims, then to declare the study of supernatural phenomena out of bounds to scientific investigation imposes artificial constraints on scientific inquiry, which potentially would deny science the noble task of purging false beliefs from the public sphere or the opportunity to discover aspects of reality that may have significant worldview implications.

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Fishman, Y.I. (2009) Can science test supernatural worldviews? Science and Education 18:165-189. [doi: 10.1007/s11191-007-9108-4

Fishman, Y.I. and Boudry, M. (2013) Does Science Presuppose Naturalism (or Anything at All)? Science & Education (published online January 7, 2013) [doi: 10.1007/s11191-012-9574-1]

John Wilkins Revisits Methodological Naturalism

Thank God John has revived Evolving Thoughts!

As usual, his latest post contains lots of food for thought [God and evolution 2: The problem of creation]. I want to pick out one morsel because it's back in the news recently.

It's the problem of "methodological naturalism" and whether it restricts science. Kairosfocus recently posted an article on methodological naturalism at Uncommon Descent [Optimus, replying to KN on ID as ideology, summarises the case for design in the natural world]. He pointed out, quite correctly, that by restricting science to methodological naturalism it means that Intelligent Design Creationism becomes non-scientific by definition.

I've argued frequently in the recent past that science is not bound by methodological naturalism [Is Science Restricted to Methodologial Naturalism?] [Accommodationism in Dover] [Methodological Naturalism]. My stance has evolved over the past few years. Back in 2007 I was a staunch defender of limiting science to methodological naturalism [Methodological Naturalism].

Jerry Coyne agrees with my current position on methodolocical naturalism. We are both upset by the way it's used to support accommodationism at NCSE [The NCSE Position on Science vs Religion] and at AAAS [AAAS Supports Accommodationism, Illogically]. If you're new to the subject, read Jerry's latest post at: Must we assume naturalism to do science?. That will bring you up to date.

John Wilkins and I have debated this controversy several time [e.g. John Wilkins Defends Methodological Naturalism]. The important point, as far as I'm concerned, is that there are respectable philosophers who disagree with the idea that science can't investigate the supernatural because it is constrained by methodological naturalism.

Here's what John said yesterday (in my time zone).

The term “naturalism”, however, is ambiguous. On the one hand it can mean giving a natural explanation through the use of scientific methods such as the use of human reasoning and observation. Or, it can mean the claim that only “natural” things exist. The first is sometimes called “methodological naturalism”, and it is the underpinning of all science, and indeed all learning about the world. The second is sometimes called “metaphysical naturalism”, although I think it is instead a claim about what exists (which is called “ontology” amongst the philosophical community). God might be natural in that sense. There is no real sharp dividing line between the natural and the supernatural that would satisfy most believers. For example, human nature for some is held to include a soul, which is divine. So let us call the second kind ontological naturalism.

Obviously I don't think that methodological naturalism is the "underpinning of all science." I think science is free to investigate claims of the paranormal (i.e. not naturalism) and can, in principle, discover things that don't meet the definition of naturalism.

What makes me nervous is that this is John's field. Is he saying that among philosophers of science the overwhelming consensus believes that that in science you can only give natural explanations? Or is he simply offering his personal opinion disguised to look authoritative?

Is there a slam-dunk philosophical refutation of the position held by the likes of Yonatan Fishman and Maarten Boudry that Jerry Coyne and I (and many others) are unaware of?

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Hank Green Talks About Junk DNA

A reader gave me a link to a video that was posted on Genetic Engineering & Biotechnology News (GEN) just a few days ago (March 25, 2013). The video was made by Hank Green of SciShow. Hank has a bachelor's degree in biochemistry and a master's degree in environmental studies.

The video is interesting for two reasons: (1) it shows how a typical scientifically literate person interpreted the ENCODE publications, and (2) it show how a business publication treats the results almost seven months later. Here's how GEN introduces the video ...

GEN brings you the best, most informative and/or entertaining biotech-related videos on the web!

In this video, Hank—who has brought you updates on the Human Genome Project, chimeras, and epigenetics—explains why your junk DNA may actually be quite valuable. Through the ENCODE project, scientists have recently revealed that junk DNA is in fact useful in ways we hadn't understood. Though there's still a lot to learn, Hank explains why it's an exciting time to be studying genes.

Watch the video and tell me what you think.

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Understanding the ENCODE Results

Josh Witten of The Finch and the Pea participated in a video discussion about the ENCODE results [see Decoding ENCODE]. The hosts are Rajini Rao, Buddhini Samarasinghe and Scott Lewis. The other guest is Ian Bosdet. The goal is to explain the controversy over ENCODE in a way that the general public can understand.

Post a comment and let me know what you think. Do you understand the issues after watching the video?

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Responding to 21st Century Atheism

I'm going to a meeting (Responding to 21st Century Atheism) on Saturday, April 13. Are you going?

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Education Is a Two-Way Street

I recently met Melonie Fullick and I've been reading her blog: Speculative Diction. Here's another post that really hits the nail on the head: Can education be sold?. As usual, you have to read the whole post but this is the part that resonates with me ...

Education works in much the same way: it is a process, one in which the student plays a necessary part, and an experience, in which the student plays a major role in the “outcome”. In fact every student actually receives a different “education”, with different outcomes, even if they’re all paying the same amount. What you pay for with tuition money is not “education”, but access to resources–libraries, expert staff, teaching and mentorship, even social contact–and access to a formal credential. Even the credential isn’t guaranteed, since students must complete academic requirements in addition to paying tuition and fees.

The assumption that education itself can be sold seems in part like a conflation of “education” and “credential”, and also an assumption that education never required anything from the student in order to be education. The idea that in the past students were not “engaged” with material is closely related to this. Of course students in the past were engaged to learn–they had to be. Otherwise they couldn’t have learned anything, because that’s how learning works. This is why “education” cannot be “delivered” like the daily paper.

The concept of education as an object is also present in debates about online learning, particularly in the recent massively hyped corporate and Ivy League versions of MOOCs. Driven as they are by the non-pedagogical need to find economies of scale, these projects envision students quantitatively, from the calculation of enrollment to the use of “learning analytics” to track behaviour (and the monetization of data). This fragmentation turns education into a series of discrete services, interactions, and measured outcomes.

Such a view of education–as something that can be delivered, sold, packaged–is part of a schema that includes the overly-simplistic “sender-receiver” model of communication, and the objectification of knowledge. These ideas are present in much of the criticism of, and commentary about, higher education; and they are pervasive in the rhetoric of education marketing and policy. The marketization of education, its presentation as simultaneously a product and a service, its increasing necessity in a difficult economy, and the financial burden placed on students through increasing tuition and fees, have all contributed to our understanding of what education is. Objectification and commodification go hand in hand; treating students as consumers means encouraging them to see education as something to be consumed–not created. Of course this is much easier than saying, “you’ve paid $6,000–now you have to do the work”, because that arrangement simply doesn’t fit with consumerist logic.

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