Come With Us to Watch "The Unbelievers"

Here's an announcement from HotDocs (The Canadian International Documentary Festival).

The Unbelievers follows evolutionary biologist Richard Dawkins and theoretical physicist Lawrence Krauss across the globe as they speak publicly to sold-out halls, advancing a thoughtful dialogue about the importance of science and reason in the modern world. Dawkins, the world’s most famous atheist, and Krauss, director of the esteemed Origins Project, are dedicated to furthering the (r)evolutionary idea that science, above all else, should inform man’s understanding of the universe. Filmmaker Gus Holwerda follows these “rock stars of reason” as they embark on a most modern crusade to encourage people to cast off antiquated ideologies and assume a purely rational approach to important current issues. Refusing to engage with those who advance divisive and extreme fundamentalist positions Dawkins and Krauss show how sometimes sensitive and provocative ideas can be discussed respectfully and with intellectual rigour. Fans, including Ricky Gervais, Cameron Diaz, Stephen Hawking, Woody Allen and Werner Herzog, share their impressions and support, while arenas full of admirers and the curious eagerly receive them. As engaging as the subjects themselves, The Unbelievers offers an exciting glimpse into two of the world’s most influential minds at work.

The opening night is Monday, April 29. Richard Dawkins and Lawrence Krauss will be there for a conversation after the show. This event is sponsored by one of Canada's big banks (Scotiabank) as part of their Scotianbank Big Ideas series. Tickets for that event sold out before I even became aware of it and you can't even buy rush tickets right now.

My colleagues, Craig Smibert and Alex Palazzo, invited me to the movies on Wednesday May 1, 2013. We'll be making our way to the TIFF Bell Lightbox for the 3:00 pm show. Maybe we'll have lunch before the movie ... would anyone like to join us? I really like the Oliver & Bonacini restaurant (LUMA) that's in the building. It's bit pricey but it's worth it. There are tons of good restaurants in the theatre district.

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Educating an Intelligent Design Creationist: Pervasive Transcription

I'm replying to a post by andyjones (More and more) Function, the evolution-free gospel of ENCODE. This was the fourth post in a series and I'm working my way through five issues that Intelligentt Design Creationists need to understand.

Educating an Intelligent Design Creationist: Introduction

Pervasive Transcription

The idea that most of the human genome is transcribed dates back to the early 1970s. Workers isolated RNA from various sources and hybridized it to DNA (Rot analysis). They measured the amount of DNA that was complementary to this RNA and discovered two things:

1. Using highly purified messenger RNA (mRNA) the amount of DNA suggested that the genome had between 15,000 and 20,000 genes.
2. Using heterogeneous nuclear RNA (hnRNA) a much larger percentage of the genome was covered. This included the repetitive DNA fraction that we now know consist mostly of defective transposons.

These discoveries lead to intensive investigation of these non-coding DNA sequences and contributed to the discovery of introns and splicing. That accounted for a great deal of the mass of nuclear RNA that never made it into mature mRNA. Still, there was lots of RNA being synthesized that couldn't be accounted for. The data showed that this fraction was very complex (lot's of sequences) but that individual RNAs were not very abundant.

The main references quoted these days are Milcarek et al. (1974), Hugh et al. (1975), Holland et al. (1980), and Varley et al. (1980) but there were dozens of papers. The work was summarized in great detail in the first edition of Gene Expression by Benjamin Lewin. Most molecular biologists knew of these results.

Andyjones commented on this finding ...

... 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 ...

Now, to my mind the first point only underlines my original point about the cult of Darwinism (word defined according to the old-school, traditional and popular usage); that it can get in the way of the practice and dissemination of science, a dysteleological worldview which stagnates interest in trying to find function, something which has only recently been picked up again by ENCODE, and only then, Larry claims, because they don’t understand evolution.

It's true that most scientists were puzzled by this pervasive transcription but gradually they learned that a lot of it was introns and the rest was probably spurious transcription or junk RNA. They reached this conclusion because most of the transcripts were of very low abundance and were turned over (degraded) very rapidly.

I don't know where andyjones got the idea that scientist "sat on" the data. He seems to have made it up.

Andyjones says ....

The idea that (almost) everything gets transcribed sometimes but only by accident, is an explanation, but it is one that requires no investigation, and inspires no investigation. It is much more convincing to an already-convinced Darwinist than to anyone else. A Darwinist says, nah, there’s nothing here to be understood, stop looking. But to others, that would be a presumptuous ‘evolution-of-the-gaps’. Anyone who has reason to suspect teleology (meaning: engineering intent) is going to look just that little bit harder, and is going to see the importance of pervasive transcription just that little bit earlier.

Many scientists wanted to find a function for all of this RNA but they failed to do so. Meanwhile, other studies showed that much of our genome was probably junk DNA. This is about the time that scientists discovered pseudogenes (early 1980s) and discovered that half our genome was transposon pseudogenes (defective transposons). Experiments showed that a lot of pervasive transcription came from those regions of the genome suggesting that the transcripts were not functional.

It's simply not true to claim that the junk RNA explanation was not based on solid evidence and it's not true to claim that it stifled investigation. It's also ironic that andyjones thinks that the "Darwinists" would give up looking for an explanation when they (Darwinists) were doing the exact opposite! It's those who prefer natural selection (Darwinists) who most wanted there to be a function for this RNA. They still do.

I wonder if we should not be a little angry that this was not popularised in the 70s! My fiancee, who has a recent biology degree, is now annoyed that this fact was kept from her … The Darwinian establishment seem to have buried it, exactly the kind of thing I wanted to warn against.

The existence of hnRNA was widely known in the 1970s. It was discussed in graduate courses when I was a student. By the late 1970s we were teaching this material to undergraduates.

By 1990, the general consensus was that most of the rapidly degraded nuclear transcripts were probably introns although it was still an open question. That's the view that Benjamin Lewin popularized in his textbook Genes IV in 1990. The next decade showed that this was wrong because hundreds and hundreds of ESTs (expressed sequence tags) were being sequenced and most of them could not be assigned to a known gene.

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Holland, C. A., Mayrand, S. & Pederson, T. (1980) Sequence complexity of nuclear and messenger RNA in HeLa cells. J. Mol. Biol. 138:755–778.

Hough, B. R., Smith, M. J., Britten, R. J. & Davidson, E. H. (1975) Sequence complexity of heterogeneous nuclear RNA in sea urchin embryos. Cell 5:291–299.

Milcarek, C., Price, R. & Penman, S. (1974) The metabolism of a poly(A) minus mRNA fraction in HeLa cells. Cell 3:1–10.

Varley, J. M., Macgregor, H. C. & Erba, H. P. (1980) Satellite DNA is transcribed on lampbrush chromosomes. Nature 283:686–688.

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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