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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Teach Students How Universities Work

I recently met Melonie Fullick and I've been reading her blog: Speculative Diction. Melonie is a graduate student at York University in Toronto (Canada). Her main interest is universities and how they work.

I highly recommend her blog and I'm going to highlight a few of her posts. The first is Mixed Messages where she talks about what students know about universities and what they should know. Here's how she begins ...

A central part of my research project is the way organizations communicate, and the organizations I focus on are universities. So when it comes to undergraduate education and university experience, an important question I think we need to ask is this: what’s the message that students receive from universities? I’ve been thinking about this lately, and was discussing it again last week with students in one of my tutorials. Here are a few of the thoughts that came out of that discussion.

You should read her entire post but here's the bottom line ...

So what’s the message that students receive from universities? From asking undergraduates, it sounds like oftentimes it’s an incoherent, authoritative, and monologic one. This tone and delivery in and of itself can be off-putting enough that students might feel uncomfortable seeking help. For example, being told “that information was/is available to you” (i.e., “you should have known better”) is not a helpful approach when students may be confused and in the middle of a crisis, seeking support. One thing that’s missing is the understanding that rather than just providing students with lists of available services, we need to de-mystify the university itself; instead of trying to create the perfect bureaucratic system (which is impossible in any case), we could show students how systems work. This is also part of the “tacit” knowledge that students gain from being in university; to help students understand the institution, we need to make that knowledge explicit–to communicate it.

I've often thought that we must not be doing a good job of education if we are graduating students with a bachelor's degree who don't understand the basics of how a university works. These are the students who will go on to decide the future of universities even if it's only because they vote. How do we "de-mystify" the university?

This reminds me of a Forbes article published last January by Susan Adams [The Least Stressful Jobs Of 2013]. You may recall that there was a bit of a kerfluffle about it in the blogosphere (e.g. I Have the Least Stressful Job!!!]. Melonie Fullick also wrote about it in More (higher ed) media madness!. Let me remind you of what Susan Adams said in her article ...

University professors have a lot less stress than most of us. Unless they teach summer school, they are off between May and September and they enjoy long breaks during the school year, including a month over Christmas and New Year’s and another chunk of time in the spring. Even when school is in session they don’t spend too many hours in the classroom. For tenure-track professors, there is some pressure to publish books and articles, but deadlines are few. Working conditions tend to be cozy and civilized and there are minimal travel demands, except perhaps a non-mandatory conference or two. As for compensation, according to the Bureau of Labor Statistics, the median salary for professors is $62,000, not a huge amount of money but enough to live on, especially in a university town.

In an ideal world, every single university graduate should know that this is ridiculous. They should know what professors really do because they have spent four years at university and they learned how the system works. How is it possible that we are graduating students who would believe something like this?

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Learning About Evo-Devo

We talked about evolutionary developmental biology (evo-devo) in my class last week. The main issue is whether the proponents of evo-devo are making a substantive contribution to evolutionary theory. Is evo-devo going to be part of an extended modern synthesis, and, if so, how? My own view, which I express to the class, is that the discoveries of developmental biology pretty much confirm what Stephen J. Gould wrote in Ontogeny and Phylogeny back in 1977.

What, then, is at the root of our profound separation? King and Wilson argue convincingly that the decisive differences must involve the evolution of regulation: small changes in the timing of development can have manifold effects upon a final product "Small differences in the timing of activation or in the level of activity of a single gene could in principle influence considerably the systems controlling embryonic development. The organismal differences between chimpanzees and humans would then result chiefly from genetic changes in a few regulatory systems, while amino acid substitutions in general would rarely be a key factor in major adaptive shifts." Differences in regulation may evolve by point mutations of regulatory genes or by rearrangement of gene order caused by such familiar chromosomal events such as inversion, translocation, fusion, and fission. Studies of banding indicate that at least one fusion and ten large inversions and translocations separate chimps and humans.

Stephen J. Gould (1977) Ontogeny and Phylogeny, Harvard University Press, Cambridge Massachusetts, USA pp. 405-406

This helps us understand the history of life, especially the evolution of animals, but it doesn't contribute to evolutionary theory.

PZ Myers is teaching a developmental biology course and his students are dealing with three take-home questions this weekend [What I taught today: O Cruel Taskmaster!]. I'd like to reproduce two of them here since they're very relevant to the debate over the importance of evo-devo.

Question 1: One of the claims of evo devo is that mutations in the regulatory regions of genes are more important in the evolution of form in multicellular organisms than mutations in the coding regions of genes. We’ve discussed examples of both kinds of mutations, but that’s a quantitative claim that won’t be settled by dueling anecdotes. Pretend you’ve been given a huge budget by NSF to test the idea, and design an evodevo research program that would resolve the issue for some specific set of species.

I'd like my students to keep in mind Richard Lenski's ongoing evolution experiment in E. coli. Recall that evolution of the ability to grow on citrate depended mostly on mutations that changed the regulation of citrate utilization genes.

Since we have many examples of mutations that affect regulation of gene expression in bacteria, yeast, and other single-cell organisms, why do the proponents of evo-devo think they're on to something special when they look at development in animals? What is there about the evolution of "form" that changes our views on evolution?

Question 2: Every generation seems to describe the role of genes with a metaphor comparing it to some other technology: it’s a factory for making proteins, or it’s a blueprint, or it’s a recipe. Carroll’s book, Endless Forms Most Beautiful, describes the toolbox genes in terms of “genetic circuitry”, “boolean logic”, “switches and logic gates” — he’s clearly using modern computer technology as his metaphor of choice. Summarize how the genome works using this metaphor, as he does. However, also be aware that it is a metaphor, and no metaphor is perfect: tell me how it might mislead us, too.

Before answering PZ's question about Sean Carroll and metaphors, I'd like my students to remember the quotation I gave them in class. Discuss the use of hyperbole and metaphor in this context.

The key to understanding form is development, the process through which a single-celled egg gives rise to a complex, multi-billion-celled animal. This amazing spectacle stood as one of the great unsolved mysteries of biology for nearly two centuries. And development is intimately connected to evolution because it is through changes in embryos that changes in form arise. Over the past two decades, a new revolution has unfolded in biology. Advances in developmental biology and evolutionary developmental biology (dubbed “Evo Devo”) have revealed a great deal about the invisible genes and some simple rules that shape animal form and function. Much of what we have learned has been so stunning and unexpected that it has profoundly reshaped our picture of how evolution works. Not a single biologist, for example, ever anticipated that the same genes that control the making of an insect’s body and organs also control the making of our bodies.

This book tells the story of this new revolution and its insights into how the animal kingdom has evolved. My goal is to reveal a vivid picture of the process of making animals and how various kinds of changes in that process have molded the different kinds of animals we know today and those from the fossil record.

Sean B. Carroll Endless Forms Most Beautiful: The New Science of Evo Devo, W.W. Norton & Co., New York (2005) p. x

I'd also like Sandwalk readers to keep in mind the recent ENCODE publications. They talked extensively about genetic circuits and regulation. In fact, their major "finding" was the idea that our genome is full of regulatory elements; so many, in fact, that most of what we thought was junk DNA is actually part of a a vast control circuit. Has this emphasis on a multitude of switches and controls been misleading or is it turning out to be correct?

I would ask a third question. The evolution of toolkit genes (i.e. transcription factors) make it possible to evolve many different body plans with only a small number of mutations. It helps explain the Cambrian explosion. Given our current understanding of evolution, is it possible to select for a evolution of a toolkit that has this potential for future evolution? Explain your answer.

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ENCODE, Junk DNA, and Intelligent Design Creationism

andyjones has replied to my earlier posting on ENCODE and junk DNA. You can read his response at: (More) Function, the evolution-free gospel of ENCODE. Here's part of what he says ...

Larry Moran has sort-of replied to my previous blogpost but disappoints with only one substantive point. And even that one point is wrong: ID is not committed to the idea that individual genomes be well-designed; that is just an expectation some of us derive based on belief in a designer which is established on other evidence. ID would still be true if only globular proteins were designed (lookup Axe), or even if only the flagellum was designed (lookup Behe), or even if only the first life form was designed (lookup Meyer – and please read their actual work, not cheap reviews, because reviewers often dont pick up on the salient points – more below). I just say this lest readers get the impression that this is ID’s strongest point, or in any sense a weak point. It is neither.

It's true that there are some IDiots who are distancing themselves from a commitment to junk DNA. There are probably some who claim that they could live with the fact that 90% of our DNA is junk.

But let's not forget that Jonathan Wells is a prominent IDiot and he wrote a book on The Myth of Junk DNA. It sounded very much like Intelligent Design Creationism is staking its reputation on finding function for most of our genome.