Science Journal Publishes More Gobbledygook

I don't know what's happening at Science these days. It got caught up in the arsenic affair last year and it recently made a fool of itself over the ENCODE publicity fiasco where it was completely duped by Ewan Birney.

Now it has published the following "perspective" in the October 12th issue. It reads like a Sokal hoax but it's perfectly legitimate. That's actually how Stuart Neuman proposes to solve the mystery of the Cambrian explosion.

Stuart A. Newman
Physico-Genetic Determinants in the Evolution of Development
Science 338:217-219 [DOI: 10.1126/science.1222003]
Abstract

Animal bodies and the embryos that generate them exhibit an assortment of stereotypic morphological motifs that first appeared more than half a billion years ago. During development, cells arrange themselves into tissues with interior cavities and multiple layers with immiscible boundaries, containing patterned arrangements of cell types. These tissues go on to elongate, fold, segment, and form appendages. Their motifs are similar to the outcomes of physical processes generic to condensed, chemically excitable, viscoelastic materials, although the embryonic mechanisms that generate them are typically much more complex. I propose that the origins of animal development lay in the mobilization of physical organizational effects that resulted when certain gene products of single-celled ancestors came to operate on the spatial scale of multicellular aggregates.

Neuman was one of the Alternberg 16, a group of scientists who met in Altenberg, Austria in 2008. Their purpose was to develop a new theory of evolution. The proceedings were collected in a book edited by Massimo Pigliucci and Gerd B. M^uuml;ller, Evolution: The Extended Synthesis.

This story has been promoted by a rogue journalist named Suzan Mazur and she has written a book on the subject. Here's her interview with Stuart Newman, The New Master Of Evolution?. Elizabeth Pennisi, a senior editor at Science, helped publicize the Altenberg 16 back in 2008 by publishing an article in Science [Modernizing the Modern Synthesis]. She has been sympathetic to the bizarre views of some Altenberg 16 members so I suspect she's behind the publication of Stuart Newman's article in Science.

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Douglas Axe on Protein Evolution and Magic Numbers

Imagine that I asked you to "prove" evolution by transforming a chimpanzee into a human. Would you recognize the fallacy that I described recently in Why Are Chimps Still Chimps?. Of course you would. Any intelligent person who understands evolution knows that chimps and humans share a common ancestor and both have evolved substantially since the two lineages diverged. In order to change a chimp into a human you would first have to "devolve" it back to the common ancestor and proceed from there. That requires a lot of changes.

Now let's think about two enzymes that are members of the same gene family but have evolved different functions. It's easiest to think of these as two enzymes that are now specific for similar but distinct substrates. Imagine that you were asked to "prove" evolution by changing one of those enzymes into the other? Would you recognize the same fallacy? Would you realize that the most likely evolutionary scenario is that the two different enzyme specificities evolved from an ancestral enzyme that carried out both reactions? [see: The Evolution of Enzymes from Promiscuous Precursors]

Changing one of the modern enzymes into the other would require many changes because in most cases the common ancestor dates back hundreds of millions of years. Many of the changes that have become fixed in the two lineages were not directly involved in selecting one of the substrates over the other (i.e. increasing specificity). They were neutral mutations fixed by random genetic drift after the enzyme became specialized for one or other of the substrates. Many would have to be "reversed" in order to re-create the dual specificity because they would have been detrimental in the ancestral enzyme.

Think about these facts as you watch Douglas Axe explain why his research shows that evolution is impossible [Video: Doug Axe on Protein Evolution's Magic Number (It's Six)].

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On Attacking the Integrity of Scientists

We are discussing the evolution/creation controversy in my course. One of the issues that comes up frequently is the role of scientific evidence. The importance of science in the 21st century cannot be exaggerated. Everyone wants science to be on their side because if your views conflict directly with scientific evidence then your case is very weak.

So, how do creationists handle this issue? They usually try to present counter-evidence or they cherry-pick the scientific literature looking for papers that lend support to their cause. But that only takes you so far. Creationists are forced to admit that the vast majority of scientists support evolution and that's a real problem for their flock.

The solution is obvious. If you can't attack the science then attack the scientists. By casting doubt on the motives of scientists you can partially neutralize the impact of science.

Here's an excellent example from today's post on Evolution News & Views (sic) [How to Talk About "Evolution"].

Better to think of opinion as sharply divided. The professors, their students and many university-educated people believe one thing (evolution is a fact) and most everyone else is suspicious. They won't believe in evolution if you tell them what the professors believe -- that life in all its complexity assembled itself as a result of a series of lucky hits; that we live in a world of random changes that sometimes "coincide" with the environment (natural selection); and that's how we got here.

To believe that, we first have to be blinded by antagonism to the normal, automatic recognition of purpose and design in nature. And for most people, this blindness has to be inculcated; by teachers, by the academy, by the culture.

As to the possibility of our reaching the professor group, the trouble with my correspondent's design versus "accidental mutation/natural selection" formula is not that it is too wordy but that the professoriate have learned to accept that accidental mutation and natural selection can explain everything under the sun.

I have often wondered: What would it take for a biology professor to see some living organism, study it and then clap his hand to his forehead and say: "Wow, natural selection couldn't possibly have done THAT!"

Answer: Nothing. They are locked into a materialist worldview, and they think that anything outside it is unscientific. They have already accepted Lewontin's Law about the necessity of a "prior commitment to materialism." They will look at any strange organism you may show them and say: "Well, it exists doesn't it? How else did it get here, if not by gradual stages, bit by bit, starting with molecules in motion, finally building up to what we see in front of us? What other choice is there?"

In such a dogmatic environment dissenters wisely keep their mouths shut and upholders of the orthodoxy firmly close their minds.

Of course they don't like it when we refer to them as IDiots or creationists but they have an answer to that one as well.

Going beyond that, some of our better-known adversaries indulge in name-calling so mechanically that they may well have ceased to understand the issues. It's as though they become unable to think about what they don't want to think about. Those who resort to slogans like "ID creationism" often show no sign of understanding what the claims of ID are, sufficiently even to be able to restate them.

Unfortunatly for the IDiots, I actually understand the issues better than they do! Here's the main tenets of Intelligent Design Creationism.

1. Darwin is evil and gave rise to Hilter. Evolutionists are wedded to atheism and materialism. Most scientists are too stupid to interpret evidence correctly. Evolution cannot account for life as we know it.
2. Life can only be explained by invoking an Intelligent Designer but we're not going to tell you how or when he/she/it did it.
3. The Intelligent Designer is not necessarily a god. We never said that so you can't accuse us of being creationists.
4. The general public is being prevented from learning the truth about creationism anti-evolutionary theory by a vast conspiracy of dogmatic scientists who control higher education (and almost everything else in some secular "foreign" countries like France or Japan).

Do you think I got it right?

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Does Environmental Change Drive Evolution?

I recently posted an article on the lack of evolution in species that have lived through several ice ages {More Evidence of Short-term Stasis]. This prompted a discussion about whether any serious evolutionary biologists really believe the opening statement in the abstract of the paper, "Conventional neo-Darwinian theory views organisms as infinitely sensitive and responsive to their environments, and considers them able to readily change size or shape when they adapt to selective pressures" (Prothero et al. 2012).

I believe that lots of biologists think like this. Let's discuss a quotation from The Blind Watchmaker (1986, p.178-179) by Richard Dawkins. How many readers agree with him?

After many generations of cumulative selection in a particular place, the local animals and plants become well fitted to the conditions, for instance weather conditions, in that place. If it is cold the animals come to have thick coats of hair, or feathers. If it is dry they evolve leathery or waxy waterproof skins to conserve what little water there is. The adaptations to local conditions affect every part of the body, its shape and color, its internal organs, its behavior, and the chemistry of its cells.

If the conditions in which a lineage of animals lives remain constant; say it is dry and hot and has been so without a break for 100 generations, evolution in that lineage is likely to come to a halt, at least as far as adaptations to temperatures and humidity are concerned. The animals will become as well fitted as they can be to local conditions. This doesn't mean that they couldn't be completely redesigned to be even better. It does mean that they can't improve themselves by any small (and therefore likely) evolutionary step: none of their immediate neighbors in the local equivalents of 'biomorph space' would do any better.

Evolution will come to a standstill until something in the conditions changes: the onset of an ice age, a change in the average rainfall of the area, a shift in the prevailing wind. Such changes do happen when we are dealing with a timescale as long as the evolutionary one. As a consequence, evolution normally does not come to a halt, but constantly 'tracks' changing environment. If there is a steady downward drift in the average temperatures in the area, a drift that persists over centuries, successive generations of animals will be propelled by a steady selection 'pressure' in the direction, say, of growing longer coats of hair. If, after a few thousand years of reduced temperature the trend reverses and average temperatures creep up again, the animals will come under the influence of the new selection pressure, and will be pushed towards growing shorter coats again.

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Prothero, D.R., Syverson, V.J., Raymond, K.R., Madan, M., Molina, M., Fragomeni, A., DeSantis, S., Sutyagina, A., and Gage, G.L. (2012) Size and shape stasis in late Pleistocene mammals and birds from Rancho La Brea during the Last Glacial–Interglacial cycle. Quaternary Science Reviews 56:1–10. [doi: 10.1016/j.quascirev.2012.08.015]

More Evidence of Short-term Stasis

A group of paleontologists recently documented stasis in birds and mammals from 35,000 years ago to today (Prothero et al., 2012).

Intelligent Design Creationists such as Douglas Axe are surprised by this result [Tar Pit Study Shows Complete Absence of Evolutionary Change]. So, apparently, are the authors even though they are evolutionary biologists and they have published this observation before.

How many Sandwalk readers are surprised by this paper?

Understanding Evolution in New England Colleges and Universities

The March issue of Evolution: Education & Outreach contains an interesting article on "Educators of Prospective Teachers Hesitate to Embrace Evolution Due to Deficient Understanding of Science/Evolution and High Religiosity" (Paz-y-Miño-C and Espinosa, 2012). The authors surveyed three groups at 17 colleges and universities in Maine, New Hampshire, Vermont, Massachusetts, Connecticut, and Rhode Island in the USA (New England states). The three groups were (1) general faculty members, (2) faculty members who were involved with training prospective teachers (educators), and (3) undergraduates.

Most of the general faculty (82%) thought that evolution was definitely true but only 54% of the students agreed. Among the educators only 71% thought that evolution was definitely true. This is a general trend. Educators tend to be more religious and less certain of evolution than typical faculty members but less religious and more accepting of evolution than the average student.

Why Are Chimps Still Chimps?

The American Biology Teacher published an issue dedicated to evolution back in February 2012. I got a chance to see this issue when I was in Ottawa for a big evolution meeting last July but it's taken me this long to blog about it.

One of the most impressive articles is Why Are Chimps Still Chimps" (Johnson et al. 2012). It answers the most common questions from students about human evolution and the evolution of our closest cousin, the chimpanzee.

You will learn about the difference between anagenesis and cladogenesis and why our common ancestor might have looked more like a modern chimpanzee than a modern human.

Johnson et al. are addressing teachers and they know it's important to directly refute students' misconceptions in class. They do a good job of pointing out those misconceptions.

Here's the conclusion of their paper.

If humans evolved from chimps, why are there still chimps? The two major misconceptions this question reflects are that evolution is (1) always linear and (2) innately progressive. The common depiction of evolution as a linear progression throughout which ape-like creatures become more like modern humans is a gross simplification (see Gould, 1989, for further discussion of the iconography). Along these lines, we encourage educators to find images of human and ape family trees in which the human–chimp common ancestor is depicted as an illustration, rather than those that use photographs of chimps to represent this common ancestor – reinforcing the very misconception we are trying to avoid. As we discussed, much of evolution results in a pattern known as cladogenesis; this involves processes that have given rise to the tree-like pattern of the diversity of life. Moreover, evolution does not necessarily equate to progress, as change is not always progressive (Ruse, 1996). It is incorrect to speak of living organisms as more (or less) evolved than other living organisms. Chimps are just as evolved as humans. The lineages leading to chimps and humans split from one another some 6 million years ago; since then, each has taken its own path.

This is an example of the misconception that we need to refute ...

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Johnson, N.A., Smith, J.J., Pobiner, B. and Schrein, C. (2012) Why Are Chimps Still Chimps? The American Biology Teacher 74:74-80. [DOI: 10.1525/abt.2012.74.2.3]

Monday's Molecule #190

Last week's molecule was carnitine (3-hydroxy-4-(trimethylazaniumyl)butanoate) or carnitine. The winner was Raúl Mancera [Monday's Molecule #189].

Name this week's molecule. Be sure to give an unambiguous name—it can be the common name or the IUPAC name. Why is this molecule important in some species?

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.)

Eschaton 2012 Is Coming!

THE WORLD IS PROBABLY NOT ENDING.
NOW STOP WORRYING, AND CELEBRATE REASON!
Come to Ottawa for a weekend gathering of scientists, philosophers, authors, academics, skeptics, rationalists, humanists, atheists, and freethinkers, where you can see presentations and join discussions on science, skepticism, gender issues, theocracy vs secularism, godless ethics, parenting beyond belief. Featured speakers include blogger PZ Myers, author Ophelia Benson, philosopher Chris DiCarlo, science education activist Eugenie Scott, and many others. You can even participate in a live recording of Canada's skeptical podcast, "The Reality Check" (trcpodcast.com).

Saturday evening we present our gala "Night at the Musuem" (held at the Canadian Museum of Nature), which includes a reception, talk by PZ Myers, and late night special events, with exclusive access to the Fossil Gallery and Earth Gallery.

The price of $275 ($225 for CFI members) includes access to the Friday night plenary session, a choice of 2 daytime tracks on Saturday and Sunday, lunches and snacks, plus the Saturday evening gala. (A limited number of volunteer discounts are available - email volunteers@eschaton2012.ca for more information.)

Eschaton 2012
November 30-December 2
Ottawa, Canada

The best event, by far, will be Saturday morning ...

9 AM: Eugenie Scott
10AM: Larry Moran "Science vs IDiots"
11AM: PZ Myers
11:30 AM: Audience Q+A, panel on science education (PZ Myers, Eugenie Scott, Larry Moran)

See you there!

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A Dishonest Intelligent Design Proponent?

Most IDiots are ignorant about evolution and they let their religious biases interfere with the proper interpretation of scientific data. We excuse their mistakes on the grounds that they don't know any better.

However, some IDiots clearly should know better. They have advanced degrees in relevant fields and they have received considerable feedback on the claims they post or the books they write. We know they have read the critiques so when they persist in repeating falsehoods, there must be another explanation. They must be lying.

Jonathan Wells has a Ph.D. in molecular biology. He has posted numerous articles about junk DNA and he was written a book on the subject (The Myth of Junk DNA). Lots of people have made comments about his blog posts and his book has been widely critiqued. Many of his claims have been shown to be false.

So what do we make of his recent post on Evolution News & Views) (sic) entitled Why All the Fuss Over Some Junk?. We are forced to conclude that Wells is dishonest. Perhaps with the caveat expressed by Peter Medawar many years ago in his review of Père Teihard's The Phenomenon of Man.

Yet the greatest part of it, I shall show, is nonsense, tricked out with a variety of metaphysical conceits, and its author can be excused of dishonesty only on the grounds that he has taken great pains to deceive himself.

An Honest Intelligent Design Proponent?

It's unusual to find a proponent of Intelligent Design Creationism who makes an honest attempt to evaluate scientific facts. Jonathan McLatchie (Jonathan M) seems to be one of those rare birds. I'm not going to refer to him as an IDiot.

Here's a bit from his latest post on Evolution News & Views (sic [Perspectives on ENCODE and Junk DNA].

The debate thus hinges on whether activity such as transcription, transcription factor association, and histone modification are signs of true function. My own view is that such activity is suggestive of functionality, but not proof. Therefore I would be cautious about claiming that these results show 80% of the genome to have function in the sense that we normally use that word.

On the other hand, the observation that the genome is buzzing with activity underscores what proponents of ID have been saying for years: not knowing what something does doesn't constitute evidence that it's doing nothing. Moreover, it wasn't long ago that Laurence Moran and PZ Myers were telling us that the genome is not even pervasively transcribed and that this amounted to evidence that the majority of our DNA is junk.

That's pretty good for someone who posts on a blog that also publishes stuff from Jonathan Wells and Casey Luskin. I wonder if they talk to each other?

On the other hand, it's not perfect. I've been arguing for years that there is good solid evidence that most of our genome is junk. I have never used the argument from ignorance that Jonathan attributes to me.

Also, I have never denied that the genome is pervasively transcribed. Instead, I have argued that pervasive transcription is something that one expects given what we know about DNA binding proteins and transcription. I've pointed out that the vast majority of our genome is transcribed very rarely—about one transcript per day in 100 cells—and this is consistent with accidental transcription. This is noise. The product is junk RNA and is has no function [Useful RNAs?] [Junk RNA] [Pervasive Transcription] [How to Frame a Null Hypothesis] [How to Evaluate Genome Level Transcription Papers ].

I discussed this thoroughly when I reviewed Jonathan Wells' book The Myth of Junk DNA [Junk & Jonathan: Part 6—Chapter 3]. Perhaps Jonathan McLatchie hasn't read my earlier posts?

Contrast McLatchie's post with that of Jonathan Wells [A Dishonest Intelligent Design Proponent?].

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Breaking News ... New Atheists Aren't Very Sophisticated

Richard Swinburne is Emeritus Professor of Philosophy at the University of Oxford (UK). He's a noted Christian apologist who has written many books defending the existence of God. According to Wikipedia, his two most important "sophisticated" priniciples are:

• Principle of Credulity - with the absence of any reason to disbelieve it, one should accept what appears to be true (e.g., if one sees someone walking on water, one should believe that it is occurring)
• Principle of Testimony - with the absence of any reason to disbelieve them, one should accept that eye-witnesses or believers are telling the truth when they testify about religious experiences.

What this means is that when it comes to religious experiences that confirm your beliefs you should abandon skepticism. I don't think these principles apply to people who have seen leprechauns or been abducted by UFOs. It probably doesn't apply to Muslims or Hindus, either. It seems like a "sophisticated" way of shifting the burden of proof.

As you might imagine, Swinburne is really unhappy with the New Atheists because they ignore all his sophisticated apologetics and simply ask for evidence of God. That's not playing fair. They probably haven't read any of his books.


There ought to be a rule for people who claim to have sophisticated arguments for the existence of god(s). They should have to describe at least one of them.

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[Hat Tip: Uncommon Descent]

What Is Evolution?

Most non-scientists seem to be quite confused about precise definitions of biological evolution. Part of the confusion is because the word "evolution" has many different meanings, depending on the context. When we talk about biology we are thinking about biological evolution and that's the term I want to define here. What do biologists mean when they refer to biological evolution?

This is a slightly modified version of a post from January, 2007 which, in turn, is a moified version of an essay that appears here. An even earlier version is on the TalkOrigins Archive.One of the most respected evolutionary biologists has defined biological evolution as follows:

Biological (or organic) evolution is change in the properties of populations of organisms ..., over the course of generations. The development, or ontogeny, of an individual organism is not considered evolution: individual organisms do not evolve. The changes in populations that are considered evolutionary are those that are ‘heritable' via the genetic material from one generation to the next. Biological evolution may be slight or substantial; it embraces everything from slight changes in the proportions of different forms of a gene within a population, such as the alleles that determine the different human blood types, to the alterations that led from the earliest organisms to dinosaurs, bees, snapdragons, and humans.

Douglas J. Futuyma (1998) Evolutionary Biology 3rd ed., Sinauer Associates Inc. Sunderland MA p.4

Why Do Students Skip Lectures?

There's an interesting article on student attendance at lectures in the latest issue of BAMBED (Biochemistry and Molecular Biology Education): Engagement of students with lectures in biochemistry and pharmacology.

The authors surveyed students to find out why they skipped classes at Monash University in Melbourne, Australia. The answers they give are not surprising, especially for the 8AM biochemistry lecture. However, the really interesting finding is that there's hardly any correlation between the number of lectures attended and a student's final grade in the course. The slight difference could easily be due to motivation and not ability to master the material.

This is a common finding in studies like this and the paper provides several references to the pedagogical literature. (In fairness, there are some studies that show a more significant correlation—students who skip classes get a much lower grade than those who attend.)

Here's my take on the issue of skipping lectures. If the lecture doesn't provide any value in terms of your final grade then why waste time going to class? Why bother giving the lecture?

I'd like to see a study comparing attendance in a course that has adopted student-centered learning where the class time is devoted to explaining difficult concepts and helping students think critically. The exams and assignments would have to measure whether students have mastered the concepts and learned how to think critically about the subject. In an ideal course, a student shouldn't be able to pass if they've skipped most of the lectures. What would attendance look like in such a course?

If students are skipping your lectures and still getting good grades then it's time to change your course. If you can't, or won't, do that then just cancel the lectures. You could record them and put them online if it makes you feel better. Your students are clearly not getting anything of value from sitting in the classroom.

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Monday's Molecule #189

Last week's molecules were cis Δ⁹-octadecanic acid (oleic acid) and trans Δ⁹-octadecanic acid (elaidic acid). Last week's winner was John Runnels. He should email me.

Name this week's molecule. Be sure to give an unambiguous name—it can be the common name or the IUPAC name. Why is this molecule important in some species?

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.)