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.)

An Online Course for Intelligent Design Creationists

About 99% of all books and posts by Intelligent Design Creationist consists of criticisms of evolution—which they mistakenly refer to as "Darwinism."

What this usually reveals is that the typical IDiot doesn't understand evolution. But there's at least one Intelligent Design Creationist who recognizes that this is a problem. Jonathan McLatchie (Jonathan M) recommends that his colleagues take an free online course in order to learn about evolution [Free Online Course: Introduction to Genetics and Evolution]. He writes,

Critics of modern evolutionary theory have an intellectual responsibility to strive to understand the paradigm that they are critiquing, preferably to a level where they can clearly articulate the key propositions of evolutionary theory and offer a standard defense of them.

Richard Hoppe, at the Panda’s Thumb blog, drew my attention to a free online course on the subject of genetics and evolution. You can, as I have done, sign up for (and read about) the course at this link.

...

I particularly recommend that those among us who don’t have a strong biology background take this course. It is very important that we ID proponents make sure we have a robust grasp of what evolutionary theory is saying and why it says it, so that no one can say we haven’t given it a fair hearing.

Wouldn't it be nice if most IDiots followed Jonathan McLatchie's advice? In just a few months they could learn that modern evolution and genetics includes all sorts of things that Darwin never knew! Imagine what a relief it would be if they stopped referring to us all as "Darwinists" and started to understand that evolution is a fact.

Not holding my breath.

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Visiting the Grand Canyon

Last week we took a helicopter from Las Vegas to Hoover Dam and the Grand Canyon. Check out the photos on Ms. Sandwalk's blog: The Magic Canyon Ride.

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Online Training of Competent, Employable, Bioinformatics Professionals

I think that undergraduate education at most universities is done very badly. There are far too many courses that consist of professors giving standard lectures to large classes with evaluations focused on "memorize and regurgitate" exams. Most courses pay no heed to student-centered learning even though there has been sound pedagogical research showing that student participation leads to better learning. Most courses and programs provide no "value-added" component that takes advantage of being physically located in an enriched scholarly environment. Most courses do not teach critical thinking.

Given the horrible status of most university courses, it's not surprising that they can be replaced by online courses where the student never needs to set foot on a university campus to get the same quality of education. This is not an endorsement of online courses, it's a comment on the poor quality of campus-based courses.

David B. Searls is an "independent consultant" who published an article in PLOS Computational Biology: An Online Bioinformatics Curriculum.

Carnival of Evolution, Number #52: the Network Edition

This month's Carnival of Evolution is hosted by Sam Wise at SOS Presents%mdash;the Carnival of Evolution #53. Read it at: Carnival of Evolution, Number 52 — the Network Edition

Welcome to the 52nd edition of the Carnival of Evolution, hosted here at The Genealogical World of Phylogenetic Networks blog.

For those of you not familiar with the Carnival of Evolution, at the beginning of every month the Carnival provides a collection of some of the most interesting of the recent blog posts about biological evolution. The Carnival is hosted by a different blog every month: last month's Carnival can be found at The Stochastic Scientist blog; and next month's Carnival will be hosted by the Sorting Out Science blog at the beginning of November.

The theme for the presentations this month is, of course, phylogenetic networks. You can skip straight on to the blog posts if you are familiar with such networks.

There's some cool stuff this month, including a summary of the ENCODE/junk DNA fiasco.

The next Carnival of Evolution (September) will be hosted by Sorting out Science. If you want to volunteer to host others, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before. Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution.

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Reddit: We are the Encyclopedia of DNA Elements (ENCODE) Consortium.

There's been a lot of talk recently about the discussion on reddit concerning the ENCODE publicity fiasco.

Here's the forum ...

AskScience Special AMA: We are the Encyclopedia of DNA Elements (ENCODE) Consortium. Last week we published more than 30 papers and a giant collection of data on the function of the human genome. Ask us anything!

It's interesting to see how some of the consortium members are responding to criticism. My personal view is that none of them seem to be very knowledgeable about genome biology and the work that has been published over the past 40 years.

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Monday's Molecule #188

Last week's molecule was N-formylmethionyl-tRNA_f^Met [Monday's Molecule #188]. Only three people came close. The winner was Mikkel Rasmussen.

Name these molecules. One of them has a well-known common name that you have to include in your answer. The other one also has a common name but you don't have to find it. You have to give the complete formal names of each molecule. Do you know the significance of these two molecules?

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.)

Douglas Axe Explains Molecular Evolution

There are several dozen scientists and graduate students in my department studying various aspects of protein evolution, structure, and folding. They've published dozens of papers but, apparently, they never realized that what they're studying is impossible. Douglas Axe, a leading Intelligent Design Creationist, sets them straight.

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[Hat Tip: Evolution News & Views: Axe: Vive la Différence]

Where Am I?

My granddaughter, Zoë, took a picture of me getting a hot dog. Can you guess where I am?

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Where Am I?

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Ewan Birney: Genomics' Big Talker

My copy of Science arrived in the mail last week and I wasn't surprised to see the article by Elizabeth Pennisi on ENCODE Project Writes Eulogy for Junk DNA. Pennisi has long been skeptical about junk DNA. She advocates the position that what makes us human is hidden in the "dark matter" of the genome. She has never lost an opportunity to promote those scientists who claim to have discovered function in junk DNA so it was natural for her to fall hook-line-and-sinker for the recent ENCODE publicity campaign [see Science Writes Eulogy for Junk DNA].

What did surprise me was a three-page spread on Ewan Birney: Genomics' Big Talker, written by Elizabeth Pennisi. This is extraordinary. I don't know of another example where a leading science journal has promoted a young scientist in this manner. Of course, it's doubly extraordinary because, in this case, Science is promoting a scientist who just made some serious mistakes interpreting his own data! The man who is so prominently featured in the Sept. 7, 2012 issue of Science magazine is coming under serious criticism for letting publicity rule his science. He has almost single-handedly¹ damaged the reputation of 400 scientists in the ENCODE Consortium and he did it, in part, because he was not knowledgeable about his own field of expertise! [see ENCODE Leader Says that 80% of Our Genome Is Functional and The ENCODE Data Dump and the Responsibility of Scientists]

UPDATE:A reader has reminded me that Science published two pages (online) on Felicia Wolfe-Simon at the time of the arsenic affair. Hmmmm ... is this the beginning of a pattern?

Viva Las Vegas!

Ms. Sandwalk and I are in Las Vegas with our friends. Posting may be a bit light for the next few days.

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Where Am I #2?

Here's another clue. Where am I today? (Click to embiggen.)

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Where Am I #1?

Can you guess where I am today? (Click to embiggen.)

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Monday's Molecule #187

Last week's molecule was the core nucleosome complex [Monday's Molecule #186] and nobody who was eligible for a win got it! That's quite shocking. Here's an easy one for today.

Name this molecule, including the name of the "R" group. You'll have to guess but there's really only one possibility in living cells. Don't forget, I need the full name of the most likely molecule given the partial structure that you see.

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.)

On the Reasoning Ability of Most Creationists

Here's an excellent example of the difference between a scientific way of knowing and the other kind. Follow this link to the full story. I'm told that reddit user jerfoo wrote the story and took the photos.

I've often admired the jigsaw puzzle analogy to understanding the evidence for evolution. It's as though we have a picture of evolution that's missing but a few pieces yet the creationists steadfastly refuse to see the image and insist that we concentrate on the missing pieces.

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[Hat Tip: Bad Astronomy]

Boudry vs Plantinga

Alvin Plantinga is a famous philosopher who is widely respected and seems to be able to publish in all the right places. He is a theist (Calvinist) and for a long time he was at the University of Notre Dame in Indiana (USA). Since his retirement from there, he has taken a position at Calvin College.

Plantinga has long advocated the accommodationist position from the perspective of Christian apologetics. I bought his latest book, Where the Conflict Really Lies, because I'm interested in the conflict between science and religion.

I've been struggling for weeks with how to explain Plantinga's case. My problem was that I found the whole book quite ridiculous and it seemed to me that Plantina's idea of logic and rationality was much closer to kindergarten philosophy than to something one might expect from a distinguished scholar. I hesitated to say that out loud because it sounds very condescending coming from a scientist.

I had to be missing something. There must be some sophisticated philosophy in there somewhere and I just wasn't getting it. I couldn't post.

Are All IDiots Irony Deficient?

As I'm sure you can imagine, the Intelligent Design Creationists are delighted with the ENCODE publicity. This is a case where some expert scientists support one of their pet beliefs; namely, that there's no such thing as junk DNA. The IDiots tend not to talk about other expert evolutionary biologists who disagree with them—those experts are biased Darwinists or are part of a vast conspiracy to mislead the public.

You might think that distinguishing between these two types of expert scientists would be a real challenge and you would be right. Let's watch how David Klinghoffer manoeuvres through this logical minefield at: ENCODE Results Separate Science Advocates from Propagandists. He begins with ....

"I must say," observes an email correspondent of ours, who is also a biologist, "I'm getting a kick out of watching evolutionary biologists attack molecular biologists for 'hyping' the ENCODE results."

True, and equally enjoyable -- in the sense of confirming something you strongly suspected already -- is seeing the way the ENCODE news has drawn a bright line between voices in the science world that care about science and those that are more focussed on the politics of science, even as they profess otherwise.

Apocalypse in Ottawa!

The end is approaching. See you in Ottawa on November 30th!

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Athena Andreadis Writes for Scientific American: Junk DNA, Junky PR

Quite a few science journalists have clued in to the fact that they were massively conned by the ENCODE publicity machine. Turns out that the death of junk DNA was greatly exaggerated.

Here's what Athena Andreadis has to say on the Scientific American website: Junk DNA, Junky PR. Athena is a professor in the Department of Cell and Developmental Biology at the University of Massachusetts Medical School.

Chris DiCarlo on the Sandwalk

My friend Chris DiCarlo recently visited Down House with his family. Here's a photo of him on the Sandwalk. Chris is a philosopher and it looks like he's trying very hard to strike a philosophical pose.

In fact, he just can't figure out which way to go to get out of there!

Chris joins a distinguished list of people whose visit to the Sandwalk has been recorded here.

Larry Moran
PZ Myers
John Wilkins
Ryan Gregory
The God Delusion
Cody
John Hawks
Michael Barton
Seanna Watson
Steve Watson
Michael Richards
Jeffrey Shallit
Chris DiCarlo

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Priceless Idiot

UPDATE: The woman in the picture, Kim Stafford, was making fun of the Tea Party with this sign [Internet FAIL: The truth about that Tea Party sorority girl you saw on Facebook.

This photo is everywhere on the internet but it's so perfect that I just have to post it even though spelling is not one of my own strengths.

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Stephen Jay Gould and Sydney Brenner Agree on Junk DNA

It's no secret that I'm a big fan of Stephen Jay Gould. I'm also a big fan of Sydney Brenner. Here's Gould writing in The Structure of Evolutionary Theory (pages 1269-1270). This is long and complicated but if you want to understand junk DNA and why it conflicts with Darwinism, then you've got to make the effort. I especially like the idea that Gould understands the difference between junk DNA, which can't be explained by any adaptive mechanism, and "selfish DNA," which isn't junk and has a Darwinian explanation. Many people don't get this.

Gould and Brenner are talking about repetitive DNA. This includes highly repetitive sequences of simple repeats and moderately repetitive sequences that include the transposons.

Gould on Darwinism and Nonadaptive Change

Some people have trouble understanding the difference between Darwinism and modern evolutionary theory.

In spite of the fact that he has been dead for a decade, Stephen Jay Gould remains the authority on challenges to classical Darwinism and the hardened version of the Modern Synthesis (sometimes referred to as Neo-Darwinism).

If you really want to understand this issue then you have to read The Structure of Evolutionary Theory. One of my criticism of those who would overthrow modern evolutionary theory is that they are often completely ignorant of the work done by Gould and his allies and they end up attacking a strawman version of modern evolutionary theory.

Gould described the essential features of Darwinism in many of his writings. The most important feature is an emphasis on natural selection as the mechanism of evolution. In much of his work Gould emphasizes the roles of contingency, constraints, and non-gradualistic evolution as extensions of Darwinism. However, he doesn't forget direct challenges to Darwinism in the form of nonadaptive mechanisms that don't, under any circumstances, fit within the Darwinian framework.

These are complicated issues and that partially explains why so many people have not been able to follow Gould's reasoning. He doesn't help by using a writing style that requires your full attention. The advantage of that style is that he doesn't dumb down the subject and he covers all the exceptions and qualifications.

Here's Gould explaining why some features could arise as one form of adaptation then shift to serve another adaptive role (functional shift) (page 1246-1247). These features are called exaptations since they did not originally arise as adaptation to their present role. (Think of a defective transposon that becomes a regulatory sequence.)

Nevertheless, also emphasized throughout, ... the basic concept of exaptation remains consistent with orthodox Darwinism (while expanding its purview and adding some structural clarification and sophistication) for an obvious reason: the principle of quirky functional shift does not challenge the control of evolution by natural selection as an adaptational process. Unpredictable shift of function may establish the ground of contingency, and may imply a rule for structural constraints upon phyletic pathways. But this principle does not undermine the functionalist basics of evolutionary change because features so effected remain adaptive throughout: they originate from one function (presumably by natural selection), and then undergo quirky shift to a different utility.

However, the principle of functional shift, ... implies a disarmingly simple and logical extension that does challenge the role of Darwinian mechanics and functionalist control over evolutionary change. Ironically, the very simplicity of the argument has often led to its dismissal as too obvious to hold any theoretical importance—a "feeling" that I shall try to refute in this section, and whose disproof represents an important step in the central logic of this book.

The deeper challenge posed to orthodox Darwinism by the principle of functional shift flows from the implication that, if current utility does not reveal the reasons for hisorical origin, then these initial reasons need not be adaptational or functional at all—for features with current adoptive status may have originated from nonadaptive reasons in an ancestral form. In other words, and in the terminology of table 11-1, when certain aptations rack rank as exaptations rather than adaptations, the coopted source will be identifiable as an ancestral structure with either adaptive origins (for a different function) or nonadaptive origins (for no function at all). ...

The general conclusion may be stated in a simple manner, but I believe that the resulting implications for evolutionary theory are both profound and curiously underappreciated: If many features that operate as adaptations under present regimes of natural selection were exapted from ancestral features with nonadaptive origins—and were not built as adaptations for their current use (or exapted from ancestral features with adaptive origins for different functions)—then we cannot explain all the pathways of evolutionary change under functionalist mechanics of the theory of natural selection. Instead, we must allow that many important (and currently adaptive) traits originated for nonadaptive reasons that cannot be attributed to the direct action of natural selection at all and, moreover, cannot be inferred from the exaptive utility of the trait in living species. Because the subject of evolutionary biology must engage many critical questions about the origins of features, and cannot be confined to the study of current utilities and selective regimes, nonadaptationist themes therefore assume an important role in a full account of life's history and the mechanisms of evolutionary change.

In other words, lots of things can't be explained by Darwinism even if they look adaptive today.

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Monday's Molecule #186

Last week's molecules were the four common nuleosides in DNA [Monday's Molecule #185]. The winner was Matt Talarico.

This week I'm asking you to identify a complex structure made up of eight different components (top) plus one other (bottom). Name the structure making sure to be as specific as possible, Name the none components.

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.)

Read What Mike White Has to Say About ENCODE and Junk DNA

One of the good things to come out of this ENCODE/junk DNA fiasco is that I've discovered a number of excellent scientists who aren't afraid to speak out on behalf of science. One of them is Mike White, a systems biologist at the Center for Genome Sciences and Systems Biology, Washington Univ. School of Medicine, St. Louis (USA). He blogs at The Finch & Pea.

Mike published an impressive article on the Huffington Post a few days ago. This is a must-read for anyone interested in the controversy over junk DNA: A Genome-Sized Media Failure. Here's part of what he says ...

If you read anything that emerged from the ENCODE media blitz, you were probably told some version of the "junk DNA is debunked" story. It goes like this: When scientists realized that classical, protein-encoding genes make up less than 2% of the human genome, they simply assumed, in a fit of hubris, that the rest of our DNA was useless junk. (You might have also heard this from your high school or college teacher. Your teacher was wrong.) Along came the ENCODE consortium, which found that, far from being useless, junk DNA is packed with functionality. And so everything scientists thought they knew about the genome was wrong, wrong wrong.

The Washington Post headline read, "'Junk DNA' concept debunked by new analysis of human genome." The New York Times wrote that "The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as 'junk' but that turn out to play critical roles in controlling how cells, organs and other tissues behave." Influenced by misleading press releases and statements by scientists, story after story suggested that debunking junk DNA was the main result of the ENCODE studies. These stories failed us all in three major ways: they distorted the science done before ENCODE, they obscured the real significance of the ENCODE project, and most crucially, they mislead the public on how science really works.

What you should really know about the concept of junk DNA is that, first, it was not based on what scientists didn't know, but rather on what they did know about the genome; and second, that concept has held up quite well, even in light of the ENCODE results.

Way to go, Mike!

In the past week, lot's of scientists have demonstrated that they don't know what they're talking about when they make statements about junk DNA. I don't expect any of those scientists to apologize for misleading the public. After all, their statements were born of ignorance and that same ignorance prevents them from learning the truth, even now.

However, I do expect lots of science journalists to write follow-up articles correcting the misinformation that they have propagated. That's their job.

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How Do Intelligent Design Creationists Define "Creationism"?

David Klinghoffer showed up in the comments on James Shapiro Claims Credit for Predicting That Junk DNA Is Actually Part of a "highly sophisticated information storage organelle" to ask about creationism.

He didn't like the fact that I define "creationism" as belief in a creator and anyone who believes in a creator is a creationist. I identified several flavors of creationism including Young Earth Creationism, Intelligent Design Creationism, and Theistic Evolution Creationism. This is exactly the same sort of definition used by many people and it's the one described in the Wikipedia article on creationism. (It has even more flavors.)

David Klinghoffer didn't like that so he decided to make an issue of it by posting on Evolution News & Views: What Is a "Creationist"? Let's take a look at what he says in order to learn a little more about the creationist mindset.

Does the Central Dogma Still Stand?

Lots of people don't understand the Central Dogma of Molecular Biology and that's probably why there are so many articles announcing its death. The article and book by James Shapiro is just one example [Revisiting the Central Dogma in the 21st Century].

The correct version of the Central Dogma of Molecular Biology is .... [see Basic Concepts: The Central Dogma of Molecular Biology]

... once (sequential) information has passed into protein it cannot get out again (F.H.C. Crick, 1958)

The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. (F.H.C. Crick, 1970)

Eugene Koonin has an article in Biology Direct entitled Does the central dogma still stand (Koonin, 2012).

Groupthink Science And That 'Junk DNA'

The IDiots (e.g. Tom Bethell) over at Evolution News & Views are gloating about a comment made on The Wall Street Journal website [Why ENCODE Is a Significant Defeat for Darwinism].

The WSJ article is: Groupthink Science And That 'Junk DNA'.

Anyone with even the slightest understanding of the evolutionary process knows that evolution is too relentlessly efficient to have allowed most, or even large sections, of DNA to be "junk" ("'Junk DNA' Theory Debunked," U.S. News, Sept. 6). Any intelligent scientist would have simply said, "I don't know."

Unfortunately, this says something important about the quality of contemporary Ph.Ds. Groupthink has become pervasive in part because of how research is now financed: grants. The disillusioning sociological aspects of scientific research that Thomas Kuhn identified more than four decades ago have become more pronounced, not less.

Tom Shillock

Portland, Ore.

This is exactly backwards, in my opinion. The real problem is that many scientists think, incorrectly, that natural selection would have removed all junk DNA so they are looking for reasons why it isn't junk. If they can't find evidence then they just make up a story or re-define the word "function." They don't have even the slightest understanding of evolution, just like Tom Shillock.

UPDATE: Shapiro and Sternberg Anticipated the Fall of Junk DNA.

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James Shapiro Claims Credit for Predicting That Junk DNA Is Actually Part of a "highly sophisticated information storage organelle"

Do you remember James Shaprio? He's the University of Chicago scientist who claims to have discovered a new theory of evolution in his book evolution: A View from the 21st Century [see my review in NCSE Reports]. The book criticizes the old hardened version of the Modern Synthesis and never mentions things like random genetic drift or Nearly-Neutral Theory. It's difficult to imagine how someone could criticize evolutionary theory without understanding population genetics but he managed to pull it off.

You might also recall that he's the scientist who criticized the Central Dogma of Molecular Biology when he clearly didn't understand it [Revisiting the Central Dogma in the 21st Century]. I was shocked to learn that he had published a paper with the title "Revisiting the Central Dogma in the 21st Century" without ever bothering to read the literature to find out how Francis Crick actually defined the Central Dogma. (In fact, Shapiro misrepresented Crick's view.) It goes to show you how silly you look when you criticize something you don't understand.

ENCODE/Junk DNA Fiasco: The IDiots Don't Like Me

Casey Luskin has devoted an entire post to discussing my views on junk DNA. I'm flattered. Read it at: What an Evolution Advocate's Response to the ENCODE Project Tells Us about the Evolution Debate.

Let's look at how the IDiots are responding to this publicity fiasco. Casey Luskin begins with ...

University of Toronto biochemistry professor Larry Moran is not happy with the results of the ENCODE project, which report evidence of "biochemical functions for 80% of the genome." Other evolution-defenders are trying to dismiss this paper as mere "hype".

Yes that's right -- we're supposed to ignore the intentionally unambiguous abstract of an 18-page Nature paper, the lead out of 30 other simultaneous papers from this project, co-authored by literally hundreds of leading scientists worldwide, because it's "hype." (Read the last two or so pages of the main Nature paper to see the uncommonly long list of international scientists who were involved with this project, and co-authored this paper.) Larry Moran and other vocal Internet evolution-activists are welcome to disagree and protest these conclusions, but it's clear that the consensus of molecular biologists -- people who actually study how the genome works -- now believe that the idea of "junk DNA" is essentially wrong.

ENCODE/Junk DNA Fiasco: John Timmer Gets It Right!

John Timmer is the science editor at Ars Technica. Yesterday he published the best analysis of the ENCODE/junk DNA fiasco that any science writer has published so far [Most of what you read was wrong: how press releases rewrote scientific history].

How did he manage to pull this off? It's not much of a secret. He knew what he was writing about and that gives him an unfair advantage over most other science journalists.

Let me show you what I mean. Here's John Timmer's profile on the Ars Technica website.

John is Ars Technica's science editor. He has a Bachelor of Arts in Biochemistry from Columbia University, and a Ph.D. in Molecular and Cell Biology from the University of California, Berkeley. John has done over a decade's worth of research in genetics and developmental biology at places like Cornell Medical College and the Memorial Sloan-Kettering Cancer Center. He's been a speaker at the annual meeting of the National Association of Science Writers and the Science Online meetings, and he's one of the organizers of the Science Online NYC discussion series. In addition to being Ars' science content wrangler, John still teaches at Cornell and does freelance writing, editing, and programming.

See what I mean? He has a degree in biochemistry and another one in molecular biology. People like that shouldn't be allowed to write about the ENCODE results because they might embarrass the scientists.

Monday's Molecule #185

Last week's molecule was warfarin, a rat poison with another role [Monday's Molecule #184]. The winner was Matt McFarlane.

This week we're in the middle of the ENCODE/junk DNA controversy. A dispute that reveals a serious lack of knowledge of fundamental concepts in biochemistry. I'm going to go back to basics today and ask you to name these four molecules. Be careful, I'm going to insist that you use the correct unambiguous names. Name them in order from upper left to upper right to lower left then lower right.

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.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.

Comments are now open.

UPDATE: The molecules are deoxyadenosine, deoxyguanosine, deoxycytidine, deoxythymidine. This week's winner is Matt Talarico. Matt should contact me by email.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia
July 23: Raul A. Félix de Sousa
July 30: Bill Chaney and Raul A. Félix de Sousa
Aug. 7: Raul A. Félix de Sousa
Aug. 13: Matt McFarlane
Aug. 20: Stephen Spiro
Aug. 27: Raul A. Félix de Sousa
Sept. 3: Matt McFarlane
Sept. 10: Matt Talarico

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The Story of You: Encode and the human genome – video

This is really quite incredible. I don't think I've seen anything like it in my lifetime.

Two private for-profit companies, illumina and Nature, team up to promote the ENCODE results. They even suck in hire Tim Minchin to narrate it.

The average person watching this video will think that ENCODE is the best thing since sliced bread. The hype is astounding, and totally unjustified considering that we haven't learned anything of fundamental importance from the ENCODE project.

Is this what science is going to be like in the future—the person with the biggest advertising budget wins the scientific debate?

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Science Writes Eulogy for Junk DNA

Elizabeth Pennisi is a science writer for Science, the premiere American science journal. She's been writing about "dark matter" for years focusing on how little we know about most of the human genome and ignoring all of the data that says it's mostly junk [see SCIENCE Questions: Why Do Humans Have So Few Genes? ].

It doesn't take much imagination to guess what Elizabeth Pennisi is going to write when she heard about the new ENCODE Data. Yep, you guessed it. She says that the ENCODE Project Writes Eulogy for Junk DNA.

THEME

Genomes & Junk DNALet's look at the opening paragraph in her "eulogy."

When researchers first sequenced the human genome, they were astonished by how few traditional genes encoding proteins were scattered along those 3 billion DNA bases. Instead of the expected 100,000 or more genes, the initial analyses found about 35,000 and that number has since been whittled down to about 21,000. In between were megabases of “junk,” or so it seemed.