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Wednesday, September 30, 2009

The College Student’s Back to School Guide to Intelligent Design Creationism

The Evolution News website is run by the Discovery Institute in Seattle, Washington USA. In spite of the title, their goal is not to inform you about evolution. Instead, their goal is to promote anti-evolution thinking and Intelligent Design Creationism.

I'm in the middle of teaching a course about evolution and creationism so the latest posting on their website caught my eye. I urge my students to read the latest posting: Introducing The College Student’s Back to School Guide to Intelligent Design. They have lots of helpful hints about how to deal with evil Professors who oppose intelligent design. Not only that, they have a book for sale called "The College Student’s Back to School Guide to Intelligent Design." It's sort of like "Evolution for Dummies."

The main part of the book is about dealing with your Professor's "misinformed" opinions about Intelligent Design Creationism. Here's a list of nine such opinions. I better read up on how students are going to refute these arguments—at least the ones that aren't farcical or obvious strawmen.

  1. Intelligent Design Is Not Science
  2. Intelligent Design Rejects All of Evolutionary Biology
  3. Intelligent Design Has Been Banned From Public Schools by the Federal Courts
  4. Intelligent Design Is Just Politics
  5. Intelligent Design Is a Science Stopper
  6. Intelligent Design Is “Creationism” and Based on Religion
  7. Intelligent Design Is Religiously Motivated
  8. Intelligent Design Proponents Don’t Conduct or Publish Scientific
  9. Intelligent Design Has Been Refuted by the Overwhelming Evidence for Neo-Darwinian Evolution
Hmmm ... on second thought, I hope my students don't see this. It looks like a pretty devastating attack on everything I've been saying in class. I'm shaking in my boots.

Tuesday, September 29, 2009

Monday's Molecule #138: Winner

The purple molecule is cyclin bound to phospho-cyclin-dependent kinase 2 (CDK2) (yellow) and kinase-associated phosphatase (KAP) (blue). The Nobel Laureate is Tim Hunt.

There were lots of correct answers from Asia and Europe this time around but also a few from North America.

This week's winner is Joshua Johnson of Victoria University in Australia. The posting time was convenient for Australians since his email message was sent at 2 o'clock in the afternoon. There wasn't an undergraduate winner this week so I'll carry over the undergraduate prize for next week's molecule.

This is the earliest posting of a Monday's Molecule. It should make the contest open to a whole new category of Sandwalk readers, especially those in Europe who will see it long before the readers in North America are awake.

It will also work for Asian readers and a few North and South Americans who are up very late at night. (Note to the latter group: get a life! )

The molecule is a compex of three different proteins. One of them—the yellow one—has already been featured as a Monday's Molecule last April. This time I want you to identify the purple molecule. It was first identified and characterized in the organism shown below then subsequently found in lots of other species.

The Nobel Laureate from last April shared the prize with the person who discovered today's molecule. Name that Nobel Laureate.

The first person to identify the molecule and name the Nobel Laureate wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only three ineligible candidates for this week's reward: Philip Johnson of the University of Toronto, Ben Morgan of the University of North Carolina at Chapel Hill and Frank Schmidt of the University of Missouri.

Frank has agreed to donate his free lunch to a deserving undergraduate. Consequently, I have an extra free lunch for a deserving undergraduate so I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.


Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours. Comments are now open.

You Can't Go Home Again

This is a resurrected version of a steroid hormone receptor. It was derived from the modern glucocorticoid receptor (GR) gene by mutating various codons to make them like the predicted ancestral gene. When all of the mutations were introduced, the protein was expressed and its structure was determined.

Glucocorticoid receptor specifically binds cortisol but the ancient protein binds other steroids as well as cortisol. This is pretty much what you might expect. Various gene duplication events lead to a family of proteins and each family member evolved to recognize a single ligand. The fact that you can reconstruct the presumed ancestral protein and show that it bound to multiple ligands is pretty amazing. The work comes out of Joseph Thornton's lab (Ortlund et al. 2007).

Altogether there were about 60 amino acid substitutions along the lineage leading from the ancestral broad-specificity receptor to the cortisol-specific receptor but only two of these turned out to be ones that shifted the specificity. Most of the rest probably had little effect of the function or specificity of the protein. This is the expected result. Most amino acid substitutions during evolution are neutral.

If there are really only two key amino acid substitutions that change specificity then it should be possible to convert a modern glucocorticoid receptor into one that recognizes a broad range of hormones by merely changing two amino acids. In other words, you could revert to the ancient form by reversing evolution and only a few mutations should do it.

Can you go back in time this easily? Apparently not, according to a recent paper from the same lab (Bridgham et al. 2009). Carl Zimmer is on top of this story in a article he published in yesterday's issue of the New York Times "Can Evolution Run in Reverse? A Study Says It’s a One-Way Street."

There's no conceptual advances in this paper, at least for those scientists who have a proper understanding of evolution. Some of the neutral changes along the pathway prepared the way for additional changes that were not possible in the ancestor protein. In other words, strictly neutral changes can add up to significant differences in structural stability making it possible for some adaptive change to occur that could not have otherwise occurred.

This isn't a breakthrough, it's an excellent study that confirms what was predicted on the basis of what we know about evolution. Here's how the authors describe their result in the abstract ...
Using ancestral gene reconstruction, protein engineering and X-ray crystallography, we demonstrate that five subsequent ‘restrictive’ mutations, which optimized the new specificity of the glucocorticoid receptor, also destabilized elements of the protein structure that were required to support the ancestral conformation. Unless these ratchet-like epistatic substitutions are restored to their ancestral states, reversing the key functionswitching mutations yields a non-functional protein. Reversing the restrictive substitutions first, however, does nothing to enhance the ancestral function. Our findings indicate that even if selection for the ancestral function were imposed, direct reversal would be extremely unlikely, suggesting an important role for historical contingency in protein evolution.
Because of "historical contingency" you can't reverse evolution. The path that lineages follow as they evolve is determined, in part, by chance and accident and not by natural selection alone.

You can't go home again.

Bridgham, J.T., Ortlund, E.A., and Thornton, J.W. (2009) An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461:515-519. [PDF]

Ortlund, E.A., Bridgham, J.T., Redinbo, M.R., and Thornton, J.W. (2007) Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317:1544-1548. [PDF]

Monday, September 28, 2009

Naked Adaptationism

Most other mammals think that humans are excessively ugly. They probably see us in the same way we see naked mole rats. We (mostly) have no hair.

What happened to our hair? There are many explanations for human hairlessness but they all share one common characteristic—they are adaptationist just-so stories.1

If you're looking for the best example of an adaptationist then you need look no further than Elaine Morgan, author of the Aquatic Ape speculation [see Elaine Morgan and Aquatic Apes]. She has written an article for last week's issue of New Scientist: Why are we the naked ape?. It won't come as a big surprise to learn that she dismisses all of the speculations about the evolution of hairlessness, except one: we lost our hair because our ancestors lived in the water.

That's not the point I want to make. Here's what Elaine Morgan says in the first few sentences.
RIGHT from the start of modern evolutionary science, why humans are hairless has been controversial. "No one supposes," wrote Charles Darwin in The Descent of Man, "that the nakedness of the skin is any direct advantage to man: his body, therefore, cannot have been divested of hair through natural selection."

If not natural selection, then what?
The idea that our lack of hair might just be an accident is completely foreign to someone like Elaine Morgan. She's probably being deadly serious when she asks the question, "If not natural selection, then what?" For adaptationists, natural selection is the only game in town and no other sorts of explanation are possible.

If it's genetic and visible, then it must be an adaptation. If one just-so story is refuted then make up another one to take it's place. That's what the article is all about. One by one, she dismisses sexual selection, overheating on the savannah, neoteny, avoiding parasites, evaporating sweat, leaving only aquatic ape speculation that hasn't been refuted, or so she claims.

One of the problems with the adaptationist program was described by Gould and Lewontin (1979), "If one adaptationist argument fails, assume that another must exist ...." Why not start thinking about other, non-adaptationist explanations?

Why is that so hard?

1. The one exception is the idea that our nakedness is an epiphenomenon resulting from neotony.

Gould, S.J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc. R. Soc. Lond. B 205:581-598.

Science Education by Press Release

Futurity was officially launched on September 15th.
As an online research magazine, Futurity highlights the latest discoveries from leading universities in the United States and Canada.

Who is Futurity?

Duke University, Stanford University, and the University of Rochester lead a consortium of participating universities (see list below) that manages and funds the project. All partners are members of the Association of American Universities (AAU), a nonprofit organization of leading public and private research universities.

Futurity aggregates the very best research news. The content is produced by the partner universities, and submitted to Futurity’s editor, Jenny Leonard, ( for consideration. The site, which is hosted at the University of Rochester, covers news in the environment, health, science, society, and other areas.
We're talking about press releases. Most of the information comes from press releases written by the "leading" universities. Does anyone see a problem with that?

Carl Zimmer does. He rightly points out that universities and reasearch hospitals have a vested interest in promoting the work done at their institutions [Apocalypse Via Press Release].
What Futurity does do, however, is allow universities and research institutions to go straight to the reader. Originally, press information officers at these places wrote press releases, which, as the name implies, were things intended to get the attention of the press in the hopes that they’d cover something you’re doing. Futurity calls what it publishes “news,” but it’s still being written by employees of the organizations that are the subject of that news.

I have great respect for some public information officers; the stuff they write is, in some cases, wonderfully clear and informative. There’s good information to be had on Futurity. But I always treat press releases as a starting point. I do not, for example, assume that a piece of research is actually important just because a press release says it is. Imagine a press release with the headline, “Minor study published that is really not all it claims to be.” Such things just don’t exist.
This makes a lot of sense. I really like the fact that Carl is speaking out against the excesses of bad journalism and the gross misunderstandings of science education. He's exactly right about university press releases. They are entirely one-sided—don't look for balance from a PR department.

Not only that, most press releases are horrible. I think it's fair to say that many of the worst examples of science journalism come from university press offices. That's not to say that they're all bad. I've seen some pretty good examples from my own university and from some others, but they are the exceptions, not the rule.

How soon we forget. Remember The Darwinius Affair?

You can't blame science journalists for getting their science wrong if they get it straight from the horse's mouth, right? Wrong! Read Carl Zimmer and learn how real science journalist should behave. They should investigate a story to see if the hype is justified.

Investigative science journalism is the subject of yesterday's posting by Bora Zivkovic over on A Blog Around the Clock. He points out that most science journalists do not investigate in spite of the fact that this is often what they claim to be doing. This is what distinguishes the average science journalist from the good ones, like Carl Zimmer.

That much we know. Where Bora and I part company is when it comes to press releases. Here's what Bora says ...
While we have all screamed every now and then at some blatantly bad press releases (especially the titles imposed by the editors), there has been generally a steady, gradual improvement in their quality over the years. One of the possible explanations for this is that scientists that fall out of the pipeline as there are now so many PhDs and so few academic jobs, have started replacing English majors and j-school majors in these positions. More and more institutions now have science-trained press officers who actually understand what they are writing about. Thus, there is less hype yet more and better explanation of the results of scientific investigation. Of course, they tend to be excellent writers as well, a talent that comes with love and practice and does not necessitate a degree in English or Communications.
That's not been my experience. Just look at the main page on the Futurity website for examples of bad science journalism. As I write this, the top story is ....
Wonder drug may treat cancer, addiction

UC IRVINE—A drug in development to treat cancer could have the added benefit of helping prevent relapse in people trying to overcome cocaine addiction.

In mice conditioned to cocaine, drug-seeking activity was inhibited faster and to a greater extent with sodium butyrate than without it, neuroscientists at the University of California-Irvine say.

"Our results are exciting because sodium butyrate taps into fundamental molecular mechanisms, providing a novel approach to understanding and treating drug addiction," says the study’s lead author Marcelo Wood, assistant professor of neurobiology and behavior....
That's sounds just like the kind of story that could come from the PR office of a political party or the head office of a major pharmaceutical company.

Yom Kippur

My lunch buddy isn't here today. At first I was worried, maybe he's sick or been in a car accident? Then I realized that it's Yom Kippur, the most sacred of the Jewish holidays.

This is the Day of Atonement, for Jews. It's a day characterized by fasting, prayer, and seeking forgiveness. This is the one day of the year when attending synagogue is practically mandatory—even for secular Jews.

Who are "secular" Jews, you might ask? They're people who belong to the culture of Judaism but who don't believe in God. That can be a substantial percentage of Jews in some countries. Even in Israel, about 30% of the citizens are atheists (

I'm pretty sure this phenomenon (secular "religion") is quite common. I know lots of secular Roman Catholics and secular Anglicans.

Happy Yom Kippur1 to all Jews, secular and otherwise.

1. It seems a bit strange to be wishing happy Yom Kippur on a day devoted to atonement but I'm told this is appropriate for an atheist or other goya.

A Young Scientist in Italy

Like John Wilkins, I too have visited Italy.

Whereas John is interested in spandrels, I was more interested in the native wildlife.

John is there now [An Adaptationist in Piazza San Marco], I was there in prehistoric times.

John is old and wise, I was young and naive. (I didn't even know about spandrels back then.)

I had a Michelin guide, I bet John doesn't have a Michelin guide!

An Adaptationist in Piazza San Marco

John Wilkins of Evolving Thoughts is currently in Venice, Italy. He has just visited the Basilica San Marco (St. Mark's Basilica) according to What I am doing on my holidays….

This visit is significant since the Spandrels of San Marco are famous in evolutionary biology. They are part of the attack on adaptationism launched in 1979 by Gould and Lewontin. This is a paper that every student of evolution should read. Here's an online version: The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme.

John has been struggling with adaptationism for almost fifteen years. When he first began studying evolutionary biology he, like many others, was unaware of the importance of random genetic drift and other anti-adaptationist perspectives. He certainly didn't know that random genetic drift is by far the dominant mechanism of evolution in terms of frequency of allele fixation. Over time John has developed an unusual perspective on adaptionism—one that I don't really understand.

Here's how he explains it in his latest posting ...
This is interesting, I think, in the context of Gould’s and Lewontin’s paper. It shows that claims of things being adaptive or not depend crucially on what one counts as the “task” of a structure. Since I think that everything is subjected to selection pressure at all times (sometimes not enough to overcome the noise of statistical properties), counting what is, and what isn’t, adaptive is a bit of a personal call, in the absence of access to the historical processes of particular traits. I am becoming more of an adaptationist these days.
The idea that many alleles might be slightly beneficial or slightly detrimental isn't very controversial. But that's not what John is saying. As I understand him, he's saying there can be no such thing as a truly neutral allele. He seems to be saying that anyone who believes otherwise is making a "personal call." A personal call that he believes is wrong since he thinks (i.e. his personal call) that everything is subject to natural selection.

He's also making a somewhat trivial point that doesn't contribute to the debate, as far as I'm concerned. Many alleles that are slightly beneficial are lost due to random genetic drift and many alleles that are slightly deleterious are fixed by random genetic drift. To me, that says that adaptationism can't explain all of evolutionary biology. To call yourself an adaptationist while knowing that slightly deleterious alleles can be fixed by random genetic drift seems somewhat unsatisfying.

John has a paper in the latest issue of Biology and Philosophy, an issue devoted to Adaptationism. It's not a very enlightening issue, from my perspective. The main problem with adaptationism isn't that it can't explain adaptation and it isn't that some just-so stories are wrong. The main problem is that adaptationists don't even consider any other alternatives to fixation by natural selection. Everything, especially everything with a visible phenotype, is automatically assumed to be adaptive and the arguments proceed from there.

One of the papers I liked was Seven Types of Adaptationism by Tim Lewens (Lewens, 2009). The seven types are:
A Empirical adaptationisms

1. Pan-selectionism–natural selection is the most significant of the evolutionary forces that act on populations.
2. Good-designism–evolutionary processes tend to result in organisms with suites of well-designed traits. Most lineages are highly evolvable.
3. Gradualism–adaptation is always the result of selection acting on gradual

B Methodological Adaptationisms

4. Weak heuristic adaptationism–those traits that are adaptations are likely to be correctly recognised as such only if we begin by assuming that all traits are adaptations.
5. Strong heuristic adaptationism–only by beginning to think of traits as adaptations can we uncover their true status, whether they are adaptations or not.

C Disciplinary Adaptationism

6. Explanatory adaptationism–an evolutionary biologist’s proper business is the study of adaptations.

D Epistemological Adaptationism

7. Epistemological optimism–investigators have access to the data that reliably discriminate between conflicting evolutionary hypotheses.
There are problems with all seven forms of adaptationism but the nice thing about Lewens' paper is that he effectively refutes #4, #5, and #7. In the case of methodological adaptationism it's just not true that the default assumption has to be adaptation. Evolutionary biology will be just as productive in the long run if drift is the default assumption and adaptation has to be proven.

In explanatory adaptationism, the assumption is that all of the interesting parts of evolution are adaptations and fixation of alleles by random genetic drift is so boring that it might as well not even be evolution. This is the stance taken by many adaptationists, like Richard Dawkins. As you might imagine, it doesn't take much effort to refute that kind of argument. One's personal opinion about what's interesting and what's not interesting should not play a role in determining how everyone else should go about studying evolution.

Gould, S.J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc. R. Soc. Lond. B 205:581-598.

Lewens, T. (2009) Seven types of adaptionism. Biol. Philos. 24:161–182. [doi: 10.1007/s10539-008-9145-7]

Monday's Molecule #138

This is the earliest posting of a Monday's Molecule. It should make the contest open to a whole new category of Sandwalk readers, especially those in Europe who will see it long before the readers in North America are awake.

It will also work for Asian readers and a few North and South Americans who are up very late at night. (Note to the latter group: get a life! )

The molecule is a compex of three different proteins. One of them—the yellow one—has already been featured as a Monday's Molecule last April. This time I want you to identify the purple molecule. It was first identified and characterized in the organism shown below then subsequently found in lots of other species.

The Nobel Laureate from last April shared the prize with the person who discovered today's molecule. Name that Nobel Laureate.

The first person to identify the molecule and name the Nobel Laureate wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only three ineligible candidates for this week's reward: Philip Johnson of the University of Toronto, Ben Morgan of the University of North Carolina at Chapel Hill and Frank Schmidt of the University of Missouri.

Frank has agreed to donate his free lunch to a deserving undergraduate. Consequently, I have an extra free lunch for a deserving undergraduate so I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.


Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours. Comments are now open.

Sunday, September 27, 2009

Extreme Atheists Are Like Extreme Religious Fundamentalists

Joshua Rosenau blogs at Thoughts from Kansas but don't be confused by the geography. He actually lives in California and works at the National Center for Science Education (NCSE).

His most recent posting concerns an issue that is often raised when we discuss the compatibility of science and religion [see On cracks]. The issue is outlined in a quotation from Kevin Padian, who is a strong supporter of NCSE and a vocal opponent of creationism.
The two kinds people who believe that religion and evolution can not coexist are extreme atheists and extreme religious fundamentalists. Everyone else doesn't really have a problem. [A majority] of Americans believe that a belief in god is compatible with evolution.
Many atheists interpret this kind of statement as an insult and Jerry Coyne called it "an anti-atheist crack." This prompted Joshua Rosenau to respond like this.
First, note that Kevin Padian is a fairly open atheist, so if this line were "anti-atheist" it would have to be a sort of self-hating atheism. Second, how is it factually wrong? Some atheists (but not all) think science and religion are incompatible. Some religious fundamentalists also think this. There are also a bunch of people in the middle of the spectrum of belief who do not think that. Whether these represent a majority of Americans depends how you ask the question and what you do with undecided responses, but it is absolutely the case that most Americans belong to religious groups whose governing bodies have asserted the compatibility of science (including evolution) and their brand of religion.

What, then, makes Padian's factually correct statement about the beliefs of some atheists a "crack"? Is there any method at all to Coyne's outrage
Yes, Josh, there's a reason why some atheists are annoyed at remarks like that. Here's a list ....
  1. Padian disagrees with those of us who argue that religion and science are almost always incompatible. By labeling his opponents as "extreme atheists" he is trying to marginalize us. That's insulting.
  2. He insults us by associating us with our worst enemies (religious fundamentalists) and suggesting that we think alike.
  3. He uses the argument of popularity to support his position. Imagine that he lived in a country where a majority of citizens were atheists and believed that religion was incompatible with science. Would that change his opinion? Why should non-Americans, like Richard Dawkins for example, form an opinion based on whether or not it agrees with a majority of Americans? It's a silly argument. Either religion and science are compatible or they aren't. Since when did the opinion of the average American become relevant in debates like that?
If you are truly interested in the actual debate about compatibility then those kind of statements are completely useless in advancing your position.

On the other hand, if your primary objective is accommodationism—creating a comfortable place for theistic evolutionists—then Padian's statements make a lot of sense. It's a political argument, not a philosophical one. It's called "framing" and it's the official position of NCSE.

Kevin Padian is the President of the National Center for Science Education so it's not surprising that Josh defends him and the official NCSE position. Unfortunately, that defense involves alienating many former allies who happen to disagree with NCSE on the accommodationist issue. Those of us who disagree think that NCSE should be adopting a neutral position with respect to the overall compatibility of science and religion.

NCSE should continue to opposes the more obvious examples of incompatibility as manifest by the creationist attacks on evolution but it should not be in the business of defining those other areas where science is supposed to be perfectly compatible with religious beliefs.1

UPDATE: Jason Rosenhouse weighs in: Who Rejects Evolution?

1. What are those areas? I wonder if Josh or Kevin has a list?

Dead Fish Thinking

One of the popular techniques in psychology these days is to analyze brain activity in an MRI machine. In a typical experiment, the subject will be shown various images and the machine will maps those parts of the brain that are responding.

In the latest study, a group of psychologists showed a bunch of photographs to a dead salmon and measured the brain activity. The results were announced in a poster: Neural correlates of interspecies perspective taking in the post-mortem Atlantic Salmon: An argument for multiple comparisons correction. Apparently, the salmon was thinking about the photos.

Here's the method ....
Subject. One mature Atlantic Salmon (Salmo salar) participated in the fMRI study. The salmon was approximately 18 inches long, weighed 3.8 lbs, and was not alive at the time of scanning.

Task. The task administered to the salmon involved completing an open-ended mentalizing task. The salmon was shown a series of photographs depicting human individuals in social situations with a specified emotional valence. The salmon was asked to determine what emotion the individual in the photo must have been experiencing.

Design. Stimuli were presented in a block design with each photo presented for 10 seconds followed by 12 seconds of rest. A total of 15 photos were displayed. Total scan time was 5.5 minutes.

Preprocessing. Image processing was completed using SPM2. Preprocessing steps for the functional imaging data included a 6-parameter rigid-body affine realignment of the fMRI timeseries, coregistration of the data to a T1-weighted anatomical image, and 8 mm full-width at half-maximum (FWHM) Gaussian smoothing.

Analysis. Voxelwise statistics on the salmon data were calculated through an ordinary least-squares estimation of the general linear model (GLM). Predictors of the hemodynamic response were modeled by a boxcar function convolved with a canonical hemodynamic response. A temporal high pass filter of 128 seconds was include to account for low frequency drift. No autocorrelation correction was applied.

Voxel Selection. Two methods were used for the correction of multiple comparisons in the fMRI results. The first method controlled the overall false discovery rate (FDR) and was based on a method defined by Benjamini and Hochberg (1995). The second method controlled the overall familywise error rate (FWER) through the use of Gaussian random field theory. This was done using algorithms originally devised by Friston et al. (1994).
The point of the study was to show that you need to be aware of false positives and make the effort to filter the data in order to remove them.

The bigger point, as far as the rest of of us are concerned, is that all aspects of science are complicated and we need to be appropriately skeptical. There's a tendency in the popular press to treat all these brain activity studies as gospel truth because they use a fancy machine.

[Hat Tip: John Hawks]

Friday, September 25, 2009

University of Toronto Enrolment

There's some discussion about enrolment at the University of Toronto in the comments to University Students Aren't as Intelligent as They Used To Be.

Some people seem to be under the impression that enrolment at the University of Toronto has not increased recently. Here's the data from the 2009 Enrolment Report.

Enrolment has doubled since 1970 with most of the increase occurring in the past ten years as the echo boomers reach university age. The participation rate is also increasing. We currently have about 64,000 students (actually they're full-time equivalents (FTEs), but who's quibbling?). There are roughly 13,000 graduate students and 51,000 undergraduates.

Expansion is a good thing. I support it. However, it would be nice to have the extra resources that are required to do a good job of teaching these extra students.

Atheists in America

A recent survey of religious beliefs in America resulted in 15% of the population saying they did not belong to any religion. This group, referred to as the "Nones," is the fastest growing segment having just about doubled over the past two decades.

What do these people actually believe? Are most of them atheists? The answers are in the following detailed report: American Nones: The Profile of the No Religion Population.

What does this group think about evolution? The results are surprising.

Among the general public, only 38% think that evolution is definitely or probably correct. This number only rises to 61% among the nones! 17% of them are certain that humans didn't evolve. What in the world are they thinking?

Well, it turns out that the "no religion" category hides a great deal of diversity. When asked about the existence of God you get the following responses ...

More than half of them believe in some sort of supernatural being and only a small percentage qualify as atheists.

An even smaller percentage will actually admit to being an atheist or an agnostic in spite of the fact that their answers to other questions identify them as atheists or agnostics. The "belonging" category refers to the answer to the question, "What is your religion, if any?" It's a way of allowing respondants to self-identify as atheists or agnostics.

As you can see from the data, almost 90% prefer to identify themselves as having no religion rather than label themselves atheists or agnostics. This group includes, of course, those people who really are religious but just don't belong to a particular religious group.

We conclude from this data that about 12% of Americans don't believe in God—or at least have serious doubts—but only 2% admit it. This number is considerably higher in other industrialized nations according to Atheists, agnostics, and non-believers probably represent a majority of the population in Sweden, Denmark, Norway, Japan, and the Czech Republic and they are close to a majority in Finland, France, South Korea, Estonia, and Germany.

[Hat Tip: Razib Khan]

University Students Aren't as Intelligent as They Used To Be

It's a well-known fact that the average intelligence of university students has been declining over the past four or five decades. This is true in spite of the fact that the average university grades have been going up.

The decline in average intelligence is exactly what one would expect, as Razib Khan explains on his blog Gene Expression: College students are not as intelligent.1

Surprisingly, the typical student at my university doesn't want to hear this. You'd be impressed by the number of explanations they can come up with to refute the data. Maybe we'll see some of them in the comments. Are they scientific explanations?

You might also be surprised at the reluctance to accept the fact of grade inflation. The most common explanation for grade inflation is that today's students are smarter than those of the 60s and 70s and that's why they get higher grades.

1. This is not an argument against increasing the participation rate and expanding university enrolment. I'm in favor of that. Let's just realize that there are consequences that universities need to deal with.

The real question we need to address is gradation rate. In an ideal world, what percentage of those who enter university should graduate? Should it be 100%? 50%?

Swine Flu and "The Canadian Problem"

TV, radio, and newspapers in Canada are abuzz with the lastest studies on swine flu. According to "preliminary reports" your chances of getting swine flu are increased if you get/got? the regular flu shot. This is prompting Canadian public health officials to recommend holding off on the regular flu shot until after you get the swine flu shot ... which won't be available until November.

The so-called "preliminary data" doesn't make any sense as public health experts on Effect measure point out: Once more on the vaccine question.

The confusion isn't helped by ambiguous reporting such as this from Canadian Press: Study linking flu shots, swine flu raises concern abroad, prompt changes at home.
The data, referred to as "the Canadian problem" by some scientists outside this country, are reported to link getting a flu shot last year with double the risk of contracting swine flu this year.

The link, if real, is to mild disease. One person who has seen the study says it seems to suggest that those who got a seasonal flu shot were less likely to develop severe disease if they became infected than those who hadn't received the shot.
Say what?

Nobody else is reporting a connection between this year's swine flu and whether or not you got a flu shot last year. Part of the problem is that Canadian health officials might be basing decisions on a flawed study. That's unacceptable.

One of the most disturbing aspects of this situation is that the actual study may not be available for some time. According to Canadian Press ...

Drawn from a series of studies from British Columbia, Quebec and Ontario, the work is led by Dr. Danuta Skowronski of the British Columbia Centre for Disease Control and Dr. Gaston De Serres of Laval University.

They have submitted the paper to an unnamed scientific journal and are therefore constrained about what they can say about the work. Journals bar would-be authors from discussing their results before they are published.

"For me, it's very important that we respect the peer-review process as good scientists. Because the implications ... are important," Skowronski said in an interview Wednesday.

"And if there are methodologic flaws, we need to be assured that every stone was turned over to make sure what we're reporting is valid."
This is unethical behavior at many levels. First, journals have no right to block access to essential information that's needed to make public health decisions in the middle of a pandemic. That journal should be identified and forced to defend it's policy. Second, no reputable scientists should agree to such an embargo in the first place. Third, if the journal and the scientists enter into a deal to remain silent then how come we know about this study? It sounds like the authors may want to have their cake and eat it too.

SEED Magazine

The last issue of SEED magazine was published in June. Since then, I've been scanning the shelves of my local convenience stores looking for the latest informative article by PZ Myers and the latest fuel for complaints about the quality of science journalism.

No luck so far. According to the SEED website ...
We are currently finishing an exciting redesign that will be on press this fall. This will also be our first issue with the new tagline.
This sounds ominous. Is the print version of SEED dead?

Internet Connection Speed Test

I think I have a pretty good internet connection but many of my friends tell they have much faster connections. Here's a site that tests your upload and download speeds:

I don't know how reliable these are, but here are my results (avg. of five trials):

          DOWNLOAD:  8290 kbps
          UPLOAD:        8080 kbps

I'm pretty happy with my connection through the University of Toronto. Are there better ones out there?

There's another speed test at It gives a difference result for upload speeds.

In the first student labs we ran back in 1987 we downloaded DNA sequence files via a 28.8 kbps modem. That was 22 years ago and the connection speed has only increased about 300×. Doesn't Moore's Law say that the improvement should have been more than 1000-fold?

Thursday, September 24, 2009

Creationist Thinking about Spontaneous Generation

It's not surprising to discover that creationists are opposed to the idea that life began by purely natural processes. After all, that's at the heart of the dispute between creationists and scientists.

One of the rhetorical tricks used by creationists is to refer to the origin of life as "spontaneous generation." Why is this a trick? Because the term is most commonly associated with an old-fashioned view of spontaneous generation as a process that occurs regularly when new living things spring into existence. The idea was that the maggots on rotting meat arose spontaneously, for example, without the need for pre-existing life.

This notion was put to rest once-and-for-all by nineteenth century scientists; notably, Louis Pasteur. We all know that spontaneous generation of this sort doesn't happen. The creationists take advantage of this when they talk about abiogenesies—the origin of life. If they can confuse their audience by associating abiogenesis with discredited spontaneous generation, then that's a good thing, as far as they are concerned. They know what they're doing and that's what makes it despicable.

This brings me to Denyse O'Leary, Toronto's own version of IDiot. Last month she posed the following question on her blog: Is accidental origin of life a doctrine that holds back science?.
Accidental origin of life is the basic thesis of origin of life researchers. Life all just somehow sort of happened one day, billions of years ago, under the right conditions – which we may be able to recreate. But there is a constant, ongoing dispute about just what those conditions were.

Here is the problem I have always had with accidental origin of life: It amounts to spontaneous generation. However, banishing the doctrine of spontaneous generation played a key role in modern medicine’s success. If we assume that life forms (for medical purposes, we focus on pathogens) cannot start spontaneously, then they must have been introduced. Hence, we can develop procedures for a sterile operating room or lab.

If life can be spontaneously generated, why isn’t it happening now? Conditions for life today are probably as good as they have ever been, and maybe better. For over 500 million years they have obviously been good for complex life forms, and for billions of years they have been good for simple ones.
You can win a creationist book for the best response to her question.

Well, the results are in and the prize goes to StephenB. Here's part of his response. Presumably, this is the best argument the IDiots have to offer on what science is all about.
The accidental origin of life idea hurts science because it militates against the vital principle of causation, the rational and indispensible standard on which science is based. The first question any researcher asks is this: “How did it happen? or—What caused it? Yet, the concept of spontaneous generation popularizes the idea that physical events can occur without causes—that there need not be a “how”—that they can “just happen.”

Consider the following proposition: Streets don’t just “get wet.” Using the scientific and philosophical principle of causation, we understand that something had to cause the streets to get wet. So, we say that if the streets are wet, then it must be raining, or else someone turned on a fire hydrant, or we look for some other reason. But if, as Darwinists or postmodern cosmologists claim, physical events do not always need causes or necessary conditions, that is, if something really can come from nothing, then streets can indeed just get wet. With this mind set, science is severely compromised. If, indeed, something can appear spontaneously or without a cause, why cannot it happen again somewhere else in some other situation?

In keeping with that point, if one thing can “just happen,” then why cannot anything just happen? Why not everything? Under these circumstances, how could the scientist know which things were caused and which ones were not? Science would become an intellectual madhouse where the impossible is affirmed with confidence and the obvious is dismissed with disdain, which, come to think of it, is not a bad description of Darwinst epistemology. For Darwinists, and for postmodern cosmologists, a universe can pop into existence, life can come from non-life, and, yes, streets could, in principle, just “get wet.” Science cannot survive this irrational mind set indefinitely.
Are there any evolutionists out there who believe that the first living cell just "poofed" into existence without any cause or antecedents? If you believe this then please post a comment below.

If nobody admits to holding such a belief, then how do we account for the fact that the IDiots misunderstand and misrepresent science?

Wednesday, September 23, 2009

Next-Generation DNA Sequencing

There's a real revolution under way in terms of our ability to collect sequence information. The so-called Next-generation DNA sequencing technology relies on the ability to sequence billions of single DNA molecules simultaneously.

How does it work? I was planning on writing up a blog posting to explain the technology since so many experiments rely on it. I kept putting it off but that turns out to be a good thing 'cause others have explained it much better that I ever could have. Watch this video from Helicos.

[Hat Tip: ScienceRoll]

Tuesday, September 22, 2009

Nobel Laureate: Ivan Pavlov


The Nobel Prize in Physiology or Medicine 1904

"in recognition of his work on the physiology of digestion, through which knowledge on vital aspects of the subject has been transformed and enlarged"

Ivan Petrovich Pavlov (1849 - 1936) (Иван Петрович Павлов) won the Noble Prize in 1904 for his contribution to understanding the physiology and biochemistry of digestion. Part of his contribution was the discovery that some of the digestion enzymes needed to be activated before they could work in the stomach [Monday's Molecule #133].

Pavlov is famous for his work with dogs. Most people know of his studies on conditioned reflexes where he was able to show that the mere anticipation of food caused dogs to salivate. He is famous as one of the founders of modern psychology but the Nobel Prize was for a different study where he examined the stomach secretions of dogs by redirecting secretory ducts to the exterior where the secretions could be collected and analyzed. Pavlov was actually more of a biochemist than a psychologist!

Pavlov had a large, well-equipped lab with many workers. In that sense he was much more of a professional scientist than many of the other biological scientists of the late nineteenth century. Pasteur was another example. Many others, like Charles Darwin, worked alone and didn't seek out students.

The knowledge gained from his studies on digestion had no practical application in medicine. They simply advanced our understanding of how our bodies work. In presenting the Nobel Prize the presenter, Count K.A.H. Mörner, took pains to make this point clear and to pronounce it a good thing. Science for the sake of knowledge.

One gets the impression that the audience at the award ceremonies needed to hear that.

Here's part of the Presentation Speech that describes Pavlov's contribution.

Nobel Laureates
In the early days opinions on the course of digestion were speculations as to what was termed as «cooking» or «grinding» in the stomach etc. So long as the digestive processes could not be observed or investigated directly in the stomach no real knowledge could be obtained. An accident turned physiological research in this field in a direction which has later become very important. In the 1820's a young man sustained a gunshot wound in the stomach and developed a gastric fistula which to some extent permitted the gastric processes to be studied. Observations were carried out on this man by the American physician W. Beaumont. This accidental path of investigation, allowing actual observation of processes taking place in the digestive tract, was later followed by many workers using animals. Technique is an important factor in such experiments and has been perfected in a masterly way by Pavlov, whose animals remain in good health, without any injury to the function of their digestive tract, permitting observation and systematic investigation over an almost unlimited period.

These methods for the study of the physiology of digestion established by Pavlov have been taken up by various physiological institutions, but above all much important work was performed in his own laboratory. From this has followed a far-reaching transformation of our knowledge in this field which has also been enriched by new fundamental facts.

The following may be mentioned as an illustration.

The digestive canal can be influenced in various ways by the nervous system. When we remember that the nervous system can induce not only the secretory processes as well as the movements of various parts of the system, but also can bring such processes to a standstill, that it controls the blood supply to these organs and that sensory nerves arise from them, we can get an idea of the complexity one encounters. The complications become still greater when it is realised that we must take into account not only nervous pathways having their origin in the brain or the spinal cord, but also the sympathetic nervous system, and that we have further to pay attention to the interdependence between the different parts of the digestive system through the nerves, so that variations in the behaviour of one may affect that in other organs.

It is in the nature of things that cognition of the scope and character of the functional interdependence of the nervous system and the digestive organs is of great importance to the knowledge of the physiology of these organs. It is also clear that one can only hope that answers to these complicated questions will advance step by step by much research. In this respect Pavlov has acquired very great merit. He has revealed new points of view and has fruitfully stimulated the solution of these problems, and through his methods has made it possible to reach conclusive analysis of them.

The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

[Photo Credit: Pasteur [Hulton Archive/Getty Images]

Monday's Molecule #137: Winner

This is poliovirus and the Nobel Laureates are John Enders, Thomas Weller, and Frederick Robbins. This week's winner is Frank Schmidt of the University of Missouri.

One of the Nobel Laureates, Frederick Robbins, is a graduate of the University of Missouri.

Frank has generously agreed to donate his free lunch to a hungry, deserving, undergraduate so there may be two winners next week.

Today's "molecule" is actually several molecules, one of which is shown in a diagram below the electron micrograph. You have enough clues to identify this virus. As soon as you get the right answer it will lead you directly to one or more Nobel Laureates.

The first person to describe the "molecule" and name the Nobel Laureate wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only three ineligible candidates for this week's reward: Maria Altshuler of the University of Toronto, Philip Johnson of the University of Toronto and Ben Morgan of the University of North Carolina at Chapel Hill.

All of the recent winners are in a position to accept their prize so there haven't been any recent winners who donated the free lunch to a deserving undergraduate. Consequently, I do not have an extra free lunch for a deserving undergraduate so I'm not going to continue to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.


Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours. Comments are now open.

The Devil Among Us: America's First Witch Hunt

Here's a clip from the movie The Devil Among Us: America's First Witch Hunt. It's about the first witches who were executed in the colonies of New Haven and Connecticut in New England. (See: The Hanging of Goodwife Knapp in 1653.)

The Hanging of Goodwife Knapp in 1653

Roger Knapp was born about 1618 in England and came to New England in the early 1640s. He eventually settled in Fairfield in the colony of New Haven in 1644 (now Connecticut). Not much is known about Roger Knapp except that he is listed as a farmer and an Indian trader.

His wife is known only as "Goodwife" Knapp—a title that’s equivalent to "Mrs." Knapp in modern times. (Sometimes shortened to “Goody”. Women with a higher status in society were referred to as “Mistress.”) In 1653 Goodwife Knapp was accused and convicted of witchcraft and executed by hanging in Try’s field outside the village of Fairfield. (None of the witches executed in New England were burned at the stake.)

Nothing is known of the trial of Goodwife Knapp or what she was accused of. This was right in the middle of the epidemic of witch trials and executions in England and Scotland and the phenomenon naturally made its way to the new colonies. Typically, the witch was accused of associating with the Devil, sometimes intimately. The “evidence” was usually a series of unusual happenings that occurred in the presence of the accused, or strange behavior that was deemed to be inappropriate. In many cases, the accused women seem to be rather more outspoken than others—in other words, they didn’t know their proper place.

Men who were accused of witchcraft were also people who were not satisfied with the status quo.

One of the books put on line by Googel is The Salem Witch Trials: a Reference Guide (by K. David Goss). It recounts the trial of Anne Hibbins who was hanged in 1656.
Anne Hibbins (1656) was censured by Boston church leaders for her contentious behavior in repeatedly accusing a local craftsman of overcharging for his labor. She was furthermore charged with supplanting her husband’s position in dealing with this problem, violating the puritan belief that wives should submit themselves to the leadership of their husbands. For this offense, she was unrepentant. She was removed from membership in the Boston church and found guilty of witchcraft in 1654 after the death of her husband. Although the magistrates denied the initial vedict, a second trial was held before the Massachusetts Great and General Court. Anne Hibbins was convicted a second time of witchcraft and executed in 1656. In his assessment of this tragedy, Governor Thomas Hutchinson, in his "History of Massachusetts," places the blame for this conviction upon the people of Boston who disliked Anne Hibbin’s contentious nature. He wrote that the trial and the condemnation of Anne Hibbins for withcraft was "a most remarkable occurrence in the colony," for he found tha is was her temper and argumentative nature that caused he neighbors to accuse he of being a wtich.
It’s very likely that Goodwife Knapp was hung for the same reasons three years earlier in Fairfield in the New Haven Colony.

The remarkable thing about the Goodwife Knapp execution is not the trial itself but the aftermath. Roger Ludlow, the Deputy Governor of Connecticut, had been fighting on and off for several years with his neighbor Mary Staples (wife of Thomas Staples, also known as Staplies). In 1651 Ludlow won a suit against Mary Staples for slander but this did not put and end to their dispute.

During the trial and imprisonment of Goodwife Knapp, Roger Ludlow and his supporters tried to get her to affirm that Mary Staples was a witch but Knapp refused. Just before the execution, Ludlow claimed that Goodwife Knapp came down the ladder and whispered in his ear that Mary Staples was, indeed, a witch.

Ludlow told this story to his friends, Rev. John Davenport and his wife, and it soon spread to the entire village of Fairfield. Accusing someone of witchcraft was a very serious charge—especially just after Goodwife Knapp had been hanged. When Thomas Staples heard that Ludlow was making these accusations against his wife he filed a defamation suit against Roger Ludlow.

The trail took place in May, 1654. There are several accounts on the internet taken from books that have recently been scanned. The best and most readable is from The Witchcraft Delusion in Colonial Connecticut by John M. Taylor. This is from the trial records and some of the descriptions are quite graphic, particularly the account of the examination of Goodwife Knapp’s body for witch’s teates.

There’s another good account in Witch-Hunting in Seventeenth-Century New England: A Documentary History 1638 ... by David D. Hall.

The role of the Sherwood family in the trial is described in A Changing America: Seen Through One Sherwood Family Line 1634-2006.

The reason for my interest in this trial is that many of my ancestors lived in Fairfield at the time and their names are mentioned in the account. Some of my ancestors were friends of the Staples and defended Mary Staples while others sided with Roger Ludlow. Ludlow lost the case and he left Fairfield the following year (1654), making his way eventually back to England and then to Ireland where he remained for the rest of his life.

By an extraordinary coincidence, my good friend and former best man at my wedding, Charles Beach, is a descendant of Mary Staples and Thomas Staples. Their daughter, Mary Nicol Staples (1630-1677) married John Beach (1623-1677).

My living relatives might be interested in our connections to the trial: here they are.

These are ancestors of Isabelle Hooper Burns (1862-1923) the mother of my maternal grandfather. More specifically, they are direct ancestors of her mother’s mother, Esther Treen (1807-~1891).

Here are the names of people mentioned in the defamation lawsuit. Our direct ancestors are underlined. (Some of these have subsequently been proven to be incorrect = strikeout.)

John Banks (1619-1684), attorney for Thomas Staples. (He is my great9-grandfather. Most of the others are from this generation or one generation earlier: great10)

Witnesses Andrew Ward (1597-1659) and his wife Hester Ward = Hester Sherman (1606-1666).

Witnesses: Goodwife Barlow = Ann Ward (?-1684) and her husband John Barlow (1599-1674)

Witness: Goodwife Sherwood = Mary Onge? second wife of Thomas Sherwood (1586-1655). Thomas' first wife, my ancestor, was Alice Tiler1 (1585-1635).

Witness: Goodwife Odell (Odill) daughter-in-law of John Odell (1574) and Joan Bingley (1581-1640).

Witness: Mr. Jones is John Jones (1591-1665).

Witness: Goodwife Lockwood is Susan (Susanna) Norman (1616-1661) wife of Robert Lockwood (1600-1658).

Witness: Deborah Lockwood (1636-?), 17 years old at the time of the trial and my great9-grandmother. She is the daughter of Robert Lockwood and Susanna Lockwood.

Witness: Thomas Lyon (1621-1690).

Witness: Rebecca (Rebecka) Hull is Rebecca Jones, wife of Cornelius Hull and daughter of John Jones (1591-1665) and Sarah UNKNOWN (1599-1650).

Witness: Thomas Barlow was the second husband of Rose Sherwood, daughter of Thomas Sherwood (1586-1655) and Alice Tiler1 (1585-1655).

Goodwife Pell is not an ancestor of mine but she has an interesting connection. She is Lucy Pell, wife of Thomas Pell who later founded Pelham, in what is now the Bronx, New York City [The Involvement of Thomas Pell's Family in the Witchcraft Persecution of Goody Knapp].

1. Usually given as Alice Seabrook but this is almost certainly wrong according to A Changing America: Seen Through One Sherwood Family Line 1634-2006, Volume 1 By Frank P. Sherwood.

The drawing of the hanging of Ann Hibbins and the map of the colonies in 1650 are from the HTY277 website of the University of Maine at Farmington.

Monday, September 21, 2009

More Junk DNA Fallacies

BiOpinionated is a blog written by a molecular biologist named Nils Reinton. He tries to see every side of an argument but there are times when this attempt goes astray.

The "debate" over junk DNA is an example. Here's how Nils responed to claims by Ryan Gregory and me that most of our genome is junk [How to have your cake, eat it, and then complain].
First: State that most of our genome is junk.

Second: When more and more promoters, enhancers, repressors and other regulatory elements are discovered, claim that this of course was not included in the definition of “most of the genome”. The perfect excuse because it means you’ll never be wrong.

Last: Complain when the press does not understand that “most of our DNA” actually meant “much of our DNA , but with a lot of exceptions” and that science reporters don’t intuitively know which exceptions these are.

Post written using the zpen in dire agony over extremely poor science communication from the same persons who most eagerly criticize science communication from others.
[see the original article for links - LAM]
Oh dear. There's so much wrong with the logic of this posting that I hardly know where to begin.

Nils is mostly upset about a recent posting on Genomicron: The Junk DNA myth strikes again (next up: media hype). This isn't very complicated so let me give you the short version.

Most of our genome is junk. That does not mean that all of our genome is junk and it certainly never meant (among intelligent scientists) that all of our non-coding DNA is junk. Here's a short list of non-coding DNA that is absolutely essential in our genome: all genes that produce functional RNAs instead of proteins; all regulatory sequences including enhancers; sequences that control splicing and other RNA processing events such as capping and polyadenylation; some 5′-leaders and 3′-tails of mRNA; chromatin domain markers (regulatory); scaffold attachment sites (SARs); some recombination hotspots; origins of replication; centromeres; telomeres.

Ryan was complaining about a paper that's about to be published in Molecular Biology and Evolution. The authors say this in their abstract.
Protein-coding sequences make up only about 1% of the mammalian genome. Much of the remaining 99% has been long assumed to be junk DNA, with little or no functional significance.
I agree with Ryan Gregory that this is extremely misleading. It implies that there are legitimate scientists who think that all non-coding DNA is junk. It would be far better to say something like this ...
Genes that encode proteins, and other genes, make up only a few percent of our genome. If you add in all of the other DNA sequences that are known to be essential you still can only account for no more than 5% of our genome. Most of the rest is thought to be junk DNA with no biological function. There are no respectable scientists who think that none of it will ever be shown to have a function but the general consensus among the defenders of junk DNA is that the vast majority of these DNA sequences, consisting mostly of defective transposons and pseudogenes, will turn out to have no function.
The authors of the paper go on to present evidence that about 5.4% of non-coding DNA has a function.

Big deal. That's not much more than what the textbooks have been saying for several decades.

Nils, there's an interesting debate going on about the amount of junk DNA in our genome. You're welcome to participate but please make sure you understand the issue and, please, don't spread false information. When we say that most of our genome is junk that does not mean that some of what we now consider to be junk DNA won't turn out to have a function. We're not that stupid—please don't imply that we are.

What we're saying is that the vast majority of DNA sequence in our genome is junk. I think the amount of junk is going to be >90%. That still leaves room for discovering a function for about twice as much DNA as we already know to be functional.

Get back to me when someone publishes solid evidence that more than 10% of our genome is essential.