Ford Doolittle talks about transposons, junk DNA, ENCODE, and how science should work

Here's more from the interview with Ford Doolittle [The Philosophical Approach: An Interview with Ford Doolittle].

Gitschier: I want to close with what you describe as your “latest rant.” How did you get on function?

Doolittle: Well, I’ve always been on that.

Back in 1980, people were talking about transposable elements as if their function was to speed evolution; that they exist because of their future utility. And I’ve never liked that kind of idea. I didn’t like it in terms of introns. And Dawkins had just published The Selfish Gene in 1978.

Carmen Sapienza, a student of mine who now works on eukaryotic imprinting, and I wrote a paper which was rejected by Science after seven referees. But we heard that Leslie Orgel and Francis Crick were working on something like this, so we sent it to them. They said, “If you submit it to Nature, we will tell Nature not to publish ours without publishing yours, and to publish yours first,” etc., which was very nice.

That paper, seemingly now very simplistic, said you don’t need to suppose that transposable elements are there for the purpose of speeding evolution. These are selfish things, and natural selection will favor such elements that can make copies of themselves in genomes and then spread horizontally to other genomes within the species. These are basically parasites. I think many people would now accept this, but it was radical at the time.

People don’t like to think that the human genome has junk in it. This came back when the ENCODE papers came out a few years ago and were touted as spelling the “demise of junk DNA.” That got my dander up.

I wrote a perspective in PNAS, and Dan Graur had a much more vituperative thing in Genome Biology and Evolution. I don’t think the ENCODE people have given up; they had a kind of semi-apology in PNAS, which wasn’t really an apology.

It is the same as the tree of life issue, but until we actually have some agreement about what we mean by words we are going to get into these arguments, and in my mind, there are two devastating things you can say about the ENCODE people.

One is that they completely ignored all that history about junk DNA and selfish DNA. There was a huge body of evidence that excess DNA might serve some structural role in the chromosomes, but not informational. They also ignored what philosophers of biology have spent a lot of time asking: what do you mean by “function?” And you can mean one of two things: we might mean either what natural selection favored, which is what I think most biologists mean, or we might mean what it does. Some people might say, “Well the function of this gene is in the development of cancer,” but they don’t really mean that natural selection put it there so that it would cause cancer. These are not-so-subtle differences.

I think many molecular biologists and genomicists, in particular, think that each and every nucleotide is there for a reason, that we are perfect organisms. It is almost as if we were still theists thinking God doesn’t make junk; we just now think natural selection doesn’t make junk. I think there is a deep issue about the extent to which we are noisy creatures and the extent to which we are finely honed machines. I think the latter view informs much of genomics, and I think it is false.

ENCODE wouldn’t have got funded had they said 80% of the human genome is just junk, transposable elements.

Gitschier: It is justifying itself, post hoc. They are the big players with a lot of money. It’s like a machine—“We can do it, so let’s just do it!”

Doolittle: It’s a juggernaut is what you are saying.

My other objection is that it is false ontology. I think all of our science suffers not only from the big science motivation, but from what I call “positivism.”

A couple of times we submitted papers saying, “Everybody’s doing something this way, and it doesn’t work, and it is wrong to do it this way.” And Nature would write back, “We’re not interested in negative reports like this. What does work?” And we say, “We don’t give a damn what does work, it is important to know that what people are doing now is not working.”

There is no critique in science, very little. You can’t actually say, “This doesn’t mean what people say it means.” You’ve got to be “positive;” you’ve got to be moving the program forward all the time. I don’t think that is right.

Now, and down the road, we’re going to tackle directly relevant questions, like what is the meaning of function in the concept of genomics? There are legitimate evolutionary constructs in which you can address transposable elements, and people have not really explored that. Questions about the tree of life, again, and some of the questions we’ve been through are things that continue to interest me and which have a strong philosophical component as well as a data-related component. That’s what I’m interested in pursuing.

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Ford Doolittle talks about the tree of life

There's an interview with Ford Doolittle in PLoS Genetics [The Philosophical Approach: An Interview with Ford Doolittle].

Ford has lots of things to say about the origin of introns, the tree of life, transpsosons, ENCODE, and the meaning of "function." Here's the bit about the tree of life.

Why did they bury Darwin in Westminster Abbey?

I'm gradually starting to work on my book about evolution by accident. The first chapter is "Darwin Died in 1882." The point I'm making is that evolutionary biology is a 21st century discipline not one that's stuck in the nineteenth century.

I was re-reading an old article from the 2006 issue of Skeptical Inquirer with the title¹ I picked for this blog post. The author is W.G. Weyant, an historian at the University of Calgary (Calgary, Alberta, Canada). He says,

Why, then, did they bury Darwin in Westminster Abbey? The brief answer is "because he was dead," but that, while true, clearly is not the whole story."

The whole story is interesting because it reflects the attitudes of late Victorian society in England. This was a time when scientists were honored even if, or especially because, their ideas were upsetting. It appears to be an age when smart, rational, people were admired.

I don't know if this is still true in Europe but it's not true in Canada and it's certainly not true in the USA. Actors and singers are admired, but not intellectuals. I wonder what late Victorian society would have thought on seeing the memorial services for Francis Crick and Michael Jackson? I wonder what they would have thought of Ted Cruz?

Weyant also writes,

Approximately a decade after publication of the "Origin of Species" in 1859, most educated Englishmen, including many of the clergy, had accepted the fact of evolution. More that a few of them were uneasy about where the evidence and their reason were taking them, but they went nevertheless.

That's an interesting way of putting it. Today, we see many people who are faced with the same uneasiness but the response is quite different. When the choice is faith or facts, they choose not to follow the path of reason.

I think we're finally beginning to realize that science and religion are not compatible, confirming the worst fears of educated Victorians back in 1882. Jerry Coyne's new book is likely going to start a serious debate, one that has been largely ignored in the interests of accommodationism.

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1. I wasn't the first to do this; see Why did they bury Darwin in Westminster Abbey?

Jerry Coyne is coming to Toronto!

Save this date: June 10, 20015.

Jerry Coyne is coming to Toronto to talk about his book. He'll be arriving from Vancouver and Imagine No Religion 2015. I'll see him there but I'm not sure I'll be back in Toronto in time. [Centre for Inquiry Canada: Jerry Coyne]

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Are biochemistry instructors going to treat evolution as a core concept or are they going to teach to the MCAT?

The American Society for Biochemistry and Molecular Biology (ASBMB) has recommended that biochemistry courses concentrate on core concepts rather than details. It has defined five categories of core concepts that are essential in understanding biochemistry and molecular biology [see ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function].

Theme

Better BiochemistryI strongly support the concept of teaching core concepts even though I disagree with many of the actual concepts that are proposed. Here are the five core concepts with links to my discussions.

1. evolution [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution ]
2. matter and energy transformation [ASBMB Core Concepts in Biochemistry and Molecular Biology: Matter and Energy Transformation]
3. homeostasis [ASBMB Core Concepts in Biochemistry and Molecular Biology: Homeostasis]
4. biological information [ASBMB Core Concepts in Biochemistry and Molecular Biology: Biological Information]
5. macromolecular structure and function [ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function]

Molecular Evolution Exam - April 2015

Here's the final exam in my course. Students have to answer the first two questions and three of the next five questions. How would you do?

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1. Choose a subtopic from your essay and explain it better than you did in your essay and/or rebut the comments and criticisms made by the marker/grader.


2. Michael Lynch says in The Origins of Genome Architecture ....
   

   Nothing in Evolution Makes Sense Except in the Light of Population Genetics
   Evolution is a population genetic process governed by four fundamental forces, which jointly dictate the relative abilities of genotype variants to expand through a species. Darwin articulated a clear but informal description of one of those forces, selection (including natural and sexual selection), whose central role in the evolution of complex phenotypic traits is universally accepted, and for which an elaborate formal theory in terms of changing genotype frequencies now exists. The remaining three evolutionary forces, however, are non-adaptive in the sense that they are not the function of the fitness properties of individuals: mutation (broadly including insertions, deletions, and duplications) is the fundamental source of variation on which natural selection acts; recombination (including crossing-over and gene conversion) assorts variation within and among chromosomes; and random genetic drift insures that gene frequencies deviate a bit from generation to generation independently of other forces. Given the century of theoretical and empirical work devoted to the study of evolution, the only logical conclusion is that these four broad classes of mechanisms are, in fact, the only fundamental forces of evolution. Their relative intensity, directionality, and variation over time define the way in which evolution proceeds in a particular context.

   Do you agree with Lynch that “Nothing in Evolution Makes Sense Except in the Light of Population Genetics”? If so, why isn’t population genetics taught in introductory biology courses? If not, why not?


3. Imagine that identical female twins were born to a woman in 1000 AD. Imagine that you could find a direct descendant of each twin in 2015. If you sequence the complete genomes of the descendants, approximately how many differences would you expect to find? How do these compare to the differences between any two randomly selected individuals from the same part of the world? Explain your reasoning and describe any assumptions you make. Think carefully before you answer. The second question is the most important one. (Human mutation rate = 130 mutations per generation. Haploid genome size = 3.2 × 10⁹ bp.)


4. Why do some scientists think that there is no unique tree of life?


5. Many people believe that recombination evolved because it increases genetic variation in a population and this provided a selective advantage over species that didn’t have recombination. Do you agree with this explanation for the evolution of recombination? Why, or why not? What are the other possibilities?


6. What is “evolvability ”and why could it be important in evolution? Why are some scientists skeptical of this claim?


7. Richard Dawkins once wrote,
   

   Even the most ardent neutralist is quite happy to agree that natural selection is responsible for all adaptation. All he is saying is that most evolutionary change is not adaptation. He may well be right, although one school of geneticists would not agree. From the sidelines, my own hope is that the neutralists will win, because this will make it so much easier to work out evolutionary relationships and rates of evolution. Everybody on both sides agrees that neutral evolution cannot lead to adaptive improvement, for the simple reason that neutral evolution is, by definition, random, and adaptive improvement is, by definition, non-random. Once again, we have failed to find any alternative to Darwinian selection, as an explanation for the feature of life that distinguishes it from non-life, namely adaptive complexity.
   
   Richard Dawkins (1986) The Blind Watchmaker. p. 304

   Can you describe situations in Richard Lenski’s ongoing evolution experiment where neutral or deleterious alleles were essential for adaptive change?

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Nature reviews Nessa Carey's book on junk DNA

Read it at" Genetics: We are the 98%. Here's the important bit ...

Finally, Junk DNA, like the genome, is crammed with repetitious elements and superfluous text. Bite-sized chapters parade gee-whizz moments of genomics. Carey's The Epigenetics Revolution (Columbia University Press, 2012) offered lucid science writing and vivid imagery. Here the metaphors have been deregulated: they metastasize through an otherwise knowledgeable survey of non-coding DNA. At one point, the reader must run a gauntlet of baseball bats, iron discs, Velcro and “pretty fabric flowers” to understand “what happens when women make eggs”. The genome seems to provoke overheated prose, unbridled speculation and Panglossian optimism. Junk DNA produces a lot of DNA junk.

The idea that the many functions of non-coding DNA make the concept of junk DNA obsolete oversells a body of research that is exciting enough. ENCODE's claim of 80% functionality strikes many in the genome community as better marketing than science.

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Nessa Carey doesn't understand junk DNA

Nessa Carey is a science writer with a Ph.D. in virology and she is a former Senior Lecturer in Molecular Biology at Imperial College, London.

She has written a book on junk DNA but it's not available yet (in Canada). Judging by her background, she should be able to sort through the controversy and make a valuable contribution to informing the public but, as we've already noted Nessa Carey and New Scientist don't understand the junk DNA debate.

Casey Luskin has a copy of the book so he wrote a blog post on Evolution News & Views. He's thrilled to find someone else who dismisses junk DNA and "confirms" the predictions of Intelligent Design Creationism. I hope Nessa Carey is happy that the IDiots are pleased with her book [New Book on "Junk DNA" Surveys the Functions of Non-Coding DNA].

Human mutation rates - what's the right number?

There's some controversy over the rate of mutations in humans. The latest summary comes from science journalist Ewen Callaway, a Senior Reporter for Nature, writing on March 10, 2015: DNA mutation clock proves tough to set.

Theme

Mutation

-definition
-mutation types
-mutation rates
-phylogeny
-controversies
Let's review what we know. The first thing we have to do is define "mutation" [What Is a Mutation?]. A mutation is any alteration of the nucleotide sequence of a genome. It includes substitutions, insertions, and deletions.

The mutation rate can be described and defined in many ways. For most purposes, we can assume that it's equivalent to the error rate of DNA replication since that accounts for the vast majority of substitutions. Substitutions are far more numerous than most insertions and deletions. (But see, Arlin Stoltzfus on The range of rates for different genetic types of mutations).

Happy 10th birthday to YouTube!

The first video was posted to YouTube on April 23, 2005 [see YouTube]. I took this photo (right) a few years ago near my daughter's place in Playa Vista, California. It's a production facility, YouTube Space LA, on the site of the former Howard Hughes airport.

The main purpose of this post is to give me an excuse to post one of my granddaughter's favorite YouTube videos (below top). She's a big fan of YouTube and so is my two year old grandson—he likes videos of rocket launches (below bottom).

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Does natural selection constrain neutral diversity?

Razib Khan is an adaptationist and he's discovered a paper that gets him very excited: Selectionism Strikes Back!.

Here's the paper and the abstract.

Corbett-Detig, R.B., Hartl, D.L., Sackton, T.B. (2015) Natural Selection Constrains Neutral Diversity across A Wide Range of Species. PLoS Biology Published: April 10, 2015 doi: 10.1371/journal.pbio.1002112

The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude, levels of genetic diversity within species fall in a comparatively narrow range. Although theoretical arguments have invoked the increased efficacy of natural selection in larger populations to explain this discrepancy, few direct empirical tests of this hypothesis have been conducted. In this work, we provide a direct test of this hypothesis using population genomic data from a wide range of taxonomically diverse species. To do this, we relied on the fact that the impact of natural selection on linked neutral diversity depends on the local recombinational environment. In regions of relatively low recombination, selected variants affect more neutral sites through linkage, and the resulting correlation between recombination and polymorphism allows a quantitative assessment of the magnitude of the impact of selection on linked neutral diversity. By comparing whole genome polymorphism data and genetic maps using a coalescent modeling framework, we estimate the degree to which natural selection reduces linked neutral diversity for 40 species of obligately sexual eukaryotes. We then show that the magnitude of the impact of natural selection is positively correlated with Nc, based on body size and species range as proxies for census population size. These results demonstrate that natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species. This implies that natural selection may provide an explanation for this longstanding paradox of population genetics.

It is impossible for someone like me to evaluate this paper. Can someone take a look to see if it's valid?

How many selective sweeps must there every 50,000 years in order to remove substantial amounts of neutral diversity from junk DNA?

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Mississauga Mayor Bonnie Crombie agrees to abide by Surpeme Court ruling banning prayers at city council

Shortly after being elected last Fall, the new Mayor of Mississauga, Bonnie Crombie, decided that the City Council would continue to say a prayer before each council meeting. She voted in favor of continuing the practice even though she heard the arguments against it and even though she knew that the Ontario Court of Appeal (in 1999) had ruled it illegal [Mississauga council debates removing Lord’s Prayer from meetings].

Crombie, who is Catholic, said she doesn’t have a problem with the recitation of the prayer. But, she does want to touch base with the municipality’s 11 councillors to get their opinions.

She has already heard lot of different ideas from her peers, such as leaving the practice the way it is to replacing it with a non-denominational blessing to even rotating a prayer from a different faith before each meeting.

"I don’t think there’s anything wrong with (reciting the prayer)," said Crombie. "But, I am asking each councillor about it and there is a diversity of opinion."

...

Larry Moran, who described himself as an atheist, is also a University of Toronto professor and an advisory fellow with the Centre for Inquiry Canada, an organization he said strongly supports the separation of religion and government.

He wrote a blog post condemning the practice in Mississauga earlier this year and Moran estimates about 30 per cent of Canadians aren’t religious. He strongly believes the Lord’s Prayer before council should come to an end.

"There is no reason to invoke any of the gods at a public meeting of any government body," said Moran. "It sends the wrong message to … citizens who don’t believe in those gods or who believe in other gods. Nobody has been able to tell me why religion has to be mixed in with government business."

Now Bonnie Crombie says she will obey the law—no mention of fairness or of consideration for non-Christians in the community. Oh well, at least she's not going to fight it and cost the city lots of money.

The Toronto Star reports that the mayor of Oshawa plans to ignore the Supreme Court decision. I bet he backs down after talking to the city lawyers [Oshawa mayor plans to keep Lord’s Prayer].

Brampton Mayor Linda Jeffrey stopped the practice of reciting the Lord's Prayer before council meetings earlier in the year and today Mississauga Mayor Bonnie Crombie indicated her council will now do the same, after the Supreme Court decision. At the beginning of the year she supported keeping the Lord's Prayer in Mississauga council meetings.

"Today’s ruling sets a precedent and the City of Mississauga will abide by the Supreme Court’s ruling," Crombie said.

At the beginning of the year Crombie supported keeping the Lord's Prayer in Mississauga council meetings, after Councillor Carolyn Parrish had pushed to remove it from council meetings.

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Story-telling and the origin of eukaryotes

Austin Booth and Ford Doolittle have just published a paper that discusses the origin of eukaryotes (Austin and Doolittle, 2015). They point out that many of the stories about this event are not grounded in fact. Read the paper.

Writing for public audiences, and often even for themselves, biologists are not loath to make simplifying claims about uniqueness and importance that are rhetoric disguised as fact. Such generalizations serve purposes in the doing of science, but are often not themselves testable scientific claims and are subject to biases. Evolutionary biology may be especially vulnerable to hype, as suggested by the frequency with which revolutionary evolutionary claims in top-notch journals are debunked. Additionally, anthropocentrism, as it grades into "zoocentrism" and then "eukaryocentrism," surely remains a subtle distorter of objectivity.

Our aim here is to critique general claims about the uniqueness and special importance of eukaryogenesis, with an aim to making them more open to question and conceptual and empirical analysis. We ask (i) whether eukaryogenesis entailed such a "genuinely unlikely sequence of events" as to justify belief in its uniqueness as a process, (ii) if, as is often claimed, eukaryogenesis has a problematic or unique theoretical status in evolutionary biology, (iii) what intrinsic features might have conferred on eukaryotes their presumed "richer evolutionary potential," and (iv) if this greater potential might be just a presumption, an illusion reflecting eukaryocentric bias.

There are many useful ways of understanding evolution, and their articulations can be intellectually valuable and experimentally fruitful. We advocate a more self-conscious pluralism that would require not that we stop telling eukaryogenesis stories but that we do recognize them for what they are. We do not claim to know whether there is any best story, any theory by which the apparent differential success of eukaryotes can be objectively probed and causally rationalized. What we have questioned here is whether premises of existing theories have been objectively formulated and whether, despite widespread acceptance that eukaryogenesis was "special," any such notion has more than rhetorical value.

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Booth, A. and Doolittle, W.F. (2015) Eukaryogenesis, how special really? Proc. Natl. Acad. Sci. (USA) Published online before print April 16, 2015 [doi: 10.1073/pnas.1421376112]

Canada bans prayers at city council meetings

The Supreme Court of Canada has ruled that prayers at the opening of city council meetings are not consistent with a secular society [Quebec town can’t have prayers at council meetings, top court rules].

The Supreme Court decision is at: Mouvement laïque québécois v. Saguenay (City). The decision appears to be unanimous (9:0) provided I'm reading it correctly.

The state’s duty of religious neutrality results from an evolving interpretation of freedom of conscience and religion. The evolution of Canadian society has given rise to a concept of this neutrality according to which the state must not interfere in religion and beliefs. The state must instead remain neutral in this regard, which means that it must neither favour nor hinder any particular belief, and the same holds true for non‑belief. The pursuit of the ideal of a free and democratic society requires the state to encourage everyone to participate freely in public life regardless of their beliefs. A neutral public space free from coercion, pressure and judgment on the part of public authorities in matters of spirituality is intended to protect every person’s freedom and dignity, and it helps preserve and promote the multicultural nature of Canadian society. The state’s duty to protect every person’s freedom of conscience and religion means that it may not use its powers in such a way as to promote the participation of certain believers or non‑believers in public life to the detriment of others. If the state adheres to a form of religious expression under the guise of cultural or historical reality or heritage, it breaches its duty of neutrality. The Tribunal was therefore correct in holding that the state’s duty of neutrality means that a state authority cannot make use of its powers to promote or impose a religious belief. Contrary to what the Court of Appeal suggested, the state’s duty to remain neutral on questions relating to religion cannot be reconciled with a benevolence that would allow it to adhere to a religious belief.

This seems so obvious to most people that it's a wonder why anyone ever thought that reciting prayers at city council meetings was justified.

Now, let's see how long it takes for other cities to stop the practice.

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Hat Tip: Canadian Atheist

The Virtual Cell Animation Collection

I'm interested in science education in general and teaching biochemistry and molecular biology in particular. A recent publication in PLoS Biology caught my eye ...

Reindl, K.M., White, A. R., Johnson, C., Vender, B., Slator, B.M., and McClean, P. (2105) The Virtual Cell Animation Collection: Tools for Teaching Molecular and Cellular Biology. PLoS Biology 13(4): e1002118 DOI: 10.1371/journal.pbio.1002118

The paper focuses on the value of short animations for teaching biochemistry and molecular biology to advanced high school students and college students.

There's nothing in the paper about the scientific accuracy of the presentations or the pedagogical approach and this is unfortunate. The animations only show complex eukaryotic cells in spite of the fact that the American Society for Biochemistry and Molecular Biology recommends an evolutionary approach to teaching. The fact that the videos emphasize eukaryotes leads to some interesting descriptions of fundamental processes.

Look at the video on transcription regulation for example [Regulated Transcription]. The textbooks teach this using simple systems such as E. coli transcription then they move on to more complex prokarotic systems such as the lac operon. Then they cover the eukaryotic examples pointing out how they differ from the simple bacterial systems. This has always been a successful approach to teaching the basic concepts of transcription and transcription regulation. ¹

Is the approach taken by the authors of The Virtual Cell Animation project better? I don't think so. What do you think? Does anyone out there teach transcription without introducing it first in bacteria?

Let's not forget my favorite example of biochemical misconceptions: the Citric Acid Cycle. Did you know that it's sometimes called the "tricarboxylic acid cycle" because three CO₂ molecules are released for every pyruvate molecule? ²

The carboxylate groups on citrate, isocitrate etc. are shown as -COOH instead of COO^- as in the textbooks. I don't know why they did this ... it leads to some extra protons being released in the reactions.

The authors make a very common mistake with succinate dehydrogenase. They show FADH₂ as one of the products of the reaction whereas the IUBMB database shows that the real final product is QH₂ [see Succinate Dehydrogenase]. I don't understand why biochemistry teachers can't check out a leading textbook (or the scientific literature) before producing a video.

Did you know that some of the reactions of glycolysis are irreversible? Check out the video on Glycolysis to find out which reactions have this interesting property. ³ There is no video on gluconeogenesis and that's surprising because the synthesis of glucose is far more important than glycolysis in most species.

I wonder if the editors of PLoS bothered to watch the videos or whether they just assumed that they were scientifically accurate and pedagogically sound? I'm guessing that they didn't see the need to review the videos and simply concentrated on whether all the words in the article were spelled correctly.

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1. There's a separate video on the lac Operon. How many errors, flaws, or missed opportunities, can you spot?

2. Silly me. I always though it had something to do with the fact that two of the key intermediates (citrate and isocitrate) were tricarboxylic acids. Most of the others are dicarboxylic acids.

3. Maybe I'm quibbling. In my textbook I describe these reactions as "metabolically irreversible" because the activities of the enzymes are regulated. That's not the same as saying that the reactions are irreversible.

Stupid Harvard press release illustrates the importance of author responsibility

Bonnie Prescott is a Senior Science Writer at the Beth Israel Deaconess Medical Center at Harvard Medical School. She has written a press release concerning pseudogenes and cancer: Evolutionary Relic: Pseudogenes in the human genome may lead to cancer development.

Here are the first five paragraphs ...

Pseudogenes, a subclass of long noncoding RNA (lncRNA) that developed from the human genome’s 20,000 protein-coding genes but has lost the ability to produce proteins, have long been considered nothing more than genomic "junk."

Yet the retention of these 20,000 mysterious remnants during evolution suggests that they may in fact possess biological functions and contribute to the development of disease.

Now, a team led by investigators at Harvard Medical School and the Cancer Center at Beth Israel Deaconess Medical Center has provided some of the first evidence that one of these noncoding "evolutionary relics" actually has a role in causing cancer.

In a new study published in the journal Cell on April 2, the scientists report that, independent of any other mutations, abnormal amounts of the BRAF pseudogene led to the development of an aggressive lymphoma-like disease in a mouse model, a discovery suggesting that pseudogenes may play a primary role in a variety of diseases.

The new discovery also suggests that with the addition of this vast "dark matter" the functional genome could be tremendously larger than previously thought—three or four times its current known size.

There are many things wrong with that description but I'm not going to elaborate. If you don't know what's wrong you probably won't be interested in this post anyway.

I want to discuss two rules that should be enforced for every press release.

1. The press release must include the complete citation, including a link (doi). If This means delaying the press release for a day or two after the embargo is lifted then that's a small price to pay.
2. The press release should always include a notice from at least one author affirming, in writing, that the press release is a complete and accurate report of the results and conclusions that have been published in the peer reviewed literature.

This press release did not contain a citation. In this case, the paper has been published online but there's no volume number or page number because it hasn't appeared in the journal. Here's the citation ...

Florian A. Karreth, Markus Reschke, Anna Ruocco, Christopher Ng, Bjoern Chapuy, Valentine Léopold, Marcela Sjoberg, Thomas M. Keane, Akanksha Verma, Ugo Ala, Yvonne Tay, David Wu, Nina Seitzer, Martin Del Castillo Velasco-Herrera, Anne Bothmer, Jacqueline Fung, Fernanda Langellotto, Scott J. Rodig, Olivier Elemento, Margaret A. Shipp, David J. Adams, Roberto Chiarle, Pier Paolo Pandolfi (2015)The BRAF Pseudogene Functions as a Competitive Endogenous RNA and Induces Lymphoma In Vivo Cell published online April 2, 1015. [doi: 10.1016/j.cell.2015.02.043]

There. That wasn't so hard, was it?

I can't read the paper because it's behind a paywall but the abstract suggests that the authors really do think their work applies to most pseduogenes. The press release quotes the senior author, Pier Paolo Pandolfi, and while his views aren't nearly as idiotic as the beginning of the press release it does suggest that he isn't a fan of junk DNA.

In order to confirm that the views expressed by Bonnie Prescott are an accurate representation of the views in the peer-reviewed paper, it would be nice to see a note at the bottom of the press release signed by multiple authors. It would state that they stand by the press release and that the views in the press release represent those views that have passed peer review.

I call this "Author Responsibility" and I think it should be a requirement in all press releases.

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Hat Tip Dan Graur: Shouldn’t Press Releases from @Harvard be Less Asinine?

James Lunney doesn't get no respect - does he deserve it?

James Lunney has quit the Conservative Party of Canada and decided not to run in the next federal election. He's upset because he doesn't believe in evolution and lots of people, including me, are pointing out the stupidity of his views. Because those views are based on religion, he interprets this to be an attack on his faith.

Here's what he says on his website [Evolution Controversy].

Maybe it’s because I am tired of seeing my faith community mocked and belittled. To not respond is to validate my accusers and worse yet, imply that I lack the courage of my convictions to stand–up for what I believe. This is not a legacy I wish to leave behind. Many of you colleagues represent constituencies beyond the ones who elected you; I hope that no member of any faith community in Canada is compelled to defend the beliefs of their community in the future.

Freedom of Religion and conscience are fundamental freedoms in Canada. Bigotry cloaked in defense of "science" is as intolerable and repugnant as bigotry from any other source.

It is contrary to our multi-racial, multicultural and multi-faith character and the tolerance for diversity that defines us as Canadians.

I know members on all sides of the house are concerned about bullying in general and cyber-bullying in particular. The government has brought in new legislative measures to address some aspects of this brutal phenomenon and there are many social actions like the pink shirt initiative that seek to shield the vulnerable.

We are living in an era where knowledge is increasing at an astounding pace; there are so many technical advances it is hard to keep up and what we refer to in general as "science" has been parsed into more and more diverse pursuits of knowledge.

I urge you to read the entire article that he posted on April 1st 2015. See if you think he deserves the respect he craves. He sounds like a kook to me.

How many times have we heard this stuff before? And how many times have we seen this style of writing?

So is "Evolution Theory or Fact?

The late Stephen Jay Gould stated: "a fact is something that is proven to the extent that to not believe it is perverse"!

That translates to: a fact is something that my friends and I believe, AKA eminence-based science. There’s a lot of that in health-care, where it’s known as eminence-based medicine as opposed to evidence- based medicine. There are people in the medical world expressing concern about the immense influence of KOLs (Key Opinion Leaders) with influencing public policy and decision making in directing scientific inquiry

Darwin’s brilliant and convincing construct that defined a century and a half of scientific belief, is in crisis because of astounding advances in molecular biology and it’s all about THE CELL.

You have 80-100 trillion cells, 200 cell types, all reading the same genetic library, but as different as they are, working together in specialized communities to perform astonishing synchronized manufacturing, recycling, transport, packaging and delivery functions. Twenty-five thousand miles of blood vessels if you strung them end to end; that is a trip around the world at the surface.

Every cell is worlds within worlds of nanotechnology finely tuned and regulated.

Darwin’s elaborate construct is stalled at the cell; even the simplest prokaryotic cell is infinitely beyond the odds of ever coming together by random, undirected process.

Jame Lunney is attacking evolutionary biologists and their acceptance of the scientific evidence for evolution, which happens to be their area of expertise. It seems ironic that he accuses others of bigotry and bullying.

James Lunney is a chiropractor and he has a B.Sc. (science). He says, "I have a background in Science: my credentials modest as they are, are superior on this file to many in this chamber and most of my critics."

That explains a lot.

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Poor James Lunney resigns from the Conservative Party because of bullying over his religious beliefs

Some of you may recall James Lunney, Conservative Party Member of Parliament for Nanaimo-Alberni in British Columbia. He's a chiropractor who spoke out against evolution back in 2009 [James Lunney: Creationist, Chiropractor, Conservative].

More recently, he defended another MP who didn't believe in evolution. He was mocked and ridiculed in the popular press and now he has decided to resign from the Conservative Party and sit in the House of Commons as an Independent. That's not working out so well according to CBC News [James Lunney defends views on evolution in House of Commons].

One day after he announced he was leaving the Conservative caucus to better defend his religious beliefs, Nanaimo-Alberni MP James Lunney attempted to do just that from his new seat in the corner of the House of Commons reserved for independent MPs.

But despite his best efforts, he was unable to convince House of Commons Speaker Andrew Scheer that the "cyberbullying" and "crowd-shaming" that he claimed to have experienced after questioning the science behind evolution constituted a breach of his parliamentary privilege.

Imagine that! He was unable to convince Parliament that making fun of his silly beliefs is wrong! This is exactly how the Canadian public SHOULD deal with people who act like kooks.

Wanna hear about his beliefs? This is what he said in Parliament ....

Speaking to CBC News Power & Politics host Evan Solomon on Wednesday evening, Lunney said that he was tired of seeing his faith community bullied.

...

Lunney described evolution — or, as he calls it, "macro-evolution" is "a theory in crisis."

"Scientists are not able to speak their mind on that — at least half of them who feel this way, they're gagged by an old construct," he argued.

"There's a whole generation of kids being taught that what they're taught in Sunday School or in church is garbage, it's wrong, it's false, and it's simply a form of bullying that's no longer acceptable. It's not scientifically tenable, it's a disservice to science… it's not freedom of religion if your views are put down by your peers."

Freedom comes in several forms. If you live in a free society then you have to be prepared to accept criticism of your most cherished beliefs. You can't hide behind religion to protect you when you act like an IDiot. Pointing out the stupidity of a Member of Parliament is not bullying

As far as I'm concerned, this is exactly how freedom should work.

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On the "ethics" of germ line DNA editing

Edward Lanphier, Fyodor Urnov, Sarah Ehlen Haecker, Michael Werner and Joanna Smolenski have published a comment in Nature with a provocative headline "Don’t edit the human germ line. They are asking scientists to agree " not to modify the DNA of human reproductive cells." The idea is that editing the genome of sperm or egg cells produces changes that will be passed on to future generations and this poses certain dangers.

Physiologists fall for the Third Way

I looked forward to this "conversation" because I was already familiar with Denis Noble and his strange views of evolution [A physiologist thinks about evolution]. Noble reiterated his view of modern evolutionary theory at the meeting. He thinks that modern evolutionary theory (The Modern Synthesis or Neo-Darwinism) is all about random mutation and natural selection. He thinks it is based on the views of Richard Dawkins in The Selfish Gene. Neither he nor Michael Joyner (an anaethesiologist at the Mayo Clinic) have learned about random genetic drift or Neutral Theory and neither of them have much knowledge of population genetics. In other words, they are pretty ignorant about evolution even though they feel entitled to attack it.

The President and Vice-President arrive in Boston

There's a shuttle bus that runs between my hotel in Boston and the convention center where Experimental Biology takes place. I went down to the hotel lobby this morning to catch the shuttle bus. The first clue that something was amiss was the four policemen in their yellow jackets sitting in the lounge. Their big bikes were parked just outside. The second clue was a larger than normal number of people waiting for cabs and shuttle buses.

All of a sudden, the cops left and so did all the taxis and shuttles without any passengers. That was also a clue.

The hotel informed us that there would be no shuttles to the conference center this morning, no shuttles to the airport, and no taxis because the President of the United States and the Vice-President were arriving.¹ This requires shutting down I90 for several hours.

I decided to eat breakfast in the restaurant and wait out the disruption. (There wasn't anything interesting going on at the meeting this morning anyway.) I watched the motorcade go by on the Interstate. There were about a dozen cars lit up like Christmas trees, including an ambulance with lights flashing. Most of the lights were blue but there was a pretty mixture of yellow, red, orange, and green.

Judging by the number of angry people in the lobby, I can understand why the President and Vice-President need so much protection.

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1. They are attending the opening of the Edward M. Kennedy Institute.

Interdisciplinary Research

I'm at the Experimental Biology meetings in Boston and yesterday I dropped into a session on "Training the Mind of an Interdisciplinary Scientist." There were talks on how to resolve disputes among member of the interdisciplinary team, and on how to choose a problem that your customers want solved (from an engineer). There are was also a talk from the University of Missouri-Kansas City about their graduate program. Every single graduate student has to choose an interdisciplinary problem for their thesis topic and they have to take a half dozen courses in each of two disciplines (at least).

The only experience I've had with being interdisciplinary is when I tried to understand what computer scientists were interested in and whether we could work together on some problems. We couldn't. The gap was too large. So biochemists have just adopted the tools and techniques of computational sciences and moved on.

Very few of my colleagues are doing interdisciplinary research and they seem to be getting along just fine. Is this whole "interdisciplinary" thing just a fad? Do you know anyone whose main area of investigation spans two distinct disciplines?

I got the distinct impression from the session that there's pressure from university administrations and granting agencies to become interdisciplinary. Is this true?

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Plant biologists are confused about the meanings of junk DNA and genes

A recent issue of Nature contains a report on plant micro-RNAs (Lauressergues et al., 2015). The authors found that certain genes for plant micro-RNAs encoded short peptides in the micro-RNA precursors and those peptides seemed to have a biological function. What this means is that part of the longer precursor RNA that is cleaved to produce the final micro-RNA may have a function that wasn't recognized. If you thought that the part of the precursor that was thought to be discarded as useless junk was, in fact, junk, then you were wrong—at least for some genes.

This is not a big deal and the authors of the paper don't even mention junk DNA.

The paper was reviewed by Peter M. Waterhouse and Roger P. Hellens in the same issue (Waterhouse and Hellens, 2015). They think it's a big deal. Here's what they say,

Student essays about evolution

Students in my molecular evolution course have to write an essay. They can pick any topic they like as long as it's related to evolution and some controversy in the scientific literature. I have to approve the topic. The idea is that the students have to critically evaluate both sides of an issue and pick a side that they can defend.

The essays tell me a lot about what things are interesting in the course and how well the students understand the topics. Here are this year's topics.

• Education: Misconceptions in Evolutionary Biology
• Are Transposable Elements Junk?
• RNA World Hypothesis
• Evolutionary Psychology and Biology: A Comparison
• The End for the Alternative Search for Complexity
• C-Value Paradox: Why Junk DNA Looks So Good
• Will Humans Ever Be Perfectly Evolved?
• Epigenetic Inheritance: A Turning Point in Evolution?
• Back to Basics (about evolutinary biology eduaction)
• The Relationship between Natural Selection and Artificial Selection
• Foreign Gene Incorporation in Agriculture and in the wild: Debunking Anti-GMO Rhetoric and the "Unnatural" Fallacy
• Enhancers: An Evo-Devo Perspective
• Will humans stop evolving?
• Genomic Screening: Currently Not Worth the Trouble
• The Decade Long Argument Over Junk
• What Is a Gene?
• Sex: Is It Really Advantageous?
• A Critical Analysis of Stephen Meyer's Darwin's Doubt; The Explosive origin of Animal Life and the Case for Intelligent Design
• The Role of Natural Selection in the Process of Biological Human Evolution
• The Struggle Between Humans and Bacterial Evolution
• Drifting Away: Perspectives on Modern Evolution
• The Continuing Struggle Against Junk DNA
• The Evolution of Influenza A: Antigenic Drift at Work?

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Another successful prediction of Intelligent Design Creationism?

The genetic code is redundant. Many amino acids have multiple codons ranging from two to six. The different codons for the same amino acid are called "synonymous" codons.

As sequences of protein-coding genes began to accumulate in the 1980s, it became apparent that different synonymous codons were used preferentially in different species. The phenomenon became known as codon bias. By 1990 it was known that the frequency of codon usage was correlated with tRNA abundance. As a general rule, there is a different tRNA for each codon and if multiple codons exist for a given amino acid then insertion of that amino acid into protein will depend on different tRNAs carrying the same amino acid.

Quantifying the "central dogma"

There was a short article in a recent issue of Science that caught my eye. The title was "Statistics requantitates the central dogma."

As most Sandwalk readers know, The Central Dogma of Molecular Biology says,

... 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)

You might wonder how you can quantify the idea that once information gets into protein it can't flow back to nucleic acids. You can't, of course.

The authors are referring to the standard scheme of information flow from DNA to RNA to protein. This is often mistakenly referred to as the Central Dogma by those scientists who haven't read the original papers. In this case, the authors of the Science article are asking whether the levels of protein in different cells are mostly controlled at the level of transcription, translation, mRNA degradation, or protein degradation.

Mary Lyon (1925 - 2014)

Mary Lyon died on Christmas day last December. She was 89 years old.

She was a famous mouse geneticist who spend most of her working career at the MRC labs in Harwell, United Kingdom (near Oxford). The labs are known as an international center for mouse genetics.

Mary Lyon is famous for discovering the phenomenon of X chromosome inactivation. This is when one the the X chromosomes of female mammals is selectively inactivated so that the products of the X chromosome genes are quantitatively similar to the dosage in males where there's only one X chromosome. The phenomenon used to be referred to as Lyonization.

I never met Mary Lyon but from what people say about her, I'm sure I would have liked her. Here's an excerpt from the obituary in Nature: Mary F. Lyon (1925 - 2014).

Lyon was a central figure in twentieth-century mouse genetics. She laid the intellectual foundations and developed the genetic tools for the use of mice as model organisms in molecular medicine, cell and developmental biology and in deciphering the function of the human genome. Lyon was editor of Mouse News Letter from 1956 to 1970, a publication that had a key role in establishing a mouse-focused research community in the pre-Internet age. She also helped to develop a common language for the field by chairing the Committee on Standardised Genetic Nomenclature for Mice from 1975 to 1990. Her pivotal contribution was recognized by the naming of the Mary Lyon Centre, an international facility for mouse-genetic resources, opened at Harwell in 2004, and by the creation of the Mary Lyon Medal by the UK Genetics Society in 2014.

Because everything Mary said was so carefully thought through, she could be difficult to talk to: on the phone, it was easy to think you had been cut off. She did not suffer fools gladly, but was a great supporter of the bright young scientist, often eschewing authorship of publications to enhance the profile of junior collaborators. She was intellectually rigorous but not dictatorial. When I began my PhD with her in 1977, she gave me a handful of papers, showed me the genetic tools — mice carrying the various mutations and chromosomal rearrangements — and said, “do something on X-inactivation”. That degree of academic freedom was exhilarating, coupled as it was with the safety net of robust critique.

... Her first love was mice, although she always had a cat — a tortoiseshell, of course.

X chromosome inactivation is one of the classic examples of epigenetics, sensu stricto. It was the subject of one of my most popular posts of all time: Calico cats. Calico cats almost always have to be female but there are very rare examples of male calico cats. Can anyone figure out why?

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On the handedness of DNA

Double-stranded DNA forms a helical structure where the two strands are twisted into a helical shape. If you think of the base pairs forming a ladder then imagine that the entire ladder could be distorted by rotating the ends relative to each other. The result would be the helical shape of DNA. The twisting results mainly from the attraction between the planar base pairs (rungs of the ladder.) They are "happier" when they are stacked close together right on top of each other. (The "force" is called "stacking interactions.")

This is not how DNA is actually built since there's never a time inside the cell when the DNA forms a ladder-like structure that's not helical, but you get the picture. [The Three-Dimensional Structure of DNA]

The final form of double-stranded DNA on the right is a cartoon used to illustrate certain features. I've deliberately drawn it with about 10-11 base pairs per turn so you can see the shape of the helix.

Conrad Black attacks the shabby, shallow world of the militant, atheist

Conrad Black, also known as Baron Black of Crossharbour, KSG, was stimulated by a conversation with Christian apologist, and physicist, John Lennox. Black decided to write a column for the National Post (Toronto, Canada): Conrad Black: The shabby, shallow world of the militant atheist.

Richard Dawkins tweeted ...

Conrad Black seems to be at large again. Spot the factual errors, illogicalities and failures to understand.

Good advice. I wonder how many can be packed into a brief diatribe?

Keep in mind that no matter how many strawmen are erected, the important issue is whether gods exist. If you are a Christian, and you are going to attack the "shabby, shallow world" of atheists then the very least you can do is present your strongest case for the existence of gods.

Check out Conrad's Black's evidence for the existence of gods. (Warning: you will have to ignore all the rhetoric about the benefits of religion because it isn't relevant. On the other hand, there's a certain enjoyable irony in reading about how Christians are more moral than atheists.)

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How the genome lost its junk according to John Parrington

I really hate it when publishers start to hype a book several months before we can read it, especially when the topic is controversial. In this case, it's Oxford University Press and the book is "The Deeper Genome" Why there is more to the human genome than meets the eye." The author is John Parrington.

The title of the promotion blurb is: How the Genome Lost its Junk on the Canadian version of the Oxford University Press website. It looks like this book is going to be an attack on junk DNA.

We won't know for sure until June or July when the book is published. Until then, the author and the publisher will have free reign to sell their ideas without serious opposition or push back.

Here's the prepublication hype. I'm going to buy this book and read it as soon as it becomes available. Stay tuned for a review.

Junk DNA comments in the New York Times Magazine

It's always fun to be quoted in The New York Times Magazine but there's a more serious issue to discuss. I'm referring to a brief article about online comments after Carl Zimmer published a piece on "Is Most of Our DNA Garbage?" a few weeks ago. If you read the comments under that article you'll discover that we have a lot of work to do if we are going to convince the general public that our genome is full of junk.

Richard Lenski answers questions about the long-term evolution experiment (LTEE)

Richard Lenski has a blog called Telliamed Revisited. He's been answering questions about his long-term evolution experiment and the latest answers are at: Questions from Jeremy Fox about the LTEE, part 2.

"Did the LTEE have any hypotheses initially, and if so, how were you going to test them?

Short answer: Yes, the LTEE had many hypotheses, some pretty clear and explicit, some less so. (What, did you think I was swimming completely naked?)"

Well worth reading ....

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Economist Stephen Moore explains why we should mistrust science.

Stephen Moore is an conservative economist who writes for the Wall Street Journal. Here's a quote from the Wikipedia article ...

In a February 2, 2011 appearance on HBO's Real Time with Bill Maher, Moore stated "I say the Reagan tax cuts were the greatest economic policy of the last 50 years" and added "the lowest income people had the biggest gains" during the 1980s. Politifact.com found Moore's assertion to be false.

Moore thinks he's in a position to explain why scientists should not be trusted [The myth of ‘settled science’].

The magazine [National Geographic] is incredulous that so many skeptics "believe that climate activists are using the threat of global warming to attack the free market and industrial society generally."

Wait. Climate change activists are using the issue as a means of attacking free-market capitalism. This past summer major environmental groups gathered in Venezuela to solve leading environmental problems like global warming, concluding: “The structural causes of climate change are linked to the current capitalist hegemonic system.”

How is it paranoia to believe that the climate change industry wants to shut down capitalism when the movement plainly states that this is its objective? And how can a movement be driven by science when its very agenda violates basic laws of economics? I am no scientist, but I’m highly skeptical of a movement whose first advice is to steer the U.S. economy off a cliff toward financial ruin.

Well, there you have it. According to Stephen "I am no scientist" Moore, science can't be trusted because it violates the basic laws of economics, like those laws that Ronald Reagan must have obeyed when he instituted the greatest economic policy of the last 50 years.

QED

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Are gods a delusion?

John Lennox is a mathematician from Oxford (UK). He likes to attack the so-called "new atheists" and defend the idea that Christianity is rational. He is just finishing up a tour of North America. This video is a recording of a talk he gave at a church in the Toronto suburbs on March 14, 2015.

It's quite similar to the presentation he gave a few days later at the University of Waterloo (Waterloo, Ontario, Canada). Jeffrey Shallit went to that talk (bless his heart) and reports on the major fallacies and distortions [John Lennox - Talk #1: "Do Science and God Mix?"]. As you watch the video you'll see that John Lennox is a very good speaker. He sounds very, very, convincing in the tradition of many other religious Oxford professors and even atheist ones like Richard Dawkins.

As you listen and watch, you gradually come to the realization that the lecture is all about Irish charm and humor. Most of his arguments don't make any sense as we know from listening to them many times over the past few decades. How many times have we heard the argument that so-and-so Nobel Laureates were Christians so science and religion must be compatible?

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Apparently it really is impossible to teach Intelligent Design Creationists about evolutionary theory

Last week I asked an important question, "Is it impossible to educate Intelligent Design Creationists on evolutionary theory?.

The reason I asked is because in spite of our best efforts over several decades, the Intelligent Design Creationists still don't understand modern evolutionary theory. We see this all the time whenever they start criticizing evolution. It gets them into all sorts of trouble, especially when we debate junk DNA.

Many of their objections to evolution would be easily answered if they only understood that there's more to evolution than natural selection and the appearance of design. They would understand why Michael Behe is wrong about the edge of evolution, for example, and why their pseudoscientific probability calculations are nonsense. They can't possibly understand molecular evolution and phylogenetic trees based on sequences unless they understand that it has almost nothing to do with "Darwinism" and the appearance of design.

Do offensive pictures justify violence?

This video raises many complicated issues. It's a confrontation between students and anti-abortion protestors on the University of Oregon campus on March 10, 2015.

Most of the buzz on the internet is about the first policeman who tried to defuse a potentially violent confrontation by telling the main protestor that he did not have the right to free speech on a private university campus. He almost succeeded in getting the protestor to hide his offensive signs.

When the sargeant showed up, he overruled his officer and told the protestor he could display his signs and stay on the campus. I agree with the sergeant but I have a great deal of sympathy with what the first policeman was trying to do.

How do Intelligent Design Creationists interpret "extraordinary evidence"?

Marcello Truzzi was one of the founding members of the Committee for the Scientific Investigation of Claims of the Paranormal (CSICOP). Back in 1978 he said, "An extraordinary claim requires extraordinary proof." Carl Sagan popularized this idea as "Extraordinary claims require extraordinary evidence."

The basic idea has been around for centuries.

We often use this saying when we encounter gullible creationists making extraordinary claims. For example, a few weeks ago Vincent Torley claimed that back in the 1600s a monk named St. Cupertino was routinely seen to fly through the air on numerous occasions [see What counts as "evidence"?].

Casey Luskin agrees with Lawrence Krauss ... teach the controversy

Casey Luskin suggests that we should teach science properly [How Should We Teach Evolution?].

Science education theorists agree that students learn science best when they learn about arguments for and against a particular concept. A 2010 paper in the journal Science observes that "[c]ritique is not, therefore, some peripheral feature of science, but rather it is core to its practice." The paper found that students learn science best when they are asked "to discriminate between evidence that supports ... or does not support"4 a given scientific concept.

Science education is about teaching students the facts of biology, but also about teaching them how to think like scientists. When students are told that Darwinian evolution is a "settled theory" or that there "is no controversy over evolution," that not only misinforms them about debates taking place among scientists, but it fails to teach students how to use critical thinking on these important scientific questions. When evolution advocates demand that students should not learn about scientific weaknesses in evolution, the real losers are the students who are denied opportunities to learn about all of the evidence and are prevented from studying different legitimate scientific viewpoints regarding Darwinism.

I agree with Luskin and Krauss.

They disagree about the probable outcome of this kind of education but let's put it to the test.

If we did, I predict that Casey Luskin will be sorry he ever mentioned critical thinking.

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Lawrence Krauss advocates "teaching doubt"

There's a robust pedagogical literature on misconceptions and how difficult it is for educators overcome them in the classroom. The current overwhelming consensus is that you have to address those misconceptions head-on and show why they are wrong. You are doomed to failure if you just try to correct misconceptions by teaching the correct idea in the hope that students will see the light all by themselves.

That's why you must "teach the controversy." This applies in spades to the evolution/creation debate. You can't expect creationists to abandon their misconceptions about evolution if all you do is expose them to the latest information about evolution and evolutionary theory. They are already armed with all kinds of objections, rationalizations, and misconceptions about evolution and they'll listen politely while saying to themselves that it's all a bunch of lies.

You need to show them why the idea of a 6000 year old Earth is wrong and why it's foolish to say there are no transitional fossils.

Lawrence Krauss makes the case in The New Yorker [Teaching Doubt].

One thing is certain: if our educational system does not honestly and explicitly promote the central tenet of science—that nothing is sacred—then we encourage myth and prejudice to endure. We need to equip our children with tools to avoid the mistakes of the past while constructing a better, and more sustainable, world for themselves and future generations. We won’t do that by dodging inevitable and important questions about facts and faith. Instead of punting on those questions, we owe it to the next generation to plant the seeds of doubt.

This approach works in most of the Western industrialized world but it probably can't work in America. That's because Americans have set up a system where you can't challenge religious beliefs in public schools because it's a violation of their Constitution. That's to bad because it means that science teachers can't do their job.

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IDiots say that evolution violates the Second Law of Thermodynamics

Over on the main "science" blog of the Intelligent Design Creationists, that famous scientist, kairosfocus, says on Piotr (and KS, DNA_Jock, VS, Z et al) and “compensation” arguments vs the energy audit police ..., quoting that other famous scientist Granville Sewell,

The discovery that life on Earth developed through evolutionary "steps," coupled with the observation that mutations and natural selection -- like other natural forces -- can cause (minor) change, is widely accepted in the scientific world as proof that natural selection -- alone among all natural forces -- can create order out of disorder, and even design human brains, with human consciousness. Only the layman seems to see the problem with this logic. In a recent Mathematical Intelligencer article ["A Mathematician's View of Evolution," The Mathematical Intelligencer 22, number 4, 5-7, 2000] I asserted that the idea that the four fundamental forces of physics alone could rearrange the fundamental particles of Nature into spaceships, nuclear power plants, and computers, connected to laser printers, CRTs, keyboards and the Internet, appears to violate the second law of thermodynamics in a spectacular way.

There's obviously a problem. The IDiots have to believe and trust one set of scientists and not another.

Since the evidence for evolution is overwhelming, the Second Law of Thermodynamics must be wrong.

Stupid chemists.

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Photo credit: Aubrey Hirsch

The University of Toronto ranks 16th in the world!

The latest Times Higher Education World Reputation Rankings for 2015 are out [The World Reputation Rankings]. This ranking list universities by their academic reputation. It has little to do with undergraduate education, which in most cases, is just an important sideline for these universities.

The University of Toronto ranks #16 on this list. I mention this because many people in the USA are unaware of the quality of universities in other countries. They will not be surprised to learn that Harvard is #1 but do they know that Cambridge is #2 and Oxford is #3?

Canada has three universities in the top 40 (McGill #35 and the University of British Columbia #37 are the other two). Our population is 35 million.

The USA has twenty-one universities in the top 40. It's population is 320 million.

The United Kingdom has seven in the top 40 with a population of 65 million.

It won't be long before China takes over.

It seems pretty obvious that the number and quality of universities is proportional to the wealth and the population of countries in the "Western" English-speaking world. It is not obvious that any one country can claim to be better than the others at fostering good universities. If you had to pick a country, it looks like the United Kingdom would be the clear winner.

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Is it impossible to educate Intelligent Design Creationists on evolutionary theory?

We all know how much creationists like to label their opponents as "Darwinists." What you don't know is that many of us have spent decades trying to teach creationists about modern evolutionary theory and why is is much more than just mutation plus natural selection. Some Intelligent Design Creationists seem to get it but then they quickly revert to the old rhetoric.

So, the question is whether the Intelligent Design Creationists really understand modern evolutionary theory or not. If they do, then they must be lying when they claim that it's just natural selection and "Darwinism." It can't be excused as ignorance in that case. Alternatively, if they don't understand modern evolutionary theory then they must be stupid.

Which is it?