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Monday, March 30, 2015

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.

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?

Friday, March 27, 2015

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?

Wednesday, March 25, 2015

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.

Monday, March 23, 2015

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?

Sunday, March 22, 2015

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.

Saturday, March 21, 2015

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.)

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.

Wednesday, March 18, 2015

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 ....

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. 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.


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?

Tuesday, March 17, 2015

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.

Monday, March 16, 2015

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.

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.

Sunday, March 15, 2015

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.

Photo credit: Aubrey Hirsch

Thursday, March 12, 2015

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.

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?

Wednesday, March 11, 2015

A physicist tries to understand junk DNA: Part II

Yesterday I posted some comments on a blog post by physicist Rob Sheldon [A physicist tries to understand junk DNA ]. My comments were based on what I had seen on Uncommon Descent but it turns out that was only a summary of a longer post that appeared on Evolution News & Views (sic): More on Junk DNA and the "Onion Test".

The longer post doesn't add very much to the argument but it does have something interesting at the bottom. Here's what Rob Sheldon says about the Onion Test and junk DNA.

Tuesday, March 10, 2015

A physicist tries to understand junk DNA

Rob Sheldon has a PhD. in physics and a M.A. in religion.1 With two strikes against him already, he attempts to understand biology by discussing evolution, junk DNA, and the Onion Test [Physicist suggests: “Onion test” for junk DNA is challenge to Darwinism, not ID]. As you might imagine, posting on Uncommon Descent in support of Intelligent Design Creationism leads directly to strike three.

The Onion Test was created by Ryan Gregory in 2007 [The Onion Test] and published in the scientific literature by Palazzo and Gregory in 2014. It goes like this. Take your favorite hypothesis suggesting that most of the DNA in the human genome is functional and use it to explain why the onion, Allium cepa, needs a genome that is five times larger than the human genome. Then explain why closely related species of onion need twenty times more DNA than humans.

Monday, March 09, 2015

Learn to think like a scientist

There's a course at MIT (Boston, USA) called "7.00x Introduction to Biology - The Secret of Life." It's a very popular MOOC (online course). Here's the trailer for the course. In it, Eric Lander tells you that if you take his introductory biology course you will learn to think like a scientist and you will be able to understand the latest breakthroughs.

Here are the week one lectures that focus on biochemistry. I don't have time to go through it all but check out the description of ATP beginning at 2:13. This is not how good teachers explain the importance of ATP in the 21st century but it is how it was taught 40 years ago.

Saturday, March 07, 2015

Get a job as a dissertation writer

Jerry Coyne has found a posting for a job in Toronto [see Dissertations for sale!]. You can see the original at: Dissertation Writers wanted for Work from Home Position. It's suitable for retired professors and post-docs who can't get any other job.
We are a medium sized, cloud-based consultancy headquartered in New York, but with consultants spread across the globe, from Asia to South America. We primarily handle Academic Consulting for Doctorate level clients, and we currently have several job openings in the Academic Research department.

Job responsibilities:
Your main responsibility will be to assist our clients in conducting the research needed needed to complete their theses, dissertations, or journal articles, and then writing drafts for portions of those documents, such as a Literature Review, Introduction or Discussion chapters.

The job will involve communicating with clients by email and by phone to understand their specific needs, provide suggestions on how to improve their research, and finally write a draft of the document itself. It will also involve engaging in ongoing discussions with clients after the first draft, and revising/rewriting the document to our clients' satisfaction.

*This is strictly a work-from-home position*, and any applicant should view this as a strong incentive.

Please note that this is a *full-time position*.

- Applicants must possess a meticulous nature and an extremely high attention to detail.
- A very positive and upbeat attitude (particularly as relates to phone calls and email communication with clients).
- Native English speakers only.
- A 4-year college degree is an absolute must, preferably from a well-known university.
- Ghostwriting or Technical Writing experience is desired, but not a must.
- Tutoring and/or research experience is also a bonus.

Compensation for the successful applicant is very generous. As we expect very few applicants to have directly applicable work experience in this field, there will be an extensive training program before the candidate is taken on in a more permanent capacity. Training will be paid, at USD 4,000/month, and is projected to last 3-4 months. Following successful training, pay will be USD 85,000 - USD 100,000/year.
I've chaired quite a few Ph.D. exams for humanities students and I reckon I could bang out a pretty good thesis in a few months.

As for journal articles, the ENCODE Consortium could hire me for $8000 per month.

Friday, March 06, 2015

Here's a good example of a tenured professor who should be fired

I am a staunch defendant of academic freedom but tenure doesn't protect you from gross misconduct. Here's an example where a Professor of Philosophy at UNC faced dismissal hearings and, wisely, decided to resign. I'm betting that ethics wasn't her specialty.

Why did she resign? Read about it at: Jan Boxill, implicated in UNC scandal, resigns.

Apparently Boxill was counselor to the women’s basketball team and she participated in a scheme to give athletes decent grades in "courses" that didn't exist or required minimal work. Some of the courses were in African and Afro-American Studies (AFAM) and some were philosophy courses.
[The Provost's] letter to Boxill said there was "compelling evidence that over a period of several years you knowingly participated in grossly improper practices in your roles as a member of the faculty and an academic advisor to student athletes."

The letter, released Thursday, accused Boxill of several acts of misconduct:

▪ Requesting that AFAM employees provide specific grades to students.

▪ Steering athletes to AFAM courses that she knew were not overseen or taught by faculty, required only a paper and were graded by former office manager Deborah Crowder.

▪ Editing and writing portions of text inserted into the papers of the students she tutored.

▪ Allowing students to enroll in independent study classes in philosophy that required little academic work.
Bye-bye Boxhill.

How to promote science according to new AAAS CEO Rush D. Holt

As the name implies, the American Association for the Advancement of Science (AAAS) is a group of American scientists dedicated to "advancing" science. It was formed in 1848 and over the years it has evolved into a sophisticated lobby for advocating and defending science funding as well as an organization that promotes science to the general public. It publishes several journals, including Science and Science: Translational Medicine.

The new CEO and Executive Publisher of Science is Rush D. Holt, Jr.. He is the son of a former United States Senator (Rush D. Holt Sr.). Rush D. Holt Jr. obtained a Ph.D. in physics in 1981 and taught courses in physics, public policy, and religion at Swarthmore College from 1980 to 1986. He is a Quaker.

Thursday, March 05, 2015

Don't misuse the word "homology"

Here's the latest science news from The Allium": Evolutionist Loses It As Colleague Conflates Homology and Similarity Yet Again.
Evolutionary biologist Dr. Constance Noring shot and killed her microbiology colleague and formerly good friend, Dr. Dan Deline when, for the umpteenth time he used the word homology when he really should have said similarity.
Read the rest. I sympathize with Professor Noring. This could have been me if Canadians were allowed to buy handguns.

C0nc0rdance reads from Dobzhansky defending accommondationism

Here's how COncOrdance explains his latest YouTube video.
To celebrate Darwin Day, Feb 12th, 2015, I offer the words of Dobzhansky, who was a central figure in the modern evolutionary synthesis with his 1937 book, "Genetics and the Origin of Species". Dobzhansky was also a deeply religious man who believed that God had a hand in the process of evolution, a view I don't share, but try to understand.

Dobzhansky cites Teilhard de Chardin, who was a biologist, a theistic evolutionist, and a controversial figure who described evolution as cosmic attainment of perfection, a concept I also strongly disagree with.

This is an excerpt from the original work:
The American Biology Teacher, Vol. 35, No. 3 (Mar., 1973), pp. 125-129. [Nothing in Biology Makes Sense except in the Light of Evolution]
I'm not sure what purpose is served by reading from Dobzhansky's book where he praises Pierre Teilhard de Chardin. Keep in mind that Teilhard's most famous book was reviewed by Peter Medawar who described it like this: "... the greater part of it, I shall show, is nonsense, tricked out with a variety of metaphysical conceits, and its author can be excused of dishonesty only on the grounds that before deceiving others he has taken great pains to deceive himself."

That's pretty much the consensus view of Teilhard these days. It's also pretty common to point out that science as a way of knowing conflicts with religion as a way of knowing in spite of what Dobzhansky said 46 years ago.

Here's the video ....

Is most of our DNA garbage?

Carl Zimmer's article on junk DNA has appeared in the online edition of the New York Times magazine at: Is Most of Our DNA Garbage?.

Carl was in Toronto and Guelph last December gathering information for his article. You can see that Ryan Gregory is featured and my colleague Alex Palazzo gets quoted.

Here's a picture of us having dinner. That's Alex on the left, second from left is some old dude who everyone ignores, Ryan is next and Carl Zimmer is on the right.

Carl is still the best science journalist on the planet and I appreciate that he has alerted the public to a serious problem in genome studies. The general public has been snowed by the ENCODE publicity campaign and by naive journalists who have enthusiastically reported that junk DNA is dead.

It is not. The most knowledgeable scientists recognize that the issue is not settled. The very best ones () know that 90% of our genome is junk.

Wednesday, March 04, 2015

Does still exist?

Several people have asked recently if still exists and if the TalkOrigins Archive is still functional. As it turns out, the current king of the newsgroup (David Greig) is going to be here (my office) either today or in the next few days to upgrade the server. The name of the server is "Darwin" and here's what it looks like (right).

Here's a link to the newsgroup: Here's a description from the Wikipedia article on
The first post to was a starter post by Mark Horton, dated 5 September 1986.

In the early 1990s, a number of FAQs on various topics were being periodically posted to the newsgroup. In 1994, Brett J. Vickers established an anonymous FTP site to host the collected FAQs of the newsgroup. In 1995, Vickers started the TalkOrigins Archive web site as another means of hosting the FAQs. It maintains an extensive FAQ on topics in evolutionary biology, geology and astronomy, with the aim of representing the views of mainstream science. It has spawned other websites, notably TalkDesign "a response to the intelligent design movement", Evowiki, and the Panda's Thumb weblog.

The group was originally created as the unmoderated newsgroup as a 'dumping ground' for all the various flame threads 'polluting' other newsgroups, then renamed to as part of the Great Renaming. Subsequently, after discussion on the newsgroup, the group was voted to be moderated in 1997 by the normal USENET RFD/CFV process, in which only spam and excessive crossposting are censored. The moderator for the newsgroup is David Iain Greig (and technically Jim Lippard as alternate/backup).

The group is characterized by a long list of in-crowd jokes like the fictitious University of Ediacara, the equally fictitious Evil Atheist Conspiracy which allegedly hides all the evidence supporting Creationism, a monthly election of the Chez Watt-award for "statements that make you go 'say what', or some such.", pun cascades, a strong predisposition to quoting Monty Python and a habit of calling penguins "the best birds".

Apart from the fun, the group includes rebuttals to creationist claims.There is an expectation that any claim is to be backed up by actual evidence, preferably in the form of a peer-reviewed publication in a reputable journal. The group as a whole votes for a PoTM-award (Post of The Month), which makes it into the annals of TalkOrigins Archive.
I forgot about penguins being the best bird. The article forgot to mention Howler monkeys.

The University of Ediacara consists of many faculty members named Chris plus some others. There's only one permanent student, me.

I won't try to name all the alumni who are still active on the newsgroup or on blogs. I'll let them confess identify themselves in the comments if they dare.

Here's the link to the TalkOrigins Archive. It contains all kinds of information on the evolution/creation debate including all the rebuttals to any argument the creationists have ever made.

Monday, March 02, 2015

Genomes and junk DNA

Here's your chance to hear about genomes and junk DNA from one of the world's leading experts. The seminar is at the University of Toronto (Toronto, Canada) in the Medical Sciences Building. It's on Wednesday, March 4th—only two days form today! The seminar room (Rm 2172) is right around the corner from Tim Hortons. Ryan is from the University of Guelph. How Canadian can you get, eh?

Sunday, March 01, 2015

The University of Toronto explains why it hosted an alternative medicine conference

I received a response from Bruce Kidd, the Principal of the University of Toronto at Scarborough on why his campus was hosting a conference on alternative medicine (see Is the University of Toronto promoting quackery and pseudoscience?). I had asked whether the university was officially involved in sponsoring the event.

Here is his complete response. He knows that I will post it on my blog.
Dear Professor Moran:

Thank you for your inquiry. The University encourages the fullest, critical investigation of scientific and social issues, including the bases of health and well-being and the various ways personal, community and environmental health can be maintained and strengthened. That is an essential part of our institutional mission. As you know, we have been debating whose knowledge counts, the methodological bases for such knowledge and the professional practices that have been developed as a result of such knowledge in the field of health for many years. That's how knowledge advances. The hosting of the Population Health and Policy Conference at UTSC yesterday was just one expression of that commitment to critical inquiry.

That being said, such hosting cannot be equated with endorsement of the various positions and points of view expressed at the conference. I have attended hundreds of conferences at U of T and other universities over the years and have never felt that the presentation of particular views meant that the hosting institution endorsed those particular views.

I hope that's helpful.

With best wishes,

Bruce Kidd, O.C., Ph.D., LL.D.
Vice-President and Principal
University of Toronto Scarborough
Professor, Faculty of Kinesiology and Physical Education
I'm all in favor of critical investigation of scientific issues and critical inquiry. I think it's a good idea for the University of Toronto to sponsored a conference where diverse points of view are presented and debated. That's how we learn to distinguish science from pseudoscience and "whose knowledge counts."

There is no possibility that this conference meets those minimal academic requirements.

Here's the welcome message from the Chair of Anthropology and the Associate Chair of Health Studies [see Population Health and Policy Conference].
Welcome to the second Population Health and Policy Conference at UTSC! This event demonstrates not only the energy and initiative of our student organizers, but also the enthusiasm of the students in the Health Studies programs at UTSC. The faculty in Health Studies are very proud of the commitment of our students.

The Health Studies programs promote an understanding of health across a spectrum of academic perspectives: from the clinical and biological health sciences, to social science and humanistic ways of knowing. What binds together these disciplinary approaches is a consciousness of the need for rigorous biological knowledge to be understood in tandem with the social milieu of human health and embodiment.

The programs are built around the bio-medical paradigm, to which the faculty in the program are unreservedly committed. This model has been spectacularly successful in increasing the life span and wellbeing of the majority of people around the world. At the same time Health Studies students learn how to view this paradigm critically through a variety of lenses, notably with respect to such issues as inequality of access, social factors that influence the prevalence of disease and the likelihood of cure, the impacts of government policy on health, and the perspectives of diverse practitioners and clients within the broad health care system. The theme of this year’s conference is Alternative Medicine and the ideas and practices it offers to complement standard health care and the biomedical model, including its emphasis on nutrition and lifestyle. As students and faculty we hold Alternative Health to the same standards of rigorous inquiry and critical appraisal that we apply to other aspects of our society.

The program covers much ground and promises to be stimulating and exciting. We look forward to seeing you there.

Prof. Michael Lambek, Chair, Department of Anthropology

Prof. John Scherk, Associate Chair, Health Studies
Apparently there are at least two ways of knowing the truth; science and the "humanistic way of knowing." I'm disturbed to see that students and faculty are holding alternative health to "the same standards of rigorous inquiry and critical appraisal that we apply to other aspects of our society." It suggests that we're in a lot more trouble than just alternative medicine.