Inciting Hatred

 
This video is making the rounds. I'm including it here because so many people have been discussing "civility" and "politeness" in the wake of the Tuscon mass killing. In my opinion, it's not lack of civility that's the problem. The problem arises when you start treating your opponents as anti-American and unpatriotic and their ideas as illegitimate (not just a difference of opinion). That's when it becomes reasonable to consider using force to prevent your enemy from destroying the country. You are protecting America against dictatorial traitors and that's exactly what reasonable citizens should do.

Glen Beck is a master of this technique. He should not be surprised if some of his followers jump to the obvious conclusion. Indeed, CUNY professor Frances Fox Piven (78 years old) has been receiving death threats ever since Beck's rant aired on television last November [Glenn Beck's Ranting Sparks Death Threats Against 78-Year-Old Sociologist]. Is anyone surprised?

Why does Glen Beck still have a job?

A note to Canadian readers. Pay attention. This is the real problem, not simple lack of politeness.

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What Did You Learn at University?

What did you learn at university? Not much, it seems, according to the data in a new book titled Academically Adrift. The book is reviewed in the latest issue if Inside Higher Ed [Academically Adrift].

The data aren't surprising. The authors of the book show that 36% of students failed to learn anything after four years of college. Of those who did learn something, the gains were very modest.

Why don't students learn?

The main culprit for lack of academic progress of students, according to the authors, is a lack of rigor. They review data from student surveys to show, for example, that 32 percent of students each semester do not take any courses with more than 40 pages of reading assigned a week, and that half don't take a single course in which they must write more than 20 pages over the course of a semester. Further, the authors note that students spend, on average, only about 12-14 hours a week studying, and that much of this time is studying in groups.

Who's to blame for this sorry state of affairs?

Debra Humphreys, vice president for communications and public affairs of AAC&U, said that she viewed the book as "devastating" in its critique of higher education. Faculty members and administrators (not to mention students and parents) should be alarmed by how little learning the authors found to be taking place, she said. Humphreys also said that the findings should give pause to those anxious to push students through and award more degrees -- without perhaps giving enough attention to what happens during a college education.

"In the race to completion, there is this assumption that a credit is a credit is a credit, and when you get to the magic number of credits, you will have learned what you need to learn," she said. What this book shows, Humphreys added, is that "you can accumulate an awful lot of credits and not learn anything."

None of this is news my colleagues and me. Problem is, there's not much we can do about it. If we increase the rigor of our biochemistry courses and start demanding more of our students then the result won't be increased learning. It will simply mean that undergraduates will avoid biochemistry courses. In fact, that's already happening since the University of Toronto has developed dozens of new programs that will award degrees in the biological sciences without ever forcing students to take a rigorous course.

This brings up a question that I often ask my students. If university is supposed to be difficult (rigorous) then it's likely that some students won't be capable of completing a degree. In an ideal setting with expertly taught, challenging, programs, what percentage of the incoming class of students should expect to complete a degree? Clearly the answer can't be 100% because that bar is way too low. Should it be 50% as it was in many universities in the past? Lower?

The graduation rate at the University of Toronto has been pretty constant over the past decade at 73-75%. I assume that many of the students who drop out do so for reasons other than the rigor of university courses (e.g., personal problems, financial problems, transfers, changing goals etc.). Let's assume that this accounts for 15% of the drop-outs.

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[Hat Tip: Uncertain Principles]

Extraordinary Claims: Psychics, Homeopathy and Christ

 

This Friday night at 7:30 p.m. CFI Canada launches the much awaited Extraordinary Claims campaign with three lectures, a panel discussion and an audience question-and-answer session, for a critical analysis of Psychics, Homeopathy and Christ. The invitation has also been respectfully extended to hundreds in the Toronto area who support one or more of these claims. The night promises to be an exciting and fascinating experience. Don't miss out!

Professor James Alcock of York University will address Psychics, Dr. Iain Martel of the Committee for the Advancement of Scientific Skepticism (CASS) will analyze Homeopathy and John Loftus, a former Christian Minister and apologist, will take on Christ. The night will be moderated by Michael Kruse, co-chair of CASS.

Date and time: Friday, January 21, 7:30 p.m. to 10:00 p.m. CFI members have advance access to seating beginning at 6:45 p.m. Non-members will be seated shortly before the presentation begins.

Location: University of Toronto - MacLeod Auditorium - 1 King's College Circle, Room 2158 Google Map

Admission prices: $8 general, $5 students and FREE for CFI members. Become a CFI member or renew.

Prepaying admission by PayPal is offered HERE. Please print out your PayPal receipt and bring it with you.

CFI members please bring your membership card and check the expiration date to ensure you can get in for FREE. If you are unsure then call Centre for Inquiry Ontario at (416) 971-5676 or e-mail info@cficanada.ca

A members-only reception is being held at 5:30 p.m. at CFI Ontario (216 Beverly St.).

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Comments Allowed at Evolution News & Views!

 
Evolution News & View is one of the main blogs for promoting Intelligent Design Creationism. Up 'till now it has not allowed comments but that has changed. Here's the new policy ...

Of course, you might want to discuss it with the scientists and scholars themselves. To that end, comments will be allowed on selected articles. All comments are held for moderation. The debate over evolution and intelligent design attracts all kinds, including those who detract from the conversation by their obnoxious behavior. In order to maintain a higher level of discourse, we will not publish comments that use foul language, ad hominem attacks, threats, or are otherwise uncivil.

By way of contrast, this blog and many others run by defenders of evolution will allow all comments except spam. We're not afraid of contrary opinions or uncivil behavior from creationists. We get them all the time.

I wonder what they're really afraid of?

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[Image Credit: Institute for Creationist Strategies: Show pride in your anti-scientific beliefs]

The Bankruptcy of Evolutionary Psychology

Evolutionary psychologists never seem to give up. Their latest folly is to pretend that women have a series of evolved behaviors to avoid rape during the time that they're ovulating.

Jerry Coyne has already commented on the study and his follow-up posting is worth reading because it highlights the responses of others who have dissected the papers [The women of Slate take on evolutionary psychology].

The bottom line is that the entire field of evolutionary psychology is in big trouble and it is bound to become a major laughing stock unless evolutionary psychologists clean up their act [Evolutionary Psychology as Maladapted Psychology].

One of Jerry Coyne's comments caught my eye because we've just been reading the Gould & Lewontin Spandrels paper in class. Coyne said,

Like the stories of the Bible, there’s no evolutionary psychology hypothesis that can be disconfirmed by data. If your story doesn’t hold up, simply concoct another story. Of course, there’s no evidence for the alternative stories, either.

In 1979 Gould and Lewontin wrote,

The admission of alternatives in principle does not imply their serious consideration in daily practice. We all say that not everything is adaptive; yet, faced with an organism, we tend to break it into parts and tell adaptive stories as if trade-offs among competing, well designed parts were the only constraint upon perfection for each trait. It is an old habit. As Romanes complained about A.R. Wallace in 1900: "Mr. Wallace does not expressly maintain the abstract impossibility of laws and causes other than those of utility and natural selection... Nevertheless, as he nowhere recognizes any other law or cause... he practically concludes that, on inductive or empirical grounds, there is no such other law or cause to be entertained. The adaptationist programme can be traced through common styles of argument. We illustrate just a few; we trust they will be recognized by all:

(1) If one adaptive argument fails, try another. Zig-zag commissures of clams and brachiopods, once widely regarded as devices for strengthening the shell, become sieves for restricting particles above a given size (Rudwick, 1964). A suite of external structures (horns, antlers, tusks) once viewed as weapons against predators, become symbols of intra-specific competition among males (Davitashvili, 1961). The eskimo face, once depicted as "cold engineered" (Coon, et al., 1950), becomes an adaptation to generate and withstand large masticatory forces (Shea, 1977). We do not attack these newer interpretations; they may all be right. We do wonder, though, whether the failure of one adaptive explanation should always simply inspire a search for another of the same general form, rather than a consideration of alternatives to the proposition that each part is "for" some specific purpose.

Plus ça change, plus c'est la même chose.

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The Science Hall of Fame

 
Science has published the Science Hall of Fame, a list of the most famous scientists of the past few hundred years. They compiled the list by counting the number of times that a scientist was mentioned in books published since 1800. The standard is Charles Darwin whose citations are set at 1000 milliDarwins. The only one who ranked higher was Bertrand Russell at 1500 milliDarwins.

Here are the top 25. The ones on the bottom have scores of 152. One remarkable thing about this list is how few of them are really famous for doing science. Many of them are cited in popular books for other reasons. Another remarkable thing about the list is that all of the scientists in the top 25 are dead.

Bertrand Russell (1872-1970) (1500mD)
Charles Darwin (1809-1882) (1000mD)
Albert Einstein (1879-1955) (878mD)
Lewis Carroll (1832-1898) (479mD)
Claude Bernard (1813-1878) (429mD)
Oliver Lodge (1851-1940) (394mD)
Julian Huxley (1887-1975) (350mD)
Karl Pearson (1857-1936) (346mD)
Niels Bohr (1885-1962) (289mD)
Alexander Graham Bell (1847-1922) (274mD)
Max Planck (1858-1947) (256mD)
Francis Galton (1822-1911) (255mD)
Robert Oppenheimer (1904-1967) (252mD)
Louis Pasteur (1822-1895) (237mD)
Chaim Weizmann (1874-1952) (236mD)
Alfred North Whitehead (1861-1947) (229mD)
Marie Curie (1867-1934) (189mD)
Robert Koch (1843-1910) (185mD)
Isaac Asimov (1920-1992) (183mD)
James Jeans (1877-1946) (182mD)
Ray Lankester (1847-1929) (175mD)
Stephen Jay Gould (1941-2002) (169mD)
Norbert Wiener (1894-1964) (163mD)
Rachel Carson (1907-1964) (152mD)
Carl Sagan (1934-1996) (152mD)

The website has an interactive table that links you to Wikipedia articles. If you click on "Karl Pearson," for example, you'll learn about his science. You can also click on the citation score to see how their citations vary over time. I've copied the charts for Dawkins and Gould so you can see how they compare.

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Homeopathy: Cue or Con?

 
Check out the Marketplace show. If you live in Canada, go to Cure or Con?, otherwise watch it on YouTube (below). Our Center for Inquiry friends in Vancouver overdose at the beginning of the show. Will they survive?

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Homeopathy on Marketplace

 
We've known about this upcoming show for several months because the producers have been contacting skeptical groups to get both sides of the story. Watch it tonight on CBC (Canada) at 8 PM.

Our Vancouver members of the Centre for Inquiry get to have all the fun!

Cure or Con?

Erica Johnson investigates one of the fastest growing alternative health treatments in the country: homeopathy. Ontario homeopaths are about to become the first province in Canada to regulate homeopathy — lending credibility to this unproven practice.

Canada's leading consumer ally takes a long hard look at the theories, and the remedies. For the first time in Canada, we conduct a test of homeopathic medicines, investigating the science behind these so-called medicines. In light of our results, we ask both the Ontario government and Health Canada why they are lending credibility to the homeopathic industry. Johnson also meets up with a rep from the world's leading manufacturer of homeopathic medicines, who admits that even the company doesn't know how homeopathy is supposed to work.

Watch, as we witness a Vancouver group of skeptics taking part in a group overdose of homeopathic remedies. Perhaps most disturbing we learn that some homeopaths are treating cancer patients with homeopathic remedies — this despite a leading cancer specialist saying there is no role for homeopathy in the treatment of cancer, that it is a "scam that is not evidence-based".

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25 Influential Atheists

 
Here's a list of The 25 Most Influential Living Atheists. How many do you recognize? Are they good people or are they all morally degenerate because they're not scared of God?

Why isn't Hemant Mehta on the list?

Here's a better list 'cause it includes some people who are much more interesting than Daniel Dennett [The 50 Most Brilliant Atheists of All Time].

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A Challenge to Fans of Alternative Splicing

There are many well-known examples of alternative splicing. These examples have been taught in undergraduate courses for 30 years and they are prominently featured in textbooks. Alternative splicing exists.

Here's the problem. The explosion of EST data in the 1990's resulted in detection of many sequences suggesting that alternative splicing was much more widespread that previously suspected. The vast majority of these claims have not been verified and many of them have been removed from the annotated genomes published in the past few years.

Now we have a whole new set of claims based on high throughput analysis of transcripts from a variety of organisms and tissues. Many workers believe that the majority of human genes are alternatively spliced and some even publish articles stating that 95% of humans genes exhibit alternative splicing. One of my colleagues who makes such a claim says that just because a gene is alternatively spliced doesn't mean that the various isoforms of RNA are functional but I think that's disingenuous. If it's going to be a meaningful term then "alternative splicing" has to imply that that at least two different versions of RNA have some biological function.

I've asked repeatedly for evidence that some particular genes are alternatively spliced to give rise to two or more functional products. It should be possible to get this information from the databases used by these researchers—the ones that support their claim of widespread alternative splicing. Unfortunately, this has proven to be difficult. Whenever I search common alternative splicing databases I'm told that those databases aren't very good and the results aren't reliable.

Here's the challenge to all researchers who believe that a majority of human genes are alternatively spliced (in a biologically relevant manner). Show me your data. Pick one of the following sets of genes and demonstrate that most of them have functional alternatively spliced transcripts. If none of the genes in the set qualifies then explain why you reject the presumed alternative transcripts shown in popular databases. This shouldn't be much of a challenge if your claim is correct.

Note that this is a two part challenge. You have to first present evidence that there are functional alternative splicing events and then you also have to present the reasons why you reject some of the data from sequenced RNAs.

Here's an example from the human gene for triose phosphate isomerase (TPI1). The Entrez Gene entry is Gene ID: 7167. The primary entry shows one alternatively spliced transcript that removes the N-terminal coding region of the protein and creates an new larger N-terminal sequence. What is the evidence that this is biologically relevant? Now check out the known transcripts that have been detected according to UCSC Genome Browser, AceView, and Model Maker. These show additional variants affecting the splice junction sequences around exons 2, 4, and 6. Are these also examples of alternative splicing? Are they functional? If you reject these variants then what's the rationale for accepting some possible transcripts as real but rejecting others? Are some of them artifacts?

The three gene sets are ...

1. Human genes for the enzymes of glycolysis.
2. Human genes for the subunits of RNA polymerase with an emphasis on the large conserved subunits [Two Examples of Alternative Splicing]
3. Human genes for ribosomal proteins.

I selected these examples because we know the structures of the proteins so we can evaluate the possibility that an alternatively spliced message might produce a novel polypeptide chain. Of course there might be other reasons (regulation?) for producing alternatively spliced transcripts. Feel free to present the evidence.

Now it's possible that I've accidentally chosen sets of genes that do not exhibit alternative splicing. If that's the case then pick any other set of genes with a common function where the structure of the protein product is known. Meanwhile, you can explain why you reject all the putative splice variants for these genes.

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What Does San Marco Basilica Have to do with Evolution?

Everyone interested in evolution should read the famous critique of the adaptationist program by Stephen Jay Gould (1941-2002) and Richard Lewontin (1929 - ). Whether you agree with them or not, it's essential that you become informed about the adpatationist-pluralist controversy—also known as the neutral-selectionist controversy. That controversy is still very much a part of the debates over evolution, although the adaptationist side tends to argue that the controversy has been settled.

It's no secret that I'm a huge fan of Gould and if I had my druthers I'd make students read every one of his books, including, The Structure of Evolutionary Theory. I'm a pluralist.

My friend John Wilkins, a philosopher, visited St. Mark's Square and the Basilica last year. He's on the opposite side of this debate and he offers the best defense of adaptationism that I've seen in recent years. You should keep an eye on his blog, Evolving Thoughts, it's a must-read for anyone who's serious about evolution. I blogged about John's version of adaptationism [An Adaptationist in Piazza San Marco].

This is a rich topic for undergraduates and there are many potential essay topics.

Michael Ruse Defends Adaptationism
Richard Dawkins' View of Random Genetic Drift
Naked Adaptationism

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Gould, S.J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. Proceedings of the Royal Society of London. Series B, Biological Sciences, Vol. 205, No. 1161, The Evolution of Adaptation by Natural Selection (Sep. 21, 1979), pp. 581-598. [AAAS reprint] [printable version]

Secret Alien Messages in Your Genome

 
Today is the first day of my course on molecular evolution and I want the students to experience the give-and-take of scientific—and not so scientific—debate in the blogosphere.

Their first assignment is to read the following quotation from an article by Paul Davies and answer the question that follows.

Paul Davies is a professor at Arizona State University. He was trained as a physicist and he lists his interests as cosmology, quantum field theory, and astrobiology. The quotation is from an article he wrote last April in the Wall Street Journal [Is Anybody Out There?: After 50 years, astronomers haven't found any signs of intelligent life beyond Earth. They could be looking in the wrong places.]

Another physical object with enormous longevity is DNA. Our bodies contain some genes that have remained little changed in 100 million years. An alien expedition to Earth might have used biotechnology to assist with mineral processing, agriculture or environmental projects. If they modified the genomes of some terrestrial organisms for this purpose, or created their own micro-organisms from scratch, the legacy of this tampering might endure to this day, hidden in the biological record.

Which leads to an even more radical proposal. Life on Earth stores genetic information in DNA. A lot of DNA seems to be junk, however. If aliens, or their robotic surrogates, long ago wanted to leave us a message, they need not have used radio waves. They could have uploaded the data into the junk DNA of terrestrial organisms. It would be the modern equivalent of a message in a bottle, with the message being encoded digitally in nucleic acid and the bottle being a living, replicating cell. (It is possible—scientists today have successfully implanted messages of as many as 100 words into the genome of bacteria.) A systematic search for gerrymandered genomes would be relatively cheap and simple. Incredibly, a handful of (unsuccessful) computer searches have already been made for the tell-tale signs of an alien greeting.

Here's the question. Assume that the aliens inserted a 1000 bp message in the same place in the genomes of every member of our ancestral population from five million years ago. At that point every organism in the species had exactly the same message in a region of junk DNA.

If you were to sequence that very same region of your own genome what would the message look like today? Would it be different from the original message of five million years ago? Is there a way of reconstructing the original message and interpreting it?

Comments will be held until tomorrow evening in order to give everyone a fair shot at coming up with an answer.

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Photo Credit: Lieutenant Ellen Ripley communicates with aliens.

How to Do Good Science

Richard Feynman (1918–1988) was a very smart American physicist who's words are often quoted ... for good reason.

Here's one quotation where he describes how good scientists should behave. It's a point I make in my class on scientific controversies and it's worth emphasizing because so many modern scientists ignore it.

Feynman is specifically referrring to "cargo cult science" but his advice applies to a lot of of modern biology as well.

There is one feature I notice that is generally missing in "cargo cult science." It's a kind of scientific integrity, a principle of scientific thought that corresponds to a kind of utter honesty — a kind of leaning over backwards. For example, if you're doing an experiment, you should report everything that you think might make it invalid — not only what you think is right about it; other causes that could possibly explain your results; and things you thought of that you've eliminated by some other experiment, and how they worked — to make sure the other fellow can tell they have been eliminated.

Details that could throw doubt on your interpretation must be given, if you know them. You must do the best you can — if you know anything at all wrong, or possibly wrong — to explain it. If you make a theory, for example, and advertise it, or put it out, then you must also put down all the facts that disagree with it, as well as those that agree with it. There is also a more subtle problem. When you have put a lot of ideas together to make an elaborate theory, you want to make sure, when explaining what it fits, that those things it fits are not just the things that gave you the idea for the theory; but that the finished theory makes something else come out right, in addition.

In summary, the idea is to try to give all of the information to help others to judge the value of your contribution; not just the information that leads to judgment in one particular direction or another.

Richard Feynman, "Cargo Cult Science" in Surely You're Joking, Mr. Feynman!

Think about Feynman's words next time you read a paper on the importance of alternative splicing, the disappearance of junk DNA, or anything about evolutionary psychology.

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Splicing Error Rate May Be Close to 1%

Alex Ling alerted me to an important paper in last month's issue of PLoS Genetics. Pickrell et al. (2010) looked at low abundance RNAs in order to determine how many transcripts showed evidence of possible splicing errors. They found a lot of "alternative" spliced transcripts where the new splice junction was not conserved in other species and was used rarely. They attribute this to splicing errors. Their calculation suggests that the splicing apparatus makes a mistake 0.7% of the time.

This has profound implication for the interpretation of alternative splicing data. If Pickerell et al. are correct—and they aren't the only ones to raise this issue—then claims about alternative splicing being a common phenomenon are wrong. At the very least, those claims are controversial and every time you see such a claim in the scientific literature it should be accompanied by a statement about possible artifacts due to splicing errors. If you don't see that mentioned in the paper then you know you aren't dealing with a real scientist.

Here's the abstract and the author summary ..

Abstract

While the majority of multiexonic human genes show some evidence of alternative splicing, it is unclear what fraction of observed splice forms is functionally relevant. In this study, we examine the extent of alternative splicing in human cells using deep RNA sequencing and de novo identification of splice junctions. We demonstrate the existence of a large class of low abundance isoforms, encompassing approximately 150,000 previously unannotated splice junctions in our data. Newly-identified splice sites show little evidence of evolutionary conservation, suggesting that the majority are due to erroneous splice site choice. We show that sequence motifs involved in the recognition of exons are enriched in the vicinity of unconserved splice sites. We estimate that the average intron has a splicing error rate of approximately 0.7% and show that introns in highly expressed genes are spliced more accurately, likely due to their shorter length. These results implicate noisy splicing as an important property of genome evolution.

Author Summary

Most human genes are split into pieces, such that the protein-coding parts (exons) are separated in the genome by large tracts of non-coding DNA (introns) that must be transcribed and spliced out to create a functional transcript. Variation in splicing reactions can create multiple transcripts from the same gene, yet the function for many of these alternative transcripts is unknown. In this study, we show that many of these transcripts are due to splicing errors which are not preserved over evolutionary time. We estimate that the error rate in the splicing of an intron is about 0.7% and demonstrate that there are two major types of splicing error: errors in the recognition of exons and errors in the precise choice of splice site. These results raise the possibility that variation in levels of alternative splicing across species may in part be to variation in splicing error rate.

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Pickrell, J.K., Pai, A.A., and Gilad, Y., Pritchard, J.P. (2010) Noisy Splicing Drives mRNA Isoform Diversity in Human Cells. PLoS Genet 6(12): e1001236. doi:10.1371/journal.pgen.1001236

Extraordinary Claims about Human Genes

Sandra Porter of Discovering Biology in a Digital World has recently attended a talk by Chris Mason of Cornell University. According to Sandra, Chris Mason made the following claims based on his analysis of RNAs from various tissues (human? mammal?). [Next Generation Sequencing adds thousands of new genes]

1. A large fraction of the existing genome annotation is wrong.
2. We have far more than 30,000 genes, perhaps as many as 88,000.
3. About ten thousand genes use over 6 different sites for polyadenylation.
4. 98% of all genes are alternatively spliced.
5. Several thousand genes are transcribed from the "anti-sense"strand.
6. Lots of genes don't code for proteins. In fact, most genes don't code for proteins.

I bet that every one of those claims is wrong.

There's a saying about extraordinary claims—they require extraordinary evidence. In this case, I'm pretty sure the "evidence" is the detection of low abundance transcripts using highly sensitive sequencing technology. Anyone who's ever learned about DNA binding proteins knows about non-specific binding and they know that spurious transcription is inevitable. In order to overthrow our view of the number of genes and how they behave, you will have to convince me that you've ruled out accidental spurious transcription (junk RNA).

I think it's somewhat disingenuous to be giving a talk where you claim we have 88,000 genes and 98% of them are alternatively spliced. (The term "alternative splicing" implies biological significance and not just splicing errors.)

In order to evaluate transcriptome data we need to know the abundance of the transcript. It's not sufficient to simply report that such-and-such region of the genome was transcribed. Researchers have got to report the average number of transcripts per cell in the tissue they are analyzing. I'm betting that if we saw that data we would instantly recognize that the so-called new "genes" are producing less than one transcript per cell. If that's the case it can't be biologically significant in a large mammalian cell.

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