Some transcription factors can be both activators and repressors! Textbooks have been saying this for decades

This is another post about a bad press release based on a lack of knowledge of the history of the field.

Here's the press release from Washington State University as reported in SciTechDaily

Scientists Discover “Spatial Grammar” in DNA: Breakthrough Could Rewrite Genetics Textbooks

“Contrary to what you will find in textbooks, transcription factors that act as true activators or repressors are surprisingly rare,” said WSU assistant professor Sascha Duttke, who led much of the research at WSU’s School of Molecular Biosciences in the College of Veterinary Medicine.

Rather, the scientists found that most activators can also function as repressors.

“If you remove an activator, your hypothesis is you lose activation,” said Bayley McDonald, a WSU graduate student who was part of the research team. “But that was true in only 50% to 60% of the cases, so we knew something was off.”

Looking closer, researchers found the function of many transcription factors was highly position-dependent.

They discovered that the spacing between transcription factors and their position relative to where a gene’s transcription began determined the level of gene activity. For example, transcription factors might activate gene expression when positioned upstream or ahead of where a gene’s transcription begins but inhibit its activity when located downstream, or after a gene’s transcription start site.

... By integrating this newly discovered ‘spatial grammar,’ Christopher Benner, associate professor at UC San Diego, anticipates scientists can gain a deeper understanding of how mutations or genetic variations can affect gene expression and contribute to disease.

”The potential applications are vast,” Benner said. “At the very least, it will change the way scientists study gene expression.”

Higher education for all?

I discuss a recent editorial in Science that advocates expanding university education in order to prepare students for jobs.

I believe that the primary goal of a university education is to teach students how to think (critical thinking). This goal is usually achieved within the context of an in-depth study in a particular field such as history, English literature, geology, or biochemistry. The best way of achieving that goal is called student-centered learning. It involves, among other things, classes that focus on discussion and debate under the guidance of an experienced teacher.

Universities and colleges also have job preparation programs such as business management, medicine, computer technology, and, to a lesser extent, engineering. These programs may, or may not, teach critical thinking (usually not).

About 85% of students who enter high school will graduate. About 63% of high school graduates go to college or university. The current college graduation rate is 65% (within six years). What this means is that for every 100 students that begin high school roughly 35 will graduate from college.

Now let's look at an editorial written by Marcia McNutt, President of the United States National Academy of Sciences. The editorial appears in the Nov. 11 issue of Science [Higher education for all]. She begins by emphasizing the importance of a college degree in terms of new jobs and the wealth of nations.

Currently, 75% of new jobs require a college degree. Yet in the US and Europe, only 40% of young adults attend a 2-year or 4-year college—a percentage that has either not budged or only modestly risen in more than two decades— despite a college education being one of the proven ways to lift the socioeconomic status of underprivileged populations and boost the wealth of nations.

There's no question that well-educated graduates will contribute to society in many ways but there is a question about what "well-educated" really means. Is it teaching specific jobs skills or is it teaching students how to think? I vote for teaching critical thinking and not for job training. I think that creating productive citizens who can fill a variety of different jobs is a side-benefit of preparing them to cope with a complex society that requires critical thinking. I don't think my view is exactly the same as Marcia McNutt's because she emphasizes training as a main goal of college education.

Universities, without building additional facilities, could expand universal and life-long access to higher education by promoting more courses online and at satellite community-college campuses.

Statements like that raise two issues that don't get enough attention. The first one concerns the number of students who should graduate from college in an ideal world. What is that number and at what stage should it be enhanced? Should here be more high school graduates going to college? If so, does that require lowering the bar for admission or is the cost of college the main impediment? Is there a higher percentage of students entering college in countries with free, or very low, tuition? Should there be more students graduating? If so, one easy way to do that is to make university courses easier. Is that what we want?

The question that's never asked is what percentage of the population is smart enough to get a college degree? Is it much higher than 40%?

The second issue concerns the quality of education. The model that I suggested above is not consistent with online courses and there's a substantial number of papers in the pedagogical literature showing the student centered education doesn't work very well online. Does that mean that we should adopt a different way of teaching in order to make college education more accessible? If so, at what cost?

McNutt gives us an example of the kind of change she envisages.

At Colorado College, students complete a lab science course in only 4 weeks, attending lectures in the morning and labs in the afternoon. This success suggests that US universities could offer 2-week short courses that include concentrated, hands-on learning and teamwork in the lab and the field for students who already mastered the basics through online lectures. Such an approach is more common in European institutions of higher education and would allow even those with full-time employment elsewhere to advance their skills during vacations or employer-supported sabbaticals for the purpose of improving the skills of the workforce. Opportunities abound for partnerships with industry for life-long learning. The availability of science training in this format could also be a boon for teachers seeking to fill gaps in their science understanding.

This is clearly a form of college education that focuses on job skills and even goes as far as suggesting that industry could be a "partner" in education. (As an aside, it's interesting that government employers, schools, and nonprofits are never asked to be partners in education even though they hire a substantial number of college graduates.)

Do you agree that the USA should be expanding the number of students who graduate from college and do you agree that the goal is to give them the skills needed to get a job?

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Undergraduate education in biology: no vision, no change

I was looking at the Vision and Change document the other day and it made me realize that very little has changed in undergraduate education. I really shouldn't be surprised since I reached the same conclusion in 2015—six years after the recommendations were published [Vision and Change] [Why can't we teach properly?].

The main recommendations of Vision and Change are that undergraduate education should adopt the proven methods of student-centered education and should focus on core concepts rather than memorization of facts. Although there has been some progress, it's safe to say that neither of these goals have been achieved in the vast majority of biology classes, including biochemistry and molecular biology classes.

Things are getting even worse in this time of COVID-19 because more and more classes are being taught online and there seems to be general agreement that this is okay. It is not okay. Online didactic lectures go against everything in the Vision and Change document. It may be possible to develop online courses that practice student-centered, concept teaching that emphasizes critical thinking but I've seen very few attempts.

Here are a couple of quotations from Vision and Change that should stimulate your thinking.

Traditionally, introductory biology [and biochemistry] courses have been offered as three lectures a week, with, perhaps, an accompanying two- or three-hour laboratory. This approach relies on lectures and a textbook to convey knowledge to the student and then tests the student's acquisition of that knowledge with midterm and final exams. Although many traditional biology courses include laboratories to provide students with hands-on experiences, too often these "experiences" are not much more than guided exercises in which finding the right answer is stressed while providing students with explicit instructions telling them what to do and when to do it.

"Appreciating the scientific process can be even more important than knowing scientific facts. People often encounter claims that something is scientifically known. If they understand how science generates and assesses evidence bearing on these claims, they possess analytical methods and critical thinking skills that are relevant to a wide variety of facts and concepts and can be used in a wide variety of contexts.”

National Science Foundation, Science and Technology Indicators, 2008

If you are a student and this sounds like your courses, then you should demand better. If you are an instructor and this sounds like one of your courses then you should be ashamed; get some vision and change [The Student-Centered Classroom].

Although the definition of student-centered learning may vary from professor to professor, faculty generally agree that student-centered classrooms tend to be interactive, inquiry-driven, cooperative, collaborative, and relevant. Three critical components are consistent throughout the literature, providing guidelines that faculty can apply when developing a course. Student-centered courses and curricula take into account student knowledge and experience at the start of a course and articulate clear learning outcomes in shaping instructional design. Then they provide opportunities for students to examine and discuss their understanding of the concepts presented, offering frequent and varied feedback as part of the learing process. As a result, student-centered science classrooms and assignments typically involve high levels of student-student and student-faculty interaction; connect the course subject matter to topics students find relevant; minimize didactic presentations; reflect diverse views of scientific inquiry, including data presentation, argumentation, and peer review; provide ongoing feedback to both the student and professor about the student's learning progress; and explicitly address learning how to learn.

This is a critical time for science education since science is under attack all over the world. We need to make sure that university students are prepared to deal with scientific claims and counter-claims for the rest of their lives after they leave university. This means that they have to be skilled at critical thinking and that's a skill that can only be taught in a student-centered classroom where students can practice argumentation and learn the importance of evidence. Memorizing the enzymes of the Krebs Cycle will not help them understand climate change or why they should wear a mask in the middle of a pandemic.

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Do Canadians "believe" in evolution?

A recent post by some anonymous blogger named "Darwin Quixote" made the following claim [see comment in: Be Careful, Evolution is Behind You]. The discussion was about teaching evolution in Ontario (Canada) schools ....

Of course I agree that these topics should be required, but I would suggest that it’s even more important that human evolution be a required topic because only 51% of Ontarians believe that humans evolved. It is likely that a significant number of teachers fall into the 49% category, and therefore leaving this topic to the discretion of the teacher becomes problematic.

This didn't seem right to me so I checked the latest polls that I could find on the internet.

Here's one by Angus Reid in 2012: Believe In Evolution: Canadians More Likely Than Americans To Endorse Evolution. The results show that 60% of Ontarians believe the following statement: "Human beings evolved from less advanced life forms over millions of years."

24% of Ontarians thought that: "God created human beings in their present form within the last 10,000 years."

16% were not sure.

The results were somewhat different in other provinces. In Quebec, for example, the number of people who accepted evolution was 71% and only 13% believed in Young Earth Creationism. In Alberta only 48% of the population accepted evolution and 35% were Young Earth Creationists.

So Darwin Quixote was off by a bit (51% vs 60%) but not by much. However, I think he makes an error by assuming that a significant number of biology teachers (in high school) would be opposed to evolution and might not teach human evolution.

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The Discovery Institute's myths and misconceptions about evolution

If students are going to learn critical thinking about evolution, they need to be exposed to controversial views and challenges concerning evolution, the history of life, and evolutionary theory. The Discovery Institute agrees with this strategy. It has published a handbook called The Educator's Briefing Packet that claims to outline what teachers should cover when they teach evolution.

As you might imagine, the Discovery Institute concentrates on showing that evolution is wrong rather than focusing on whether Intelligent Design Creationism is correct. That's partly because they don't want to advocate teaching Intelligent Design Creationism in schools.

They explain the strategy on page 7 ...

Teaching this subject objectively means presenting both the scientific evidence for and against neo-Darwinian evolution. This does not mean simply criticizing evolution or only presenting the case against the neo-Darwinian model. Rather, objective instruction means:

• Fully teaching the evidence for neo-Darwinian evolution from the textbook.
• Covering the entire required curriculum.
• Helping students understand the scientific arguments in favor of neo-Darwinian evolution as well as the scientific criticisms as they are presented in the scientific literature.

This strategy implies that students are taught something called "Neo-Darwinism" in class. Here's how they define Neo-Darwinism.

Darwin argued that natural selection had the power to produce fundamentally new forms of life. Together, the ideas of universal common descent and natural selection form the core of Darwinian evolutionary theory. "Neo-Darwinian" evolution combines our knowledge of DNA and genetics to claim that mutations in DNA provide the variation upon which natural selection acts.

Right away we have a problem since many textbooks do not describe modern evolutionary theory in this manner. The handbook doesn't explain what teachers should do if they are teaching modern evolutionarytheory instead of Neo-Darwinism but I think it's pretty obvious what the Intelligent Design Creationists would recommend if they actually understood evolution. They would still recommend criticizing it.

In a real classroom run by competent teachers, the teachers would begin by pointing out that many creationist organizations have an incorrect and distorted view of evolution and they would pass out copies of the handbook. Then they would discuss why the Discovery Institute is promoting nonsense about evolution when they claim to be experts on the subject. The class could analyze the difference between the DI version of evolution that only covers natural selection and the modern view that includes random genetic drift and population genetics. This would be a highly effective way of teaching critical thinking and exposing students to one of the most common misconceptions about evolution.

In the right hands, this could lead to a discussion about why creationists seem to resist being educated about evolution even though the correct information is readily available on the internet. The class could learn about confirmation bias, begging the question, false dichotomy, and the strawman fallacy using examples from the handbook.

The Educator's Briefing Packet contains lots of other myths and misrepresentations that are commonly found in creationist literature. Debunking and correcting these examples can also be used to foster critical thinking and teach the truth about evolution. I'd like to thank the Discovery Institute for putting them all in one place. I'd love to spend a few days in a senior high school class showing the students why these are myths and/or misconceptions.

Here's the list¹ ...

• Genetics: Mutations Tend to Cause Harm and Do Not Build Complexity. Darwinian evolution relies on random mutations which are acted on by natural selection, a blind and unguided process that has no goals. Such a random and undirected process tends to harm organisms. They do not seem capable of improving organisms or building new complex systems.
• Biochemistry: Unguided and Random Processes Cannot Produce Cellular Complexity.Cells contain incredible complexity, similar to machine technology but dwarfing anything produced by humans. Cells use circuits, miniature motors, feedback loops, encoded language, and even error-checking machinery which decodes and repairs our DNA. Many scientists have claimed that Darwinian evolution does not appear capable of building this type of integrated complexity.
• Paleontology: The Fossil Record Lacks Intermediate Fossils. The fossil record’s overall pattern is one of abrupt explosions of new biological forms and possible candidates for evolutionary transitions are the exception, not the rule. For example, the Cambrian Explosion is an event in life’s history over 500 million years ago where nearly all the major body plans of animals appear in a geological instant without any apparent evolutionary precursors.
• Taxonomy: Biologists Have Failed to Construct Darwin’s Tree of Life. Biologists hoped that DNA evidence would reveal a grand tree of life where all organisms are clearly related. Yet trees describing the alleged ancestral relationships between organisms based upon one gene or biological characteristic commonly conflict with trees based upon a different gene or characteristic. This implies a challenge to universal common descent, the hypothesis that all organisms share a single common ancestor.
• Chemistry: The Chemical Origin of Life Remains an Unsolved Mystery. The mystery of the origin of life is unsolved, and all existing theories of chemical evolution face major problems. Basic deficiencies in chemical evolution include a lack of explanation for how a primordial soup could arise on the early earth’s hostile environment, or how the information required for life could be generated by blind chemical reactions.

In all theses cases we have situations where the Discovery Institute is challenging the views of the vast majority of scientists who have devoted careers to studying these issues. That's a good opportunity to teach students how they should go about deciding who to believe when faced with scientific questions. Should you believe doctors or movie actors when trying to decide whether to vaccinate your children? Should you believe climatologists or politicians about climate change? Should you believe evolutionary biologists or religious leaders when trying to decide if evolution is true?

However, I'm not sure if we could ever have much of a discussion about these issues because the latest "ID the Future" podcast features a discussion between Nate Herbst and Casy Luskin about students who question evolution in class. As it turns out, many of those students have bad experiences because they end up feeling stupid when they challenge science in class. Luskin and Herbst recommend that they hide their beliefs in order to avoid such embarrassment [see Listen: Good Advice for Students Learning about Evolution]. Maybe that's not always a good idea, however, because Herbst and Luskin also have some stories about how they stumped the professors and caused them to change their minds about evolution and origins.

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1. I wonder who they used as an authority on evolution in order to make up these questions?

Does talk.origins still exist?

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

Here's a link to the newsgroup: talk.origins. Here's a description from the Wikipedia article on talk.origins.

The first post to talk.origins 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 talk.origins 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 net.origins as a 'dumping ground' for all the various flame threads 'polluting' other newsgroups, then renamed to talk.origins 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.

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Changing high school education: Equinox Summit and Learning 2030

I recently re-watched a program on The Agenda about high school education and what needs to be done to make it better. The broadcast was from the Perimeter Institute in Waterloo, Ontario, Canada and it featured the results of a conference on learning called the "Equinox Summit" organized by the Waterloo Global Science Initiative in collaboration with the Perimeter Institute. You can watch the final episode of the TV show at: The Agenda: What's Necessary? What's Possible?.

If you are interested in this subject, as I am, you should watch this show since it gives you a good perspective on what the "best minds" are thinking. You can make up your own mind about whether this is encouraging or not.

Here's a short video on the summit ...



The communique from Equinox Summit: Learning 2030 isn't very long so you can read it quickly. Here are the goals that this group decided on.

In order for high school graduates to reach their full potential in life, they need to be:

• lifelong learners who can identify and synthesize the right knowledge to address a wide range of challenges in a complex, uncertain world
• literate, numerate, and articulate
• creative, critical thinkers
• able to collaborate effectively with others, especially those of different abilities and backgrounds
• open to failure as an essential part of progress
• adaptable and resilient in the face of adversity
• aware of the society they live in and able to understand the different perspectives of others
• self-aware and cognizant of their own strengths and limitations
• entrepreneurial, self-motivated, and eager to tackle the challenges and opportunities of their world

To achieve these goals, we require a radically di fferent structure for learning in 2030, one in which traditional concepts of classes, courses, timetables, and grades are replaced by more flexible, creative and student-directed forms of learning. This develops deep conceptual understanding, which can then be applied in other contexts.

There's nothing radical about these goals. They're pretty much the same goals that any conference in the 1960s would have come up with. The only really new buzzword is "entrepreneurial"—that's borrowed from business and it wouldn't have been popular in the 1960s. Today every high school student has to be an entrepreneur because by 2030 nobody will be working for anyone else. They'll all be running their own businesses.¹

I've been trying to teach creative and critical thinking for a long time and I haven't come up with any really good ideas. It's probably because I'm too old. You should watch the Agenda show to see how young people are going to solve these problems.

But here's a question that occurs to me as I'm thinking critically about this problem. Let's assume that we can achieve all those goals. Let's assume that in order to graduate from high school you have to have learned how to think critically; be literate, numerate, and articulate; be able to collaborate, be entrepreneurial, be adaptable, etc.

They are laudable goals that I support, but what percentage of students entering high school can achieve them? I'm thinking that, with lots of resources and excellent teachers, it might be possible for about 50% of high school students to reach these lofty goals. The rest are going to achieve the goals of learning to be "open to failure as an essential part of progress" and how to be "adaptable and resilient in the face of adversity."

I think we might have trouble convincing most societies, and most governments, that a 50% graduation rate from high school is the price of higher standards.

I'm not even sure that all of the students graduating from the University of Toronto are literate, numerate, articulate, critical thinkers.

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1. This will save enormous amounts of tax dollars because nobody will be working for the government.

A new definition of kindness and empathy? (on educating children)

Today's version of the Toronto Star has several articles on kindness and empathy. The feature article appears on the front page of the "Insight" section. The title of the print version is "Kindness: A fledgling movement aims to instil empathy and make us a kinder, gentler, society." The online version is How to fight meanness? Try a bit of kind.¹

The article is written by education reporter Louise Brown. The gist of the article is that we need to teach empathy and kindness² and perhaps the schools should be involved. But the main teachers should be parents.

Oops! MOOCs Didn't Work Out So Good for Sebastian Thrun

From Tressie McMillan Cottom at tressiemc [The Audacity: Thrun Learns A Lesson and Students Pay].

Sebastian Thrun, founder of Udacity, one of the most high-profile private sector attempts to "disrupt" higher education discovered inequality this week. Thrun has spent the last three years dangling the shiny bauble of his elite academic pedigree and messianic vision of the future of higher education before investors and politicos. He promised nothing short of radically transforming higher education for the future by delivering taped classroom lessons of elite professors through massive open online courses. So what went wrong?

After low performance rates, low student satisfaction and faculty revolt, Thrun announced this week that he has given up on MOOCs as a vision for higher education disruption. The "godfather of free online education" says that the racially, economically diverse students at SJSU [San Jose State University], "were students from difficult neighborhoods, without good access to computers, and with all kinds of challenges in their lives…[for them] this medium is not a good fit." It seems disruption is hard when poor people insist on existing.

Thrun's goal was to market lectures by "elite" professors at places like Sanford¹. His new company, Udacity, was going to make tons of money by selling lists of successful students to private companies who are looking for talent. Guess what? It turns out that there are lots of disadvantaged students in introductory courses at SJSU who don't learn from lectures given by elite Stanford professors. Who would have guessed?

In case you've forgotten the hype that Sebastian Thrun created when he formed Udacity, read: Sebastian Thrun Will Change Education. And watch the video.

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1. My position on this is that the professors at Harvard and Stanford are not necessarily the best teachers. In my field of biochemistry, for example, we have direct evidence that professors at MIT do a horrible job of teaching biochemistry [Where Are the Best University Teachers?]. In my experience, the best biochemistry teachers are often located at small colleges where they pay attention to the latest pedagogical literature and actually read the textbooks they use in class.

On Preparing Students for the 21st Century

Yesterday I attended a meeting organized by the Ontario Ministry of Education. The theme was From Great to Excellent: The Next Phase in Ontario's Education Strategy. The idea was to promote widespread consultation before the Ontario government releases its new plan for education reform next year.

I was attending on behalf of my friend Chris DiCarlo who had to be out of town. He (and I) are promoting the concept of critical thinking; specifically, the idea that it needs to be explicitly taught in a high school philosophy course.

The Minister of Education (Liz Sandals) and several of the senior members of her ministry were there. They told us that today's students are facing unprecedented changes and that the Ontario education system has to change in order to cope. They were mostly thinking about technological change and the possibility that today's students would have new types of jobs and careers.

I'm certain that we can improve our education system but I'm not sure it's helpful, or even correct, to focus on the idea that the next generation will have to cope with situations we never faced in the past. If we could show that our existing education system did a pretty good job of preparing students for change then maybe we should turn our attention to problems other than job training and technological innovation?

Judging the Quality of MOOCs

Another journalist has written about Massive Open Online Courses (MOOCs). This one is in The New York Times: Two Cheers for Web U!.

Most of these articles about MOOCs are not very good but this one is different. The author expresses some skepticism and hit the nail on the head when he says ...

But the first thing I learned? When it comes to Massive Open Online Courses, like those offered by Coursera, Udacity and edX, you can forget about the Socratic method.

The professor is, in most cases, out of students’ reach, only slightly more accessible than the pope or Thomas Pynchon.

But that's not what I want to talk about today. I want to discuss the quality of these courses and how you might go about judging whether they are truly teaching the subject correctly.

Here's the problem. Too many people, like A. J. Jacobs, the author of today's article, assume that because the lecturer is famous or from a "top" school, the material must be accurate and up-to-date. As A. J. Jacobs puts it ...

On the other hand, how can I really complain? I’m getting Ivy League (or Ivy League equivalent) wisdom free....

With the exception of a couple of clunkers — my plodding nutrition professor might want to drink more organic coffee before class — most of my MOOC teachers were impressive: knowledgeable, organized and well respected in their field.

Students are not in a position to judge whether a professor is "knowledgeable" about the material being covered in a course. In the case of MOOCs, many students just assume that because the professor is from an Ivy League school then he/she knows how to teach an introductory course properly.

That's a very bad assumption as I've shown when I examined the biochemistry material being taught in the MIT courses Where Are the Best University Teachers?. Same is true for the courses at the Khan Academy.

I'm currently in Boston at EB2013 where I'm hanging out with biochemistry and molecular biology teachers and textbook authors. Many of these experts are not household names but they are the experts in their field, which is teaching. If you really want accurate information about the fundamental principles and concepts in biochemistry and molecular biology then you should take the courses they teach. You'll get a far better education than if you listen to professors from big-name research intensive-universities.

The recent ENCODE publicity disaster is just one example of the fact that top-notch researchers don't necessarily understand the fundamentals of subjects that are just outside of their own area of expertise.

Let's try and put a stop to this myth that the best teachers are professors from Ivy League schools. There's very little evidence to support that myth, especially in fields that I'm familiar with: evolution, biochemistry, and molecular biology,

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Mocking Friedman's MOOCs

Thomas L. Friedman is the Op-ed columnist for foreign affairs at the New York Times. He has won three Pulitzer Prizes (1983, 1988, 2002).

According to Wikipedia, Friedman has an undergraduate degree from Brandeis University (Boston, USA) and a Master's degree from Oxford (UK). He taught a class at Brandeis in 2006 but as far as I can tell that's his only experience with university outside of being a student. He does not appear to be an educator and he doesn't appear to have any expertise in pedagogy.

That hasn't prevented him from writing three opinion pieces on the imminent demise of universities and the glorious future of online courses—especially MOOCs (Massive Open Online Courses).

Come the Revolution May 15, 20012
Revolution Hits the Universities January 26, 2003
The Professors’ Big Stage: March 5, 2013

Should Chilliwack BC Permit Distribution of Bibles in Public Schools?

Here's a notice from the BC Humanist Association.

Recent secular victories in Chilliwack are at risk.

On November 13th, the Board of the Chilliwack School District deleted Regulation 518 that stated, "The Board approves the distribution of Gideon Youth Testaments to Grade 5 pupils with parental consent." At the same meeting, the Board agreed to draft a new policy to permit the "distribution of materials" by March 2013.

This new policy represents an attempt to use public schools for religious proselytizing in BC public schools.

Superintendent Evelyn Novak intends to gather feedback through February to draft the new policy. While this feedback may not be open to the public, secular voices will be heard.

Please sign the petition below to send the message to the Chilliwack School Districts that BC schools should remain secular.

Sign the Petition. You will have to identify yourself but that shouldn't be a problem if you really believe in a secular school system.

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[Hat Tip: Veronica Abbas at Canadian Atheist.]

The Revisionaries Is Coming to Television

The Revisionaries is a documentary about the Texas state board of education and their attempt to suppress science in Texas public schools.

It will be aired on PBS starting January 28th. It's due to be broadcast in my area (WNED) on Feb. 3, 2013 at 11pm and on Feb. 8, 2013 at 4am.

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[Hat Tip: Mike the Mad Biologist]

I Have the Least Stressful Job!!!

According to Careercast.com, I have the least stressful job of all jobs.¹ Here's how it's reported in Forbes magazine by web staff writer Susan Adams: The Least Stressful Jobs Of 2013.

University professors have a lot less stress than most of us. Unless they teach summer school, they are off between May and September and they enjoy long breaks during the school year, including a month over Christmas and New Year’s and another chunk of time in the spring. Even when school is in session they don’t spend too many hours in the classroom. For tenure-track professors, there is some pressure to publish books and articles, but deadlines are few. Working conditions tend to be cozy and civilized and there are minimal travel demands, except perhaps a non-mandatory conference or two. As for compensation, according to the Bureau of Labor Statistics, the median salary for professors is $62,000, not a huge amount of money but enough to live on, especially in a university town.

Another boon for professors: Universities are expected to add 305,700 adjunct and tenure-track professors by 2020, according to the BLS. All of those attributes land university professor in the number one slot on Careercast.com’s list of the least stressful jobs of 2013. The ranking comes from an annual best and worst jobs list that began in 1995 under the auspices of the Wall Street Journal.

Ironically, this article comes out just as some of my colleagues are getting the bad news about their grant applications. Those who weren't funded face the end of their research career while they are still in their 40s. It also comes out at a time when two of my colleagues are starting to think about their applications for tenure. If they are unsuccessful, they will be out of a job in their late 30s with a family to support.

None of my colleagues took a month off at Christmas and I can assure you that all of my colleagues are here for almost the entire summer running a lab full of graduate students, post-docs, technicians, and summer students. The stress of running what amounts to a small business and getting papers published on things that nobody else has ever discovered is a lot more than most people could stand.

Read to the end of the Forbes article to see how the author responds to the many comments she received. The real problem here is that a prominent journalist could actually believe what she wrote in the first place!

I love the comment from Thomas Epps ...

Given your comment above indicating that you realize the source of your article was poor at best. I think you should consider retracting this article. I know that I would be severely sanctioned for writing this type of article with such questionable sourcing in my academic job. If the same is not the case in your job, then clearly your career is not a terribly stressful one. Maybe, "web staff writer" should be on the top of the "least-stressful jobs" list?

See ...
Do College Professors Have Less Stress?
Top 10 Reasons Being a University Professor is a Stressful Job
Before Professor comes Postdoc: Lower career rung, just as much job stress

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1. I have no intention of supplying specific information about MY job but I'm happy to explain why every one of my younger colleagues is under a tremendous amount of stress every single day.

The Purpose of Education

My friends and I were talking about the purpose of education over dinner on Saturday night. This video criticizes one side of the issue; namely, the idea that the purpose of education is to prepare you for a job. It should not be the goal of education.¹

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1. But it may be a collateral benefit.

[Hat Tip: Veronica at Canadian Atheist.]

What's Happened to Universities?

The latest issue of Academic Matters has a provocative article by Ken Coates on The Quiet Campus: The Anatomy of Dissent at Canadian Universities.
Here's the opening paragraphs ...

The remarkable—a word that can be read in many different ways—2012 student protests in Quebec have stirred memories of the activist campuses of yesteryear. For faculty members introduced to the academy in the era of student activism, anti-Vietnam War protests, and general social unrest, the recent quietude of the Canadian university system has been disturbing. Universities had been transformed in the 1960s from comfortable retreats into agents of intellectual foment, social change, and political action. For a time, it appeared that the imperatives of the academy had aligned with a commitment to social justice to create a system almost ideally set to lead Canada’s transformation.

Universities had long stood apart intellectually from the Canadian mainstream, but finally, in the 1960s, began to reflect society at large. The humanities and social sciences expanded rapidly. Women, minorities, immigrants and working class Canadians came to campuses in record numbers and, later, showed up at the front of the classroom. They brought new perspectives on the issues of the day, challenging the patriarchal, middle-class hegemony that had dominated Canadian universities for generations. With some exceptions, faculty members and administrators stood behind student radicals and protestors. Many faculty members used the classroom and their writing to support hitherto unpopular causes. Universities were often at the vanguard of protests against the Vietnam War and in favour of the rights of women, Aboriginals, LGBT individuals, and minorities.

I was a student in the 1960s. Universities are no longer like that. What happened?

Canadian campuses have become distressingly quiet. It is not that the universities are without dissenters from all points on political and social spectrums. Many of the country’s most radical, creative, and outspoken commentators work or study at universities and use the campus as a pulpit. This is how it should be. But the preoccupation with practicalities—work, careers, salaries, and the commercialization of research—has transformed Canadian universities into calm, largely dissent-free places, with the greatest debates often saved for battles between faculty and students and the campus administrators. There are no structural or legal impediments to greater engagement. There is nothing stopping students and faculty from speaking out, no grand tribunals determined to impose punishments on those who challenge the status quo. We have self-regulated ourselves into near silence, and our students and the country suffer from the quiet as much as university faculty. It is more than nostalgia that brings one to yearn for days of activism and protest; it is, instead, the realization that the ideas, talent, energy and resources of the academic could and should be used to change our country and our world for the better.

Nostalgia, yes that describes my feelings exactly.

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Online Training of Competent, Employable, Bioinformatics Professionals

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

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

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

Thinking Like an Administrator

A few years ago my university (University of Toronto) decided to take a look at student evaluations. A committee was formed and this was its terms of reference.

In recognition of the need to periodically revisit practices related to the evaluation of teaching, the Course Evaluation Working Group was formed in the Fall 2009 (Appendix B) and was asked to:

1. Review current course evaluation practices across the University of Toronto and at peer institutions;
2. Review current research on course evaluation policies and practices;
3. If necessary, make recommendations to improve existing policies and practices.

This sounds like a good idea. As you know, I am very skeptical about student evaluations [On the Significance of Student Evaluations]. It's abut time that universities took a long hard look at the process with a view to abolishing student evaluations or drastically revising them and reviewing their importance in promotion and tenure decisions. It's even more important to revise the policy on using student evaluations to judge the effectiveness of part-time lecturers and teaching assistants. At the very least, their role in determining teaching awards should be critically examined.

If I were in charge of this project I would pick a committee composed almost entirely of the following groups:

• front-line lecturers in introductory classes, including tenured faculty, untenured faculty, full-time lecturers, and part-time lecturers
• teaching assistants (graduate students)
• undergraduates

There would have to be substantial representation from undergraduates since they feel strongly about the issue and any drastic changes would require their consent and cooperation.

I would avoid having any administrators on the committee since the purpose of the committee was to evaluate existing university policy. In general, administrators are reluctant to make radical changes and they have trouble thinking outside the box. Furthermore, most of them don't have time to think seriously about the issue.

Administrators think differently than I do. Here's how they constructed the committee (see Course Evaluation Working Group.

• Edith Hillan (Vice-Provost, Faculty and Academic Life; Co-Chair)
• Jill Matus (Vice-Provost, Students; Co-Chair)
• Grant Allen (Vice-Dean, Undergraduate, Faculty of Applied Science and Engineering)
• Gage Averill (Dean and Vice-Principal, Academic, UTM)
• Cleo Boyd (Director, Robert Gilliespie Academic Skills Centre, UTM)
• Corey Goldman (Associate Chair [Undergraduate], Department of Ecology & Evolutionary Biology, Faculty of Arts & Science)
• Pam Gravestock (Associate Director, Centre for Teaching Support & Innovation)
• Emily Greenleaf (Faculty Liaison & Research Associate, Centre for Teaching Support & Innovation)
• Jodi Herold-McIlroy (Wilson Centre, Faculty of Medicine)
• Glen Jones (Associate Dean, Academic, OISE) Helen Lasthiotakis (Director of Academic Programs and Policy)
• Marden Paul (Director, Planning, Governance & Assessment)
• Cheryl Regehr (Vice-Provost, Academic Programs)
• Carol Rolheiser (Director, Centre for Teaching Support & Innovation)
• Jay Rosenfield (Vice-Dean, Undergraduate Medical Education, Faculty of Medicine)
• John Scherk (Vice-Dean, UTSC)
• Elizabeth Smyth (Vice-Dean, Programs, School of Graduate Studies)
• Suzanne Stevenson (Vice-Dean, Teaching & Learning, Faculty of Arts & Science)

No students. No teaching assistants. No part-time lecturers. Very few people who are currently teaching large undergraduate courses. Almost every person has an administrative positions of some sort—most of the positions take up a considerable portion of their time and some of them are full-time jobs.

That's what thinking like an administrator looks like.

I don't think my university is unusual. We have thousands of very smart students and teachers but all the important committees seem to be composed of people with heavy administrative responsibilities. Does anyone understand the logic here?

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Where Are the Best University Teachers?

Much to my embarrassment, the University of Toronto is promoting online courses, or MOOCs [Online courses for anyone, anywhere]. These courses seem to be for information only—you can't get a university credit for them.

I'm not opposed to offering free "courses" for people who don't have easy access to a university campus. In fact, I think it's a good thing. But let's make sure we distinguish between public lectures and serious education. In my opinion, if the quality of an online course is equal to the quality of a course given on campus then all that says is that the campus-based course is lousy. We should not refer to these online examples as "university courses." They should be labelled as "public lectures."

I'll have more to say about this later but today I want to return to an issue I raised before. Is it true that the "best" universities also do the best teaching? I have suggested that the answer to this question is probabyy "no" [On the Quality of Online Courses] [Is Canada Lagging Behind in Online Education?].