Kostas Kampourakis cautions us against teaching Mendelian genetics

A few weeks ago I put up a post on Were you lied to in your genetics class?. At the time I thought it was just a fringe view being expressed by a graduate student who didn't understand genetics but now I realize that it's much more important than that.

Kostas Kampourakis is a respected scientist who is being promoted by the National Center for Science Education (NCSE) as an excellent communicator of evolution. Here's a short video (below) where he explains why teachers are making a mistake by saying that Mendel is the father of genetics and that simple Mendelian genetics can explain complex traits.

I'm struggling to understand his point. Here's what I think he means.

Kampourakis uses the example of eye color in Drosophila. He agrees that segregation of the allele responsible for eye color may follow the Mendelian rules¹ but it's wrong to assume that there's a single gene responsible for eye color in fruit flies. He thinks that the goal is to understand the complexities of development and standard Mendelian genetics gives a completely distorted view of that subject, assuming, of course, that teachers can't separate genetics from understanding development.

Part of the problem is that we use the word "trait" differently. Take Mendel's example of pea color as another example. [Identity of the Product of Mendel's Green Cotyledon Gene (Update)] What Mendel was studying was the segregation of alleles in a gene called sgr (stay-green). It codes for an enzyme involved in the degradation of chlorophyll during senescence. When the enzyme is defective, chlorophyll isn't degraded and one of the visible phenotypes is that peas stay green instead of turning yellow.

I believe that the fundamental trait is the lack of an enzyme for degrading chlorophyll and this is what I would teach my students. I would also show them that the phenotype can be easily explained once you understand the biochemistry. It shows you that the connection between the fundamental trait and the visible phenotype can be mysterious so you should be careful about jumping to conclusions.

I think that Kampourakis sees this differently. He thinks that the example of green vs yellow peas is used to teach students that the color of peas is completely determined by a single gene. He thinks that the "trait" is the develpment of seed color in peas.

Kampourakis believes that "people looking for explanations and whatever happens to them in terms of disease and their own features, they find hard to reconcile the simplistic model that they have been taught with the realities of life." I think what he means is that students are being taught that single genes will always determine complex characteristics. He attributes that to the teaching of Mendelian genetics.

If he is correct, then that kind of teaching has to stop but I don't think it's the fault of Mendelian genetics. Mendelian genetics—indeed the entire field of genetics sensu stricto—is about the segregation of alleles. It is not about development even though we have come to learn a lot about development through genetics and the phenotype of mutants. I think that genetics and development are separate topics.

Kampourakis disagrees. He says, "we need, I think, to teach genetics from a developmental perspective. We need to show that genes do not determine traits but they are implicated in development." I believe this perspective comes from a more fundamental bias that distinguishes his worldview from mine. I tend to see genetics as a subject that covers all of biology and that includes all species such as bacteria, viruses, and single-cell eukaryotes. He tends to see things from a human perspective, which is much more complex than dealing with simple organisms. I think we should concentrate on teaching students about simple well-understood model organisms and then move on to explaining how this applies to more complex organisms. Kampourakis seems to be implying that we should jump right into reaching high school students about the most challenging issues in biology.

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1. Actually, the common allele for white eye in Drosophila (see image) is X-linked so it doesn't follow the standard rules for Mendelian segregation!

Western scientists should continue to cooperate with Chinese scientists

China has become a science powerhouse and it achieved this goal, in part, by sending its young scientitsts abroad to train in universities in Canada, Australia, United States, and Europe. Many of these countries have signed scientific cooperation agreements with China but some of those agreements are in danger of lapsing as China is increasingly seen as an untrustworthy enemy.

On the importance of controls

When doing an exeriment, it's important to keep the number of variables to a minimum and it's important to have scientific controls. There are two types of controls. A negative control covers the possibility that you will get a signal by chance; for example, if you are testing an enzyme to see whether it degrades sugar then the negative control will be a tube with no enzyme. Some of the sugar may degrade spontaneoulsy and you need to know this. A positive control is when you deliberately add something that you know will give a positive result; for example, if you are doing a test to see if your sample contains protein then you want to add an extra sample that contains a known amount of protein to make sure all your reagents are working.

Lots of controls are more complicated than the examples I gave but the principle is important. It's true that some experiments don't appear to need the appropriate controls but that may be an illusion. The controls might still be necessary in order to properly interpret the results but they're not done because they are very difficult. This is often true of genomics experiments.

The seven biggest problems in science

Here's an interesting article about the biggest problems in (American) science: The 7 biggest problems facing science, according to 270 scientists. Most of them apply to science in other countries.

I've added brief comments under six of the headings. Those are MY opinions, not necessarily those of the authors. The comment under #6 is a direct quote from the article.

1. Academia has a huge money problem.
   There's not enough money to do high quality science, especially basic science.
2. Too many studies are poorly designed. Blame bad incentives.
   Some experiments are poorly designed. All scientists are under pressure to make their results seem important.
3. Replicating results is crucial. But scientists rarely do it.
   Replication is important—especially in medical studies—but I think this problem is exaggerated.
4. Peer review is broken.
   The system (peer review) isn't working well. That doesn't mean there's a better system.
5. Too much science is locked behind paywalls.
   This was never a problem in the past when you had to go to the library to read science journals. You could photocopy whatever you wanted. Now it's a problem because we want instant access from our laptops.
6. Science is poorly communicated to the public.
   "But not everyone blamed the media and publicists alone. Other respondents pointed out that scientists themselves often oversell their work, even if it's preliminary, because funding is competitive and everyone wants to portray their work as big and important and game-changing.
   
   'You have this toxic dynamic where journalists and scientists enable each other in a way that massively inflates the certainty and generality of how scientific findings are communicated and the promises that are made to the public,' writes Daniel Molden, an associate professor of psychology at Northwestern University. 'When these findings prove to be less certain and the promises are not realized, this just further erodes the respect that scientists get and further fuels scientists desire for appreciation.'"
7. Life as a young academic is incredibly stressful.
   This is not just a problem for my younger colleagues. It affects all of us. It affects morale in an academic department and it affects the way science is done.

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Here's why Alain Beaudet, President of the Canadian Institutes of Health Research, should resign

The Canadian Institutes of Health Research (CIHR) is the main source of research funding for Canadian health researchers, including those doing basic research like most of the researchers in my biochemistry department.

A few years ago, CIHR decided to revamp the process of applying for and obtaining research grants. They did this without taking into consideration the wishes of most applicants. (They did "consult," but consulting isn't the same as listening.)

The result has been a disaster. Most researchers are confused and discouraged by the new process and there's great fear that the results of the next competitions will be harmful to basic research and harmful to new investigators.

But even before the new rules came into play the funding of basic, curiosity-motivated, science was taking a major hit. Many mid-career basic researchers at the University of Toronto have lost their grants or are struggling to make do with a lot less money. This is partly due to a lack of money in the system but it's been exacerbated by a deliberate shift in priorities under the previous Conservative government of former Prime Minister Stephen Harper.

These are some of the reasons why Canadian researchers have been calling for Alain Beuadet to resign [Support basic research with new leaders at the Canadian Institutes of Health Research (CIHR)].

Science and skepticism

The National Academies of Sciences (USA) formed a committee to look into scientific integrity. A summary of the report was published in the June 26th issue of Science (Alberts et al., 2015)

I'd like to highlight two paragraphs of that report.

Like all human endeavors, science is imperfect. However, as Robert Merton noted more than half a century ago "the activities of scientists are subject to rigorous policing, to a degree perhaps unparalleled in any other field of activity." As a result, as Popper argued, "science is one of the very few human activities—perhaps the only one—in which errors are systematically criticized and fairly often, in time, corrected." Instances in which scientists detect and address flaws in work constitute evidence of success, not failure, because they demonstrate the underlying protective mechanisms of science at work.

All scientists know this, but some of us still get upset when other scientists correct our mistakes. We have learned to deal with such criticism—and dish it out ourselves—because we know that's how knowledge advances. Our standards are high.

Get Science Right (in Canada)

The Canadian Association of University Teachers (CAUT) has launched a campaign to alert the public about changes in science policy and funding. The Conservative government of Stephen Harper has shifted funds toward directed research and starved Canadian scientists who focus on basic, curiosity motivated, research.

What this means is that young scientists are finding it increasingly difficult to get funding from the government. It means that scientists in mid-career are losing their grants and this means that research technicians have to be fired, graduate students can't be funded, and post-docs have to find another position.

Why is this important? Why should you care? Those are the questions that CAUT wants to answer by sponsoring meetings across the nation to explain why it's important to "Get Science Right." Come to a Town Hall meeting at the University of Toronto (Toronto, Ontario, Canada) and learn more. The meeting starts at 7pm. It's in room 119 at Emmanuel College (Victoria Uiniversity). [Facebook: Get Science Right - Toronto Town Hall]

Let me know if you plan to attend. We could get together before or after the meeting.

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Marc Garneau and the Liberal Party of Canada support basic research

Last night I was at a small gathering of Liberal supporters at the Paramount restaurant on Yonge Street in Toronto. The event was organized by Omar Alghbra my former MP in Mississauga. The guest of honour was Liberal MP Marc Garneau who was Canada's first astronaut. He represents the Montreal riding of Westmount—Ville-Marie.

Marc Garneau is one of a small handful of MPs in the Federal Parliament who has a Ph.D. (Electrical Engineering, Imperial College of Science and Technology, London, England) He has always been a strong supporter of science and technology and I know that he is involved in forming science policy for the Liberals under Justin Trudeau. This was my chance to put in a good word for funding basic science so I made my pitch. I described to him how the current funding situation is hurting basic science research in the universities [Canada is destroying a generation of scientists].

It wasn't really necessary. Garneau is a strong supporter of basic science and, if elected, the Liberal Party intends to reverse the policies of the current Conservative Party under Stephen Harper. They will change the distribution of funds at NSERC and CIHR to support more curiosity motivated research and to move away from the emphasis on using science funding to support business. According to Garneau, they will also reverse the Harper decision to force NRC into short-term goal oriented technology development and return it to a broad organization that also invests in basic research.

I was impressed by the fact that Marc Garneau was just as passionate about basic research as I am. I'm confident that the Liberal Party understands the problem and will, if elected, take steps to improve the current situation. The next step is to make sure that the Harper government is booted out of office before they can do even more damage.

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Muzzled and mad Canadian scientists

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The Silence of the Labs

The Canadian Broadcasting Corporation (CBC) aired an episode of The Fifth Estate on Friday night. I taped it and watched it yesterday between curling matches and the Canadian figure skating championships.¹

The Fifth Estate program documents the shutting down of various government labs by the Conservative government of Stephen Harper. The title says it all: Silence of the Labs. Follow the link and you can watch the entire program. I highly recommend that you watch the first two minutes to get the gist of what's happening in Canada.

Here's part of the summary that appears on the CBC website ...

Scientists across the country are expressing growing alarm that federal cutbacks to research programs monitoring areas that range from climate change and ocean habitats to public health will deprive Canadians of crucial information.

"What’s important is the scale of the assault on knowledge, and on our ability to know about ourselves and to advance our understanding of our world," said James Turk, executive director of the Canadian Association of University Teachers.

In the past five years the federal government has dismissed more than 2,000 scientists, and hundreds of programs and world-renowned research facilities have lost their funding. Programs that monitored things such as smoke stack emissions, food inspections, oil spills, water quality and climate change have been drastically cut or shut down.

The fifth estate requested interviews with two senior bureaucrats and four cabinet ministers with responsibility for resources, the environment and science. All of those requests were denied.

On Tuesday, the fifth estate received a statement from the office of Greg Rickford, Minister of State for Science and Technology, and the Federal Economic Development Initiative for Northern Ontario.

"Our government has made record investments in science," it stated. "We are working to strengthen partnerships to get more ideas from the lab to the marketplace and increase our wealth of knowledge. Research is vibrant and flourishing right across the country."

But members of the scientific community disagree. CBC’s the fifth estate spoke to scientists across the country who are concerned that Canadians will suffer if their elected leaders have to make policy decisions without the benefit of independent, fact-based science.

The CBC is a crown corporation. That means it has to report to a branch of the government and some its Board of Directors are government appointees. A lot of its funding comes from the Federal Government.

You probably won't be surprised to learn that the CBC is also under attack from the Harper government. I don't think that pressure is going to diminish once Conservative MPs see this program.

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[Photo Credit: I took this picture during a protest on Parliament Hill in July 2012. There are videos in the Fifth Estate program but I didn't see any glimpses of me of any of my friends.]

1. So many exciting things on television—one has to have priorities. I don't watch the Leafs any more.

Canada is destroying a generation of scientists

My department is in a Faculty of Medicine and the main source of research funding for biomedical sciences in Canada is the Canadian Institutes of Health Research (CIHR). The current Conservative Government has been consistently underfunding CIHR over the past six years so that the number of grants available for basic research (e.g. biochemistry and molecular biology) has been falling.

This is the time of the year when my colleagues hear the results of the latest grant competitions. It's been a sad couple of days because four labs failed to get funding for their main research projects. Eight other labs failed to get additional funding for ongoing projects that were not part of their main grant.

What does this mean? Let's think about the consequences for labs that lose their grants. In the short term, the lab will survive until the next application deadline but it means that the Professor running the lab can't take on any new graduate students or post-docs no matter how brilliant they might be. In some cases, the department, or the university, might have to provide "bridging" funds in order to pay the salaries and stipends of people in the lab. If the Professor manages to get the grant back in the next competition then a recovery is possible but a lot of damage has already been done.

However, in many cases the second or third attempts to recover funding are not successful and the lab must shut down. That's the situation we face in our department with several active research groups that have disappeared or are about to disappear.

The first people to be let go are the post-docs who are funded from the grant. They have to scramble to find a new position and this isn't easy. It could be the end of their career.

The most expensive people in the lab are the research technicians ($50-60,000 per year¹). They have to be put on notice and they will be fired. These are scientists with advanced degrees who are the heart and soul of a research lab. They are mostly women in mid-career. Many of them will never find another position that pays as well.

Graduate students who are close to finishing can usually be helped but those at the beginning of their studies have to switch to another lab and start a new project. This may not be possible.

Our research labs have two or three undergraduate students doing research projects as part of their degree requirements. As we lose more and more active labs, we also lose the ability to train undergraduates. We also hire undergraduate to work in labs over the summer and this provides invaluable experience in preparation for graduate school. If you don't have a funded lab you can't hire students. If you lose part of your funding, the easiest way to save money is not to hire anyone.

The groups that are losing their grants are the backbone of Canadian research infrastructure. The typical lab has three or four graduate students, a post-doc, and a research technician (research associate, lab manager). It takes about $150,000 per year to sustain such a lab. The Professor who runs the lab is usually between 30 and 40 years old (mid-career). The lab is producing several papers a year in respectable journals. These labs would easily have been funded a decade ago when the success rate on grant applications was 25% but now that it's down to 15% they are being cut out of the system.

Even those labs that are still funded are affected when a colleague loses a grant. That's because there's a lot of sharing of equipment and resources and expertise. We can foresee a time when the department falls below a critical mass of active research labs and when that happens everyone will lose their grants. Morale is already at an all-time low. Students and faculty are more worried about survival than science.

A generation of mid-career scientists is being destroyed by the policies of the Canadian government. Graduate students, post-docs, technicians, and undergraduates are being affected. It might take another generation to recover if funding were to return to appropriate levels. We might never recover if something isn't done soon.

Here at the University of Toronto we used to talk about becoming a world-class research centre. We don't talk about that very much any more.

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1. Salary plus benefits.

Get Science Right in Canada

Get Science Right

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Marc Kirschner Defends Basic Science

Marc Kirschner is Chair of the Department of Systems Biology at Harvard Medical School. He's a very smart man and a well-respected scientist.¹ He has an editorial in the June 14th issue of Science: A Perverted View of “Impact” [see also: In search of big breakthroughs: why attempts to predict ‘significant’ research might backfire in The Boston Globe]

Kirschner says that the emphasis on "significance" and "impact" in making funding decisions is "misleading and dangerous." Nobody can really predict how fundamental research will affect the future. He writes ...

PZ's Wonderful Exam Question

PZ Myers has just given his students a take-home exam. Here's one of the questions [It’s another exam day! ] ...

Question 1: One of Sarah Palin’s notorious gaffes was her dismissal of “fruit fly research” — she thought it was absurd that the government actually funded science on flies. How would you explain to a congressman that basic research is important? I’m going to put two constraints on your answer: 1) It has to be comprehensible to Michele Bachmann, and 2) don’t take the shortcut of promising that which you may not deliver. That is, no “maybe it will cure cancer!” claims, but focus instead on why we should appreciate deeper knowledge of biology.

That first restriction is going to make answering the question a real challenge 'cause you have to take into account the mentality of someone who is not just scientifically illiterate but scientifically anti-literate.

Nevertheless, this is exactly the sort of thing you want your science graduates to know.

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The Proper Role of Scientific Societies

Scientific societies are made up of groups of scientists who band together for various legitimate purposes such as organizing meetings, publishing journals, promoting their speciality, and lobbying for funds. The credibility of a society depends on its area of expertise. They lose credibility when they take positions on issues outside of their discipline.

That's why many of us have been opposed to the accommodationist positions of the American Association for the Advancement of Science (AAAS) and other societies. These societies have no special expertise in epistemology/philosophy or religion yet they openly proclaim that science and religion are compatible. They should be neutral on that question. A (slight) majority of Sandwalk readers agree, according to a poll I took a few years ago [What Should Scientific Organizations Say about Religion?].

I wasn't alone in adopting this position. Jerry Coyne and PZ Myers also think that scientific societies should keep their nose out of areas that are outside of their mandate. We are united when it comes to opposing accommodationism.

Dysfunctional Science

Carl Zimmer, one of the top science writers in the world, has written an article for the New York Times with the following provocative title: A Sharp Rise in Retractions Prompts Calls for Reform. It's partly about the rise in the rate of retractions¹ in scientific journals. This is a serious problem and it's hard to figure out the underlying cause, in spite of the fact that many of the people who comment think they know the answer.

But there's much more to this story as Carl explains on his blog [Dysfunctional science: My story in tomorrow’s New York Times].

In tomorrow’s New York Times, I’ve got a long story about a growing sense among scientists that science itself is getting dysfunctional. For them, the clearest sign of this dysfunction is the growing rate of retractions of scientific papers, either due to errors or due to misconduct. But retractions represent just the most obvious symptom of deep institutional problems with how science is done these days–how projects get funded, how scientists find jobs, and how they keep labs up and running.

As usual, Carl's got it right. There's something wrong with science, or perhaps I should say there's something wrong with the biological sciences since Sean Carroll doesn't see the same problem in physics [Is Physics Among the Dysfunctional Sciences?].

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1. The rate is about 0.04%. Compare this to the rate of fraudulent creationist publications, which is close to 100%.

Sign a Petition on CIHR Funding

 
Are you a Canadian researcher who cares about the dismal CIHR funding situation?

Sign the petition at: The CIHR Individual Grants Program. It may not do much good but at least you'll have 700+ friends (latest count).

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Jonathan Wells Is a Winner!

 
This week's Egregiously stupid remark of the week by an IDiot goes to Jonathan Wells for his comment about HOX genes.

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Swine Flu and "The Canadian Problem"

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

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

The confusion isn't helped by ambiguous reporting such as this from Canadian Press: Study linking flu shots, swine flu raises concern abroad, prompt changes at home.

The data, referred to as "the Canadian problem" by some scientists outside this country, are reported to link getting a flu shot last year with double the risk of contracting swine flu this year.

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

Say what?

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

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

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

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

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

"And if there are methodologic flaws, we need to be assured that every stone was turned over to make sure what we're reporting is valid."

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

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How Granting Agencies Destroy Young Scientists

 
Peter Lawrence has an article in the latest issue of PLoS Biology: Real Lives and White Lies in the Funding of Scientific Research.

He's not saying anything we don't already know but he says it so well. Peter describes the typical example of a young researcher (K.) who is frustrated and discouraged by the way science is funded in the UK. The details may differ but it's the same basic story at universities in North America and everywhere else.

He then describes his own experience and highlights the problem.

After more than 40 years of full-time research in developmental biology and genetics, I wrote my first grant and showed it to those experienced in grantsmanship. They advised me my application would not succeed. I had explained that we didn't know what experiments might deliver, and had acknowledged the technical problems that beset research and the possibility that competitors might solve problems before we did. My advisors said these admissions made the project look precarious and would sink the application. I was counselled to produce a detailed, but straightforward, program that seemed realistic—no matter if it were science fiction. I had not mentioned any direct application of our work: we were told a plausible application should be found or created. I was also advised not to put our very best ideas into the application as it would be seen by competitors—it would be safer to keep those ideas secret.

The peculiar demands of our granting system have favoured an upper class of skilled scientists who know how to raise money for a big group [3]. They have mastered a glass bead game that rewards not only quality and honesty, but also salesmanship and networking. A large group is the secret because applications are currently judged in a way that makes it almost immaterial how many of that group fail, so long as two or three do well. Data from these successful underlings can be cleverly packaged to produce a flow of papers—essential to generate an overlapping portfolio of grants to avoid gaps in funding.

Thus, large groups can appear effective even when they are neither efficient nor innovative. Also, large groups breed a surplus of PhD students and postdocs that flood the market; many boost the careers of their supervisors while their own plans to continue in research are doomed from the outset. The system also helps larger groups outcompete smaller groups, like those headed by younger scientists such as K. It is no wonder that the average age of grant recipients continues to rise [4]. Even worse, sustained success is most likely when risky and original topics are avoided and projects tailored to fit prevailing fashions—a fact that sticks a knife into the back of true research [5]. As Sydney Brenner has said, “Innovation comes only from an assault on the unknown” [6].

You know, what's really puzzling about this phenomenon is not that we are unaware of the problem—it's that we haven't done anything about it. If the system isn't working then let's fix it.

There are several innovations that could fix the problem. Peter suggests that only the best papers from a lab should be evaluated and that young investigators could be interviewed by the granting agencies to evaluate promise. Others suggest that funds could be given to departments and the departments could distribute the money in the most efficient and effective manor.

Many scientists advocate shorter grant proposals with more of an emphasis on past productivity than on what's in the actual proposal. If you've been successful in the past then you will probably be successful in the future. It's time to stop rewarding grantsmanship and start rewarding science.

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