Becoming a grown up scientist.

Dr. Janet Stemwedel is a philosopher at San Jose State who also happens to have earned her PhD in physical chemistry, which means she has some significant street cred when discussing science. Her blog is known as Adventures in Ethics and Science, and recently she began a series on being a grown up scientist. Part 1 identifies some of the many things that professional scientists must do that graduate students are not taught, or may not even be aware of, while they are in training.

Of course, what I discovered is that there is a great deal more one needs to learn than just how to be creative, have good insights, design reasonable experiments, present reasonable data, and write clear scientific papers. (Even this much is quite a lot to learn, and some of it — like scientific creativity — is pretty hard to teach.)

Grown-up chemists also seemed to know how to write effective grant proposals, how to manage (and even mentor) graduate students, postdocs, and technicians, how to nurture productive and mutually beneficial relationships with other chemists in their sub-specialty, how to stay on top of the literature and discern which newly described results or techniques were most important (at least with respect to their own research area), how to be fair and constructive peer reviewers and how to respond effectively to referee reports on their own manuscripts, how to work within departmental politics and the politics of their discipline.

They knew how to tell when an experiment was done, when the data was good, when there was a finding that merited a paper to announce it. They knew how to work out authorship on the papers. They knew who, in their field of research, would be the hardest to convince of the new result. They knew which journal would be the best place to submit a particular manuscript and which meeting would be the best venue to present pre-publication results. And, they could conceive of three distinct follow-up projects to build on the new results.

Plus, they (at least, the grown-up chemists I was looking to as role models) seemed to know which chemists in the community were good people to talk to, collaborate with, or argue with (in the best sense of argument, where each side makes its best case and then presents its best criticisms of the other side). And they seemed to have identified the chemists around whom you’d want to watch your back.

Grown-up chemists had a huge body of unwritten knowledge to draw upon, it seemed. But hardly any of it seemed to be the focus of our graduate training — at least, not explicitly.

I must say I agree totally — there is a tremendous difference between being a grad student and being a professional academic scientist, but it’s probably the case that most of us do not realize that until we are faculty. I certainly had a profound new respect (in addition to an already considerable amount) for my former advisors when I became a professor myself.

Part 2 of Janet’s series will ask “Why don’t most advisors talk about the things grad students most want to learn from them?”. I am looking forward to the rest of her posts, and I recommend them to both students and advisors as the basis for discussion and thought.


Course evaluations.

There is more than enough discussion about the usefulness (or not) of student evaluations of courses. I will refer you to Larry Moran‘s recent discussion where you can find one perspective as well as links to other articles. More recently, there is an interesting piece in University Affairs by Brett Zimmerman of York University.

Course evaluations – students’ revenge?

To some extent, the issue appears to be that anonymous evaluations are not particularly helpful. I don’t know how it is done at most universities, but at Guelph evaluations are now done online on a volunteer basis (so the problem becomes getting them to participate) and only comments that are signed count in T&P reviews. I personally find the comments useful, if in no other way than to provide confidence that some of the new approaches I try to implement are successful.

I don’t think we want to abolish student feedback, and I think this should be part of T&P reviews, especially in disciplines like science where there can be a tendency to consider oneself a researcher first and an educator a distant second. However, unsigned comments, especially when they allow students to make insulting statements without consequences, are not useful and should be updated.


Huckabee is right for all the wrong reasons.

Over at Pharyngula, PZ points to an interview with former Arkansas Governor and presidential hopeful Mike Huckabee. As a Canadian, I have long been amused by Huckabee for reasons you can see here. The prospect of this guy becoming president is unnerving, but then so is the fact that our neighbours saw fit to elect (or at least, not not-elect) Bush. Twice.

Here is what Huckabee has to say about evolution. I have omitted the bit about teaching non-scientific alternatives in science class that preceded it, because it’s too silly to repeat (he says “all views”, but presumably he means “one other view” only).

Because, frankly, Darwinism is not an established scientific fact. It is a theory of evolution, that’s why it’s called the theory of evolution.

He’s right. “Darwinism” — a term used mostly by creationists, but also historically (e.g., Wallace) and to an extent today (e.g., Dawkins), especially in Britain — refers to natural selection as a mechanism of evolution. And it is a theory. In science, a theory is an explanation for an observed or inferred condition of the natural world that is well established through multiple lines of empirical evidence (i.e., a fact). Darwin’s theory of natural selection is one explanation for the fact that species are related through descent, which in turn has been well established in science for well over a century on the basis of fossils, biogeography, embryology, morphology, and genetics. Darwinian natural selection is not the only available explanation, and therefore represents a subset of modern evolutionary theory. That natural selection happens is an established fact (witness antibiotic resistance), but what its role is in causing large-scale evolution remains a subject of discussion among biologists.

So “Darwinism,” in the sense of meaning that the majority of evolution occurs via natural selection, is indeed not an established fact, it is a theory. Huckabee’s words are correct, even if his intent is terribly muddled. Scientific theories explain facts. If there is no established fact, then there is no theory needed.

I invite Gov. Huckabee to read more about this in a recent paper that is freely available here.


Evolution as fact, theory, and path.

As noted in my previous post, the new journal Evolution: Education and Outreach is now available online and free to download. My contribution to the first issue is “Evolution as fact, theory, and path“. Feel free to distribute this and any other papers from the journal as widely as you like, but please link to the journal website rather than re-posting papers.

There are now several available articles that discuss this important subject:


Evolution: Education and Outreach

I am very pleased to announce that the new journal Evolution: Education and Outreach will launch officially today at the National Association of Biology Teachers conference in Atlanta, Georgia. The online version is now operational as well.

You can read everything in Volume 1, Issue 1 here:

http://www.springerlink.com/content/phj263762420/

I’d say this first issue turned out quite well, especially as a first attempt that sets up the types of articles we will explore more down the line. We’re working on some exciting ideas for future issues. So stay tuned.

Download. Read. Enjoy. Share.


PhDs in science finish faster in Canada than the USA.

According to a story in the December issue of University Affairs, PhD students in Canada complete their degrees more quickly than their counterparts in the USA. (I suspect that no one completes faster than students in the UK, but that’s a rather different topic.)

The article suggests that the existence of a distinct Master of Science (MSc) degree in Canada is at least partly responsible for this difference. That is, having the option of starting in a Master’s degree lets students decide whether they are cut out for the considerably more demanding PhD program. In Canada, the expectations for originality and scope are less for an MSc thesis than for a PhD, but both are based on conducting independent research and have only a moderate course component.

The interesting thing is that with the intense pressure from the top down on faculty to get more PhDs out the door, there is a growing emphasis on doing away with the MSc and having students transfer to a PhD program without completing and defending a Master’s thesis1. The data collected by Susan Pfeiffer, which are described in the story, suggest that this is a bass-ackwards way to go about it.

Moreover, completion times are not the only consideration — students also must be competitive for postdocs, fellowships, and eventually jobs. To me, going a semester over but completing some manuscripts appears more beneficial in the longer term than getting out in no more than nine semesters post-MSc. On the other hand, only 3/4 of PhD students in Dr. Pfeiffer’s survey had completed their degrees even after 10 years in the program, which is way too long by any department’s standards.

Some students are perfectly capable of completing an MSc but may not be interested in, or qualified to attempt, the PhD. It also happens that students who do both degrees typically complete more efficiently overall than those who do just a PhD. Therefore, I feel that the option (indeed, usual requirement) of a distinct Master’s program prior to enrolling in a PhD is a good thing, and I would not want to see it vanish.

________

1) Full disclosure here: I did not complete a Master’s thesis and instead transferred to a PhD and completed the whole shebang in almost exactly 5 years of graduate studies.


The Great Dying.

There have been five major mass extinctions in the history of life since the Cambrian. The “Big Five” are the Ordovician-Silurian, Late Devonian, Permian-Triassic, Triassic-Jurassic, and Cretaceous-Tertiary events. The latter is the most famous, having resulted in the extinction of all dinosaurs except birds, and more than half of contemporary biodiversity overall. This was not the most severe pruning of the tree of life, however — rather, this took place at the end of the Permian when roughly 95% of species were extirpated. The causes of the so-called “Great Dying” remain a subject of debate, but some recent work has provided evidence for an asteroid impact (perhaps in combination with various other related or independent factors).

Anyway, the reason I bring this up is that I am trying to find out the source film for the following clip by National Geographic:

If you happen to know the title of the documentary, let me know.

Oh, and if you’re interested in the End Permian event, you can take a look at these fine books:


Why would advisors encourage students to publish?

Recently there has been some discussion in the blogosphere about student-advisor relationships in science. Some of this has been triggered by the article by Peter Lawrence in Current Biology (The mismeasurement of science) and some by the recent reports in Nature (here and here) regarding the comparatively low numbers of academic positions relative to the number of new PhDs (and be sure to see also Larry Moran‘s slightly different and perhaps more realistic take on this).

One of the recurring topics is the pressure that is often put on graduate students by their advisors to publish. Often this seems to be interpreted in a very negative way, with the advisor supposedly viewing students as little more than data-generating and paper-authoring machines (or “indentured labour”, according to one of the Nature articles) to be exploited for their own gain. As an advisor, I want to provide some alternative explanations that are not based on such nefarious motives.

At the base of this discussion is the assumption that most advisors actually do encourage/pressure their students to publish — an assumption with which I will not disagree here. What remains open is the interpretation of why this might occur. There are several possibilities:

1) The advisor does no real lab work himself and brings in graduate students as “cheap, well-trained labour” (as one Nature author put it).

I am sure this happens, especially in some larger groups, but this is not the case in my lab. In fact, one wonders how the students come already well trained. As an advisor, it can eat up an enormous amount of time and energy — which could easily be spent writing more papers by oneself — to render graduate students sufficiently competent and confident that one can trust their data as though one had acquired them oneself. Indeed, I resent the insinuation that advisors are self-centred egomaniacs with no regard for student well-being. I take my responsibilities as an advisor very seriously, I care a great deal about the success of my students as individuals, and I work hard to foster an attitude of “my success is your success and vice versa” in the lab. It’s possible that the old joke about lawyers (“99% of them give the rest a bad name”) applies to advisors, but I do not believe that this is nearly as ubiquitous as it is made out to be.

So, leaving behind the standard interpretation which I strongly reject, let us consider some other possibilities.

2) Advisors need their students to publish so that they can get funds to train more students.

Like it or not, publications coming out of a lab represent a major criterion for whether applications for funding will be supported. No publications, no money. No money, no students. Instead of being a result of megalomania, the pressure put on students to publish can also be the result of a desire to be able to accept eager students into one’s lab rather than turning them away. Current students are supported by funds acquired through the labour of others (previous students and/or the advisor), and their efforts indirectly can open possibilities for future students. Think of it as a kind of intergenerational reciprocity.

3) Students want to publish, and the advisor makes sure that they stay on track to accomplish this.

Most of the graduate and undergraduate students with whom I have worked directly have been quite excited by the possibility of seeing their names in print on a high quality piece of work. I would never discourage this, and in fact I do my best to guide them in their research so that in the end it will meet the standards necessary for publication. That may mean extra work well beyond what is required for their course or degree — but I make a point of screening students as best I can to only accept those who aim higher than the average expectation. It also means that I have to hold the student to a higher standard and to keep the pressure on at times so that their goal of publishing (which of course I share) is achieved.

4) The advisor can easily write single-author papers but wants to write papers with his students.

As with many other advisors, I could easily spend more time working on papers alone or with other PIs. There is something special about writing a paper with a student, however, especially if it is the student’s first. It’s probably not unlike the excitement of taking a young child to his or her first sporting event, movie, or other activity that a parent has done dozens or hundreds of times and which no longer has that same sparkle of novelty. It is always enjoyable to experience something again for the first time. I remember very well writing my first paper and the excitement of seeing it in print. The only way an advisor can feel that again is to go through it with a new student. In this scenario, students may not quite know how to get a publishable piece of work finished, or may not be thinking that far ahead, but the advisor knows they will be thrilled to have a paper in the end and keeps the pressure on so that it remains a possibility.

5) Publishing will help students who go on in science.

It is a given at this point that having publications is necessary for students to be competitive for future graduate student positions, postdocs, scholarships, fellowships, and eventually jobs. It makes little sense to wait until the end of one stage to publish (e.g., writing up all one’s data from one’s PhD as a postdoc), and it is far more beneficial to have established at least something of a CV before one starts looking for the next position. Advisors who care about their students’ futures will therefore keep the pressure on for them to do high quality work and to put in the effort to publish before they leave the lab.

6) Publishing will help students who do not go on in science.

There is sometimes an implicit assumption that students who plan to go on in science should be treated rather differently from those who do not. Encouraging them to publish commonly falls into this category. Let me point out, however, that not all students know if they want to go on at any given moment (such that these are not discrete categories). This is especially true in systems as in Canada where the MSc and PhD are usually done separately but both involve intensive research projects; some students use the MSc to determine whether they can/want to move on to a PhD. More importantly, it should be obvious that doing work of sufficient quality to warrant publication will help a student no matter what their career ambitions. Why? First, because it shows that while they were in science, they conducted their work at a level high enough to pass peer review and to get into print. Surely a potential employer would recognize this as an indication of intellect, work ethic, and ambition even if lab work, analysis, and writing are not part of the job for which a former student is applying. Second, because inevitably the student will be asking the former advisor for letters of recommendation in the future. If the student has done high caliber work that has been published, the advisor can feel confident recommending her. Whenever possible, I would very much like to be able to write letters about my students like “She went well beyond the normal expectations of her program and completed work of such high quality that it was published as several papers in top journals.”

7) If students and advisors are going to invest the time, then the work should be done at a publishable level.

Advisors have very little free time. If they are going to invest it in writing grants to support a student’s research and spend the time training students in the methods and analytical approaches of their discipline, going over proposals, attending committee meetings, and generally ensuring that a student has everything he needs to do his research, then there is a reasonable expectation that, in return, the work will be done at a high level. It also makes sense that if the student himself will be investing months or years on a project, that it should be done at a level worthy of publication. Both the advisor and the student win in that case, and the time will have been well invested by both. Making sure that this is true may, of course, involve pressure from the advisor.

(I hope you will forgive a small digression at this point. I don’t know how common the misconception is (perhaps it is higher among students?), but advisors are not lazy. Most university faculty work very long hours and are chronically overwhelmed with dozens of duties and commitments. No, they generally do not spend very much time in the lab (anymore), but this is because they are busy writing grants, teaching courses, giving seminars, attending committee meetings, reviewing papers, and juggling countless other tasks — many of which they consider far less appealing than the lab work that they did as students and postdocs. To have landed one of the scarce faculty jobs, they must not only have done substantial research of their own, they must have risen above the competition in this and other regards. This does not give them permission to view students as data-producing robots (even if they themselves were treated as such), but it does earn them some slack from anybody who might otherwise resent that the boss isn’t at the bench very often.)

8) If data are not published, they might as well not exist as far as the pool of human knowledge is concerned.

Data that would otherwise be considered interesting, novel, and important mean nothing if no one knows about them. And if they are never published, then effectively they might as well not exist. The goal of science to expand human knowledge should, in itself, be enough to inspire students to want to publish, but in case that is not enough, there are several practical reasons that students should be expected to generate publication-quality work. One, taxpayers fund most of the research that gets done in academic labs, and they have a right to expect a return on their investment. This does not mean that all science must be done for some specific applied reason, but it does mean that it should not be done solely for the sake of personal interest or in the pursuit of a degree. Two, everyone benefits from scientific knowledge, but unlike most individuals, students have an opportunity to add to it as well — so long as they make their results widely available. As one professor I know puts it with tongue partly in cheek, “unless you actually contribute something to human understanding of the world, you are a parasite on those who do”. Three, not publishing means that other students may waste their time in other labs, trying to develop the same methodologies and making the same mistakes, because they were unaware of the work that had been accomplished already. It is also the case that other students may replicate work that has already been completed rather than expanding on it or focusing on some other issue in need of study. Not publishing essentially means that new knowledge produced by students is lost, and the advisor has a responsibility to prevent this if at all possible.

The point here is that there are many positive reasons why students should aim to publish and why this should be encouraged and expected by their advisors. Implicit assumptions that advisors have only their own selfish interests at heart can do little more than to discourage students from trying their hand at research and to offend advisors who care sincerely about their students. The publication of exceptional research is in the best interest of both the student and the advisor, but this may not always happen without some encouragement and pressure at the right times.


Acceptance of evolution in Canada, again.

As an update to the previous post about the acceptance of evolution in Canada vs. the USA, here are some highlights from a recently published (July 3) poll by Canadian Press-Decima Research. This is useful because it breaks the issue down into young earth creationism, theistic evolution, and naturalistic evolution in the way that American polls have in some cases.

  • Less than one in three Canadians (29%) believe that God had no part in the creation or development of human beings.
  • Fewer still (26%) believe “that God created human beings pretty much in their present form at one time within the last 10,000 years or so”.
  • A plurality, but still only 34%, say that “human beings have developed over millions of years from less advanced forms of life, but God guided this process”.
  • Belief in creationism is lowest in Quebec (21%), Alberta (22%), and B.C. (22%). In Alberta, the plurality view is that God guided human development (39%), while in Quebec the plurality feels God played no part (40%).
  • Rural residents are 12 points more likely than urban dwellers to believe that God created humans in their present form. Differences by generation are not all that large. The plurality of women (37%) believes that God guided the process, while the plurality of men (35%) believes that God played no part.
  • In polls using the same question (Gallup) put to US residents, findings are different: 45% said God created humans in more or less their present form (compared to 26% in Canada), 40% said that God guided the evolutionary process (compared to 34% in Canada). Only 15% say God played no part (compared to 29% in Canada).
  • According to Decima CEO Bruce Anderson “These results reflect an essential Canadian tendency: we are pretty secular, but pretty hesitant to embrace atheism. Our views on the role of science and spirituality lack consensus but these are not polarizing issues for the most part. It’s more as though for many, these feelings are unresolved, we believe in a higher being, we know what we don’t know, are comfortable not knowing, and choose not to press our views upon one another.”