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.


The press going ape again.

Here’s a headline from the AFP in Paris (via Yahoo News):

Fossil find pushes human-ape split back millions of years

This is a heck of a lot better than some of the truly nonsensical proclamations of the press about the discovery some important fossils, namely eight molars and a canine tooth from a (presumed) ancestor of gorillas, e.g. New Fossil Ape May Shatter Human Evolution Theory. But I still have some problems with this story.

I’m no anthropologist, and I do not generally follow the specialized literature of that field closely. But as far as I know, it is now very well established that humans and chimpanzees are more closely related to each other than either is to gorillas. That is what the molecular data indicate, in any case. Here’s a representation of the relationships among our closest living relatives:

This means several things. First, that there is no natural category called “apes” that does not include humans. Humans are apes. Second, that there was no single split between the ancestors of “apes” and those of humans. Different lineages split at different times. The split between the ancestor of orangutans and the ancestor of the other apes (gorillas + chimps + humans) probably occurred first, then the split between the ancestor of gorillas and that of the remaining apes (humans + chimps), and then the split between the ancestor of chimps and humans. (And then splits between the ancestor of chimps and bonobos and various now-extinct relatives thereof, and between the ancestors of various hominins).

(Just in case it doesn’t go without saying, humans are not descended from chimps, they share a common ancestor with chimps. Chimps are cousins, not grandparents, to humans. Further, it is just as accurate to say that “orangutan ancestors diverged from the ‘human’ lineage” as it is to say that “human ancestors diverged from the ‘orangutan’ lineage”. There is no main trunk from which offshoots diverge, there are just branchings within a bush.)

In this particular news story, the reporter notes that “the new fossils, dubbed ‘Chororapithecus abyssinicus‘ by the team of Japanese and Ethiopian paleoanthropologists who found them, place the early ancestors of the modern day gorilla 10 to 10.5 million years in the past, suggesting that the human-ape split occurred before that.”

Moving the split of the ancestors of gorillas from the ancestor of chimps + humans back does not affect the “human-ape split”. Why? Because there was no such split. Move the gorilla lineage divergence back from 6-8 to 10-10.5 million years (My), that’s fine, but it does not automatically tell you when the human and chimpanzee ancestors’ lineages split, because that occurred later (nonetheless, the authors of the original paper suggest a new divergence for chimp/human ancestors at 9 My). In contrast, if you found an older split for the ancestors of humans and chimpanzees, you might have to move some splits that happened before it back also. As a result, there are arguments that pushing the gorilla lineage split back to 10 My from the current 6-8 My would require moving the orangutan lineage split way back (the authors of the original article say to 20 My).

Notably, the author of the news story also reports that “Conventional scientific wisdom, based on genetic “distances” measured by molecular geneticists, had placed the divergence between chimps and humans some five to six million years ago. Orangutans are thought to have parted company with our ancestors 13 to 14 million years ago.” As a very general proposition, and not including any nuanced discussion, gorillas would be expected to have ancestors of an age somewhere in between 5-6 and 13-14 million years, and 10-10.5 My is right in between these.

Maybe I am missing something, but as interesting and important as this discovery is for understanding some specifics of gorilla evolution, it does not shake things up that much as far as the other apes, including a certain hairless one, are concerned. That is, if these really are teeth from a direct ancestor of gorillas and not an example of convergence according to diet in a non-ancestral species, as some people have already suggested it might be. The question of why the molecular data and the fossils don’t quite agree is interesting, but that’s a pretty standard issue.

Finally, let me say once again that this sort of case is a question about the path of evolution, the specific branchings and timings thereof in the history of particular lineages, and has no bearing on the fact of evolution, namely whether or not species are related through common ancestry and descent with modification. Find me a gorilla fossil older than 500 My and we’ll talk about substantial challenges to the fact of evolutionary relationships.

———-

The original report and comments article in Nature are:

Suwa, G., Kono, R.T., Katoh, S., Asfaw, B., and Beyene, Y. 2007. A new species of great ape from the late Miocene epoch in Ethiopia. Nature 448: 921-924.

Dalton, R. 2007. Oldest gorilla ages our joint ancestor. Nature 448: 844-845.


T. rex could outrun humans?

Is it just me, or is there a major difference between

T. Rex Could Outrun Humans

(which is what LiveScience proclaimed)

and

T. rex Could Have Outrun Humans”

?

No, I am not talking about the annoying, inaccurate notation of the species name, but the (probably unintentional) invocation of an image of T. rex coexisting with and outpacing H. sapiens.

The story itself correctly says that T. rex is thought to have been able to reach speeds higher than humans. Incidentally, this is the same author who posted a previous story about which I recently complained.

Maybe I am just getting too nitpicky at this point.


A surprisingly silly interview.

LiveScience is continuing with their series on nature’s “Greatest Mysteries”. Today it’s “What drives evolution?“.

In the second paragraph, we find this intriguing question:

Natural selection is accepted by scientists as the main engine driving the array of organisms and their complex features. But is evolution via natural selection the only explanation for complex organisms?

No, it isn’t. Genetic drift also plays a major role. However, as Dawkins points out repeatedly, natural selection is the only known mechanism capable of resulting in complex adaptations. The legitimate debate is therefore about how much phenotypic (or genetic) change is adaptive and how much is a product of chance. I wouldn’t consider it a “great mystery” but a debate about the relative contributions of fairly well understood mechanisms. Dawkins sees adaptations as the only interesting things to explain. Lynch (2007) provides an equivalently extreme argument from the drift side of the aisle. But this can’t be what the author has in mind, as it is all very standard.

“I think one of the greatest mysteries in biology at the moment is whether natural selection is the only process capable of generating organismal complexity,” said Massimo Pigliucci of the Department of Ecology and Evolution at Stony Brook University in New York “or whether there are other properties of matter that also come into play. I suspect the latter will turn out to be true.”

So we see that, indeed, the discussion is not about whether processes besides selection can generate complexity (they can, though it may not be adaptive complexity). It’s about whether totally different processes are at play. Reading Pigliucci’s statement immediately brings to mind thoughts about self-organizing complexity as emphasized by Stuart Kaufman and others about 15 years ago. Interesting ideas, but they didn’t really lead anywhere. But this is not what is discussed, and it’s here that the story takes a turn for the bizarre.

“Over the past decade or two, scientists have begun to suspect that there are other properties of complex systems (such as living organisms) that may help, together with natural selection, explain how things such as eyes, bacterial flagella, wings and turtle shells evolve,” Pigliucci told LiveScience.

One idea is that organisms are equipped with the flexibility to change their physical or other features during development to accommodate environmental changes, a phenomenon called phenotypic plasticity.

Phenotypic plasticity is a “property of matter”?

The change typically doesn’t show up in the genes. For instance, in social bees, both the workers and guards have the same genomes but different genes get activated to give them distinct behaviors and appearances. Environmental factors, such as temperature and embryonic diet, prompt genetic activity that ends up casting one bee a worker and the other a guard.

The cells in my fingers typing these words are very different from the cells in my brain thinking them, but they contain the same genome. The exact details of gene regulation and cell differentiation are still being studied, but this hardly constitutes either a “great mystery” of evolution or a challenge to Darwinian mechanisms. Same goes for castes within a bee hive, which has been described as being like a superorganism.

And just to prove that this is all very standard:

If beneficial, this flexibility could be passed on to offspring and so can lead to the evolution of new features in a species. “This plasticity is heritable, and natural selection can favor different kinds of plasticity, depending on the range of environmental conditions the organism encounters,” Pigliucci said.

So, phenotypic plasticity is not a property of matter but a standard biological process, and it can be shaped by natural selection like other heritable characteristics. Nothing new here.

But then we do finally get back to evolutionary changes resulting from “properties of matter” such that the mechanisms are non-Darwinian.

Self-organization is another evolutionary force that some experts say whips up complex features or behaviors spontaneously in living and non-living matter, and these traits are passed on to offspring through the generations.

That a Lamarckian process of inheritance of acquired characters played an important role would be surprising indeed. Perhaps it is not so silly as that. Maybe the author is thinking of epigenetic changes that can be passed on. But that would still be only a minor variant of the standard Darwinian process — natural selection was conceived long before any specific rules about hereditary systems were identified. Genetic or epigenetic, if it is inherited and has effects on fitness, it can be subject to natural selection.

“A classic example outside of biology are hurricanes: These are not random air movements at all, but highly organized atmospheric structures that arise spontaneously given the appropriate environmental conditions,” Pigliucci said. “There is increasing evidence that living organisms generate some of their complexity during development in an analogous manner.”

A biological illustration of self-organization is protein-folding. A lengthy necklace of amino acids bends, twists and folds into a three-dimensional protein, whose shape determines the protein’s function. A protein made up of just 100 amino acids could take on an endless number (billions upon billions) of shapes. While this shape-shifting takes on the order of seconds to minutes in nature, the fastest computers don’t have the muscle yet to pull off the feat.

The mechanism that triggers the final form could be a chemical signal, for instance.

So are we relying purely on chance every single time a protein folds? Or is three dimensional structure consistent given a particular string of amino acids? If the latter (which it is, or we’d be dead), then this would imply that self-organizing that could go any which way is not the explanation. Rather, the string of amino acids and the conditions in which it folds (e.g., the chemistry of the cell) are heritable and have fitness consequences. Where might that “chemical signal” comes from, pray tell?

After this, there is more about phenotypic plasticity. There’s an example of butterflies with different colour patterns depending on season (so again, a question of how the environment affects gene expression during development — interesting and important to consider in evolutionary biology, but not a challenge to natural selection because the switch in colouration is adaptive).

The last example is of shorebirds called red knots which “can morph their phenotypes depending on their migration routes.”

When brought into captivity and placed in colder temperature environments, the shorebirds’ flight muscles and organs shrink to reduce heat loss. The birds pass on to offspring the capacity to make these changes.

Maybe this is an innocuous statement, like claiming “If people work out, they will get big muscles, and they pass on the capacity to get big muscles by working out to their offspring”. One could even say that some individuals’ offspring (say, Arnold Schwarzenegger’s) have a higher capacity to become muscular under conditions of heavy exercise than others’. But then, this wouldn’t be nearly as interesting as implying that soft inheritance is taking place.

Overall, this piece was really quite confused, mixing very different issues in a strange sequence, which is a shame in light of the good article they posted last week.

I still wonder what can be done to improve the accuracy of science reporting; “nothing” seems less and less like an acceptable answer.


Why are there transitional animals?

“Uh oh,” thought I upon seeing this headline from LiveScience: Greatest Mysteries: Why Are There Transitional Animals?

“This could go wrong in so many different ways,” I said to myself, “let’s see which one they went with”.

Much to my pleasant surprise, the story is actually pretty good. There’s a bit of the usual anthropomorphizing of natural selection (“it shows us how evolution could have tinkered with variation”), but overall it is a reasonable discussion of an interesting topic. I doubt the existence of so-called “transitional animals” counts as a “great mystery”, but this is made up for by an excellent quote from Jack Conrad of the AMNH in New York (where I spent a year as a post-doc).

“These early whales were basically playing the same game that crocodiles play: Wait for something to come get a drink and then pull it in the water for dinner,” Conrad said. “This is also the same game that early land vertebrates, early amphibians and early relatives of crocs and dinosaurs were playing. These animals weren’t necessarily ‘on their way’ to being anything; they were well suited to being exactly where they were.”

It is quite refreshing, after the dazed hype about human evolution over the past couple of weeks, to see a statement so on the mark.


Beneficial mutations.

A reader asked me to post about beneficial mutations as an antidote to the common creationist (mis)conception that all mutations are detrimental. I replied that this isn’t an anti-creationist blog per se (I feel that I have more interesting things to talk about, frankly), and that the issue has been covered by others (e.g., here and here). I will, however, note the following article published recently in Science:

Perfeito, L., L. Fernandes, C. Mota, and I. Gordo. 2007. Adaptive mutations in bacteria: high rate and small effects. Science 317: 813-815.

Abstract: Evolution by natural selection is driven by the continuous generation of adaptive mutations. We measured the genomic mutation rate that generates beneficial mutations and their effects on fitness in Escherichia coli under conditions in which the effect of competition between lineages carrying different beneficial mutations is minimized. We found a rate on the order of 10–5 per genome per generation, which is 1000 times as high as previous estimates, and a mean selective advantage of 1%. Such a high rate of adaptive evolution has implications for the evolution of antibiotic resistance and pathogenicity.

As they note at the end of the paper,

Given the estimates for the overall mutation rate in E. coli and its genomic deleterious mutation rate, our estimate of Ua implies that 1 in 150 newly arising mutations is beneficial and that 1 in 10 fitness-affecting mutations increases the fitness of the individual carrying it. Hence, an enterobacterium has an enormous potential for adaptation and may help explain how antibiotic resistance and virulence evolve so quickly.

It is important to be clear that this is not a matter of mutations occurring in response to need, nor of whole populations of individuals changing to become resistant simultaneously. It is the normal Darwinian process of “random” mutation (with respect to fitness, but not such that all mutations are equally likely to occur) leading to increased or decreased reproductive output of individuals that happen to carry the mutation, with the proportion of genic variants changing over many generations. The main insight is that the pool of mutations on which this blind process of natural selection acts is larger and less biased toward deleterious changes than assumed. In this case, the study not only hits a common creationist misconception head on, it also shows how understanding evolution often has considerable medical importance.


Funny faces.

As noted in an earlier post, it is quite useful to have blogs, science news, and journal index searches all delivered to a single reader. Today I noticed an interesting juxtaposition of two news stories while skimming through my aggregated list of feeds. These two headlines were given in immediate succession (and from the same source):

Handsome By Chance: Why Humans Look Different From Neanderthals
Chance, not natural selection, best explains why the modern human skull looks so different from that of its Neanderthal relative.

Facial Attraction: Choice Of Sexual Partner Shaped The Human Face
Facial attractiveness played a major role in shaping human evolution, as studies on our fossil ancestors have shown our choice of sexual partner has shaped the human face.

These two studies aren’t mutually exclusive, of course. Neanderthals may have evolved their features by chance whereas human features evolved in response to sexual selection, but it’s amusing that such diametrically opposed explanations for facial features within the genus Homo — random genetic drift versus non-random mate choice — are given right next to each other in the news feed.


____________

The news stories are based on these articles:

Weaver, T.D., C.C. Roseman, and C.B. Stringer. 2007. Were Neandertal and modern human cranial differences produced by natural selection or genetic drift? Journal of Human Evolution 53: 135-145.

Weston, E.M., A.E. Friday, and P. Liò. 2007. Biometric evidence that sexual selection has shaped the hominin face. PLoS One 2(8): e710.


So what’s new?

I must offer an apology for the delay in adding new posts. I have been back from Churchill for some time now, but am still not caught up. With the fall semester approaching, papers to finish, lectures to prepare, and grants to write, I am pretty much swamped these days. But that does not mean I have abandoned Genomicron! For now, however, the most I can offer is a short summary of what’s new since I last posted.

1) I found out that the subarctic is too hot. It was 30C (86F) in Churchill for several days, when the normal temperature for July is only about 18C (64F). Apparently it rained and cooled down after I left, but it’s something else to be sitting in polar bear country complaining about the heat.

2) We moved to the New Science Complex at the University of Guelph, and are getting settled in nicely.

3) Apparently Homo habilis and H. erectus may have cohabitated for some time. Ok. I guess to the media and anti-evolutionists this is big news, but the fact that human (or any) evolution is not simple or linear is no shock to those of us who actually study the topic. In fact, I just authored a paper (Evolution: Education and Outreach, in press) about how the fact, theory, and path of evolution are different issues and that arguments about theory or path do not bear on fact.

4) I was invited to become a “featured writer” at Scientific Blogging. It would not replace Genomicron but could be a nice venue for more detailed posts. Sounds interesting, though obviously finding the time is an issue. Anyone have thoughts on this?

5) While I have been busy, Genomicron had its 10,000th unique visitor. No alarms sounded and no balloons dropped from the ceiling, but I did smile when I noticed. So thanks everybody.

Finally, here for your enjoyment is one of my favourite pictures from the trip north.


Dr. Jay on incomplete transcription.

If you don’t read the posts by John Timmer (“Dr. Jay”) on Nobel Intent, you should. He has posted some good summaries about the ENCODE project, the anemone genome, and today presents a very interesting discussion of incomplete transcription of inactive genes based on a paper in Cell. (Basically, even inactive genes may experience transcription initiation although this is not followed through to generate full transcripts). If you’re interested in accurate and accessible summaries of newly published findings, and especially if you want some realistic discussion of the significance of new genomics research, this is a good place to start.