friendly funding

Many congratulations go out to a friend who has just secured external funding for a very cool (non-biological) research project. I'm exceedingly happy for him!!! Since the funding is coming from the Space Vehicles Directorate, this makes him, at least temporarily, a rocket scientist.



At least some of the grants we're all writing are getting funded... it brings me hope.

science fit for a princess

I've known there are journals that have some air of royalty, such as those published by the British Royal Society, or the scientific journal of King Faisal University, but I may have just discovered my new favorite obscure journal title, the Princess Takamatsu Symposia.

Princess Takamatsu's mother died of cancer, and she founded a cancer research fund that sponsored these symposia and other lectureships, which continue to this day. She also spoke out against male-only royal succession in Japan. She sounds like she was a scientifically-literate, civic-minded feminist. Her journal seems moribund since the last volume was published in 1995... and that combined with my not doing cancer research seems to assure that I'll never be able to add this title to my CV.


Princess Takamatsu of Japan, born Tokugawa Kikuko, 1911-2004

those shoes are just covered with bacteria...

While there are many reasons I can't, and wouldn't want to compete with Dr. Isis' shoe of the week, I felt I had to post this pair I saw on Etsy.



There are many creative people in the MSOE -- Mad Scientists of Etsy -- and some of the creations make perfect gifts for the hard-to-buy-for scientists in your life.

anonymity anomie

There's been a recent renewal of concerns about anonymous science blogging in the wake of DGT's (thankfully) temporary absence. People have been posting their own rules for pseudonymous blogging, and people have been debating taking their own blogs (or some of their more incendiary posts) down. DrugMonkey's appraisal seems, as usual, the wisest:

I have been flabbergasted to read comments suggesting that so many bloggers have not thought these issues through. Really.

For me, at least while I'm untenured, I don't think it makes sense to blog under my own name. I started this because I had been reading and commenting on others' (mostly anonymous) science blogs and I wanted a place to write longer reactions, and to add my $0.02 to the conversation. It's also where I can vent about topics that I might have more difficulty talking about with colleagues face to face, and to think through issues. I hope it is useful to some others and I'm not just writing for myself, but I do appreciate the chance to write something that's not a journal article/book chapter/peer review/grant.

I absolutely feel hemmed in by the prospect of giving away too many identifying details in posts. I've written anonymized posts on amazing, awful anecdotes that I feel I can't publish because I would suffer professional costs if the people/characters in the stories realize who I am. I want to share these because these blogs are how we do communicate to one another what kinds of terrible situations can and do arise in academic science, so we can try to avoid them happening to us. I'd also love to put them up because they are pretty damn entertaining... but for now, they will be reserved for late-night scary science storytelling.

I admire the experimental details posted by some scientists who blog under their real names, but I'm not sure I'd want to put up, in a google-searchable fashion, so many unpublished details of my work. (Good motivation to publish quickly, though... I could use that...) I'm very much looking forward to listening to four perspectives on this topic on Monday at 2:30pm during the "Open Science – The Risks, Rewards and Challenges" session at the American Society for Microbiology general meeting.



I am familiar with microbial evolutionist Rosie Redfield and phylogeneticist/PLoS Biology editor Jon Eisen, and both are proponents of open access publications and open science. I do not know Samuel Kaplan, though he is a former chair of ASM's publications board, or Joseph Deken, who has apparently been working on integrating computing into biology for many years.

For those not going to Philly -- and judging from the hard sell from ASM in recent months, many of us are not going this year -- you can watch this symposium live on Microbe World.

the youngest peer reviewers are often the harshest...

...illustrated by recent articles in the Chronicle and The Onion.

While I can't comment on otter research, the complaints of the humanities scholar about how graduate students read texts ring true for young scientists too.

Why is it that so many graduate students are reflexively critical of what they read? Why are they so eager to dismiss, dislike, and disrespect work that has already been done before they can even hope to begin to contribute?

I think there are some upsides to the arrogance that grad students initially bring to reading the established literature. Grad students, some of them at least, are the future of any field. It's a wonderful thing that they critically evaluate for themselves everything that's become conventional wisdom, because some of that conventional wisdom is wrong. And as we become more entrenched in academic science it's harder to spot the flaws in the conventional wisdom that we've embraced for 10, 20, 30 years...

I remain a very detailed reader and reviewer, but I'm not nearly as acerbic as I was as a graduate student. I also find I have much less time to take on accepted ideas when they are assumed in papers I review... most recently, I lost hours of a week's vacation working on my laptop trying to convince myself (or disprove the author's assertion) of one aspect of one virus' lifestyle. In the end, I now believe there isn't much/any data against the conventional wisdom, but it is crazy that I chose to spend a substantial fraction of my time at a beach house chasing this idea down. I'm too busy now, but I do envy the perspective and time that graduate students have when they read the literature, and when they assist in or write their own peer reviews.

Failures of Peer Review, Part 2

I've been confronting a few failures of peer review recently, and I think it's time to revive peer reviewing posts. Like most failures of peer review, it may very well be the editors who dropped the ball and not the reviewers -- or a combination of the two.

1. I came across a 2008 paper with an incredibly low resolution figure that prevented me from reading the labels of the data points (and there were >100 labels). This wasn't a problem of my computer (the pdf looked just as bad -- even more pixelated and harder to resolve at higher magnifications -- with several viewers), didn't get better on the print out, wasn't available at a better resolution in the html version), I asked others to try their hand at reading it with no success, etc. Now, this wasn't a very important figure to read to get the conclusions of the paper, I admit... it's more that the figure had to exist to get the paper published. But it was important to me for a study I'm trying to start, and I had to spend several hours deciphering the figure. I know that the reviewers could not have been able to evaluate the data in the published version of the figure, so either the journal published a lower resolution version than they gave the reviewers or neither/none of the reviewers actually read/checked this figure.

2. Twice in the last month I've been asked by senior scientists what I think of a recent paper in our field. I happen to know the paper well, since I reviewed it and recommended rejection on a number of solid grounds. Even though I still think the study is flawed, I must have been in the minority, since the paper was accepted with only a few changes. However few people will read the paper thoroughly enough to see the newly introduced hedging statements; in this busy day and age, all most people will read or remember are the title, the abstract and the quality of the journal it was published in.

So I gave these senior scientists my detailed rationale for why one shouldn't trust the paper's conclusions, it was easy to convince them, and I doubt either one will be citing it anytime soon. But I can't shake the feeling of being a failure myself as a reviewer, since the paper did get into the literature virtually unchanged. Rereading the review, I was constructive in my criticism, but I clearly challenged the premises of the paper, and backed up my argument with references. I reiterated the cause for rejection in more frank language in the confidential comments to the editor. And maybe, with another editor, my comments would have caused the paper to be rejected... but the next time I feel strongly about a rejection I will be tempted to use more emphatic language.

two cultures, two deadlines.

While many are talking and blogging about the two cultures these days, I want to highlight the gulf between our academic disciplines with an article from the Chronicle of Higher Education on the attempts to speed up publication in the humanities. While peer reviewers in science are being pushed for one or two week turnarounds from an increasing number of journals, the humanities are trying to move the average time from eliciting a book review to publication from year(s) to months.

The article says one of the reasons for the long turnaround is that "reviewing tends to be a rather thankless task, so it gets pushed to the bottom of a reviewer's agenda." Certainly, it's a similar situation in the sciences... but there seems to be a stronger system of reciprocal altruism in the sciences, where we all need to get our papers published, we all want them published quickly, and we do (largely) comply with the deadlines we're given. The article also highlighted the low number of reviews that can be published in each monthly/quarterly issue of a journal, and it could be that online-only journals will spur faster publication times in the humanities just as they have in the sciences.

It's not an apples-to-apples comparison between the fields: the publications being discussed are the peer review themselves.

I appreciate how quickly biology progresses these days, but it can be overwhelming. Having to keep up with online-early publications, the myriad table of contents emails, the automatic search emails, the increasingly short review times for journals... at times the slower publishing pace of other parts of academia could be very appealing.

join academia, see the world

While many others, apparently, are at Experimental Biology this week, I'm off to a small meeting in Europe. And while there are many reasons I am now a scientist, the amount of travel required by the job is absolutely one of them.

My family didn't travel much when I was growing up, and my traveling for science also started slowly and unglamorously... my first conference was in scenic Detroit. But since then, I've gone to meetings on four continents and have gathered a couple of truly unique passport stamps along the way. Most international places I've visited have been far off the tourist track, and I love the mix of work and vacation that foreign visits entail.

I even appreciate the domestic travel. One of the downsides of academia is how frequently we have to move, but one of the upsides is that we tend to move among a relatively small number of cities/regions. I almost always reconnect with a friend or a former labmate when I'm visiting someplace to give a seminar. And you can exploit this further -- I'm cultivating a collaboration that will require me to travel at least once a year to a part of the country where a good friend of mine is doing her PhD.

I know many scientists, including those without kids, who dislike the traveling science involves. But I'm enjoying getting my carry-on packed for the first conference of the "summer," and I've got my phrasebook ready...

Gossip Girl, PhD

I read an interesting first person over at the Chronicle of Higher Education. An assistant professor recounts a rumor that was spread about her in graduate school (that she was having an affair with an administrator, and that's why she got a plum teaching assignment), and how it was perceived from many different angles.

It was a good reminder of the painful downsides to academic gossiping. It's juicy to know -- and retell -- which scientists are hooking up with one another. We've all passed on gossip that later turned out to be untrue or was outdated... and we should hold our tongues more often for fear of hurting both the innocent and guilty.

But a case can be made that a certain amount of "gossiping" is necessary for social interactions in science... for instance, knowing two scientists are romantically involved can prevent awkward conversations/situations at conferences. Having heard through the grapevine that a professor is on the job market would prevent you from approaching her for a postdoc just because her lab is geographically convenient. I think that many forms of gossip serve as the way we pass on essential knowledge of the social aspects of academia more than we might like to admit.

The author of the Chronicle article wasn't sleeping with her superior, but there are many pairs of romantic partners we encounter in science, and it's not uncommon for one of the pair to be the boss of the other. Usually this is out in the open, for instance, one person is the PI of the lab and the partner is the lab manager. A non-trivial number of grad students marry their advisors... and the first part of the relationship is clandestine, if just for the fact that most universities consider such a relationship unethical. It's good politics to know that you can't behave the same way with that lab manager, that grad student, as you can with someone who isn't relating their whole day's events to a member of the faculty over dinner. And if the superior is giving advantages and plum assignments to their romantic partner underling... it's good to have advance knowledge so you might not get as upset, and to know the minefield you'd be negotiating if you complained about the unfair treatment.

Couples, if they share a lab, open their relationship up to some level of scrutiny as their relationship impacts lab interactions. I have known several people who got along great with their PIs, but not with the PI's wives, who were the lab managers. In all of these cases, the PIs slowly became converted to their wives' perspective, and a few of these students were outright asked to leave those labs. This could mean that the lab managers had more detailed knowledge of the students and were faster at seeing that the students weren't up to snuff... but that certainly isn't how the students perceive their situations. In the case of partner PIs who jointly head a lab, the same dynamics can occur. And as dual hires have become a regular occurrence, scientific divorces are also becoming more common, and these splits can have devastating effects on the career of their trainees. Even if a trainee stays with the same major advisor, they lose the benefits of the joint lab, which might have been one of the more attractive parts of taking their position, and they often lose time to switching institutions -- one, if not both, of the divorcees usually moves to a new position.

It's prudent for any prospective graduate student to try and discern lab dynamics. We hope that we get honest information from the existing lab members and, hopefully, all parties exercise discretion and not pass anything on further. When romantic partners work together, a prospective student really does have to guess at the nature and health of the partnership in order to determine how stable their six-year educational experience might be... and trying to find out information on the romantic relationships of people in a department is something that's hard not to call "gossip."

Beyond workplace romances, one person's gossip is another person's cautionary tale of unethical behavior, or how a university/professional society/journal really works. One of the most memorable things from my graduate career was the hair-raising tales of breaches of ethics that the oldest member of the department had personally witnessed in his 50 years at the university. One of the stories ended up with an unfairly blackballed postdoc killing herself, another ended up with a person graduating with a PhD even though s/he had acknowledged, in writing, that they had faked their data. All of his anecdotes were anonymized... is that the difference between gossip and sage stories passed on to younger scientists? That would certainly cover all the science bloggers who change names, create untraceable abbreviations for locations and remove details so they can relate what's been happening without as much fallout in their professional lives. I find this sharing very useful -- it's good to know I'm not alone, it's good to know what other indignities others are suffering (and if I can preemptively protect myself from them), it's good to have a place to vent about the confusing and unfair aspects of academia. Such posts may very well qualify as gossip but they also are a key aspect of professional development in 21st century academic science.

We pass on informal critiques on the quality of fellow scientists and their work to colleagues all the time. I have sometimes considered that a professional responsibility -- if you know that the conclusions of a paper are incorrect because of subsequent work the group conducted, but they neither published the new work nor retracted the paper, shouldn't you tell people how to correctly interpret that paper when it comes up in conversation? It doesn't seem like gossip to offer inside knowledge on one of the many papers that received less than perfect peer review... but is it gossip if you preface it with "well, you know they'll never correct this, but..." and roll your eyes?

I think the style of delivery is part of what we consider gossip. For instance, it's a dry and unembellished fact about some labs that they are slow to publish -- sometimes they are years behind on publications. However, that same information can be more dramatically related in a story about a frustrated student who didn't get any papers out until they were done with their first postdoc and the choice words he had for the PI... It's more entertaining to tell a fable than a fact.

I'd say some gossip is a necessary part of a researcher's apprenticeship. I imagine that discerning social relationships and passing on information about past events is part of the training for every kind of career (except for a reclusive novelist?). We need to learn what the informal hierarchies are, what's the best way to approach that dean, the de facto way things work. The problem seems to lie more in the propagation of lies than in gossip per se, and maybe in what areas of a scientist's life are up for public consumption. But we probably can't create any blocks that prevent false rumors from being spread around, not while personal candor bordering on gossip is such an important part of the social fabric of science. However, I'm not in any way suggesting we start gossiping more...

being okay with being #2...

DrJ&H has a recent post titled "It turns out I'm ok with being 2nd", but just like my last post, the title isn't what I thought it would be. DrJ&H was talking about the difficulty accepting she's THE expert in a sub-sub-field, and how she's okay being the second most expert person...

Whereas I want to post about what it's like to actually know you're the #2 young professor in my sub-sub-(sub-)field. I'm not sure how that sets me up for tenure -- is #2 good enough? -- and I'm having trouble navigating how much I should help the seeming #1 in my area when he asks for my opinions.

We are both young PIs and interested in ridiculously similar questions. Now, there isn't 100% overlap in our interests and expertise, but it's substantial, and we both have multiyear research plans that will keep bumping up against each other. We know that collaboration is one way out of this, but this has begun without great communication of what areas we're going to share, what we'll both conduct parallel work in, etc. And we have no joint funding.

While the thought of giving any competitor/colleague the ammunition with which they could scoop you would drives one to extensive email editing, it's worse with this particular frival. He's *much* faster at publishing than I am, he publishes in higher impact journals than I do (those two facts are not independent), and, for the last five years, I've had the concrete sense he's smarter than I am. This opinion isn't just based on having been blown away by him since the first time we met, it's based on the fact that several of my mentors have used the word "genius" to describe him. My postdoctoral advisor, for example, decided to decline an invitation to write a book chapter and recommended my frival -- someone who had never been associated with my mentor's lab -- instead of one of his own postdocs.

I should mention somewhere in here that my frival is also an amazingly nice and kind person. This isn't a personal, or personality conflict, in the slightest.

But having regular email contact with the frival is helping me see some cracks in the pedestal that I have put him on. We are having some intellectual disagreements, and I don't just think I'm right: his data support my side... leading to conclusions he didn't see on his own. In another instance, I was able to come up with the critical literature citations that radically changed the conclusions of another paper of his... I still don't know how much to reveal/hold back in any given conversation (the frival is a man of fewer words than I, and he never volunteers what his next steps will be), but having a peek under the hood of his gleaming, cherry red corvette of a research program has humanized him, and made me confront another iteration of impostor syndrome. He may be #1, but I'm not all that far behind at #2.

I have been trying to imagine whether there are things about me that might intimidate my frival. But of course, my frival is so perfect that he might just be the one young scientist without impostor syndrome himself...

the economic downturn hits my department

I have not yet been part of the very public, very unfortunate budget problems that have affected public institutions of higher learning... but just now, the rumors and worrying crystallized in my inbox: a proposal to hold an anonymous vote on whether to forgo the negotiated raises in our contract to help close our widening budget gap.

I'm very (very) glad to have a job, and that my university isn't laying off TT faculty. Not getting my raise, in this economic climate, isn't something I am upset about. I remember my father's salary being frozen in some years, without any cost of living increases...and those were in more flush times. So many workers in and outside of academia will make the same choice to forgo raises/have it foisted upon them. As the new fiscal year approaches... how many other academics have already decided/been told that salaries will be frozen this year? I think the universality of the problems makes losing our raises more palatable.

technically that title's true...

I was recently browsing the table of contents for the latest Applied and Environmental Microbiology, a journal that covers a very wide swath of microbiological subfields. I love reading the abstracts for interesting-sounding titles that don't necessarily pertain to my work. But I don't like it when a title lets me down. Such as:

"Interactions between Coexisting Intracellular Genomes: Mitochondrial Density and Wolbachia Infection"

Very cool idea -- both mitochondria and Wolbachia are maternally-inherited... it would make a lot of sense that they might influence one another. However, the abstract's conclusion is that they do not interact with one another. Technically, being independent of one another, not interacting, is an interaction... but it would be nice if scientists would tolerate more accurate titles reflecting negative results. But then again, I wouldn't have clicked on "Coexisting Intracellular Genomes: Mitochondria and Wolbachia do not influence each others density"... so maybe I'm part of the problem causing scientists to spin their titles in the most intriguing ways possible.

It is much more disappointing to come across a perfect-sounding title while doing a literature search, only to find out that the title, even abstract, bear little to no resemblance to what was actually done in the paper. At least we don't have to wait weeks for ILLed paper copies to get that disappointment anymore.

hot for teaching

Sometimes you just have a good lecture... the audience is listening, you're well-slept, you are getting the feedback you need to know that the class is following you. You even get questions from beyond the first row! Today, I gave a guest lecture on bacterial horizontal gene transfer, we were all collectively on, and it was an energizing experience.

It helps that I love this material -- nothing like covering conjugation, transduction and transformation for tossing in historical anecdotes, like how we first measured bacterial genomes in minutes. If that doesn't help them remember that the most commonly transferred bacterial genes due to an integrated conjugative plasmid are the ones closest to the site of integration... My asides weren't just historical, since I know a number of active researchers in the field. Amid all the talk of what good is it for large state schools to be centers of cutting-edge research, this is an example of the trickling down of research into the classroom. I was able to mention Rosie Redfield's papers, and their memorable titles (for instance, "is sex with dead cells ever better than no sex at all?"), and I was able to talk about the debate over why antibiotic resistance genes tend to be plasmid-borne, but mammalian toxin genes are usually phage-borne.

Of course, part of my excitement is because I haven't been teaching this semester, so these guest lectures are reminding me of the best aspects of lecturing -- without all the grading, emails about dead grandmothers, etc. But I'm spending the day smiling about the undergraduate student body (which doesn't always happen), and remembering that this is one of the reasons I decided against pursuing a career in industry. That, and I tried working in industry, and it was a soul-sucking experience (my PI agreed and he quit shortly after I left). But the teaching, that was part of the decision too.

anti-antibiotics

My inspirations for posts often come from what I manage to read in between deadlines and my social life, and as often as not, that means the New York Times. I don't read all the op-ed columnists... I'm in agreement with CPP about Ms. Maureen Dowd, though clearly CPP is more dedicated to reminding us that she takes up valuable column inches with her insubstantial, ill-informed populism. Which might be excusable if she were funnier, but... I read Kristof every couple of weeks, which is generally enough to keep up with his various crusades. While he's usually right, and is an articulate voice for his cause du jour, his anecdote-to-preachiness format can become stale. But lately Kristof is beating a dead horse (well, pig) that I cannot tire of: the overuse of antibiotics in livestock feed and what that means for global public health.

Here are his March 12th and March 15th columns on the topic. As a microbiologist, I tend to focus on the implications for infectious disease (the prevalence of antibiotic resistance genes in all microbes, including human pathogens), but the organ damage that comes from repeated bacterial infection that we're unable to shorten with antibiotics... another scary consequence.

I also have to give Kristof credit for the PLoS One study he cites, which comes from the lab of science blogger and awesome female microbiologist Tara Smith!

Americans' antibiotic use continues to be out of control. According to the American College of Physicians, 50% of antibiotic prescriptions each year are given to patients with viral infections, not bacterial infections. Antibiotics can help you prevent/clear up bacterial infections you have secondary to a viral infection, for instance, an ear infection that builds while one is congested with a common cold, but it cannot, will not directly clear the viral infection. Even when antibiotics are prescribed for actual bacterial infections, it irks me to no end that otherwise intelligent people do not follow the dosing instructions that come with their antibiotics. Some of my closest relatives stop their antibiotic treatments a few days early in order to have some pills to take the next time they feel an infection (possibly a viral one...) coming on. Grrrrrrr! This is wrong for so many reasons... so many reasons that I have to stop myself and maybe post about this topic another time.

But if you do have leftover antibiotics, don't flush your medicines into the water supply either... this is something I hadn't considered before finding links for this post, but flushing antibiotics also introduces those chemicals to the huge number of microbes in our wastewater and further selects for antibiotic-resistant bacteria.

As much as I could go on about all the ways that treating human infections has led to increased antibiotic resistance, including outside of developed nations with strong health infrastructures, it's something of a moot point. And that's because most of the antibiotics we use in this country are not given to humans -- they are given to healthy livestock animals. Scientific American says 70%, the UN says 50%... I think it's safe to say it's a majority of the antibiotics administered in this country every year. These drugs are not going to sick animals -- not animals suffering with bacterial infections that can and should be treated. We give antibiotics to healthy livestock because of the way we raise most of our meat in this country -- at such dense conditions, with such high bacterial loads in their environment that outbreaks of bacterial infections are inevitable.

Giving animals antibiotics also speeds their development, so our meat gets larger faster. I'm not entirely sure why this is, but I imagine that not having to spend as much energy on ones immune system would facilitate growth.

Some reading this post may know that we don't use the same antibiotics for humans and livestock. However, we effectively do. Stick a methyl group on a human antibiotic -- one that doesn't impact its antibacterial action, and it's now a livestock-ready antibiotic with the same mechanism of action... and resistances developed to livestock antibiotics show cross resistance to related human antibiotics.

I'm pretty terrified about the increased prevalence of these superbugs in communities outside of hospitals... it means the bacteria aren't at a competitive disadvantage relative to the more antibiotic-susceptible bacteria that are thought to be the majority of the bacteria in our environment. It means that humans, who carry the Staphylococcus aureus bacterium on our skins, have started carrying methicillin-resistant S. aureus as part of their normal flora. This in turn means that injuries as small as a paper cut will let those MRSA into your body...

One thing I do to reduce my antibiotic load on the environment is eating antibiotic-free meats, like the delicious local, free-range pork in a paprika sauce I ate tonight at a restaurant. I started being strict about this four or five years ago, and I definitely eat less meat than I did before. I also buy the more expensive no-hormone, no-antibiotic milk and yogurts (I can't give up my wide cheese selection though...). These small things make me feel like a more responsible microbiologist; the animal welfare improvements and the economic support of smaller farmers are secondary benefits to me. I know I'm lucky to have access to local farms that can provide these meats, and that I have the middle class income to afford them. But I think changing our agricultural policies, and what we chose to subsidize, could bring down the cost of farming that's better for public health.

challenges, indeed

I worked my way through the 52 page pdf of stimulus-package NIH challenge area grants that will be offered, and I don't think there are any calls suitable for my research. However, I did find several calls to send onto friends, and there was one hidden gem in the document:

06-RR-101* Virtual environments for multidisciplinary and translational research. Virtual networking environments like Science Commons, Facebook, and Second Life, create platforms that can eliminate many barriers in scientific collaborations. These environments integrate fragmented information sources, enable “one-click” access to research resources, and assist in re-use of scientific workflows. Funded projects would develop and implement virtual collaborative environments to facilitate biomedical and translational research, e.g. addressing issues of privacy, technology transfers, and sharing resources. Contact: Dr. Olga Brazhnik, 301-435-0758, brazhnik@mail.nih.gov

I'm not on Facebook, but I certainly understand how and why it could facilitate communication among collaborators. But Second Life??? Does it allow collaborators to work out their sexual tension virtually?? Or are there glass-and-steel biotech institutes where scientists come, wear form-fitting lab coats, prepare coffee in faux-wood alcoves near spacious conference tables and have virtual meetings?

blame the grants: biology link instead of a post

I prefer giant microbes, but this would make a very good valentine's day gift for that special scientist next year...

blame the grants: biology comic instead of a post

holy sh%t!

So I'm reading Blue Lab Coats on my lunch break today, and I'm smiling because DrDrA has been (very deservingly) selected as one of the top 50 must-read female science bloggers. I was perusing the list, recognizing most of the names (I'm not as plugged into the geology women as I could be)... and then I came upon my own blog's name and did a double take. And then I came upon DrugMonkey's name and did another double take! (He deserves an honorary second X chromosome...) I'm startled and flattered to be in such incredible company (FSP! Isis! Rosie Redfield, a microbiologist that I've met in real life!). I will use this as motivation to blog more interestingly and regularly...

There are many blogs that I would have put on such a list before mine... including Professor in Training and Young Female Scientist, two women who are very frank about their trials and tribulations in our chosen profession.

As an aside, I'm visiting a lab this week which has blue lab coats, and they do look fabulous on all of the women here (the men don't seem to wear their lab coats).

bashing Darwin day?

The hype over Darwin will not end soon -- the 150th anniversary of publishing the Origin of Species is in November and there's a major motion picture about Darwin planned for a fall release. If this hype increases scientific literacy and acceptance of evolution by the American public, whom am I to complain? I was part of an overflow crowd at the state museum last night for a Darwin Day lecture, and much of the audience was not academic -- older couples, fathers and sons, pairs of undergrads who were clearly not science majors (based on overheard conversations), even a guy in overalls who looked like he'd been on a tractor earlier in the day. Darwin Day seems to be working as extension, as a way of getting the average person to be more aware of biology and the process of science.

However, one day after Darwin's 200th birthday, we can stop some of the hero worship...

CPP posted over at Propter Doc that "if it hadn't been Darwin it would have been someone else." Yup, natural truths become evident over time and eventually someone would have articulated the theory of natural selection had it not been Darwin. But this subjunctive phrasing belies the fact that someone actually did independently come to the same conclusions before Darwin had published his theory. Darwin was scooped! Alfred Russel Wallace, a younger and bolder man, published some the same ideas based on different data without waiting for the results of 8 years of barnacle experiments for more evidence. Because of Darwin's work was known to members of the Royal Society -- some of whom had been trying to get Darwin to publish for years -- Darwin's precedence was recognized and the official paper on natural selection read to the Royal Society is authored by both Darwin and Wallace.

Some texts still refer to it as the "Darwin-Wallace" theory, and the Linnean Society gives out a Darwin-Wallace medal each year, but this is not the year to mention the shared credit to the general public. It's extremely similar to the history books lauding Newton for inventing calculus even though Liebniz published his independent derivation of calculus first. These days he who publishes first gets the credit, even if another scientist has been laboring on the problem longer, even presenting if s/he had presented the unpublished data at meetings. And as long as the publishing group did their work independently and without knowledge or malice... that's life in science, that's being scooped. Either Newton and Darwin had friends in much higher places, or the rules of science have changed.

Perhaps especially so in 2009, there are those dedicated to not forgetting that someone else did conceive of natural selection that wasn't Darwin. Almost everything discovered could have been found by someone else... could have been done years before we started working on it... it would be 10 times faster and easier for a scientist starting to work on it a decade from now. Linus Pauling's alpha helix discovered while he was sick in bed, Kekule's dream of a benzene ring, Darwin's amazement that all those Galapagos birds were still finches... could have been discovered by someone else. Perhaps with less poetry, less of a good anecdote. But it doesn't take away from these visionary scientists that they were the first to conceive of these major ideas and that they knew what to do with their inspiration from there.

Darwin Day is finally here!

At the very least, this will decrease the number of Darwin Day-planning emails in my inbox. I'll attend one lecture this evening in celebration and leave it at that. No Darwin-themed tshirts, no tortoise soup planned for dinner, but maybe I'll put on the next Netflixed disc of Planet Earth.

But you can count on Carl Zimmer and his kin to have a unique take on Darwin Day -- the words that Darwin first used in the English language, including rodeo.

NYT op-ed on science funding

Stephen Quake took over for Olivia Judson this week and wrote about his lucky experiences with funding as an early career scientist and what's wrong with the 'free market' of grants. Among his litany of accomplishments, Quake has pioneered single-molecule sequencing. I am in awe of all scientists who stepped back and asked "how can DNA sequencing be better?" while I was still feeling blessed I became a scientist at a time we could do DNA sequencing at all.

There are some minuses to Quake's idea of every scientist getting guaranteed minimal research support... because of those funds going to faculty no longer doing research (even if they claim they are), or to scientists who are not particularly good at research, mentoring, and because it holds back research that requires expensive techniques. Grants with lower dollar values going to more scientists would move the US towards other countries' funding systems. We'd have to shift how we fund personnel as well, because one can run a lab and get some experiments done on a shoestring budget, but short of using an army of unpaid undergrads, the majority of the cost of even a minimal lab budget will be salaries and stipends. But these changes have notable upsides as well, including dampening the effects of boom-bust cycles on laboratories.

As for 11-month salaries being covered by our universities -- yes please! In the current economy, however, AFT/AAUP shouldn't rise up and demand such things. It would be nice if it were more publicly known that many (most?) professors are already on summer furlough, and some schools are already furloughing faculty during the year to save money. Academics often work for free, we're not all cushy and secure in recession-proof ivory tower tenured positions. Knowing that we are sharing the pain with workers all across America might make people feel more sanguine about supporting the federal granting agencies and continuing to fund their state universities through these budget crises.

8% of my love

In this season of grants, in my first big grant-pushing year, I'm facing problems I never conceived of. One is how much of my time to allocate (on paper) to each of these projects. The basic problem is that you can't have funding for more than 100% of your time... the funding agencies are not willing to break the definition of 100% even for sleep-deprived academics. You have to devote 'enough' time to a grant for the agency to feel you will be a competent supervisor of the research and steward of their dollars, and you have to pick a small enough number so that you can potentially obtain additional grants. You can change the allocation of time you have on a project if you need to after you are funded, but I can't comment on how that affects your program officer's opinion of you and your research, or how that affects your chance of non-competitive renewal.

For shorter grants this is less of a problem; if a grant is funded and I over-estimated my time allocation, the grant will expire before it's a problem that prevents me from applying for additional funding.

I know I'm living in a fantasy world to contemplate this ever being a problem for me. I'm not going to get enough grants to be anywhere near a 100% time allocation in the next few years. However, I have to list my projected time allocation for all pending grants when I submit additional applications... and it's starting to add up. This is also on my mind because I am going to be a co-PI on a grant where the only funding that would come to my lab would be summer salary and travel support for me (no money for equipment or trainees). I am contemplating what percent allocation of my time I have to put down for this project in order to ensure one month of summer salary wouldn't be cut from the budget, while preserving enough of my time for grants I'm submitting that can support students.

I also thought of this because of a recent discussion over at Drugmonkey, where it was brought up that percent allocation could be used as a proxy for "lab with too much money" as a rational reason to give lower marks to grants from very comfortable, established labs. I was an ad hoc reviewer on a grant recently that had two PIs -- one junior and not published at all in the proposed experimental system, and one senior who is the queen of the experimental system. But the Queen PI has so many grants she could only allocate 8% of her time to the proposed research. While I think this PI is very good at juggling her responsibilities, it certainly made me wonder whether she'd give the project the attention and expertise it would need. I have seen grants where subcontractors allocate very low (5%) amounts of their time, but this was the first single-digit allocation for one of the major PIs I'd seen. There were other weaknesses in the grant, it wasn't a perfect, incredible proposal with this being its sole potential flaw...

Percent time allocation to different research projects was something I'd never thought about before this year. I have thought about the amount of time I devote to preparing lectures (too much) and the amount of time I spend writing papers up (too little), but I have always just rotated around my research projects as deadlines demand and my interests dictated.

Now we know what NSF employees had been doing in the low-funding-rate years:

looking at porn at work. One particular employee (no longer with the NSF) spent 20% of his time looking at porn and paying $40,000 on his credit cards for chat sites. Nature's blog refers to the NSF's porn-at-work problem as "systemic."

The ranking Republican on the Senate Finance Committee wants a full investigation of the extent of these abuses of government computers and taxpayer-funded salary before the NSF gets their fraction of the stimulus package... which will more likely result in the extra funding for NSF being cut out of the bill than stalling the stimulus package.

*sigh*

The very first problem I ever had in lab management was that an undergraduate I was supervising was using a lab computer to look at porn. I discovered this because it was his first day and he did not yet have his own account on the lab computers, and so he was using my login. I wasn't snooping on his activities, but the following day, when I began typing in a URL into my browser... a site that I hadn't visited, nor one that I thought was particularly work-appropriate popped up. It's apparently gone offline in the last 9 years, otherwise I would have provided the link. I quickly confirmed that it was a porn site, and since my PI was out of town, I decided to solve the problem by sending the undergrad a polite email that said that some sites are better viewed in the dorm than at work. The undergrad never referenced having received this email, and he got his own account, so I have no idea whether he repeated his salacious websearching.

When I asked the PI about it later, he said he would have not said or done anything about it. I don't think I overreacted, but what would others have done, especially in light of the computers having been purchased on federal grants?

Fixing peer review, part 2

I saw this over at DrugMonkey. Cell, a biology GlamourMag, claims that it is redefining its publication standards and policies in response to the digital publishing era:

One issue in particular that we at Cell will be focusing on in 2009 is redefining what constitutes a "publishable unit" in the age of electronic journals and how we can best present the information content of a scientific article online. [...] The scientific article of the future will no longer be tied to the constraints of a printing press and will take advantage of all the opportunities afforded by the web to introduce a hierarchical rather than linear structure, increased graphical representations, and embedded multimedia. Inherent in our thinking about the scientific article of the future is the need to address the current unchecked growth in the amount of supplemental and supporting material and to identify constructive, well-defined guidelines for what is reasonably and appropriately included in a unit of scientific advance.

I agree with everything DrugMonkey said -- what should be in the paper should be in the physical paper. However, I am heartened by one aspect of expanding supplementary online material: I would like to return to an earlier practice of reporting genetic analyses and require that sequence alignments used in publications be publicly available as supplementary material. This would not take up a large amount of space (the nexus file format, which I would propose as the standard, is both compact and informative -- it will preserve annotations of genomic regions if the authors wish to add them).

How would this improve science, and why is this being filed under "fixing peer review?" First and foremost, it allows future groups to build upon previously published work, and know concretely how their analysis differs from the published work. If you start with a published (as supplementary material online) alignment, and you have a serious problem with aspects of the older alignment (e.g., they neglected to take conserved secondary structures into account), this gives you an important point for discussion to explain why you results do not match up with previous results. We would no longer have to speculate -- we could test such an assertion. Secondly, it will speed up research, as fewer groups would have to reinvent the wheel and re-do the same work that has been done by other groups. And, as I argue in the first point, this does not mean that the published work would be used as an unevaluated black box -- it can, and hopefully will, be critiqued and refined. The reason it is on my mind at the moment, however, is the way this will assist peer review. I just spent far too many hours yesterday trying to replicate an alignment in a manuscript I was reviewing to test a theory I had about a phylogenetic tree in it. If my theory were correct, it would undermine all the paper's conclusions, but I could not see if my theory was even plausible without seeing at least a partial alignment. Had the authors been required to upload their alignment with their manuscript, this would have taken me less than five minutes to check. Under our current system... let's not discuss how long it took. I know some will say that I should have just suggested the reanalysis without attempting it, but I have learned the hard way that if you don't provide evidence (a hint of reanalysis, citations) for your comments in peer review, the authors sweet talk the editor and convince them you didn't know what you were talking about.

When sequence analysis was a new field, journals published the entire alignments in the physical paper journals. This quickly became impractical, as computing power and algorithms advanced, and it no longer was required or encouraged to publish your alignments. However, you are always supposed to supply your alignment to any and all people who contact you after your paper is published, and some attempts have been made at alignment repositories (EMBL's closed in 10/2008). After all, bioinformatic analyses based on nucleotide or amino acid sequences are only as accurate as the alignments underlying them. I think requiring alignments as supplementary online material would be a fantastic requirement for the increasingly digital age. Some journals already require this, but none of those I regularly read or review for. Maybe this is not what Cell meant at all... but I'm running with this.

Plus, I am in favor of anything that improves my time-to-completed-review. (I have peer reviews #5 and #6 of 2009 on my computer today. I need to speed things up or I'll never get tenure)

doing it for love

A number of science bloggers have been pretty quiet in 2009... maybe like me they were working on grants. There's good reason to be more excited about grants in the near term: NSF funding rates might not be as dismal as they have been in previous years, and science funding might be included as part of a stimulus package. Despite the current optimism, people are talking about working without funding, or with very very little funding. And even if the funding taps are opened full blast, there will be hard times ahead (boom-bust funding cycles), and some people will be asked to work on a shoestring lab budget, or work for free. As far/near as I can tell, working for the love of science, not financial security, has been asked of generations of scientists (less now than in the past, it seems)... but it's definitely not the sort of thing we advertise to prospective scientists.

Many of us work in labs for credit, or just as volunteers, as undergraduates. Whether this is a time-honored tradition or exploitation has been discussed in the comments here. Regardless, I don't think many undergraduates would think that this early donation of time is a harbinger of future sacrifices they might be asked to make for science.

In the old days, students paid universities for the privilege of being a graduate student. In some places, those "old days" weren't so long ago; one of my friends has a 2000 PhD and he had to pay for his tuition and went without a stipend for all semesters he wasn't a teaching assistant (and the stipend was very low when he did receive it, but the accompanying tuition remission was a big benefit). Before anyone tries to guess which university inflicted this on him, let me say his PhD was in biology, in an arguably biomedical field, the school is a large state R01, and he was a stellar graduate student. He just happened to want to work in a lab that while well-respected, was not well-funded. He had a previous career in computer programming in order to save the money to attend graduate school and specialize in the field of his choosing. In general, however, grad students today go to programs and labs where they are supported through four (maybe five or six) years through a combination of RAs and TAs, and don't have to go into the same levels of debt as humanities graduate students while getting a PhD. If their PI runs out of funding early on in their graduate career, the students often change labs rather than work for free and wait for the lab to become better funded. These are perfectly rational decisions, but the same financially-sound decision making doesn't apply when you are an older, getting-ready-to-graduate student whose lab runs out of funding. Especially if you had a guarantee of five years of funding from your advisor when you started, and you need a sixth year... it's not uncommon to have to donate your time for a semester, a year at the end of your graduate work.

Until fairly recently, this unpaid last year of the thesis was codified in the UK. PhDs are supposed to take three years, and students receive three years of support, though funding in the fourth year is now more common for biomedical graduate students. For students outside of these well-funded fields, any funding for the fourth year is ad hoc and is not merit-based.

I spent a semester unfunded at the end of my thesis, but that was more my choice than necessity. I defended and could have gone straight to my postdoc, but I wanted some time to destress and to finish up experiments in my thesis lab. I asked my PI to pay health insurance coverage and the registered student fee (this came to less than $1000), and I spent about half of my time in the lab, but came and went as I pleased. I have known students who had more penurious PIs who wanted the students themselves to pay these continuing student registration fees -- while they had no income -- so I consider myself lucky.

Most postdocs would not entertain the idea of working for free, but I have two friends who have done this. The first I have already blogged about, and she is doing a postdoc in her "spare time" while carrying a full teaching load in order to pay the rent. She is doing so in the city where her spouse has an official, paid postdoc. The other stayed in the town in which he did his doctoral work while his wife finished her degree. Both of these friends were unpaid postdocs for two years, and both had a partner with some kind of income at the time. This also took care of their health insurance needs. In both cases, these free postdocs would not be working for free but for their geographic restrictions.

The working for free does not stop once we get professorships. Many PIs go without summer funding -- calendar year contracts are an endangered species outside of medical schools, and summer salary was a routine casualty in the tight budgets at NSF over the last few years. Even when a PI has summer salary in the budget, there are advisors who, in shoestring budget times, choose to forgo their summer salary to give a graduate student another year's stipend and benefits.

There are concrete downsides to our working for love and not money. Many of us are not independently wealthy, and so we incur credit card debt to help us live through our unfunded patches. [Note: even if you receive a stipend you may be eligible for a Stafford Federal Loan while you are a graduate student... many are interest-free until you graduate and it's a much, much better option than carrying credit card debt for years] It harms our ability to save for retirement, build up a house downpayment, do all those fiscally responsible adult things that we see some of our friends doing. It can stress our relationships when we work all day (and night) and yet are not bringing home any bacon. Similarly, working in science and working a second job in order to pay the bills can create a stressful home environment. Yet, I know very very few people in science who haven't worked at least a few months unpaid while pursuing a science career. I have no idea how common this sacrifice is in other careers (especially those that require much less schooling; I know medical students go greatly into debt and might be laughing at this post). Is working for free one of the ways we distinguish the passionate from the complacent? Is this a continual initiation rite that we ask even professors to go through? Has it become more common while we were living in Bush administration budgets, and will it be more or less common in the next few years?

People I'm taking for granted

I have been busy working on grant applications lately, and I want to publicly, if anonymously, thank all of my non-scientist friends for their support as I work through this.

I am grateful for my supportive academic friends, too! But it's something special to get encouraging and inquisitive Twitters from distant friends who don't particularly care what I study. It's important to them because it's important to me... and maybe because I tend to gesticulate wildly when I tell funny anecdotes about my work.

(Besides, my scientist friends are still on the hook to read my drafts... they'll get their thanks later ;-))

The force of PSAs is on our side...

The TV just informed me that January is national mentoring month. January 22nd is "Thank your mentor" day.

It's not good when the things you've been blogging about are part of a problem big enough and hopeless enough for public service announcements...

Professorial Advisory: explicit content

There's a lively discussion over at YFS about various aspects of mentoring and sexism (street smarts, how men pass on information to male students, etc). There is a recurring theme of unstated expectations, of mentors, mentees and of people who are evaluating the junior scientists.

Ideally our supervisors would be true mentors, and want to help us figure out what it is we want to do, and to help us achieve our goals. In reality, professors often only want students who are very sure they want to go research track, in academia or industry. This is largely because professors, especially those earlier in their careers, need trainees who will be motivated to publish many papers, as an ambitious trainee would want to do.

After the mentorship is over, though, what are the benefits to the advisor of the trainee becoming a prominent member of the scientific community? What do advisors need/get from former advisees?

1. Reflected glory and success. Their work is partially attributable to you... when you go up for full professor it will look good that you trained a couple of bright, active R01 assistant profs. Maybe some schools quantify it -- you get to add 10% of the papers published by former trainees to your publication count...
Pedigree can be a very big deal in certain fields, but it primarily benefits the trainee. Sometimes people will say they want a "BigName" person to fill this symposium slot, or faculty position, etc.

2. Someone who owes you a few who is a colleague in your field. Need something onerous reviewed? Want to know the latest review on XYZ without doing a search? Want someone whose vote you can maybe influence on that committee? (That last one is speculation -- the other two I happily do for mentors on a somewhat regular basis)

3. Advance knowledge of the cool results coming out of the mentee's lab. We all want to know new things first!

4. A network of people whom you can rely on to train your future students. If your mentee was a tissue culture savant, send your new student who is struggling to the mentee's lab for a month or two.

But your mentees can't review your grants, probably shouldn't review your papers... there's a potentially lifelong conflict of interest. I suppose the mentee's trainees -- the academic grandchildren -- will not have such conflicts and could be favorably disposed towards the original mentor. Collaborations with former mentees can also be problematic for the mentees. We're supposed to be illustrating our independence in our pre-tenure years, and we have to obtain funding and publish without our PhD and postdoctoral advisors. So there are some things mentors cannot expect from former mentees.

While enumerating the concrete benefits to having successful trainees, I realized, with the exception of reflected glory, they all rely on the mentor-mentee having cordial relationships. Cordial relationships, however, can't just be assumed. Many people have discussed toxic mentor-mentee relationships on blogs, and some (many?) of these trainees survive and stay in science. For instance, one of my colleagues is the most successful trainee to date of his famous postdoctoral advisor, but they left things so badly, they haven't spoken since a very abrupt end to the fellowship. There probably is a positive correlation between getting along with your advisors and succeeding in ambitious academic/industry careers, but it's no guarantee, and no requirement.

Maybe I'm missing something important from my list (please tell me in comments!), but if the major impact that trainees have on their mentors' career success is from papers published while working together... then as long as the mentee pursues a 'sufficiently' ambitious track while with working with BigName, PI... it doesn't matter so much what they do afterwards. Even if they drop out of science to home school ten children... or opt for one of the many career tracks that require a PhD that are not academic research. Yes, someone whose career ambitions won't be advanced by publishing may have trouble feigning enthusiasm for publishing. And if the PI is under the false impression that the student wants to be/should be publishing, the PI will become disappointed, frustrated and perhaps resentful of the student. However, if students are honest about their less-than-R01 goals, many PIs repay their candor by investing less in the student... so what can be done to create realistic expectations on both sides?

I feel it's the advisor's job to train people in the ways and means of science, and it's the trainee's job to figure out how to use that knowledge in their life. We will overinvest in some trainees, and underinvest (a failure of debatable magnitude on our part) in others, but it's our job to invest somewhat in our trainees. Ideally, our trainees also recognize they have a vested interest in their advisor's career success.

Some mentors don't begin investing in trainees until the trainee has jumped through hoops and concretely proven their intentions to stay in science... but that means 1) all the trainees are getting subpar mentoring in their first few years in that lab, and 2) the PI has absolute power in determining what's an appropriate level of sacrifice or productivity to show such intent. I bet these PIs do not reveal their secret formula to their trainees, and I'm equally sure they change the formula, move the line for trainees based on personal prejudices. Would it help mentors to be more explicitly contractual with their mentees? For instance, inform the student early on: "whatever you want to do, I need you to write the first draft of at least three first-authored papers from a PhD thesis." Or: "I expect that you will fulfill your teaching requirement as part of your degree, but I don't like my students to take so much time away from research and I will not support you if you want to TA additional classes."

PI-trainee contracts would also force PIs to think about their expectations and what they are prepared to offer a student. Some of the unconscious mentoring/gender bias issues being discussed at YFS might be resolved if professors had to articulate what it is they do to provide mentorship. They would necessarily become more aware of how they differently treat each trainee, and it could be a step towards limiting unconscious preferential treatment.

I know some PIs who thrive on keeping their students unsettled, on edge, not knowing the PI's expectations... I can't comment on whether that makes the lab more productive, but I am certain it's not useful for the trainees to spend years marinating in stress hormones. I imagine individual PIs would craft their own contracts, reflective of their lab cultures and mentorship styles. Short of that, it might be worthwhile for departments to ask for specific mentoring plans in annual faculty reviews... and perhaps elicit feedback from the students on the mentoring, under the promise of anonymity. But people gossip, and the anonymity would likely fall apart.

I know that some granting agencies have been asking for mentorship plans on training grants, and that could be one of the first steps towards codification of what trainees should expect of their PIs.

I have trouble knowing how honest, how contractual to be with mentees, especially when such discussions are not expected or typical when joining a lab. I feel that if you tell a first year PhD student what you genuinely expect of them over a ~5 year PhD, they will run screaming from your lab and will work for someone who is less upfront with them, even if eventually that PI expects as much, or more. Even if that PI's unstated expectations will cause problems down the line. By the time that student is a 3rd or 4th year, and has enough background and experience to realize that the upfront PI might have been a much better mentor... they have hitched their wagon to a less palatable, less productive situation. However, I see being open about expectations early on as one of the only ways to make sure that my mentees feel comfortable discussing whatever career plans they are considering with me, and to make sure they know what it is I want/need from them even if they don't want to stay in science.

Like any contract, like any cooperative agreement, either side can choose to unilaterally end the cooperation. A student can choose another mentor, a student can drop out... but a PI can also take a job in a place to which the student is unwilling to move. Or the PI can leave science (this happens even when the scientist is tenured). Or the PI could say the student has repeatedly violated the expectations both the student and PI agreed to, and that the PI would like to end the mentorship. These are unavoidable possibilities, and I don't know how to smooth these situations. I think how well it goes is up to the individual maturity of the PI and trainee, and formal agreements won't necessarily help these potentially tense situations.

My perspective may sound very naive, and it's because I can't speak from the other side... yet. My department has a tradition of some students going into policy positions, so I absolutely will end up mentoring people who will have different career goals from my own. I look forward to having students that will become science journalists, or go to work for the government, including (dare I dream?) at a funding agency. What's bad about having a student who goes to a primarily four year college -- if you two still get along, wouldn't this create synergistic opportunities for creative 'outreach' and 'broader impacts' for future grants? I also hope I don't feel negatively about students who completely eschew science and academia. If you care about your mentees, and they are happy doing what they are doing, and send christmas emails assuring you of this... that has to count for something. I don't know how successful I will be at this, or how frustrated I will be after a few years. I remember being chilled by reading Too Many Bad Apples on the CofHE a while ago, and I don't know how confronting dishonesty in my mentees will affect me. My strongest mentor experienced this (masters student plaguerized large portions of a thesis... from a book the mentor had on his bookshelf!) and it did not change his warmth and his willingness to extend himself to his subsequent students.