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Friday Sprog Blogging: Kids Day at SLAC 2010 hazards and mitigations.

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Longtime friend of the Free-Rides LO has been instrumental in hooking the Free-Ride offspring up with Kids Day @ SLAC. Finally the year has come when the younger Free-Ride offspring meets the age requirements to join the elder Free-Ride offspring. As is our practice, we prepared by reviewing the safety information:

Dr. Free-Ride: So, we’re talking about Kids Day @ SLAC. I’m showing you the logo for this year’s Kids Day @ SLAC. There seems to be some sort of — I don’t know if that’s a laser beam or something. Looks interesting. But, the part we need to discuss has to do with the safety information. “All children must wear long pants, Kids Day T-shirts” — which you guys will get from LO and put on when you get there — “closed-toe shoes, no jewelry, and long hair must be pulled back. Please review the hazards and mitigation information on the workshops.” Younger offspring, let’s look at workshop B.

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Harvard Dean sheds (a little) more light on Hauser misconduct case.

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Today ScienceInsider gave an update on the Marc Hauser misconduct case, one that seems to support the accounts of other researchers in the Hauser lab. From ScienceInsider:

In an e-mail sent earlier today to Harvard University faculty members, Michael Smith, dean of the Faculty of Arts and Sciences (FAS), confirms that cognitive scientist Marc Hauser “was found solely responsible, after a thorough investigation by a faculty member investigating committee, for eight instances of scientific misconduct under FAS standards.”

ScienceInsider reprints the Dean’s email in its entirety. Here’s the characterization of the nature of Hauser’s misconduct from that email:

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Friday Sprog Blogging: please stand by.

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Dr. Free-Ride is pinned down in committee meetings for a while.

There will be a conversation with the Free-Ride offspring posted later today. In the meantime, here are whiteboard traces of a science-y conversation the sprogs had recently with Dr. Free-Ride’s better half.

On our whiteboard

Yeah, I find the “sand” thing worrisome, too.

Is objectivity an ethical duty? (More on the Hauser case.)

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Today the Chronicle of Higher Education has an article that bears on the allegation of shenanigans in the research lab of Marc D. Hauser. As the article draws heavily on documents given to the Chronicle by anonymous sources, rather than on official documents from Harvard’s inquiry into allegations of misconduct in the Hauser lab, we are going to take them with a large grain of salt. However, I think the Chronicle story raises some interesting questions about the intersection of scientific methodology and ethics.

From the article:

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Practical chemical engineering.

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It’s day two of my training course, and as I contemplate my mug of decaf, I am suddenly flashing back to a question that was rumored to be part of the chemical engineering qualifying exam in my chemistry graduate program. As it’s an intriguing problem, I thought I’d share it here:

In the dead of winter, a professor sends his grad student out into the cold to fetch him a hot beverage from the cafe. “Coffee with two creams, and make sure it’s HOT when it gets to me!” the professor barks.

Shivering from fear as much as cold, the grad student procures a 12-ounce styrofoam cup of hot coffee and two little containers (maybe 20 mL each) of half and half at the cafe. To maximize the temperature of the coffee when it is delivered to the prof, should he add the half and half to the coffee before he walks it through the cold or after?

Feel free to work together on this problem, and please show your work in the comments.

More on strategies to accomplish training.

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Earlier this week, I mentioned that I had powered through some online training courses that I needed to complete by the (rapidly approaching) beginning of my academic term. In that post, I voiced my worries about how well I’d be able to retain the material I took in (and, one hopes, absorbed to at least some extent) in one long sitting at my computer.

As it happens, I am spending today and tomorrow at full-day training sessions (about nine hours per day, including breaks) covering related material at much greater depth and breadth. Obviously, this affords me the opportunity to compare the two modes of content delivery.

One thing I’ve noticed is that I seem to have retained substantial chunks of the material presented in the online training. (Sure, retaining it for two days is maybe not a huge accomplishment, but these have been subtle details — and I’m pretty sure I have students who can forget material more rapidly than this once the quiz on the material is behind them.)

It’s possible, though, that my retention of that material will be better because I’m using it in this live training. I’ll really have no way to tell which bits of the overlapping material stick in my head because of the online training and which stick because of the live training since I’m doing both in rapid succession. (Too many variables!)

The live training has so far been more interactive during the presentation of material, with speakers taking questions and asking us questions. (They’ve also distributed clicker-like devices that we’ll be using during the presentations after lunch.) There haven’t been any quizzes on the material (yet), but there will be breakout groups in which our active participation is required.

We’ve also been presented with gigantic binders containing handouts with slides for each of the presentations (complete with space for our own notes), related articles, and extensive listings of additional resources (including online resources). These binders have been adding to my sense of actively engaging with the information rather than just having the information wash over me. Plus, my binder will now be my first stop if I need to look up a piece of information from this training, which I personally will find easier than digging through my Firefox bookmarks.

A disadvantage of this training is that it eats up two calendar days set far in advance by the trainers, in a particular location far enough from most of the participants’ home bases that they need to book lodging for a couple nights. As well, owing to the A/V needs of the presenters and the aforementioned gigantic binders, the cost per participant of the training session is significant.

Why, you might ask, am I doing both of these overlapping training programs in rapid succession?

Strictly speaking, the live training sessions I’m doing today and tomorrow are not required of me. However, given responsibilities that stem from my committee appointments, this training is a really good idea. It will help me do my job better, and I’m bringing home resources I can share with other committee members who can benefit from them. The training may be taking up eighteen hours of my life right now, but I anticipate what I’m learning may save me at least that many hours of spinning my wheels just in the coming semester.

The online training was something I was required to take, but it strikes me as the minimal amount of information adequate to prepare someone for my committee duties. Plus, the online training is being required of a larger population at my university than just members of my committee, so we committee members are also doing the online training to ensure that we understand how well it’s working for the other people taking it.

One thing I’m thinking in light of this week of training is that my committee might want to find a way to offer periodic opportunities for live training on campus (at least as a companion to the online training if not as a substitutable alternative). If we want the people who are partaking of the training to have more than a minimal grasp of the material on which they’re being trained, recognizing different learning styles and building in more open-ended interactivity might bring about better results.

Data release, ethics, and professional survival.

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In recent days, there have been signs on the horizon of an impending blogwar. Prof-like Substance fired the first volley:

[A]lmost all major genomics centers are going to a zero-embargo data release policy. Essentially, once the sequencing is done and the annotation has been run, the data is on the web in a searchable and downloadable format.

Yikes.

How many other fields put their data directly on the web before those who produced it have the opportunity to analyze it? Now, obviously no one is going to yank a genome paper right out from under the group working on it, but what about comparative studies? What about searching out specific genes for multi-gene phylogenetics? Where is the line for what is permissible to use before the genome is published? How much of a grace period do people get with data that has gone public, but that they* paid for?

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*Obviously we are talking about grant-funded projects, so the money is tax payer money not any one person’s. Nevertheless, someone came up with the idea and got it funded, so there is some ownership there.

Then, Mike the Mad Biologist fired off this reply:

Several of the large centers, including the one I work at, are funded by NIAID to sequence microorganisms related to human health and disease (analogous programs for human biology are supported by NHGRI). There’s a reason why NIH is hard-assed about data release:

Funding agencies learned this the hard way, as too many early sequencing centers resembled ‘genomic roach motels’: DNA checks in, but sequence doesn’t check out.

The funding agencies’ mission is to improve human health (or some other laudable goal), not to improve someone’s tenure package. This might seem harsh unless we remember how many of these center-based genome projects are funded. The investigator’s grant is not paying for the sequencing. In the case of NIAID, there is a white paper process. Before NIAID will approve the project, several goals have to be met in the white paper (Note: while I’m discussing NIAID, other agencies have a similar process, if different scientific objectives).

Obviously, the organism and collection of strains to be sequenced have to be relevant to human health. But the project also must have significant community input. NIAID absolutely does not want this to be an end-run around R01 grants. Consequently, these sequencing projects should not be a project that belongs to a single lab, and which lacks involvement by others in the subdiscipline (“this looks like an R01” is a pejorative). It also has to provide a community resource. In other words, data from a successful project should be used rapidly by other groups: that’s the whole point (otherwise, write an R01 proposal). The white paper should also contain a general description of the analysis goals of the project (and, ideally, who in the collaborative group will address them). If you get ‘scooped’, that’s, in part, a project planning issue.

NIAID, along with other agencies and institutes, is pushing hard for rapid public release. Why does NIAID get to call the shots? Because it’s their money.

Which brings me to the issue of ‘whose’ genomes these are. The answer is very simple: NIH’s (and by extension, the American people’s). As I mentioned above, NIH doesn’t care about your tenure package, or your dissertation (given that many dissertations and research programs are funded in part or in their entirely by NIH and other agencies, they’re already being generous†). What they want is high-quality data that are accessible to as many researchers as possible as quickly as possible. To put this (very) bluntly, medically important data should not be held hostage by career notions. That is the ethical position.

Prof-like substance hurled back a hefty latex pillow of a rejoinder:

People feel like anything that is public is free to use, and maybe they should. But how would you feel as the researcher who assembled a group of researchers from the community, put a proposal together, drummed up support from the community outside of your research team, produced and purified the sample to be sequenced (which is not exactly just using a Sigma kit in a LOT of cases), dealt with the administration issues that crop up along the way, pushed the project through (another aspect woefully under appreciated) the center, got your research community together once they data were in hand to make sense of it all and herded the cats to get the paper together? Would you feel some ownership, even if it was public dollars that funded the project?

Now what if you submitted the manuscript and then opened your copy of Science and saw the major finding that you centered the genome paper around has been plucked out by another group and publish in isolation? Would you say, “well, the data’s publicly available, what’s unscrupulous about using it?” …

[L]et’s couch this in the reality of the changing technology. If your choice is to have the sequencing done for free, but risk losing it right off the machine, OR to do it with your own funds (>$40,000) and have exclusive right to it until the paper is published, what are you going to choose? You can draw the line regarding big and small centers or projects all you want, but it is becoming increasingly fuzzy.

This is all to get back to my point that if major sequencing centers want to stay ahead of the curve, they have to have policies that are going to encourage, not discourage, investigators to use them.

It’s fair to say that I don’t know from genomics. However, I think the ethical landscape of this disagreement bears closer examination.

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The value of (unrealistic) case studies in ethics education.

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Dr. Isis posted a case study about a postdoc’s departure from approved practices and invited her readers to discuss it. DrugMonkey responded by decrying the ridiculousness of case studies far more black and white than what scientists encounter in real life:

This is like one of those academic misconduct cases where they say “The PI violates the confidence of review, steals research ideas that are totally inconsistent with anything she’d been doing before, sat on the paper review unfairly, called the editor to badmouth the person who she was scooping and then faked up the data in support anyway. Oh, and did we mention she kicked her cat?”.

This is the typical and useless fare at the ethical training course. Obvious, overwhelmingly clear cases in which the black hats and white hats are in full display and provide a perfect correlation with malfeasance.

The real world is messier and I think that if we are to make any advances in dealing with the real problems, the real cases of misconduct and the real cases of dodgy animal use in research, we need to cover more realistic scenarios.

I’m sympathetic to DrugMonkey’s multiple complaints: that real life is almost always more complicated than the canned case study; that hardly anyone puts in the years of study and training to become a scientist if her actual career objective is to be a super-villain; and especially that the most useful sort of ethics training for the scientist will be in day to day conversation with scientific mentors and colleagues rather than in isolated ethics courses, training modules, or workshops.

However, used properly, I think that case studies — even unrealistic ones — play a valuable role in ethics education.

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Some thoughts on online training courses.

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I don’t know how it is where you are, but my summer “break” (such as it is) is rapidly winding down. Among other things, it means that I spent a few hours today in front of my computer completing online training courses.

I find myself of two minds (at least) on these courses.

On the one hand, many of these courses do a reasonable (or even excellent) job of conveying important information — broken down into modules that convey reasonably sized bites of content, enhanced with videos, case studies, and links to further information which one might bookmark for future reference. Indeed, the online training courses themselves can be accessed as a source of information later on, when one needs it.

It’s hard to beat the convenience of the online delivery of these courses. You start them when you’re ready to take them, and you can do a few modules of a course at a time, or pound through them all in one sitting. You don’t need to show up to a particular place for a particular interval of time, you don’t need to find a parking space, you don’t even need to change out of your pajamas.

Plus, many of these online training courses simplify record-keeping for whomever is responsible for ensuring that the folks who are supposed to take the course have actually taken it (and performed to the specified level on the accompanying quizzes) by emailing the completion reports to the designated official.

On the other hand … if you’re pounding through a 26-module course in one sitting (as I did today), you have to wonder a little about retention. Passing a quiz on a module immediately after you’ve read through that module may be do-able, but I’m less certain that it would be as easy to pass a month later. Indeed, if there had been a single big quiz after the 26 modules (rather than a quiz on each module that you take immediately after the module), I’m not sure I would have scored as well.

I imagine, too, that this mode of training is not necessarily beloved by people who have not made their peace with multiple choice tests. As well, for people who need to discuss material in order to understand it, the online delivery of modules may be a lot less effective than a live training with other participants.

What have your experiences with online training courses been? To you find them an adequate tool for the job, a poor fit for your learning style, or a big old waste of time?

Building a critical reasoning course: homework.

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I’m still working on planning that “Logic and Critical Reasoning” course I mentioned in an earlier post. As I noted there, the course is meant to give the students exposure to symbolic logic (looking at the forms of the arguments expressed with Ps and Qs, using rules of inference and truth-tables to evaluate the validity of those arguments, etc.), as well as to help them grapple with the arguments people make in natural language. While there’s clearly a connection between argumentation in the wild and formal arguments, students frequently need some time to get used to the Ps and Qs and not-Ps and backwards Es and upside down As.

In the normal course of things, getting used to symbolic logic means homework, and homework means grading. But, I’m looking at an enrollment of about 65 in a semester where there’s no earthly chance of money for graders. And, as you might recall from the last post on the course, the students are also required to write argumentative essays totaling a minimum of 3000 words. Among other things, this means I already have a substantial grading load for this course before the students do a speck of symbolic logic. However, symbolic logic is one of those things that seems to require practice if it’s to stick in your brain.

Luckily, my colleague Anand Vaidya shared a strategy with me that I hope will give the students the practice and feedback they need without drowning me in additional grading. We’re going to do “homework” in class.

The idea will be to save time at the end of each class period to work problems. Maybe there will be a set of five for the students to work individually, after which they will tell me how to do them at the board (asking questions as needed). Then there will be another set of five problems for the students to work in small groups, after which the groups will explain how to solve them and more discussion will follow. Maybe we’ll conclude by tackling some especially challenging problems together.

None of the problems will be handed in or graded. However, every two weeks we will have a quiz covering material that includes such problems. Presumably, this will give the students a strong incentive to come to class, do the problems, participate in the discussion, and ask questions until they understand. (Anand’s experience with has been that the students discover by the second quiz that they cannot blow off the problems worked in class, at least not if they want to do well on the quizzes.) I’ll probably make the problems available on the course website for those who might miss the class meeting (or who want to recapture the magic by working the problems again later), and I’ll entertain further questions on them during office hours, but it will be the students’ responsibility to make sure they know what we go over in class.

I am assuming here that grading quizzes will require less labor than grading homework assignments would (at least for the amount of homework required to master the material in advance of the quizzes). I’m also assuming that actually making up (and photocopying) the quizzes will be less work than grading all that homework would be. (There’s probably also a subconscious calculation about the amount of paper I’d be schlepping back and forth, one that favors the quizzes slightly.)

That’s my plan for the symbolic logic course content. The argumentative papers obviously won’t work this way. More on them in an upcoming post.