Archive for: November, 2011

The Thanksgiving feast and sleepiness: let's crowdsource some data!

A few years ago, we talked about the role turkey consumption might (or might not) play in post-Thanksgiving-feast fatigue. The oft-heard hypothesis is that the tryptophan in turkey gives you the yawns, but there was the suggestion that carbohydrates from starchy and sweet side dishes were an accomplice -- and that eating additional protein might counteract the tryptophan's soporific effects. Also, the amount you eat may be involved in how your body prioritizes consciousness relative to digestion.

It gets complicated pretty fast when we don't eat standardized lab chow.

Also, in passing, let me note that for all its association with tryptophan, turkey doesn't even crack the top 50 in this list of tryptophan-rich foods. (Number one: stellar sea lion kidney.)

Bora has a nice discussion of what tryptophan is up to in your body. Myself, I'm interested in working out observable patterns in Thanksgiving dining-and-yawning experience. Once we know what the patterns are, then we know what we need to explain with a biochemical mechanism.

To this ends, let's conduct some citizen science (and, come Friday, to collect some reports from the field).

Here is a form for data collection (*.doc format).

Ideally, we'd all want to sit down to the same Thanksgiving meal together (having all gotten a good night's sleep the day before, etc., etc.). Sadly, that's not going to happen. However, maybe you can rope those with whom you are dining on Thursday into participating.

Depending on the vibe at your Thanksgiving table, you can either ask the diners to keep track of what kinds of foods they eat, or you can assign your guests particular consumption objectives. Then, before dessert, have everyone do a quick assessment of his or her energy level.

With luck, we'll get data for the following variations:

  • High-tryptophan food (like turkey), high carbohydrate intake. (Prediction: sleepy)
  • High-tryptophan food, low carbohydrate intake. (Prediction: not sleepy)
  • Skip the high-tryptophan food, high carbohydrate intake. (Prediction: sleepy)
  • Skip the high-tryptophan food, low carbohydrate intake. (Prediction: not sleepy)
  • High-tryptophan food, high carbohydrate intake, extra protein. (Prediction: not sleepy)
  • High-tryptophan food, low carbohydrate intake, extra protein. (Prediction: energetic)
  • Skip the high-tryptophan food, high carbohydrate intake, extra protein. (Prediction: not sleepy)
  • Skip the high-tryptophan food, low carbohydrate intake, extra protein. (Prediction: frighteningly energetic)

Of course, if you track participant input a bit more precisely, maybe we'll stumble upon some other factor that turns out to be important, like vitamin A or sage.

If you use my form, you can return your results to me (as a *.doc or scanned into a PDF) by email: dr - dot - freeride - at - gmail - dot - com. I'll compile the responses and we'll see if we can make sense of the data.

See you back here on Friday morning with your results!

2 responses so far

Desperately seeking session chairs for Pacific APA.

Hey you professional philosophers (including graduate students):

I'm on the program committee for the Pacific division of the American Philosophical Association, and we are working hard to finalize our program for the upcoming meeting in Seattle (April 4-7, 2012).

For some reason, there was a larger-than-usual pool of submissions this year, and apparently we were not sufficiently draconian in our refereeing (lesson learned!), because there are still a bunch of sessions where we're trying to find session chairs.

The primary duty of the chair is to introduce the session's speakers (briefly) and enforce time limits.

A caveat: you can't chair if you are already on the program in some other capacity (since there's a rule that one may only appear on the program once).

I am looking for a chair for a metaphysics/philosophy of science session, one for a philosophy of biology session, and one for a biomedical ethics session. If you are interested and able to chair one of these sessions, please email me ASAP! (dr - dot - freeride - at - gmail - dot - com)

If you are a philosophical type who is already planning to attend the Pacific APA this coming April, is not on the program already, and would be willing to chair some other session, email me your information (name, email address, institutional affiliation) and I'll pass it on to our program committee chair so we can call on your services as needed.


One response so far

Some ethical decisions are not that hard: thoughts on Joe Paterno.

Ethical decision-making involves more than having the right gut-feeling and acting on it. Rather, when done right, it involves moving past your gut-feeling to see who else has a stake in what you do (or don't do); what consequences, good or bad, might flow from the various courses of action available to you; to whom you have obligations that will be satisfied or ignored by your action; and how the relevant obligations and interests pull you in different directions as you try to make the best decision. Sometimes it's helpful to think of the competing obligations and interests as vectors, since they come with both directions and magnitudes -- which is to say, in some cases where they may be pulling you in opposite directions, it's still obvious which way you should go because the magnitude of one of the obligations is so much bigger than of the others.

The ethical decision-making strategy I teach my students (drawn from Muriel J. Bebeau, "Developing a Well-Reasoned Response to a Moral Problem in Scientific Research") is one I find useful in all sorts of real situations (which is pretty much the point of an ethical decision-making strategy). Occasionally, this means applying it to evaluate whether a decision which someone else describes as "really tough" actually is.

For example, on the downfall of Joe Paterno, I encountered comments on the ethical decision he had to make (and on how well or badly he did with that) like this:

If this guy met his “legal obligations” by reporting the report, not something he saw himself even, then why isn’t that enough? He likely would have preferred to do even less. And he’s not the police, he isn’t charged with investigating and finding out the facts.

and this:

We all have to balance competing ethical obligations all the time, let’s at least do each other the courtesy of admitting that it’s difficult.

Is it difficult?

If you would rather not think about a situation where a responsible adult had to figure out what to do when child rape was reported to him, you probably don't want to read the rest of this post. I don't blame you. However, if you should find yourself in a relevantly similar position as the responsible adult, whether you want to think of it or not, you'll be on the hook to do good ethical decision-making of your own.

Let's have a look at the bare-bones of the JoePa case: A graduate assistant tells the head coach that he has witnessed an emeritus member of the coaching staff in the team's shower facilities performing a sex act on a 10-year-old. The head coach need to figure out what to do.

Who are the interested parties here?

  • The head coach, who needs to make the decision about what to do.
  • The child who was abused, who has an interest in being protected from future abuse.
  • The graduate assistant, who has an interest in being an effective member of the football program, as well as in not being punished for being a whistleblower.
  • The emeritus member of the coaching staff. He has an interest in maintaining his reputation and relationship with the football program, and in being treated fairly. If he didn't actually abuse the child, being treated fairly may amount to something different than if he did commit the abuse.
  • Law enforcement agencies have an interest in getting information about criminal acts so they can investigate them, establish the evidence for a prosecution, and stop criminal acts that are ongoing.
  • The football program, the university, the university community, and the larger society. These communities have a bunch of interests, including continuing a successful football program that lots of people enjoy, keep kids in the community safe from abuse, and upholding the values off the institutions and communities.

The head coach is (I hope) thinking through possible courses of action that include taking the matter to the police or taking the matter to the university's athletic director. He might also be considering what would happen in the case that he does nothing. What are the possible consequences of these various courses of action?

If he takes the matter to the police:

  • The police may act to stop the emeritus matter of the coaching staff from committing further abuse.
  • The police will likely launch an investigation of the allegations to determine whether they are grounded. The police investigation will also collect evidence that may be used in a prosecution.
  • The head coach's relationship with the emeritus matter of the coaching staff may be damaged.
  • The reputation of the emeritus matter of the coaching staff will likely be damaged.
  • The administration of the athletic department and the university might be upset at the unfavorable light cast on them by the incident, if the allegations become public.
  • The reputation of the football program with the university community and the broader community may be tarnished by news of the incident.
  • It may take a bunch of time to cooperate with the police investigation.

If he takes the matter to the university's athletic director:

  • The head coach's relationship with the emeritus matter of the coaching staff may be damaged.
  • The reputation of the emeritus matter of the coaching staff will likely be damaged.
  • The administration of the athletic department and the university might be upset at the unfavorable light cast on them by the incident, if the allegations become public.
  • The reputation of the football program with the university community and the broader community may be tarnished by news of the incident.
  • It may take a bunch of time to cooperate with the police investigation -- if the university's athletic director passes the matter onto the police.
  • The abuse may stop -- if the athletic director passes the matter onto the police.
  • If the athletic director doesn't pass the matter onto the police, the head coach may have to involve the police himself, which may anger the athletic director.
  • Or, if the athletic director doesn't pass the matter onto the police, the head coach may have to spend a lot of time trying to convince him to involve the police. This may anger the athletic director and be emotionally draining to the head coach.
  • If the athletic director doesn't pass the matter onto the police, the head coach may feel guilty that he didn't do more to stop the abuse.

If the head coach decides to do nothing:

  • The abuse may continue, and more kids may be abused.
  • The reputation of the football program and the university may remain intact.
  • In the event that the situation becomes public later, the reputation of the football program and the university may be badly damaged -- as might the reputation of the head coach.
  • The head coach's relationship with the emeritus member of the coaching staff may remain intact. Or, it might not.
  • The head coach's relationship with the graduate assistant may suffer.
  • The reputation of the emeritus member of the coaching staff may remain intact.
  • The head coach's conscience may be troubled.

What are the head coach's obligations here?

  • To protect those who cannot protect themselves.
  • To protect his team.
  • To uphold the values of the athletics program, the university, and the larger community.
  • To protect the reputation of the athletics program, the university, and the larger community.
  • To protect colleagues from unfair treatment (but not from just consequences)
  • To provide the information he has about the child abuse to law enforcement so they can investigate the allegations to determine whether there is evidence to support them.
  • To maintain his own integrity and good conscience

I take it there is no ethical obligation to avoid headaches or awkward moments with one's colleagues.

Looking at these obligations, nearly all seem to pull in the direction of the head coach doing something, rather than doing nothing. Indeed, they strike me as all pulling in the direction of doing something effective, rather than passing the buck to a higher-up and being done with it.

Some might argue that there's a conflict between the obligation to protect those who cannot protect themselves and the obligation to protect colleagues from unfair treatment. However, it seems like the head coach should be able to uphold his obligation to protect colleagues from unfair treatment without having to cover up what was reported to him (and without that allegation being buried by an administrator higher up in the hierarchy). Indeed, as a grown-up, the emeritus member of the coaching staff has far more resources to secure fair treatment than does the 10-year-old child.

How people make decisions tells us something about what obligations and interests they take most seriously. Do they care more about the values of their organization or its reputation? Do they care more about vulnerable people or about people they know personally who might be hurting those vulnerable people? Do they choose blissful ignorance over the involvement that might be required to obtain accurate information, or to pass on the information they have (no matter how uncertain it might seem to them) to the people whose job it is to conduct investigations in these sorts of cases?

(I'm not claiming here that police investigations of allegations of child rape are perfect. However, they seem likely to do better by the potential victims and other vulnerable members of the community than not investigating such allegations at all.)

Some ethical decision-making is hard. There are cases where we are bound by strong obligations that pull us in different directions.

But this particular case really isn't that hard. It may require effort to do the right thing, but figuring out what the right thing to do is here is not rocket science.

16 responses so far

Scientific authorship: guests, courtesy, contributions, and harms.

DrugMonkey asks, where's the harm in adding a "courtesy author" (also known as a "guest author") to the author line of a scientific paper?

I think this question has interesting ethical dimensions, but before we get into those, we need to say a little bit about what's going on with authorship of scientific papers.

I suppose there are possible worlds in which who is responsible for what in a scientific paper might not matter. In the world we live in now, however, it's useful to know who designed the experimental apparatus and got the reaction to work (so you can email that person your questions when you want to set up a similar system), who did the data analysis (so you can share your concerns about the methodology), who made the figures (so you can raise concerns about digital fudging of the images), etc. Part of the reason people put their names on scientific papers is so we know who stands behind the research -- who is willing to stake their reputation on it.

The other reason people put their names on scientific papers is to claim credit for their hard work and their insights, their contribution to the larger project of scientific knowledge-building. If you made a contribution, the scientific community ought to know about it so they can give you props (and funding, and tenure, and the occasional Nobel Prize).

But, we aren't in a possition to make accurate assignments of credit or responsibility if we have no good information about what an author's actual involvement in the project may have been. We don't know who's really in a position to vouch for the data, or who really did heavy intellectual lifting in bringing the project to fruition. We may understand, literally, the claim, "Joe Schmoe is second author of this paper," but we don't know what that means, exactly.

I should note that there is not one universally recognized authorship standard for all of the Tribe of Science. Rather, different scientific disciplines (and subdisciplines) have different practices as far as what kind of contribution is recognized as worthy of inclusion as an author on a paper, and as far as what the order in which the authors are listed is supposed to communicate about the magnitude of each contribution. In some fields, authors are always listed alphabetically, no matter what they contributed. In others, being first in the list means you made the biggest contribution, followed by the second author (who made the second-biggest contribution), and so forth. It is usually the case that the principal investigator (PI) is identified as the "corresponding author" (i.e., the person to whom questions about the work should be directed), and often (but not always) the PI takes the last slot in the author line. Sometimes this is an acknowledgement that while the PI is the brains of the lab's scientific empire, particular underlings made more immediately important intellectual contributions to the particular piece of research the paper is communicating. But authorship practices can be surprisingly local. Not only do different fields do it differently, but different research groups in the same field -- at the same university -- do it differently. What this means is it's not obvious at all, from the fact that your name appears as one of the authors of a paper, what your contribution to the project was.

There have been attempts to nail down explicit standards for what kinds of contributions should count for authorship, with the ICMJE definition of authorship being one widely cited effort in this direction. Not everyone in the Tribe of Science, or even in the subset of the tribe that publishes in biomedical journals, thinks this definition draws the lines in the right places, but the fact that journal editors grapple with formulating such standards suggests at least the perception that scientists need a clear way to figure out who is responsible for the scientific work in the literature. We can have a discussion about how to make that clearer, but we have to acknowledge that at the present moment, just noting that someone is an author without some definition of what that entails doesn't do the job.

Here's where the issue of "guest authorship" comes up. A "guest author" is someone whose name appears in a scientific paper's author line even though she has not made a contribution that is enough (under whatever set of standards one recognizes for proper authorship) to qualify her as an author of the paper.

A guest is someone who is visiting. She doesn't really live here, but stays because of the courtesy and forebearance of the host. She eats your food, sleeps under your roof, uses your hot water, watches your TV -- in short, she avails herself of the amenities the host provides. She doesn't pay the rent or the water bill, though; that would transform her from a guest to a tenant.

To my way of thinking, a guest author is someone who is "just visiting" the project being written up. Rather than doing the heavy lifting in that project, she is availing herself of the amenities offered by association (in print) with that project, and doing so because of the courtesy and forebearance of the "host" author.

The people who are actually a part of the project will generally be able to recognize the guest author as a "guest" (as opposed to an actual participant). The people receiving the manuscript will not. In other words, the main amenity the guest author partakes in is credit for the labors of the actual participants. Even if all the participants agreed to this (and didn't feel the least bit put out at the free-rider whose "authorship" might be diluting his or her own share of credit), this makes it impossible for those outside the group to determine what the guest author's actual contribution was (or, in this case, was not). Indeed, if people outside the arrangement could tell that the guest author was a free-rider, there wouldn't be any point in guest authorship.

Science strives to be a fact-based enterprise. Truthful communication is essential, and the ability to connect bits of knowledge to the people who contributed is part of how the community does quality control on that knowledge base. Ambiguity about who made the knowledge may lead to ambiguity about what we know. Also, developing too casual a relationship with the truth seems like a dangerous habit for a scientist to get into.

Coming back to DrugMonkey's question about whether courtesy authorship is a problem, it looks to me like maybe we can draw a line between two kinds of "guests," one that contributes nothing at all to the actual design, execution, evaluation, or communication of the research, and one who contributes something here, just less than what the conventions require for proper authorship. If these characters were listed as authors on a paper, I'd be inclined to call the first one a "guest author" and the second a "courtesy author" in an attempt to keep them straight; the cases with which DrugMonkey seems most concerned are the "courtesy authors" in my taxonomy. In actual usage, however, the two labels seem to be more or less interchangeable. Naturally, this makes it harder to distinguish who actually did what -- but it strikes me that this is just the kind of ambiguity people are counting on when they include a "guest author" or "courtesy author" in the first place.

What's the harm?

Consider a case where the PI of a research group insists on giving authorship of a paper to a postdoc who hasn't gotten his experimental system to work at all and is almost out of funding. The PI gives the justification that "He needs some first-author papers or his time here will have been a total waste." As it happens, giving this postdoc authorship bumps the graduate student who did all the experimental work (and the conceptual work, and data analysis, and drafting of the manuscript) out of first author slot -- maybe even off the paper entirely.

There is real harm here, to multiple parties. In this case, someone got robbed of appropriate credit, and the person identified as most responsible for the published work will be a not-very-useful person to contact with deeper questions about the work (since he didn't do any of it or at best participated on the periphery of the project).

Consider another kind of case, where authorship is given to a well-known scientist with a lot of credibility in his field, but who didn't make a significant intellectual contribution to work (at least, not one that rises to the level of meriting authorship under the recognized standards). This is the kind of courtesy authorship that was extended to Gerald Schatten in a 2005 paper in Science another of whose authors was Hwang Woo Suk. This paper had 25 authors listed, with Schatten identified as the senior author. Ultimately, the paper was revealed to be fraudulent, at which point Schatten claimed mostly to have participated in writing the paper in good English -- a contribution recognized as less than what one would expect from an author (especially the senior author).

Here, including Schatten as an author seemed calculated to give the appearance (to the journal editors while considering the manuscript, and to the larger scientific community consuming the published work)that the work was more important and/or credible, because of the big name associated with it. But this would only work because listing that big name in the author line amounts to claiming the big name was actually involved in the work. When the paper fell apart, Schatten swiftly disavowed responsibility -- but such a disavowal was only necessary because of what was communicated by the author line, and I think it's naïve to imagine that this "ambiguity" or "miscommunication" was accidental.

In cases like this, I think it's fair to say courtesy authorship does harm, undermining the baseline of trust in the scientific community. It's hard to engage in efficient knowledge-building with people you think are trying to put one over on you.

The cases where DrugMonkey suggests courtesy authorship might be innocuous strike me as interestingly different. They are cases where someone has actually made a real contribution of some sort to the work, but where that contribution may be judged (under whatever you take to be the accepted standards of your scientific discipline) as not quite rising to the level of authorship. Here, courtesy authorship could be viewed as inflating the value of the actual contribution (by listing the person who made it in the author line, rather than the acknowledgements), or alternatively as challenging where the accepted standards of your discipline draw the line between a contribution that qualifies you as an author and one that does not. For example, DrugMonkey writes:

First, the exclusion of those who "merely" collect data is stupid to me. I'm not going to go into the chapter and verse but in my lab, anyway, there is a LOT of ongoing trouble shooting and refining of the methods in any study. It is very rare that I would have a paper's worth of data generated by my techs or trainees and that they would have zero intellectual contribution. Given this, the asymmetry in the BMJ position is unfair. In essence it permits a lab head to be an author using data which s/he did not collect and maybe could not collect but excludes the technician who didn't happen to contribute to the drafting of the manuscript. That doesn't make sense to me. The paper wouldn't have happened without both of the contributions.

I agree with DrugMonkey that there's often a serious intellectual contribution involved in conducting the experiments, not just in designing them (and that without the data, all we have are interesting hunches, not actual scientific knowledge, to report). Existing authorship standards like those from ICMJE or BMJ can unfairly exclude those who do the experimental labor from authorship by failing to recognize this as an intellectual contribution. Pushing to have these real contributions recognized with appropriate career credit is important. As well, being explicit about who made these contributions to the research being reported in the paper makes it much easier for other scientists following up on the published work (e.g., comparing it to their own results in related experiments, or trying to use some of the techniques described in the paper to set up new experiments) to actually get in touch with the people most likely to be able to answer their questions.

Changing how might weight experimental prowess is given in the career scorekeeping may be an uphill battle, especially when the folks distributing the rewards for the top scores are administrators (focused on the money the people they're scoring can bring to an institution) and PIs (who frequently have more working hours devoted to conception and design of project for their underlings rather than to the intellectual labor of making those projects work, and to writing the proposals that bring in the grant money and the manuscripts that report the happy conclusion of the projects funded by such grants). That doesn't mean it's not a fight worth having.

But, I worry that using courtesy authorship as a way around this unfair setting of the authorship bar actually amounts to avoiding the fight rather than addressing these issues and changing accepted practices.

DrugMonkey also writes:

Assuming that we are not talking about pushing someone else meaningfully* out of deserved credit, where lies the harm even if it is a total gift?

Who is hurt? How are they damaged?
*by pushing them off the paper entirely or out of first-author or last-author position. Adding a 7th in the middle of the authorship list doesn't affect jack squat folks.

Here, I wonder: if dropping in a courtesy author as the seventh author of a paper can't hurt, how either can we expect it to help the person to whom this "courtesy" is extended?

Is it the case that no one actually expects that the seventh author made anything like a significant contribution, so no one is being misled in judging the guest in the number seven slot as having made a comparable contribution to the scientist who earned her seventh-author position in another paper? If listing your seventh-author paper on your CV is automatically viewed as not contributing any points in your career scorekeeping, why even list it? And why doesn't it count for anything? Is it because the seventh author never makes a contribution worth career points ... or is it because, for all we know, the seventh author may be a courtesy author, there for other reasons entirely?

If a seventh-author paper is actually meaningless for career credit, wouldn't it be more help to the person to whom you might extend such a "courtesy" if you actually engaged her in the project in such a way that she could make an intellectual contribution recognized as worthy of career credit?

In other words, maybe the real problem with such courtesy authorship is that it gives the appearance of help without actually being helpful.

(Cross-posted at Doing Good Science)

6 responses so far

From the cave of grading remote base: apparently stable patterns.

I'm one of those people who is rather less confident about the existence of universal regularities in our world (and this has at least as much to do with the research component of my misspent scientific youth as it does with Hume and Popper and the whole problem of induction).

Nonetheless, if I had to bet money on certain patterns being stable features of my world, here's where I'd lay my chips:

  • Not coming to lecture more than three times in the part of the semester preceding the midterm will be highly correlated with not doing well on the midterm. (My lectures seem to add value; who knew?!)
  • Not actually address the question that has been asked will be highly correlated with earning very few of the available points.
  • Using many, many words in the space available to answer the question (especially if they don't engage with the question) is less likely to earn points than using fewer words that present a clear answer.
  • The ability to use a sanctioned cheat-sheet on the midterm means I'll see a sizable proportion of papers (maybe 33%) where students have simply recopied on to their test papers every single thing they put on their cheat-sheet about philosopher X, regardless of what a question is asking them about philosopher X. This strategy seems to make it hard for the students using it to notice when they have "lost the plot" in their answers.
  • In at least 10% of the papers, I will encounter the phrase "solve science" and will need to pause for a facepalm or a headdesk.
  • That rascal DrugMonkey will put up a post to which I want to respond before the end to my grading is anywhere in sight. (Seriously, am I the only blogger with grading who has an angel on one shoulder and DrugMonkey on the other?)

8 responses so far

Musings from cave of grading remote base.

Casa Free-Ride, the location for the primary cave of grading, is currently abuzz with hammering and sawing and other noises, not to mention colder than usual on account of the removal of a ceiling and a bunch of obsolete insulation. So, I have decamped to a local cafe that has tables, heat, free wifi, and food and drink, establishing a remote grading outpost until it's time to move in a soccer-ward direction.

I have always operated under the assumption that, if I'm going to occupy a table at a cafe to plow through grading (or writing, etc.), it is appropriate to purchase food and drink. (Today's purchase: large coffee and chocolate truffle cheesecake.) The food can be a useful carrot (though not a literal one) to help me press through the task at hand: get through grading this section of the exam on 30 more papers and earn three more bites of cheesecake.

But, such a grading strategy carries with it the risk of getting chocolate truffle cheesecake on the papers being graded.

Indeed, in my grad school experiences with industrial scale grading (largely of exams for general chemistry and first term organic chemistry), there was nearly always some sort of food in play while we graders were marking the hundreds of papers we had to mark.

And, since solo-grading makes my mind wander, I'm now wondering what kinds of conclusions students might draw from the various and sundry stains that accompany the check marks and comments on their returned work. What might they make of

  • Coffee (cup ring)
  • Coffee (spilled)
  • Red wine
  • Tequila-scented salt crystals
  • Orange smudges consistent with Cheetos or Doritos
  • Smeared Cheez-Whiz
  • Pizza grease
  • Bacon grease
  • Chocolate
  • Creme Fraiche and/or raspberry coulis
  • Cigarette ashes
  • Singe marks and/or holes burned through the paper
  • Fish scales
  • Blood

I haven't returned papers with each of these extra additives, and students seem not to comment (to me) on the odd coffee or chocolate stain on an exam paper.

My hunch is that they cannot detect the presence of tear stains at all. But maybe empirical research is in order here?

7 responses so far