Nuance matters in systems biology

David Baltimore once famously issued a dictum (and this is a paraphrase because my memory fails me): "If not (at least) two-fold, then too bad!" As a systems biologist I believe that there is a lot of interesting biology between one-fold and two-fold, and that four-fold is not the same as two-fold.

One of the striking aspects of the whole media coverage of the persecution of President Claudine Gay has been the complete lack of nuance in the description of her "plagiarism". The one exception has been The Harvard Crimson. In an editorial piece, they state quite accurately (with wisdom beyond their years) that:

"But not all plagiarism is equal.

Plagiarism offenses lie on a spectrum. As defined by Harvard’s undergraduate “Guide to Using Sources,” it includes both misrepresentation of others’ ideas as one’s own and misattribution of borrowed material. Both matter, but the latter category, into which Gay’s allegations fall, is less serious by far."

In stark contrast, news outlets such as The New York Times, Washington Post, CNN, etc. repeat almost verbatim the posts from Free Bacon about the "40 examples of plagiarism" as if critical thinking and nuance were not part of the job description.

I have examined roughly 10 of the examples, and in my opinion they range from not plagiarism (e.g. defining a variable), to insignificant plagiarism (e.g. sloppy paraphrasing with attribution), to minor plagiarism ("plagiarizing" an acknowledgments section). 

There are one or two exception that I deem to be serious plagiarism on par with say plagiarizing a passage from Wikipedia without attribution.

Nuance matters both in biology and in the non-biological world. It gives me comfort that the younger generation recognizes what we in the older generation do not.

"Plagiarism from Wikipedia"

Plagiarism from Wikipedia:

"Contributors to the online encyclopedia Wikipedia license their submitted content under a Creative Commons license, which permits re-use as long as attribution is given. However, there have been a number of occasions when persons have failed to give the necessary attribution and attempted to pass off material from Wikipedia as their own work. Such plagiarism is a violation of the Creative Commons license and, when discovered, can be a reason for embarrassment, professional sanctions, or legal issues.

In educational settings, students sometimes copy Wikipedia to fulfill class assignments [1]. A 2011 study by Turnitin found that Wikipedia was the most copied website by both secondary and higher education students [2]."

Why I grade on a curve

As scientists we are taught early in our training that an experiment is worthless without the proper scientific control: “Where's the control?” “Don’t waste clean thoughts on dirty data!” Of course without a control, an experiment does not provide dirty data, it provides no data.

I work with white yeast cells. One day I notice some red colonies on a plate. Eager to make a discovery, I examine the red yeast cells under the microscope. To observe their inner workings, I shine a bright light on the cells for an hour, and watch them grow and divide. After 60 minutes I notice that they stop dividing, grow an enormous vacuole, and then die. 

"Wow!" I exclaim to no one in particular, "These red cells are defective!"

Student: But you were shining a bright light on them for 60 minutes; maybe that killed them.

Professor: I have imaged the white cells for 10 minutes, and they were fine. I’m sure I could image them for an hour and they would be fine.

Student: Maybe you should do the control experiment, and subject the white cells to the intense light for 1 hour and see what happens.

Professor: Nah, I have used the white cells for my whole career. They are wild-type. My friends use the white cells, as does the whole yeast community. I believe with deep conviction that there is something wrong with the red cells.

In my opinion, the best coverage of the trials and tribulations of President Claudine Gay of Harvard University has come from The Harvard Crimson. The journalists there have been tireless in their pursuit of the truth, rather than defaulting to the spin provided by right-wing media outlets.

Yesterday, they published a series of op-eds on the resignation of President Gay. One was written by Issac J. Bailey, a former Harvard Nieman Fellow, who opened his piece with the following:

"It’s obvious what must happen now that Claudine Gay has resigned from Harvard’s presidency. All institutions of higher education must commission independent reviews into the work of their respective presidents, tenured faculty, and other top academic officials. They must weed out anyone who made citation errors like Gay — even if these errors were minor, and even if they were made decades ago.

The new standard is not excellence, not brilliance, but perfection.

To commit to anything less would be to admit that Gay was singled out for being a Black woman. To do anything other than dust off the dissertations and research papers of every academic in a leadership position — leaving racist, sexist, and ableist stones unturned — would be to acknowledge that what happened to Gay wasn’t about upholding academic integrity."

Yes, this is almost the proper scientific control, but I would take it one step further. Every university president needs to have his academic record gone over with a fine-tooth comb by a highly motivated individual who is out to get him, and then have the results published by an organization that is also out to get him.

Do I expect the new interim President of Harvard to be subjected to this level of scrutiny? Of course not.

As Mr. Bailey states, President Gay was singled out because of her race and gender for extreme scrutiny that her white male predecessors and successors will never experience. In effect, and I am using the term loosely, figuratively, she was "lynched" by which I mean that she was punished harshly and unjustly because of her race and gender by those motivated by racist and sexist animus.

What do you think motivated the individual to do the painstaking work to find evidence of the "plagiarism"? Will this person perform the same "duties" on the new interim President? Why not?

When assessing the severity of President Gay's "plagiarism" we have no control data points to compare to. As Mr. Bailey insightfully points out, she is being compared to some platonic scholarly ideal. This is why I grade on a curve.

Grading a student or anyone on some idealized scale based on some idealized standard does not acknowledge the imperfections of the assessment instrument which are too many to enumerate. A lot of subjectivity goes into the making and grading of any exam. Grading on a curve allows one to discern the objective signal from the subjective noise. For example, an instructor may have a deep-seated subjective conviction about his teaching abilities, but the class performance on the exams provides a more objective measure.

The proper control has not and will never be done, and there will be no control data points to construct a meaningful curve. But lo and behold a second data point has suddenly materialized. Two intrepid reporters at Business Insider analyzed the graduate thesis of the wife of Bill Ackman, who has led the crusade against President Gay. What did they find?

"An analysis by Business Insider found a similar pattern of plagiarism by Ackman's wife Neri Oxman, who became a tenured professor at MIT in 2017.

Oxman plagiarized multiple paragraphs of her 2010 doctoral dissertation, Business Insider found, including at least one passage directly lifted from other writers without citation.

Her husband Ackman has taken a hardline stance on plagiarism. On Wednesday, responding to news that Gay will remain a part of Harvard's faculty after she resigned as president, he wrote on X that Gay should be fired completely due to "serious plagiarism issues."

My reaction to all of this is a feeling of disappointment, but not surprise.