Lots of people asking how I would do graduate admissions differently. I don't claim to have a magic bullet, but I can point to some specific things we (US molecular biology PhD programs, although this can probably generalize somewhat) are doing wrong that are easily fixable.

https://twitter.com/mbeisen/status/1876342955382038766

Let me say at the outset that we should strive to give anyone who wants to spend their time learning how to do science the opportunity to do so. But I will stipulate here that space in graduate programs is limited and so some form of selection is necessary.

Since Steve Sailer and his the scientific racism crowd is swarming all over the @AllofUsResearch (embracing the UMAP figure, of course), I thought it would be useful to compile threads that explain why so many geneticists have been criticizing it. For starters, here is the paper.

nature.com/articles/s4158…

As a former journal EIC, I want to take issues with this claim by Science's EIC that negative interactions between scientists and editors are driven by a lack of respect for people who don't run research labs. Yes, there are scientists who think that everyone outside of their circle of elite PIs exists solely to further their uniquely indispensable role in scientific progress. These people treat nearly everyone like shit, and it sucks to have to interact with them regularly.

nobody seems to want to simultaneously acknowledge two truths about COVID origins: 1) that senior scientists, to some tangible extent, seem to have coordinated in the spinning of a story for a high profile publication and 2) this is a normal, everyday practice in modern science both of these things are bad, but you can't come to a full and honest understanding of (1) without understanding (2)

All power to people who want to imagine a better world where graduate students interview faculty to see if they're worthy of being on their thesis committees. But does it actually work this way anywhere?

https://twitter.com/arjunrajlab/status/1678476362389274624

IME what actually happens is we say to students "You passed your quals, now go form a committee", and in the guise of empowering them to form their own intellectual and mentoring path, place the burden on them to form a committee.

I don't have a lot to add to the @Nature story about @eLife. It reported accurately about the efforts of Randy Schekman and a few dozen editors to derail what we are doing, gave them a chance to explain their motivations, and us a fair opportunity to reply. We have a large (~1000 people) & diverse editorial board. There are many editors who are enthusiastic about our efforts. There are also many - probably the majority - who understand the desire and need for change, but aren't confident the community is ready for it.

Now that I've had a chance to see peoples' questions about @eLife's new publishing model, time for a thread for a thread with some details and answers.

elifesciences.org/articles/83889 The headline change is that we will no longer be making accept-reject decisions following peer review, and will instead by publishing public reviews and assessments of every paper we review.

Accepting and rejecting papers is an archaic practice that is terrible for science. It strips peer review of its value & institutionalizes the practice of judging scientists based on where, rather than what, they publish. It's time for this system to go.
elifesciences.org/articles/83889 We all know that a science publishing system that uses peer review to sort papers into 25,000 different journals makes absolutely no sense. What we are doing @eLife is making science publishing make sense - for today's technology and today's science.

You know what I don't want to ever hear again? A single complaint from anyone about how efforts to fix science publishing are going to affect their society or society journal. Because far more than anyone else it is scientific societies who are responsible for creating this mess. Back in the mid 90s when it was clear that the Internet offered an opportunity to make the outputs of science publishing freely available to everyone, scientific societies invented journal paywalls.

It's worth spending some time discussing what this new @whitehouse Open Science policy does and doesn't do, and what is still be to determined. whitehouse.gov/ostp/news-upda… For starters, the reason this is a big deal is that it is the first time, in over twenty years of #openaccess initiatives from both Congress and White House, that the policy focused exclusively on what is best for the public, without any baked in concessions to publishers.

I remain confused. People seem to think this posting is "explained" as the extending of a non-salaried teaching position to someone holding a different salaried research appointment. But at UCs such appointments are explicitly exempt from search requirements. So what's going on?

https://twitter.com/migarciagaribay/status/1505287346563940353

Indeed, as far as I can tell, none of the versions of this that people are finding "exculpatory" - courtesy appointments of various sorts or granting of teaching privileges to non-faculty researchers - would merit conducting a search at a UC.

I want to add one more thing here. @BrunaLab is right in the narrow sense that APCs are problematic, but they are not the problem. The problem is publisher greed, and fecklessness from scientific leaders and senior scientists who are complicit in a deeply broken system.

https://twitter.com/BrunaLab/status/1494448296915574785

It is important to remember that APCs arose in response to one of the most fundamental inequalities in science - the erection by greedy journal publishers of paywalls that limit access to the scientific literature to people at wealthy academic institutions in wealthy countries.

Did a quick read of @BrunaLab's study of APCs and the geographic diversity of authors. It's really good, and is another important reason why we need to move beyond APCs to a publishing system that is free for everyone to read AND publish direct.mit.edu/qss/article/2/… Publishing biases are incredibly difficult to address, and there are always a bazillion caveats, which they acknowledge, but they did as good a job as one can do with this kind of question.

I recently read @AliceDreger's "Galileo's Middle Finger" which is an account of her efforts to change how intersex newborns are treated by the medical profession, but also series of profiles of academic outcasts and how their work and ideas landed them in hot water. It's not a perfect book, but I am extremely glad it was recommended to me. I learned a ton and I emerged with a really deep respect for Dreger, and a feeling that academia would be far better if there were more people with her courage.

What I learned from years on graduate admissions committees is that they don’t predict success - they determine it. Everyone has a pet theory, rarely based on evidence, and never based on good evidence, about what makes a successful student. And, because the admitted pool is enriched for students who meet whatever criteria happen to be in the ascendancy, and because some of these students succeed, we convince ourselves that we were right and keep doing it.

it's a cartoon explaining a classic result in microbial evolutionary biology that (largely) resolved the question of whether selection acts on preexisting variation or if the selection induces mutations to occur (it won Salvador Luria and Max Delbruck a Nobel Prize)

https://twitter.com/Rossputin/status/1465487200640851972

the idea is as follows - you take a population of cells and divide them equally into a bunch of tubes and let them grow for several generations - then you pour the cells onto plates, apply some selective pressure to the cells, and count the number of colonies that grow

I don't think any of the primary authors of the Stanford seroprevalence study are on Twitter, but there are some questions about the work that I haven't seen asked elsewhere that I would love to see addressed at some point. medrxiv.org/content/10.110… 1) The paper mentions that adults were allowed to bring one child with them, and that 889 children registered. It's unclear how many children were actually tested but this suggests that on the order of 1/4 of participants were children of a participating adult.

It's interesting to see how, at every stage of this pandemic, people leap from the event being unusual to the virus defying the normal rules of its kind, when in reality it's the confluence of a range of fairly typical features that have fueled this pandemic. This has important consequences for how people respond to the pandemic. Instead of continuing to expect highly unusual things to happen, it's far better to understand what is going on as a series of predictable things that follow from the basic biology of this virus.

I want to reboot the conversation about this patent, and, crucially about patents in general. Let me start by saying that it was not my intent to single out @anshulkundaje, as the problems with this patent are widespread across all of academia. But it is a useful case study.

https://twitter.com/mbeisen/status/1199348013077917696

There are four overarching issues to discuss. 1: Should there shouldn't be patents in academia? 2: How patents have corrupted universities. 3: Why the arguments for academic patents are flawed. 4: And how this patent manifests these issues.

I want to give a little more background and detail on some of the new things we're doing at @eLife elifesciences.org/inside-elife/e… If you read this and have questions or concerns, I'd love to answer them. The motivation for all this is that people have been talking for decades - as long as I've been in science - about how we need to move beyond journal titles in how we evaluate works of science and the scientists who carry them out. And yet, we still do, and it's getting worse.

Since there's been a lot of discussion today about @eLife prompted by @TanentzapfLab, I thought it would be a good time to discuss several initiatives we're taking to reshape peer review. I'll say at the outset - as I've said many times before - I think journals are an anachronism - a product of the historical accident that the printing press was invented before the Internet. I want to get rid of them.