Michael Eyes Out πŸŽƒ Profile picture
I study how flies are made & how fungi control their behavior. I fight to make science open and fair. EIC of eLife. My conflicts https://t.co/J9KHBEPpVt
The Monarch Diaries Profile picture 1 added to My Authors
30 Nov
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.
I’m not saying that everyone is equally likely to succeed in graduate school in its current form and that there are not predictors of success. I am saying we don’t - and given our methods can’t - know with confidence what they are.
Read 9 tweets
30 Nov
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)
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
in the original experiment the selective pressure was exposure to a lethal virus, but it can and has been repeated with almost any condition where the growth of the bacteria requires a mutation not found in the original cell
Read 10 tweets
3 Nov
Lots of discussion here, but I really don't think it's that complicated: it reifies racism and abets racists to routinely assign population labels, especially socially constructed ones, to groups of individuals based on genetic data or for use in genetic studies.
That is not to say that the use of such labels is never scientifically justified, as @arbelharpak points out. But there should be a very high bar for their use, and it should be for very specific, clearly articulated purposes.
It is simply untenable to claim - correctly - that race is not a scientific concept, and then turn around and casually use race as if it IS a real scientific entity in papers. And substituting geographic labels for socially constructed race doesn't solve the problem.
Read 10 tweets
22 Aug
I hope we get some more clarity from Whitehead about what led to Sabatini's dismissal. Was there overwhelming evidence that the institution couldn't ignore? Or does this represent a shift in the way institutions are handling harassment allegations against prominent faculty?
Obviously, full transparency is impossible to protect people who spoke up. But that has often bogusly used by institutions as an excuse to provide zero transparency when they take no action, and I hope that doesn't happen in this case.
It is as important to demand transparency when institutions do act against their prominent faculty as it is when they don't. Because as much as I have faith in Ruth Lehmann as a person, I have zero faith in the institution she leads (or any academic institution for that matter).
Read 5 tweets
16 Apr
A decade ago my close colleague in science and publishing Pat Brown came to me with some data on the climate impact of animal agriculture published by the UN fao.org/3/a0701e/a0701…. This report (aspects of which are controversial) motivated me to begin looking at the issue.
Zoom ahead 12 years and I've finally had a chance to write up some work I've done myself on the problem that has convinced me that we are, if anything, underestimating the scale of the problem. A preprint describing the work is available here: biorxiv.org/content/10.110…
All the code and data I used are available here: github.com/mbeisen/meatle…
Read 33 tweets
18 Mar
Since it seems it's "You need an SNC paper to get a job" season again, there are a couple of things about the faculty hiring system that seem often to get glossed over, and I'm curious what people think about them.
I want to start by stipulating that, in the US there is no hard rule about what you "need" to get published, but there is, for sure, a strong correlation between publication record and faculty search success. What I'm interested in is why this correlation exists.
When discussing this fact, nearly everyone seems to jump from correlation to causation - assuming that people hired to faculty positions with SNC paper got their jobs *because* of those SNC papers. But what's the evidence that this is true?
Read 20 tweets
16 Jan
There are good political/social reasons for wanting SARS-CoV-2 to have entered humans directly from animals, and many pushing the WIV lab accident hypothesis have nefarious intent. I am nonetheless surprised at the degree of confidence people express in a natural origin.
I've looked at a lot of the evidence, and, while the direct transfer from bats remains the strongest hypothesis, the case is far from airtight. And it might never be, because even if it were true, we'd be lucky to find evidence in wild bat populations that would erase all doubt.
And there is an at least plausible case for lab accident too, in that the virus first appeared in the rough vicinity of a lab that is studying precisely this kind of virus and doing the kind of experiments that, if something went wrong, would lead to disaster.
Read 15 tweets
22 Dec 20
Editor: I am your editor.
Author: Well, I didn't ask you to edit my paper.
E: You don’t choose your editor.
A: Well how'd you become editor, then?
E: @LadyOfTheLake, whose profile says their science shimmers like the purest samite, held aloft your preprint from the bosom of bioRxiv, signifying by divine providence that I was to oversee its review. That is why I am your Editor.
A: Listen. Strange scientists in labs distributing preprints is no basis for a system of publication. Supreme editorial power derives from a mandate from the authors, not from some farcical acceptance ceremony.
Read 5 tweets
21 Dec 20
why do people treat current peer review system as if it was optimized to help authors and advance science when its primary features - pre-publication review by 2-3 people, binary decisions, exclusive publication rights - are products of limitations of the technology of the day?
the system has its uses - and we have so completely integrated it into the structures of scientific careers that it is difficult to change it - but can we not at least try to imagine a better system, one that is designed to function in the 2020s instead of the 1870s?
imagine you were charged with designing a system of science community and peer review in the alternative universe where the internet was invented before the printing press - what would such a system look like?
Read 6 tweets
21 Dec 20
I understand the concern - in a world where scientists are judged on the basis of journal citations, anything that might interfere with getting one is scary. But these concerns should be addressed at journals, not at @biorxivpreprint or overlay journals being created around it.
We made a decision @eLife not to do unsolicited reviews because we view what we do as in large part a collaboration with the authors to improve their work. And we let authors control when their reviews get posted so they don't worry they'll interfere w/publishing their paper.
But at same time, we see the presence of reviews published by others as augmenting, not interfering w/ this process. We'll give authors a chance to respond & have great confidence that our editors can integrate this information into the review process fairly and conscientiously.
Read 10 tweets
1 Dec 20
While we talk about the future of science publishing, we need to also have a conversation about how to fund it. The problems with the subscription model is obvious and needs no elaboration. But it's clear that the APC/author pays model doesn't really work either.
Back at the dawn of the #openaccess era, when @BioMedCentral and @PLOS adopted APCs, we knew it was imperfect, but it was the only viable way to cover costs that didn't require locking papers behind paywalls.
It was our expectation that this was a transitional state - that the funders who ultimately provide the money for science publishing would realize that it doesn't make sense to fund research infrastructure like publishing with transaction fees of any kind.
Read 10 tweets
1 Dec 20
I am excited to announce today that @eLife is transitioning to a new model based on author-driven publishing (preprints) and public post-publication peer review and curation elifesciences.org/articles/64910…
Our moves are designed to catalyze the desperately needed transition of science from the slow, exclusive, and expensive "review then publish" model born with the printing press to a "publish then review" model optimized for the Internet.
We have been inspired by the embrace of preprinting by our community. A recent internet audit showed that the authors of 70% of papers under review @eLife had already published their work on @biorxivpreprint @medrxivpreprint or arXiv.
Read 17 tweets
19 Nov 20
Vaccine, Vaccine, Vaccine, Vaccine
I’m begging of you take it when you can
Vaccine, Vaccine, Vaccine, Vaccine
Please take it just because you can
COVID symptoms often lead to death
With flaming head and no more breath
With pallid skin and loss of taste and smell.
It shut down schools and businesses
And made us all social distance
But it cannot compete with my
Vaccine
Just two small shots of RNA
Will keep this bad virus at bay
Thanks to the scientists for making this
Vaccine
Read 7 tweets
3 Sep 20
Like many people, I've been thinking a lot about the Electoral College, and more specifically the "National Popular Vote" movement, and a disturbing/terrifying idea occurred to me.
en.wikipedia.org/wiki/National_…
For those who don't know, there is an ongoing effort to getting states to agree to allocate their electors to the winner of the national popular vote provided that enough other states agree to ensure the NPV winner would get the 270 electoral votes needed to win.
I like the approach of hacking the Electoral College, since actually eliminating it would require a constitutional amendment that would be much more difficult to pass. But it is probably doomed to failure since there is not a good incentive for enough states to sign on.
Read 18 tweets
6 Aug 20
as much as I and probably most other people want to move on from the BAM/SB affair, i feel like I as an individual, and many of us as a community, haven't fully reckoned with what happened, or more significantly why it happened, and what our roles in it were
so as not to bury the lead - I fucked up - and owe both an apology, and more importantly an accounting of what happened and a promise to not do so again, to the many people BAM has bullied, gaslit and undermined the past several years
the fuckup is not by falling for SB's grift - it was well crafted and targeted instincts of mine that i don't think are bad - but rather having played a part in conferring a sense of continued legitimacy on BAM - a legitimacy she abused in myriad destructive ways
Read 19 tweets
19 Jul 20
The media are, rightly, taking a lot of heat for spreading false fears about COVID-19 immunity. But's its worth tracing the origins of this particular case back to where it starts.
The article that prompted this discussion was pegged to a @medrxivpreprint paper from researchers at King's College who monitored neutralizing antibodies to COVID-19 in 65 patient in the three months following symptom onset. medrxiv.org/content/10.110…
The raw data are pretty simple. Most of the people in the study (95%) produced a high titer of neutralizing antibodies, with the titer declining after a peak around 21 days post onset of symptoms, with a lot of inter-individual variation in magnitude of response and kinetics.
Read 25 tweets
13 Jul 20
Since the dawn of the Internet, it has been clear that we need and have the opportunity to build a system of scholarly communication free of limitations of print: a system freely accessible to all authors and readers with a new model of peer review optimized for a digital age
The ideal system would feature: 1) universal author-driven publication (currently known as preprints) as the primary means of communication, 2) robust and multi-faceted post-publication peer review and curation, and 3) direct funding to eliminate all paywalls & transaction costs
This is, and has been, technologically feasible for a quarter century. There has been progress towards this goal in various places - expansion of preprint servers, growth of #openaccess, funder mandates, creation of overlay journals. But progress has been frustratingly slow.
Read 15 tweets
20 Apr 20
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 odd that no mention of this was made elsewhere in the paper. Was there a correlation between antibody positive adults and their child? If one assumes high intrafamily spread, as has been widely reported, this would lead to an approximately 33% overestimate of the prevalence.
Read 7 tweets
11 Apr 20
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.
You can see this from the very beginning of the pandemic involving the zoonotic origins of the virus. Lot's of hand-wringing a fear mongering about this - but the reality is that many human viruses were very recent transfers from wild or domesticated animals.
Read 16 tweets
9 Nov 19
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.
Using a hierarchy of journals to convey what editors & reviewers think of a paper is bad: it's overly simplistic & fails to capture the multidimensionality & nuance of the assessment - it also enables a toxic culture in which people are judged by where and not what they publish.
Read 37 tweets
28 Jul 19
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.
More specifically, I want to get rid of pre-publication peer-review and the whole "submit - review - accept/reject - repeat" paradigm through which we evaluate works of science and the scientists who produced them. This system is bad for science and bad for scientists.
Read 34 tweets