While it’s fun to banter about what constitutes a good lab, the part of this that is uncomfortable to discuss is that leaving a bad lab is in many cases near impossible. Few universities offer much support and PIs can and do retaliate, in some cases ending careers.
My first committee meeting of a biology student @UCBerkeley, when I was still a junior prof., resulted in a student breaking down in tears as he told us of abuse his advisor was inflicting on him. We brought this up with the advisor and department.
What happened? A few years later the professor was promoted to chair of the department.
Some universities do, at least, cover funding for a semester for students who switch labs. But few places have formal policies in place even for that. And while it’s easier for students with fellowships to transfer labs, PIs can retaliate.
I’ve heard of and seen cases of PIs badmouthing students who left their labs in direct attempts to harm future employment prospects.
It’s also hard for PIs who want to help students. Earlier in my career a student came to me once complaining that his PI was clueless about the research, unhelpful, abusive in interactions and asked me to just offer scientific mentorship.
I did, and while the student never joined my lab, we worked together and wrote a paper. His PI then insisted that he be last author on the paper even though he wasn’t involved at all in the research. Claimed I was “stealing” his student. Some PIs view students as their property.
There are few sanctions ever imposed on PIs for abusing students. When discussed at faculty meetings, it’s inevitably students who get blamed for any conflicts with their advisors.
As a math professor @UCBerkeley I attended a faculty meeting once where profs. talked about students who were having trouble graduating. One student had been in the program 10 years and hadn’t written a thesis. His advisor was asked what the problem was.
He replied “I gave him a problem but he’s an idiot. You want me to give him another problem to work on?” Everybody laughed.
The same advisor had one student who left after working with him for 5 years. One day, after presenting him work she’d been doing for 3 years, he just laughed at her and said “oh, didn’t I tell you this was solved 2 years ago?” Another prof. “rescued” her so she could graduate.
She wrote a beautiful thesis in a new area shortly thereafter.
Of course it’s good advice to tell students to choose labs carefully. But the advice that’s really needed is for PIs, not students. The advice is to create environments in their departments where students don’t have to choose labs carefully, because all labs are “good”.
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If you're working on spatial transcriptomics, I think you'll find @LambdaMoses' "Museum of Spatial Transcriptomics", which analyzes the field via its metadata, to be an incredibly useful resource. biorxiv.org/content/10.110… 1/11
The museum is organized as a main paper that provides an overview of a book (i.e. the Supplementary Material) which is based on a database of papers in the field compiled by @LambdaMoses. First the database... docs.google.com/spreadsheets/d…
It contains several hundred papers. 2/11
To undertake a comprehensive study of the field, @LambdaMoses read all these papers carefully, starting with "prequel" literature to establish historical context. The database has detailed metadata including a summary of each paper. This timeline is just of the prequel. 3/11
Yesterday I posted a piece about @OrchidInc's polygenic embryo selection. I thought, based on a press release I read, that they were the first company to undertake polygenic embryo selection. 1/ liorpachter.wordpress.com/2021/04/12/the…
The press release started w/ "Orchid, the first preconception system to quantify how a couple's genetics impacts their future child's health, today announced a $4.5M seed round..". It went on to describe the company's polygenic embryo selection product. 2/ prnewswire.com/news-releases/…
I naïvely assumed that Orchid is the first company to embark on polygenic embryo selection, but TIL that is not the case. In fact, more than two years ago, an article in @TheEconomist discussed myome.
In September I wrote a blog post reciting several false #covid19 claims and predictions made by Levitt over the course of the pandemic. That is not an "ad hominem attack". I reported Levitt's claims (with references). liorpachter.wordpress.com/2020/09/21/the… 2/14
Levitt, for his part, has responded to criticism of his failed predictions with non-sequiturs about attacks on free speech.
There is a lot of focus on the importance of reproducible science for facilitating replication of published research. That's all good, but reproducible science has another benefit: when adopted by a group it is an incredible accelerant for research *in that group*. 2/
Consider the paper we wrote on whole animal multiplexed #scRNAseq. The @GoogleColab notebooks Tara Chari wrote for the analyses were a monumental effort, but she did not start from scratch. 3/
The design is simple and elegant. A single motor drives the shaft of the tube rack, which is coupled to the dispenser arm via a spiral track. This ensures both rotate in tandem. 2/
The device is easy to 3D print and build, and can be assembled from off-the-shelf parts in less than an hour for $67.02. This low cost, and the straightforward assembly, is possible thanks to the design around a single motor. Amazing work by @annekylosaurus & @sinabooeshaghi. 3/