Before money is invested in infrastructure? Sure. But that's a second order issue right now when the continuation of the business as a going concern is very uncertain even without infrastructure investment.
Senior Lecturer in Bioinformatics at the University of Sheffield. Likes gene regulation, 3' UTRs, non-coding RNA and dancing. He/Him/His Also at IanSudbery@genomic.social
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Before money is invested in infrastructure? Sure. But that's a second order issue right now when the continuation of the business as a going concern is very uncertain even without infrastructure investment.
But most of us will have to choose one or the other.
By living in Europe and building businesses in the US, you cheat in a way that would make Europe unlovable and American bad for business if everyone did it. Make you choice - bold and risk taking, with a poornquality of life, or staid and risk averse, but with a good quality of live.
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Well, that will depend on how much they are allowed to increase prices.
“I don’t want asylum seekers to live on my street” is genuinely a wild thing to say as a notionally progressive politician
If you reach out to me on the basis of my preprint and I've heard of you or your journal before, great! If I've not, then you (and possibly your whole publisher) are going straight on my block list. Sorry if you are a legitimate, but new journal, but it's the only way to control my inbox.
Sex Matters has deleted his page from its website - but the internet never forgets. web.archive.org/web/20241107...
www.ucu.org.uk/article/1415... If you work for the University of Sheffield and you're sick of seeing your university vandalised and its staff exploited, please vote. If you don't, please support our struggle. We are fighting for you too. @ucu.org.uk @sheffielducu.bsky.social #university #sheffield
Well, you could read this as "you (the market) made this mess, you pay to clean it up".
I think de-centering Joyce was one of the biggest mistakes the film made. Along with making the home pseudo-hogwarts, and making it underthreat as the main motivation, rather than just the club members being nosey.
You sell your house and rend the apartment in your 60s. The cost of the flat you pay while you are still independent then cover the later higher cost of the care home. They generally have quite a low maximum age for moving into the sheltered housing section, to make sure you pay for long enough.
We do have places a bit like cooper's chase near me (an ordinary part of the north): communities of new build one/two bed apartments around central facilities and a care home. Not quite as nice as (book) Cooper's Chase, and nothing like the film one. www.averyhealthcare.co.uk/care-homes/l...
Same way as poor kids on council estates like reading books about fantastical boarding schools.
Ron was clearly a knowing dig at trade union bosses (although possibly his famous son contributes). In fact, I'd always sort of thought of Joyce as a kind of Audience surrogate, who finds herself in this wonderful world of rich people who were (or used to be) important. Maybe even their pet normie
To be fair to the books, I think this is acknowledged at least in the original. There is a whole thing about Joyce not feeling like she fits in because she was just a nurse that her financier daughter was paying for while everyone else was a famous psychiatrist, or high up in the secret service.
That said, we are not expected to have both volume and quality. The "your job is in trouble" threshold is one 3* in a five year period. The promotion threshold is two 3.5-4* in each two year rolling period. That takes grants, but you'll be in trouble quicker for not having grants, than papers.
I wouldn't say that DORA is ignored by REF or the institutions per se, more that the individuals on the internal REF panels more or less ignore what they are told by the instution. Not that I blame them, given the number of articles they are given to assess and the time line.
Having recieved reviews and seen the reviews others recieve (as a fellow reviewer) and how the editors handle them. I might even know some of the editors. I'm sure it's not foolproof, but I can't believe the rate of milled papers is as high as such venues as some others.
I'll look out for your piece. I don't doubt paper mills target high impact journals, but I would have thought it harder to get through at some journals than others. I deliberately didn't include things like CNS in that list, but journals where I've been on both ends of the editorial process.
They're is s difference between IF and reputation. Both are inaccurate measures of the quality of a paper in s journal. But reputation is much harder to game.
Our papers are all evaluated by two or three poor sods on the REF stocktake committee. Of course they use journal names (even if told not to). People are close enough to each others work to have heard of the journals, but often not close enough to actually evaluate the papers.
Genome Biology, Genome Research, NAR, OUP Bioinformatics, PLoS Computational Biology, EMBO, elife, Molecular Cell, Nat Comms. These are these are pretty much the only sorts journals our internal REF panel cares about. So far, I don't think paper mills are common at this type of journal.
But are papers published in the journals that publish paper mills likely to get you past a REF stocktake? There are at least some journals I still trust to have be likely paper mill free (of course nothing is guaranteed). These also happen to be the places internal REF panels care about.
Labour's cowardice in the face of extremism iandunt.substack.com/p/labours-co...
An evergreen thread: Race/Ethnicity is *not the same* as genetics, and you can't use Race/Ethnicity as a sort of stand-in for genetics. These two concepts are connected via aspects like skin colour, but the connection is alot less profound and categorical than most people think.
No. I'm definitely worse. To the extent that I've wondered if they're is such a thing as pandemic acquired ADHD.
Congratulations. I can't think of anyone more deserving.
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In that article you state that there are things that could be done that would make it harder for an illiberal government to move quickly. But couldn't they just pass a bill that said "everything passed by the previous government is repealed"?
Public law practitioners: have you been involved in litigation regarding automated decision making by Government, or do you think you might be in future? The @publiclawproject.bsky.social are keen to speak to you.
Fucking ICE just disappeared two of our neighbors from their car; they had the courtesy to put the car back in the driveway , but left their 5 lb dog inside the house to die. Is America great again now‽ #MAGA
Would they? There is no right to costs in employment cases, and it would presumably cost lots to appeal (at least if you wanted any chance of winning).
But it would be lovely if such a thing were possible.
I think it would be lovely if there were a machine that could unerringly determine who was right and who wrong in law in any dispute. Obviously there is no such machine, because a) the law doesn't work like that and b) no such machine exists that could make unerring decisions if it did.
And if you think the employee with limited legal resources got a bad deal from ACAS, they'd almost certainly have faired even worse at tribunal.
Their role IS to press for a resolution. They are the conciliation service, their job is to foster conciliation between the two parties to a dispute. In theory who is in the the right or wrong is supposed to be immaterial (which is why this statement from the head is so odd).
I've been trying to put my finger on what it is that makes new nervous about the "writing is thinking" response to the use of genAI in academia. And its this: a throughly well elebaorated and completed thought process is a necessary but not sufficient condition for good writing.
If you mock a fascist for being fat, you mock fatness. If you mock a fascist for being fascist, you mock fascism. Stay on target.
NEW Yes, an incoming illiberal and radical UK government would have absolute constitutional power By me Substack: emptycity.substack.com/p/yes-an-inc... Personal blog: davidallengreen.com/2025/08/yes-...
The lack of constitutional reform is not even about good government anymore. It is about a clear and present danger to liberal democracy.
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Can across this quote on the purpose of universities from the 1963 Robins report on UK HE. Like, wow, this guy gets it. Why can't politicians be like this today?
Its frightening because so often DAG makes things seem less sensational, less breathless, less world changing than other commentators outlets. It means when he says "this is the real thing", that it hits harder.
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Depends if you calculate that average over a 24 hr period or just office hours.
Also, how can you argue that you are against credentialism, and then argue that you want the credential to mean something again?
Having now read the original article, why does it not surprise me that this guy is a fan of IQ, thinks its an important measure of someones worth, and that an IQ of 125 is not anything to write home about?
Getting a PhD is not easy. clauswilke.substack.com/p/getting-a-...
Finally, while entry to government funded doctoral training programs is fiercely competitive, if you can fund yourself (about £30k a year) entry usually is down only to the judgement of the supervisor.
Consequently the viva/defense is a real exam that takes place in private and is performed by two examiners, at least one of which must be from a different uni. People can and do fail. Outright failure is rare, but being asked to go away and redo parts (within a time limit) is very common.
However, some of what you sa in the specifics y isn't quite true for the British system. The biggest difference is that there is a 4 year limit. This means you must submit by 4 years at the latest irrespective of whether anyone thinks you are ready.
This is often the problem I have with people who would like us to see PhD as a general purpose but just higher degree. Degrees can be a process of ranking people or a way of educating them. I fear we are losing the battle against ranking as a purpose at high-school and undergrad, but not yet PhD.
I 100% agree with the principles you state here. A PhD is not a credential, it's an experience. It's valuable not for the piece of paper you get, but for the experience you gain along the way. Inckuding the experience of pushing yourself to finish something. I wish more undergrads saw BSc that way!
The proposed solutions are either generate synthetic null data to measure FDR (assumption laden), or use permutation (transcriptomics usually to low n... I think?). So I don't know what the answer is
However, if this is violated, its usally believed that BH still provides an upper bound on the expected number of false discoveries, and thus is safe. This paper claims that while the above holds on average, indevidual experiments may have very large numbers of false discoveries.
The BH proceedure calcaulates the expected false discovery rate in a multiple testing situation. (that is some experiments have more false discoveries, some less, but it will give the average). Its also known that BH usually assumes that tests are independent.
Thoughts on this? I've only skimmed it so far, but seems to claim that experiments that have positive correlation between features (e.g. genes in transcriptomics) can have a lots of false positives if using BH. genomebiology.biomedcentral.com/articles/10....
Just had a very informative conversation / whiteboard session with my postdoc about attention network segregation on AI stuff. My "emotional understanding" of AI is ... deepening.
I don't think that anyone would argue that things that increase productivity are necessarily damaging, only that our incentives mean that we risk letting things that are damaging through if they are seen as improving productivity.
4. Science of Science, with its data-intensive descriptive approach is useful, but insufficient. Metascience, with its laser focus on a replication crisis in psychology, likewise. We need broader humanistic thinking about the social processes involved in the construction and valuation of knowledge.
Nothing will prepare you. Absolutely phenomenal.
This, and also further in that if Trump and Putin were actually in a loving relationship that would improve my opinion of them because they seem like people incapable of anything except self-love. And similarly (a bit personally as someone with a mild form of brachydactyly) the small hands jokes.
I quite like the idea of more granular papers, with less bloat and maybe just one key experiment/figure, but then a greater emphasis on reviews that tie a series of single experiment papers together.
I think we have too problems - one is that there is just too much published, much of it not particularly interesting. But also the stuff that is published is already too bloated in an attempt to get noitced above the deluge.
4-space K&R. I like to have the enclosed lines seperate from the control lines, but having the opening brace on its own line feels like a waste, while having the closing brace on its own line feels neccessary for seperation.
here is the Jewish cultural perspective: you don't get an education in order to become rich. you try to make money so that you have more time for education, the greatest and most reliable joy in life. this is like complaining that raising children or falling in love isn't better paid
I think there is another way to read the quote. It could be read as not neccessarily implying that scientists have to be particularly intelligent, only that the level of intelegence they need is higher than one would expect was needed to see the down sides if a life in science and run a mile.
I suppose this is the point when I should say again that: the amount of money the videogames industry brings into the UK economy every year is *more than double* the value of the fishing and steel industries *combined* what this country is really good at is producing culture
NEW BLOGPOST: Why did the jury acquit Ricky Jones? thesecretbarrister.com/2025/08/16/w...
What a gem. A wonderful reminder of why we do this.
If someone you know buys into claims about "genetic optimization" of embryos using polygenic scores of cognition, just send them our 2024 paper on Beethoven & musicality. We wrote it to help communicate limits of individual-level genetic predictions & complexity of links between DNA & behaviour. 🧪👇
The natural sciences are liberal arts: part of and inseparable from the essential kit of human fluorishing that includes the humanities, social sciences, and fine arts. Science is beautifully, inherently humanistic--look how it excites people, almost universally!
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I think a good rule of thumb is to spend at least as much time thinking about your data as you did obtaining it. It's common for people to spend a lot less time thinking than doing which gives rise to all kinds of problems.
And if you care about details and specifics, you are probably going to try to replicate the results yourself anyway.
It helps that when I say 1,000s of papers most won't be very interesting. They'll be filming in details rather than changing underlying principles, and papers that do change underlying principals tend not to be published in The International journal of Natural Cellular Science (yorkshire).
Doing a directed literature search is a different matter, and if something is directly relevant, you can't really ignore it. But you can calibrate your levels of scepticism.
That leaves more than that just "glam mags" and my friends. For us glam means science, cell and the nature family. There are at least 2 tiers, probably 3, between there and the journals I talked about above. Plenty to provide more papers than I have time to read.
If I'm just "keeping up", then I'm very selective. And I'm afraid that does mean no journals published by MDPI or Hindawi, and only unfamiliar Elsavier or Wiley journals if I know the authors or if the title is particularly exciting. I trust preprints more than many journals (do fraud posts them?)
Here is how I put it to students... there are 1,000s of papers published in my field a year (or a month, depending on your definition). You can't possibly read them all, so you need to prioritise. How you do that prioritisation depends on your goal.
Agree. I'm sure fraudulent "paper mills" are indeed on the rise... but I'm also sure I'm not reading and citing fake papers in my work... and most of my colleagues aren't either. Fake papers are a problem, but they aren't necessarily polluting the work of other scientists to a great degree.
Right, I get that. But my experience has been that people use that tooling, not to inspect and explore, but to put it into a text based format.
Even you and I are guilty to an extent. Who didn't convert raw sequence to fastq as soon as they download it?
And that's where really good BAM APIs exist (eg pysam). Hell i even review code where people use pysam only to call to_string and then use text parsing. Things are much worse for fielders with less good tooling.
Hmm... your get your point, c and your are correct in the ideal world. But we also need to be realistic. Do you have any idea how many people are out there where the first thing they do when they get a bam file is convert it to sam so they can parse it with R dataframes or awk or python readline?
The other big one is of you are working in Google always hit "refresh" before and after copy/pasting text with a reference in. The word integration is much less fragile than the Google docs in my experience (except the case in the last skeet where Google completely currupts it).
We use Zotero, because ots basically the only thing that works with Google Docs, as far as I'm aware. They're are several things you need to be careful of though: the big one is never open a word file with zotero links in it in GDoc, not even to view it. Immediate scrambling (and vice versa).
Our collaboration with Tony Mustoe's lab us out today. MPRA libraries and possible cryptic splicing in MPRA reporters, or reporters in general. The additional novelty here is that such events are controlled or influenced by AU-rich sequences. www.nature.com/articles/s41...
The Daily Mail lead with a photo of triumphant Irish and Ghanaian heritage Lioness players + another anti-immigration story. What hypocritical graceless fuckwits.
They want magical STEM based industries. That isnthey want someone else paying for the STEM research to be done.
One of the stranger themes the past 20 years or so, was governments shouting for more STEM in school but then systematically defunding STEM jobs and universities. Many STEM graduates, few jobs. What was that about
#bioinfo4women #ISMBECCB2025 women in bioinformatics slack invite link (for 30 days) in case anyone wants to join: join.slack.com/t/women-in-b...
Just when most people have gotten the hang of presenting PowerPoints onto a second screen, laptops here at the University have started believing they have three screens.
It's a spectrometer. As a spectrometer it's great, but it's affected by things other than Nucleic acid. If you have the proper ones that can give you the full spectrum, then you can see whether to trust the concentration estimate. But you definitely can't just read the number off.
It’s actually even worse: they show it as a gel, which is pure fluorescence units, but a BioAnalyzes records as the molecules pass a single point sensor and critically _fails to normalize for different molecule speeds_ This results in a near-logarithmic overcounting of large molecules!
My DCD means that I have a digit span of only 4. And that's when I'm concreting soley on a number being read to me in a test. I don't stand a chance with 8 digits in the middle of a presentation. To be honest, I struggle with author, journal, date during the 15s these things are flashed up for.
This is your regular reminder that the BioAnalyzer/TapeStation reports fluorescence units, not # of molecules. Left is bioA trace, and right is fragment size calculated from either read output (blue) or transformation of BioA trace (black). Fig 3 from journals.plos.org/plosone/arti...
"Science is not just something I do; it’s a core facet of who I am. If science is taken from me, an important piece of me will be gone."- @feliciatuchman.bsky.social @sciforgood.bsky.social Bravo, friend! So well done. We can't just switch off what inspires us, especially when it is under attack.