So is Carl, who started this discussion. What point are you trying to make?
Professor of Computational Biology, Imperial College London MRC Investigator, Computational Regulatory Genomics, MRC Laboratory of Medical Sciences Interested in eukaryotic promoters, enhancers and long-range developmental regulation
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So is Carl, who started this discussion. What point are you trying to make?
Einstein cared about concrete solutions to his equations. That supports what I wrote above.
Read again what I wrote. Yes, theoretical physics is mostly mathematics. But most of pure mathematics is not used in theoretical physics and theoretical physicists don’t care much about it - until somebody shows that some part of it can be useful for what they do.
Biologists, and other scientists, as scientists, don’t care for things that don’t help them do their research better in a way they and their colleagues perceive as better. Physicists don’t care about much of maths, either. Einstein definitely didn’t have a broad knowledge of theoretical mathematics.
How do you measure the degrees of separation? Neither two of the three gentlemen ever published anything academic together. All three knew each other well. (I am a biologist. My Erdős number is 3. As a measure of overlap, degrees of separation mean very little indeed :) )
Policy Exchange is a think tank. A “think tank” is an euphemism for “propaganda cell”.
Gail’s, probably.
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And now government doctors got my entire channel removed. Don’t worry. I won’t base my entire identity around this or claim it is worse than covid. 😂
I finished listening to it a few weeks ago and greatly enjoyed both the book and your narration. A fine piece of writing!
If anybody needs advice on good fountain pens, I’d be happy to help.
The guest is David Collum, a rabid conspiracy theorist who is still a professor of chemistry and chemical biology at Cornell. Tenure should probably not be able to protect academics against the consequences of lunacy such as this.
The original post did.
P.S. I have never said or thought that philosophy of science is a bad thing. Just that it cannot do things for science and scientists that some people here claim it can (and should).
I don’t know, but C. P. Snow had a suggestion why, back in 1934 :) Seriousy: in my field (genomics) very few scientists do philosophy of science. My conjecture is that there is too much to do in genomics itself. It appears to be more common in fields in which progress has slowed down.
AI bros have their own philosophers. So do neo-Nazis, Russian nationalists, eugenicists and Human Extinction Movement. There is a philosophy and philosophers for every occasion.
A basic requirement for a sensible peer review is that reviewer 1) knows enough to understand the basic idea; 2) is aware what they do not understand (they do not have to understand everything); 3) is able to follow the arguments in response to reviewers. Most journalists would fail all three.
Yep. Insisting on a universal definition of some biological concepts amounts to "doing things with words" in a way that would inevitably make the resulting definition less useful. We use operative definitions that might differ according to context; there is no problem as long as we are aware of it.
I have no reason to contest that. As for unifying different fields of science, I do hope that philosophy of science does a better job of it than some scientists did (e.g. I found E.O. Wilson's "Consilience" terrible in both ambition and execution).
I do not oppose your point - I just think that it is the scientists that should ultimately judge how relevant anything is for their science. Even if philosophers don't accept that as a principle, it is what will happen in practice anyway.
P.S. Thanks for the paper link - looks very interesting and relevant, and indeed, it seems that we do agree on many things.
I've had such discussions before. It always goes thus: somebody claims philosophy is relevant for sciences, I ask for details/evidence, and in the end I get "why do you think philosophy should be relevant for sciences?" :) I don't; it is the OP who did.
" I'd ask: perhaps it's a mistake to think that philosophy should be relevant to sciences?" - That is the exact claim Carl made in the original post I reacted to - because I thought it might be a mistake.
I am more interested in philosophy of science and read more on it than (conservative estimate) 95% of my colleagues, and I just see no evidence that it puts them at any disadvantage as scientists relative to myself. Many are thoughtful and brilliant scientists, who excel at spotting problems.
I agree. I am just disagreeing, based on historical data, with the claim that philosophers of science have special insight or skills that will make scientists do science better.
In the long run, peer review is also curative. You learn things for the future from it and learn when it is necessary to ask for help from knowledgeable colleagues before planning, let alone submitting your next work.
Most botanists are pragmatic and know they do not have anything as sharp as mammalian or avian reproductive barrier to make it the main criterion. And those who work on asexually reproducing species know that, in their case, the species is no more special than the taxonomic ranks above and below it.
Who will recognise those issues and their consequences when they occur? Historically, it's the people with the domain knowledge, not philosophers. Uncritical use of AI is not unlike uncritical use of statistical methods by those who don't understand them well - there's peer review/feedback for that.
Scientists will judge any new technology on what it enables them to do, or do better, in their work and how - because, in the end, that is how science works. If somebody suggests to me how to do things better, or to avoid pitfalls, it must be better in a way that is relevant to me and my colleagues.
A big issue is the training of future scientists. AI can be used to make it easier for them to learn (which is good) or to make it easier for them to avoid learning (which is bad). With today's students, the latter is becoming a MASSIVE problem, calling for big changes in how learning is assessed.
In the end, scientist themselves will decide which future research papers are interesting based on what they themselves can build on, and spot problems caused by overreliance on AI, just like they historically spotted problems with overreliance on other approaches.
Nothing. I tend to agree with most of it. But it is in essence an opinion piece - well written and referenced, but still. It implies that there are intrinsically better and worse ways of doing science, and that AI will encourage worse ways. Other philosophers might argue the opposite just as well.
And our domain knowledge makes us see why insisting on unifying definition is a waste of time - the definition would have to be so abstract as to be useless for practical work. (I cannot say anythiing about how psychologists use "control", but I doubt that they are unaware of how they do it.)
Yes, the same word in different context can have different operating definition (like "species" - different in vertebrate zoology and in microbiology; or "gene" - different in population genetics and genomics). We know that without philosophy guiding us.
I am not asking for any timeless ideal, but for things most people can agree upon and build on. Historically, scientists have done quite well in that regard. Yes, ideas have been disputed, but many were subsequently resolved – because of a shared idea of what it means to resolve them.
I have read more on species concept than you think. See the above excerpt re Metalogical Society - what you are doing is another case of philosophers identifying "a hot mess" in science -> most scientists finding it uninteresting and unimportant for what we actually do -> you insulting us for it.
Only philosophers of biology and some zoologists fuss about the concept of species. Most biologists who have any use for the concept know that there is no definition that can be made to work for all branches of the tree of life. And no working biologists have need for a unifying definition.
Even if he was "inspired" by it when working on wave mechanics, and not retroffited it in his later reminiscences (which is common), it was a set of poetic analogies rather than anything that could pass as a serious philosophical argument. That's not what Carl or philosophers of science had in mind.
Whatever rubbish there is to clear in science, I am still waiting for a convincing example of any such rubbish having been cleared by philosophy of science in the past. Scientists always had to clean their own rubbish, and I suspect that they will do it in the future, too. Nobody else can help much.
This makes no sense at all... Plus, even Kuhn did not accept how most philosophers interpreted his account of scientific revolutions ;)
Give me an example where they have done it.
Could you provide some instances where any of Einstein's classic papers cited a philosopher or a work of philosophy? (I tried and failed). Mach was both a philosopher and physicist. Was his actual physics better for it? From "The Search" (1934) by C.P. Snow (of the "Two Cultures" fame).
OK, give me examples where a philosopher discovered a hole in a scientific argument that scientists missed. You can be trained in logic to perfection, yet without the domain knowledge you are unlikely to be able to spot any errors. Errors reducible to faulty syllogisms are rare in science.
No, that is not my perspective. I am just pointing out that that perspective is implicit in some of the claims thrown around here, and when I do, there is always a retreat to “clarification” and pluri-perspectivism - which offer very little useful guidance to working scientists.
Exactly, they take different views, with no resolution. Even the most unsavoury ideas and history came with support by some philosopher or another. Hardly a recommendation for being the right ones to clarify issues, let alone help resolve them…
I assume that claims like “Philosophers/philosophy of science can offer concrete tools for academic research (in science)” is based on some concrete evidence and historical examples. If not, what is it based on? Conviction that it is self-evident?
Maybe. But we should definitely do something differently this time.
“Clarify” is probably one of the most unclear concepts that philosophers use to describe what they do. It can mean anything and lacks broadly accepted criteria for what it means to successfully clarify something. I recommend bingweb.binghamton.edu/~dietrich/Pa... - quite relevant for your claims.
“Applied philosophy of science” has always occurred in science - with or without philosophers. Scientists have always thought about what they did, on multiple levels. The evidence that they need external help, or that external help historically made a critical difference, is a bit stretched.
The problem with conversation is that there are no objective criteria on what course to take in the end. There aren’t even objective criteria for what’s important. Heavyweights tried in the past - and gave up. From. R. Crawshay-Williams, “Russell Remembered”:
Don’t get me wrong, there is clear value in what they do, but to claim they are able to make scientists do science better, “better” should be something that other scientists can recognise as better.
To those who believe that philosophy of science offers concrete tools for advancing research, I say this: Show, don’t tell. Philosophers of science are often convinced in their abilities to do things for which there is precious little evidence that they have ever done them.
Archaea are often surrounded by bacteria. But is there ever active conflict between the two? Can archaea kill bacteria? If so, how do they do it? Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...
After nearly twenty years in the making, our attempt at understanding what makes the chaetognath phylum so unique has finally been published! www.nature.com/articles/s41... with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1
A tourist from Texas using “flat” and “tube”?
I meant primarily the scientists, especially the most prominent ones.
What is truly depressing is how little pushback against it there is relative to the gravity of the situation.
Nobody today uses this term in the mindset of "cold war driven, triumphalist rhetoric" or "assumes all state interventions are equivalent provided we don’t like them". Lysenkoism wasn't about the exact way in which Lamarckism was wrong, but about how scientists who thought it was wrong were treated.
What RFK Jr and his ghouls are doing has more than enough parallels with what Lysenko did that it needs to be resisted and fought against. In that context, arguments like "well it is not exactly the same because some things in Soviet Union were different" miss the point completely.
“Lysenkoism” in common parlance means pseudoscience enforced by high officials in charge of science, and rejection of legitimate science and scientific arguments, on specific topics, for ideological reason. It does not have to have all the elements of the original phenomenon that gave us the term.
This argument sounds very much like “it must not be called X unless it comes from the X region of France”. Many perfectly legitimately used terms would be dismissed using this criterion. Many political phenomena arose in a specific political context, which doesn’t mean they do not apply to others.
What is probably not a good idea is telling your colleagues what to do and how to use their time.
This has never meant to be solely or predominantly a science forum. People post whatever is most pressing or interesting for them in the circumstances they are. The fact that what is most pressing for them now is not the what you are interested in doesn’t mean that they are using the platform wrong.
If you had a job in US academia, what is happening in US politics would be of critical importance to you now. It is difficult to discuss science if everything you need to do your research has either been taken away or might be taken away any day.
Your choice of people to follow must be very, very unusual. For me it is still very much nothing like Twitter, in a good way.
Wrote a big review with my friend and colleague @varshneylab.social on the state-of-the-art in CRISPR used experimentally in vivo. We wanted to focus on their use in experimental vertebrate animals (apparently passé now but we persist).
Of all the bullshit positions, the one I loathe most is "yOu LiBz mAdE tEh fAsCiSmZ hAppEn" as if fascism is not a cyclical political phenomenon that always has behind it the same violent insecure inadequate men who yearn to dominate and those that support it have no agency or moral responsibility.
It is widespread. Proposals solving biological problems w/computational methods are rejected because they are seen as less valuable than those generating new data, and told to apply to computer science calls, where they would be reviewed by panels of people doing cryptography and quantum computing.
There is a growing violent movement which senior politicians and media organisations are now not only seeking to justify, but actively encouraging. Why it's time for politicians to instead start standing up to the wholly illegitimate concerns of the far right www.adambienkov.co.uk/p/illegitima...
That is what I meant when I said that they are put in an environment of better (existing) students and postdocs.
Is it really so surprising? Top institutions attract more PhD students and postdocs to apply, so better ones get recruited in average, and then they are put in environment of better PhD students and postdocs. There are great people at other institutions, too, they are just fewer and farther between.
I am glad to announce that the #DANIO-CODE Data Coordination Center is back online at a new home: danio-code-dcc.genereg.net Thank you all for your patience and sorry for any inconvenience!
#IZFC2025 #zebrafish #DANIO-CODE data coordination centre is back online. Note changed address: danio-code-dcc.genereg.net
Quite possible - but the repression could still be Polycomb-mediated, especially since you notice that the MusD demethylation is constitutive there. And many developmental loci have Polycomb marks that spread widely from the target gene itself.
... when Fgf8 is activated, the whole locus loses Polycomb, and MusD finds itself derepressed. If this is true, that means that it is not the Fgf8 enhancers that control its promoter but just its Polycomb repression, which is in sync with that of Fgf8. This is all speculation, of course.
... notes that Fgf8 is kept silent by near-locus wide Polycomb binding, which spreads into your insertion region. It might be that Fgf8's Polycomb spreads across the MusD element, preventing DNA methylation and H3K9me3 deposition. So it is silent as long as Fgf8 is, and...
As far as I know, MusD promoter is active in somatic cells as long as it is not (DNA) methylated or heterochromatinised (H3K9me3). Why does it respond like Fgf8 here? It might be a sensor of the entire enhancer landscape (which we know that the Fgf8 promoter is), or alternatively...
Weight loss improves health but What happens to cells in the fat during weight loss? Intriguingly, immune cell numbers decrease but their activated states persist w chronic inflammatory potential. Beautiful work from neighbors @mrc-lms.bsky.social Will Scott et al www.nature.com/articles/s41...
Nice work! It looks like the TE works like an enhancer trap recapitulating the regulatory input in a genomic regulatory block (GRB). A 2005 paper by Tom Becker "caught" a number of these blocks in zebrafish this way doi.org/10.1242/dev.... and we interpreted how they work in doi.org/10.1101/gr.6...
Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁 Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5
A new study, published today in Nature, reveals the hidden benefits of weight loss on fat tissue. A better understanding of how weight loss leads to health improvements at a molecular level could help inform the development of therapies for diseases such as type 2 diabetes in the future.
bsky.app/profile/adam...
This is a periodic reminder that every method of research evaluation can be gamed. As this shows, even the cheats can be cheated - if a reviewer outsources their brain to a LLM, the authors will happily try to influence how the LLM does its job. techcrunch.com/2025/07/06/r...
I know; but despite everybody knowing it is a good return on investment, the funding is always in short supply, and politicians across the political spectrum are often quick to cut it further.
Where will we get the money to pay them?
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I don't think the teaching is the problem. It's the learning. Serious learning requires a serious investment of students' time and effort, and students use ChatGPT to circumvent that investment - to produce essays and problem solutions with little effort and little learning.
With current assays and take-home exam format, the primary application of ChatGPT is to avoid the *doing*. And I disagree that evaluation is less important. We owe it to the best students to recognise them as such.
I often hear, in derogatory context, about students studying just to pass (or ace) an exam, as opposed to studying to truly learn and understand. If one can pass (or ace) an exam without having properly learnt and understood the matter, it is the exam that’s inadequate, not the student’s attitude.
Even before ChatGPT, I don't think most UK or US students would have done well on the kind of exams we were subjected to.
I agree. Most of us couldn't write after four years and 40 exams. That has to be taught, too. Then it needs to be tested in a way immune to ChatGPT. There is a basic distinction between using new technology to help one learn (good) vs. using it to avoid learning (bad). How you test it is crucial.
It is different because style and structure were not important, as long as you arrived at the correct solution or demonstrated that you knew what you were asked. And it was all done in a classroom - no take-home exams. Only a thesis at the end of 4 years, which counted as only one grade out of 40.
Same here. STEM and medical students in continental Europe were never asked to write essays. In written exams we were asked to solve problems or show factual knowledge, with pen and paper. Most exams ended with an oral exam (after the written one). I had nearly 40 oral exams in four years.
Sequence-alignment is not the best way to detect conserved cis-regulatory elements? Tobi Zehnder from Vingron-Lab developed #IPP a synteny based algorithm with @ferencmueller.bsky.social, @borislenhard.bsky.social& @da-bar.bsky.social We used it to find conserved enhancers with diverged sequences
URGENT: FlyBase has lost practically all its funding overnight; even user fees are tied up in denied grant funding. 🤬🤯 Any lab using @flybase.bsky.social please donate using the link in post below. This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.
Stop blaming yourself for other people’s deficiencies. With some - many - people, you cannot compete with liars who will tell them what they want to hear. Only grave consequences that they themselves feel have any chance of getting through the noise and garbage.
A dissociative is a noun here: adf.org.au/drug-facts/d...
Have you seen the results of local elections in England two weeks ago? They are watching the ship wreck and voting for its copy at home: www.thenorthernecho.co.uk/news/2518106...
And then, in 2029, with Farage as PM, move somewhere else again?
In the UK, it is the same (only 65 + vulnerable on NHS). It is not that they are antivaxxers, but rather that the government thinks it is OK to save money on things such as this. I am not sure which is worse.