IsoDDE: mixed-race love child of Biology and Information Science has a great future

One of the most exciting stories we have followed at this blog is the way new AI systems are suddenly speeding up the production of new drugs and other biological molecules (see LSS 1 12 20 et al) This week has seen another exciting step in the form of a new AI tool from Isomorphic labs. Read this piece, Drug discovery AI is akin to Alpha Fold 4 from Nature Briefing

Isomorphic Labs — a biopharmaceutical spin-off of Google DeepMind — has unveiled a new, powerful artificial-intelligence tool for predicting how proteins interact with drugs. The tool, called IsoDDE, can outperform other AI systems such as the open-source Boltz-2 and physics-based methods at determining binding affinity between a protein and potential drug. These skills have impressed scientists, but they highlight that IsoDDE is proprietary, and the technical paper that accompanied its announcement offers scant insight into how to achieve similar results.

Nature | 5 min read

The research and development of new drugs is one of the most arduous tasks that befalls the intelligent community. The central problem is pretty simple: how do you get your marvellous new drug to stick to a protein, and make the whole thing work the way you want it to? Proteins are not hard rigid statues of marble: they are soft, spongy and change shape in unpredictable ways when you put a new drug up against them. That’s the gap in function into which all that time, money and thought disappears. In theory new AI tools like Iso DDE (and others on the way no doubt) should rapidly speed the whole process by predicting myriad of possible shape changes as the molecular systems are brought together.[2] Moreover, to predict new bits on the target protein which we hadn’t thought of, where the drug might be made to stick to, And possibly, to crunch the numbers around all those new bits of protein, polypeptide and other molecules which are thrown up in the research process, to see if they have any likely uses as well. When we were young, Information Science and Biology were completely different disciplines with different faculties, buildings and career paths. It’s funny to watch them coming together so fructiferously, to produce such exciting offspring

[2]https://storage.googleapis.com/isomorphiclabs-website-public-artifacts/isodde_technical_report.pdf

#drugs #medicines #researh #AI #biology #health

Can your cat save you from cancer?

Cats: our feline friends: variously cute, lovable, admirable and beautiful. They’re becoming more and popular as pets. Which brings several advantages in the treatment of cancer, believe it or not. Like dogs, their nearest rival, they are exposed to all the same molecular slings and arrows of everyday domestic life-cleaning products- foods, fuels, what have you-as we are. But we also share more genetic material with them then we do with our canine chums. Moreover cancer is rapidly becoming a major cause of mortality in middle aged to elderly cats just as it is to humans in that stage of. It’s a set up for ground breaking studies. And Miguel Ángel Criado for El País and Helen Briggs of the BBC have two excellent reports on a groundbreaking study which has done exactly that. (teaser: one of these links is in Spanish, and one in English-can you guess which?)

The study, co-led by the learned Dr Louise van der Weyden of the Wellcome-Sanger Institute is the first really large map of oncogenic(cancer related) aspects of the cat genome. It’s full of intriguing details, which you can read by clicking on the marvellous articles which we have hyperlinked. But we could not resist a tiny spoiler, concerning Dr Weyden’s discoveries around the gene FBXW7 , a tumour‑suppressor gene whose loss helps drive aggressive forms of human breast cancer. Intriguingly, the same gene is frequently mutated in feline tumours. This cross‑species echo suggests that cats and humans may share a conserved vulnerability in the FBXW7 pathway, making our kitties unexpected partners in understanding this cancer mechanism.

And the conclusion? We need to help cats to help us. You could give to a cancer charity [3] You could give to a cat charity[4] But knowing our readers to be generous types we have included sufficient hyperlinks for you to do both!

[1] El mayor mapa genético del cáncer de los gatos abre la puerta a tratamientos compartidos con humanos | Salud y bienestar | EL PAÍS

[2]https://www.bbc.co.uk/news/articles/cvg3n7j8xyqo?at_campaign_type=owned&at_link_type=web_link&at_format=link&at_ptr_name=facebook_page&at_link_origin=BBC_N

[3] https://www.cancerresearchuk.org/get-involved/donate?

[4] Cats Protection | UK’s Largest Cat Welfare Charity

#cancer #breast cancer #cats #medicine #health #research #genome #oncology

Another thank you-with special regard to our last post

Every so often we put out a thank you message here. Today’s has been particularly prompted by our earlier blog R+D=GDP……(LSS 22 2 26) in which we drew attention to the achievements of the Swiss nation, whose attainments in scientific research have done so much to afford their citizens the good life.

We have had a number of responses, from many lands , which suggest we got something right We wondered what that might be. And someone in the office came up with this. “the world is full of many belief systems. Religions, philosophies, rationalisations, call them what you will. Many of these in turn are no doubt strongly held and deeply felt by their adherents. and we would contradict non of them. But sometimes, just sometimes, a simple truth is lying there in the statistics or the history books or somewhere. A sudden flash of enlightenment to illuminate the path of all of us. And the Swiss statistics are just one such example” That’s the gist of it anyway.

We hope you enjoyed the blog. And the beautiful pictures with which we illustrated it: compared to some countries they were not difficult to find . If they tempt you to visit that happy land to find out for yourself, be warned ! The general consensus is that it can be a bit pricey. [1] Both of which observations are, in our opinion, proof perfect of a high-GDP, well-run country, where even the mountains get taken in and cleaned. And a stark warning to countries who have suddenly decided to cut all their major R and D products. Oh well. Perhaps their children will earn a living entertaining Swiss tourists at rodeo shows.

[1]https://www.neverendingfootsteps.com/cost-of-travel-switzerland-budget/

#switzerland #USA #GDP #research #science #economics

R+D=GDP A maths lesson the Swiss can teach the world

Sit quietly in any pub or cafe and you will soon learn why the economy is performing so badly. Most of the diagnoses centre round a few simple tropes: wages are too high, holidays too long, taxes are too heavy, hours worked are too short…….Now, we would not dare to cross the opinions of the towering intellects you find in the bar of the Dog and Duck (it’s physically unsafe anyway ) But we dare to offer an alternative explanation for why economic growth works so well for some countries, just for your consideration, gentle readers. And the answer is: the amount that each country spends on Research and Development,

Let’s take Switzerland as our shiny example. It’s a tiny country constituting only 0.1% of the world’s population. But its R and D spend (3.4% of GDP) puts at 6th place in the global ranking of R&D. The result is a highly diverse export orientated economy, a well embedded public-private sector ecosystem of research institutes, universities schools and so on. All of which puts it almost at the top of the GDP per head league. . There are local advantages: it has strong stable institutions, membership of the EU single market and a low defence spend. Other countries share all or some of these advantages to a greater or lesser extent. We could argue for paragraphs about the pull and tug of these various factors. But we think one lesson is unavoidable, writ both large and small

Writ large, technology is the true game changer for economies. The advent of steam power in the industrial revolution utterly transformed both the out put and wealth of the nations which adopted it. However many hours humans and their animals laboured, they could never match the colossal output capabilities of powered engines. And technology only grows from a huge ecosystem of more general research and scholarship. Current debates aside, Industrial Revolutions are rare. But they can be mimicked by a pipeline of small steady innovations in many fields, which achieve the same things. This is the lesson writ small, which the Swiss have learned par excellence. Tap room philosophers may be excellent at the book keeping needs of their various small enterprises. But they are blind to the bigger lessons: on this matter and many others.

[1]https://www.aboutswitzerland.eda.admin.ch/en/research-and-development

[2]https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1023591/niesr-report.pdf

#R&D #science #technology #universities #investment #GDP growth

Stanford’s new discovery is a marvel-but can we really call it a vaccine?

Today we are happy to present one of the best news stories we’ve ever covered in our long years on this blog. It’s the announcement of a new type of vaccine from Stanford University. But it’s so mind bogglingly different from all the others we’ve come across that we genuinely wonder if it should be called vaccine at all! The details may be found in this crisp article from the excellent James Gallagher of the BBC [1] Essentially, it’s a nasal spray, so far tested only in mice, that offers protection against several viruses including colds, flu and COVID 19. Also against bacteria such as Staphylococcus aureus and Acinetobacter baumannii, two long known antibiotic resistant inhabitants of these pages.

Now, traditional vaccines have worked the same way ever since the pioneering work of Jenner. One organism=one vaccine, with the immune system trained to recognise one small target area of the invading organism. It’s as precise as a sniper; but can only ever protect you against one disease. The brilliant team at Stanford have taken an utterly new approach and decided to tackle the pathway by which a whole bunch or organisms make their attack. In this case the lungs. So it doesn’t matter if you are hit with a COVID 19 virus, the common cold, flu, the bacterial chums we noted above or even certain allergens. The macrophages of the lungs have been fired up and stand ready to repel any hostile borders-and will remain that way for several months[2]

Right, back to the question we started with: as this is so different from anything we were taught in school, can we really call it a vaccine? Well. If you define a vaccine as “ a molecular entity that trains the immune system to respond more effectively to a future biological threat” then yes, it is. But compared to the old ones it is a conceptual leap of awesome power. We doubt it will replace “old -skool” specific vaccines; their efficacy is just too good to waste. But as a completely new, game changing intellectual concept-well we think the sky’s the limit

[1] Single vaccine could protect against all coughs, colds and flus, researchers say – BBC News

[2] Science (2026)
“An intranasal vaccine activating innate immune danger pathways protects mice against diverse respiratory pathogens.”
Published: 19 February 2026

Lead author: Dr. Olivia Martinez, PhD
Stanford University School of Medicine
Department of Microbiology & Immunology

#health #vaccine #colds #flu #antibiotic resistance #virus #bacteria #immune system

Meet the influencers trying to clean up the internet

The invention of the internet has been a mixed blessing. On the one hand, you can instantly discover how many stars a Thai restaurant in Benidorm has earned. On the other, it has unleashed a torrent of unregulated and often misleading information — particularly on subjects like medicine and meteorology, where accuracy can genuinely matter. Now, a gallant group of educated rationalists has taken it upon themselves to counter some of this misinformation, as reported by Nature Briefing.: Science Influences go viral:

To combat the swathes of scientific misinformation circulating on social media platforms such as TikTok, scientists and medical experts are taking strategies straight out of the influencer playbook. Some content creators try to ‘pre-bunk’ misinformation by reaching a broad audience with peer-reviewed evidence on topics such as climate change. Others, such as Doctor Mike, challenge it head-on by fact-checking specific claims, including those by US health secretary Robert F. Kennedy Jr. The task can be difficult for individual creators, who can face personal backlash, but it’s important to meet audiences where they are, says creator Simon Clark. Research has shown that these efforts can help to shift the dial on issues such as vaccine hesitancy.Nature | 10 min read

We’ve often thought that the world of the internet is a bit like those old Victorian towns in the early Industrial Revolution, where their were no regulations about anything. So anyone could belch out anything they liked from their chimneys. And could put almost anything in a tin and call it food. Gradually laws were passed regulating pollution. Other laws imposed strict standards on what could be produced and sold. That was for physical things, of course. Isn’t time we had the same safeguards on all things digital?

#internet #pollution #misinformation #rational #fact check

Air Pollution and Alzheimer’s: grim news

We’ve written a lot about air pollution over the years (LSS passim) Mainly to say that air pollution, particularly in the form of PM_2.5 particles can do all sorts of harm to your lungs and circulatory systems. A fact well-attested by some of the sharpest medical minds on the planet as this WHO report shows[1] But now there is increasing evidence that these pesky particles may play a big part in the massive wave of dementia and neurodegenerative disease that is sweeping across the world. The latest evidence is summarised by Professor Eef Hogervorst for The Conversation.[2] And it’s pretty grim.

Air pollution and the deadly particles it chucks out are associated with all kinds of activities beloved of certain US politicians and their followers. Fossil fuels; road transport; old style heavy industries; good ol’ boys roun’ the barbecue fire, and that sort of thing. But how do you measure it, and separate out other plausible causes? A rather nifty US study started by mapping Medicare claims for dementia by postcode and PM _2.5 particle density. Other factors such as smoking, bad diets and poverty were also considered. The latter was admirably controlled by factoring in Medicaid eligibility, a sure indicator of low wealthin the US. We often use the phrase Killer Quote here: this time it’s more than a rhetorical flourish

…….pollution levels in the areas studied were, on average, about twice as high as the limit set by the World Health Organization (WHO). ………..The researchers found that the increased Alzheimer’s risk in polluted areas remained even after taking high blood pressure, stroke and depression into account

Eef goes on to explain how and why PMs are pulverising your grey matter: but click on! For she does it much better than we ever could.

And our thoughts, gentle readers? Firstly, the work confirms other reports we’ve noticed [3] Secondly the impressive size of the sample. Above all the careful attempts to control other factors such as diet and poverty; we know you prefer thoughtful scholarship over blind jumping to conclusions. Nothing is yet conclusive: but the hypothesis that air pollution causes other forms of dementia fits the available data so very much more closely than anything else does seems to us to be as close to one as you can get.

[1] WHO global air quality guidelines: particulate matter (‎PM2.5 and PM10)‎, ozone, nitrogen dioxide, sulfur dioxide and carbon monoxide

[2] https://theconversation.com/air-pollution-may-directly-contribute-to-alzheimers-disease-new-study-275873?utm_medium=email&utm_campaign=Latest%20from%20The%2%5B2%5D

[3] The effect of ambient air pollution (PM2.5) on dementia risk | Nature Aging

#air pollution #fossil fuels #smoke #alzheimers #dementia #WHO #health #medicine

How a frozen bacterium might stop the great ESKAPE

For microbiologists the great ESKAPE is not an old film on the telly at Christmas. It’s a classification of the six most deadly antibiotic resistant bacteria which they work with. These are of course: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.In other words, the bacteria that most effectively “escape” the effects of antibiotics, and thus sit at the heart of our current global antimicrobial‑resistance crisis. Now hope that they might be controlled is emerging from the icy caves of the Carpathian Mountains. And you might be forgiven for thinking that at first sight it actually makes things worse.

Because frozen in the ancient soil of Carpathian caves lies a bacteria with the snappy name Psychrobacter SC65A.3 -and it’s no less than 5,500 years old. We we’ve got two covers for you today: one in Spanish from that excellent newspaper El País by Miguel Ángel Criado and one from the Mail by Shivali Best. Both wax eloquent on its dangers: it seems resistant to at least a dozen of the best-known antibiotics. But here’s the rub: the same evolutionary toughness which let it develop these remarkable powers of resistance has also let it develop remarkable powers as an enemy of other bacteria. Including many of those on our ESKAPE list.

The natural tendency of people is to look at the scary side of anything: and thereby jump to the worst possible conclusions. We know that our readers are the ones who suspend belief a little longer, and always look deeper. In the long run that’s the only type of thinking that will release us from the antibiotics resistance crisis. And many others

[1] Hallada una bacteria helada hace 5.000 años capaz de plantar cara a superpatógenos | Ciencia | EL PAÍS

[2] Prehistoric killer superbug discovered in 5,000-year-old ice is resistant to 10 modern antibiotics, study warns | Daily Mail Online

#antibiotic resistance #microbiology #medicine #health #bacteria #ESKAPE

Recovering Rivers: Yangtse shows the way

Photo by Lucia Barreiros Silva on Pexels.com

The greatest problem in conservation and pollution control is that as soon as someone introduces a new measure, however reasonable, someone else pushes back. Try to control traffic pollution(demonstrably toxic) and all the van drivers get up in arms. Try to restrict smoking, and there’s a huge uproar crying freedom, autonomy and the right to die in peace. Yes, progressive ideas may be rational and based on scientific evidence and of long term benefit. But all too often, they can give people something to lose here, now, in the short term. Everyone really, truly need conservation and pollution projects to succeed quickly, here, now as well. The answer suggests Jonathan Watts of the Guardian, is lying on the banks of the Yangtse river in China and its called Evolutionary Game Theory [1]

The Yangtse had got into a pretty sorry state over the 70 or so years up to 2020. Too much fishing, too many dams. too much pollution. An iconic species called the Baiji dolphin (Lipotes vexillifer) was even driven to extinction, a heart-breaking tragedy if ever there was one. Something had to be done. And instead of just imposing bans and top down heavy handedness, the authorities boxed clever Check this out form Jonathan:

[the policy}t was designed according to the principles of evolutionary game theory, to assess how the three main bodies affected – communities, local governments and central government – would behave depending on different applications of punishments and rewards……The government spent about $3bn on compensating and finding alternative employment for about 200,000 fishers, scrapping many of the 100,000 boats involved.

In other words ordinary people were not treated as reckless ignoramuses, but just strugglers like the rest of. They were both brought in and bought in. a lesson many governments and well meaning reformers could do well to learn from. Now the great river, one of the undoubted wonders of the world, is starting to recover. Albeit a little groggily in places. Combine that with China’s CO₂ emissions starting to flatten out, and their huge lurch towards renewable power, and you may get a glimmer of hope indeed.

[1]https://www.theguardian.com/environment/2026/feb/12/china-yangtze-river-recovery-after-fishing-ban

#evolutionary game theory #conservation #ecology #pollution #communities #fishing #angtse

Friday Night: a feast for the real St Valentine

Who was the real St Valentine anyway? Legend says that he was a Christian citizen martyred at Rome on 14^th February 269 and buried among the tombs on the Via Flaminia. Trouble is, the evidence is shaky. For one thing, the Eastern churches celebrate his day on 6^th July: so what was the real date? He doesn’t even get a mention in lists of saints, compiled in the Fourth century: and even his earliest appearances occur in somewhat shaky sources [1] And the Emperor then reigning Claudius II Gothicus (not the bloke from Robert Graves) has no record as a persecutor, having many more pressing matters in his in-box [2] But whether there was a real Valentinus or not, he has left us a feast which we still celebrate today: Christians of all makes and now many non-Christians too. So with the aid of a little research we thought we’d take you back to the sort of food and drink he might have f known in that cold winter day in Rome in 269 AD.

The first thing: this isn’t the opulent capital of a superpower depicted in the movies any more. The Empire has been racked by civil wars climate change and invasions for over a century. A terrible pandemic, the Plague of Cyprianus, is raging: it will carry off the Emperor and many citizens in the next few years. And Rome reflects this downturn: it is starting to look scruffy and uncared for, because the money is running out, and the Emperor is nearly always on the frontiers. But a sort of middle class, the Decuriones still survives. It’s the stratum a real Valentinus might have come from. And tonight the paterfamilias of a modest family wants to push the boat out in honour of his older brothe, who is about to return to active service with the prestigious Legio V Macedonia, in Dacia.

All the Hollywood togas, silks and linens have vanished too. People dress in rough woollen tunics with equally serviceable hooded cloaks to keep out the weather. Much is influenced by military styles: the brother even wears braccae, a curious new garment which encloses the legs in tubes of cloth joined at the top and belted at the waist. And the food reflects Rome’s beleaguered state. As this is special, there is a first course of bread (panis secundarius) and some cheese, olives and pickled vegetables. Wine is served: rough red stuff from Campania: Gaul has long been cut off by a military rebellion. It will be well watered and served in earthenware cups. The main course will be a type of stew usually made from herbs. As tonight is special, a little expensive pork has been added. Desserts are simple too: a few raisins, dried figs maybe even some honeyed dates, as Africa is still under the rightful Emperor. And the talk is not of literature or Courtesans, but of battles, taxes, and who is still alive.

Ok it’s fiction But there really was a Valentinus, this is the world he would have known. Pretty rough, pretty humble. Compare it to the pink prosecco, chocolate and lavish meals that so many will be gobbling down tomorrow. And whatever your troubles, think yourself lucky.

[1] Saint Valentine – Wikipedia

[2] Claudius Gothicus – Wikipedia

For a general history, try

Goldsworthy, Adrian. Rome: The Eclipse of the West. London: Weidenfeld & Nicolson, 2003.

#christianity #st valentine #roman empire #history #church #food #drink