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

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

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

Two new stories give fresh hope on cancer

Two stories give us hope of real progress in understanding and treating cancer. The first from the excellent Emma Gritt of the Mail [1] concerns the work of the great Dr Mariano Barbacid whose work has been so crucial in elucidating and developing the whole theory of oncogenes and the role they play in cancer. His team has been studying the effects of three drugs on the KRAS gene, deeply implicated in the development of the pancreatic form of the disease. But: don’t read us, read Emma-she knows a lot more than we do

The second story, from the inimitable Ian Sample of the Guardian [2] concerns the application of the Google Deep Mind AI tool to study genetic drivers of cancer-and other diseases too. To quote Ian:

“We see AlphaGenome as a tool for understanding what the functional elements in the genome do, which we hope will accelerate our fundamental understanding of the code of life,” Natasha Latysheva, a DeepMind researcher, told a press briefing on the work.

Once again click!. You’ll get a lot more from Ian than you will from us.

Both stories blend into two of our old LSS favourites. Firstly, the use of AI to look at complex biological patterns which humans alone struggle to perceive. (LSS 1 12 20 et seq) Secondly, that repeatable frequencies in DNA may be tied, probabilistically, to repeatable patterns of symptoms. Veteran readers will recall our hopes that this methodology may apply to psychiatric disorders too: (LSS 18 12 25 and 29 12 25). Of course, we expect to learn of environmental and epigenetic factors as well. But if we are right, these genetic advances may provide a firmer starting point for future investigations than we have now. How much more is achieved when facts are sacrosanct, not convenient entities to be selected and disposed according to the immediate convenience of their user! A lesson which certain US politicians and the news channels which so fanatically support them would do well to learn.

[1] Huge pancreatic cancer breakthrough as scientists achieve ‘permanent disappearance’ of disease with new triple-threat approach tested in lab | Daily Mail Online

[2]Google DeepMind launches AI tool to help identify genetic drivers of disease | Genetics | The Guardian

#AI #deep mind #cancer #genes #DNA #medicine #health #oncogenes #psychiatric disorder #heart disease

AI =New drugs and medicines 17 times faster

Good heavens, but it takes a long time to get a new medicine in use. To go from first concept to everyday pharmaceutical use in the high street can take from 10 to 15 years on average. There’s all that Discovery and Initial research: followed by Preclinical Testing, Clinical Trials, and Regulatory Review. Quite right too: we support all this red tape , as there no point in killing the people (or animals) we’re trying to cure. Occasionally things are permitted to speed up (think mRNA vaccines during the COVID-19 pandemic) But we admit the whole thing can be a tad frustrating, particularly for a blog like this one, ever campaigning for new forms of antibiotic and other ways to combat resistant micro-organisms,

Which is why we support every endeavour to speed the process of drug development up. None more so than when its exponents try fresh thinking, as the ingenious Dr Alex Shalek of MITI. Read this AI offers drug-screening shortcut from Nature Briefing

An artificial intelligence (AI) model trained on complex data from human cells could bypass the need for time-consuming drug-screening in the race to develop new medicines. The model, called DrugReflector, was trained on data about how each of nearly 9,600 chemical compounds perturbs gene activity in more than 50 kinds of cell. Researchers found that DrugReflector was up to 17 times more effective at finding compounds that could affect the generation of certain blood cells than standard screening, which depends on randomly selecting compounds from a chemical library.Nature | 4 min read
Reference: Science paper

Dr Shalek and his admirable team think they have accelerated the process by anything between 13 and 17 times, as you will discover if you drill down on the links which we have provided.

It’s easy to bemoan the modern trend for instant narcissistic gratification, where every want is satisfied by the click of a button and a funny little man showing up in a blue van a few hours later. Of course it is essential to test new drugs, and maintain the high standards which we in the educated community hold ourselves to. You can’t run a drugs company at the same moral and intellectual level that you run a popular newspaper. But anything that speeds things up safely, as this technique appears to do, will save many lives and much suffering. We hope we’ve cheered up your morning break.

#drug development #medicine #health #AI #research #mRNA vaccine

How good teaching won a Nobel Prize

For our next look at this year’s Nobels, we thought we’d showcase the three brilliant researchers who share the prize for Chemistry. For those who need to come up to speed here’s Nature Briefing’s story, Chemistry Nobel for Supersponge MOFs

Chemists Susumu Kitagawa, Richard Robson and Omar Yaghi have won the Nobel Prize in Chemistry for developing the world’s most porous solid materials, known as metal-organic frameworks (MOFs). Structured like molecular scaffolding, MOFs contain vast caverns of internal space; Nobel committee chair Heiner Linke likens them to “Hermione’s handbag in Harry Potter — it can store huge amounts of gas in a tiny volume”. In the 30 years since they were first developed, they have become part of efforts to capture carbon from the air and remove ‘forever chemicals’ from water, among many other applications.Nature | 4 min read

Now, we in no way would distract from the accomplishments of Drs Kitaga or Yaghi. But what we want to do here is tell a very human story of how the third laureate, Dr Robson, got involved in the first place.

One day he was constructing large wooden models of crystal structures for undergraduate chemistry lectures at the University of Melbourne. These models—representing structures like sodium chloride and fluorite—were made from coloured wooden balls (atoms) connected by rods (bonds), carefully drilled at precise angles using trigonometric calculations. We’ve all seen them, they are stand by of every A level and undergraduate teaching room

As Robson assembled these models, he noticed something profound: the components seemed “invested with information,” naturally predisposed to form the intended structure. This observation led him to wonder: what if molecules could behave similarly—self-assembling into predictable, extended structures using chemical bonds instead of rods? That question planted the seed for MOFs, which he began exploring seriously about a decade later.

It’s funny how learning is a holistic thing. Research informs teaching. And teaching informs research. Oddly enough artists like Leonard Bernstein and Stephen Sondheim found the same thing, if you substitute “creative writing” for research. Perhaps its the idea of responding to questions, looking at the bigger picture. Or in Robson’s case, taking time out to play creatively with models. If you have found the same, oh readers, let us know. Meanwhile tell your Government to keep funding research and universities. As we saw in the last blog- they’ll get their money back.

#chemistry #nobel prizes 2025 #metal organic frameworks #carbon capture #climate change #science #research

Nobel Prize for Economics shows this blog was right all along

Back in the dark days of January 2021, when the world economy was reeling from the savage hit of the COVID-19 pandemic, we published a short blog called How to Get some Free Money(LSS 2 1 21) Everyone at that time was worried about the colossal debts their governments had run up to pay for the catastrophe-were we all to be bankrupt for ever? Our point was that Science and Technology were the key to economic success. Encourage them. and you will grow your way out of debt. However hard a medieval peasant worked and saved he could never hope to achieve the productive levels of a man with a steam driven plough.

How comforting then, to find that better, more profound minds have demonstrated this truth at a Nobel level. By incredibly detailed studies Joel Mokyr, Phillipe Aghion and Peter Howitt [1] have looked at archives, crunched the numbers, weaved out feedback loops and carried out any number of other careful ratiocinations to prove the point. You can read more here [2] if you like graphs and words and things. But for us three things stand out.

There has to be abstract learning first. Many of the ideas and processes that drove the industrial revolution had appeared a hundred years before as the abstruse discoveries of thinkers like Newton and Hooke, which the average man in the street would have called “bonkers!”. There has to be a social ecology of skilled and trained workers, able to quickly deploy and develop the new ideas. In the eighteenth century this meant craftsmen like watchmakers and weavers. Now it means experts in AI and biotechnology. Finally a society must be open to rapid change: and welcome it where possible. For if you do not, someone will rapidly steal your markets with a new idea you could have developed but didn’t, because the old ways were tied and tested(think Kodak and digital cameras) [3]

All of which has relevance now, especially in the United States of America and the UK. In both those countries there is a growing movement to throw over renewable energy technologies and move back to coal and oil as soon as possible. We understand the fears and share some of the nostalgia for a bygone age which the proponents of this U turn so plainly demonstrate, Yet we also recognise that other countries will not. They will adapt clean green technologies rather fast. Not only will this leave the Anglo-Saxon economies hopelessly far behind. Their pollution will also make them a dangerous threat to other places in the world. Places which may seek to shut down that danger by whatever means necessary.

[1]https://www.nobelprize.org/all-nobel-prizes-2025/

[2]https://www.nobelprize.org/uploads/2025/10/advanced-economicsciencesprize2025.pdf

[3]https://www.forbes.com/sites/chunkamui/2012/01/18/how-kodak-failed/

#science #technology #growth #innovation #digital cameras #renewable energy

Round Up: Gulf Stream collapse. stem cells rule the world, and much more

an ever-so-slightly flippant look at stories from near and far:

Gulf Stream Collapse If the Atlantic currents fail, life as we know it in western Europe will be pretty much unsustainable. The very fact that this comes from the impeccably right-wing Mail shows it is not climate change zealotry https://mail.yahoo.com/d/folders/86/messages/AA5iTI1EuaNWaFvEagvLiAbCFXc?.intl=uk&.lang=en-GB&.partner=none&.src=fp

The new political landscape Believe it or not, we feel a bit sorry for all those avid class warriors of the last century (both sides) as all their efforts now seem a waste of time. The world runs on identity, not economics as the immensely learned Professor Curtice shows in the Conversation

https://theconversation.com/how-britains-new-political-divide-delivers-voters-to-reform-and-the-greens-259613?utm_medium=email&utm_campaign=Latest%20from%20The%20Conversation%2

Stem Cells #1 An eye to the future Over twenty years ago, The Most Intelligent Man Whom We Have Ever Met was predicting a rosy future for stem cells. Today’s first proof he was right comes from this marvellous new treatment for blindness in the Mail

https://www.dailymail.co.uk/sciencetech/article-14839199/Man-blinded-Fourth-July-fireworks-grows-new-eye.html

Stem Cells #2 The sweet smell of success More proof of the prescience of the this same Most Intelligent Man Whom We have Ever Met is again from the Mail(our researchers seem to read little else) with this rather nifty advance in diabetes therapies

https://www.dailymail.co.uk/sciencetech/article-14842321/Major-breakthrough-10-patients-diabetes-CURED.html

Genes back in fashion Full twenty five years ago, and more (that’s enough declamation-ed) we used to delight in boring Police Officers and other uninterested visitors how important the human genome project was going to be. Proof we were on to something comes in this intriguing article in the Guardian where scientists are trying to recreate the whole thing from scratch in a test tube

https://www.theguardian.com/science/2025/jun/26/synhg-uk-synthetic-human-genome-project-dna-genetic-code

And the music? Although never giant fans of the work of Mr David Dundas-we tend to prefer JS Bach and the Baroque lot) we cannot, in the light of the foregoing, avoid putting up his famous ditty about “waking up in the morning putting his old blue jeans on”, or something like that Jeans/genes-geddit?

https://www.bing.com/videos/riverview/relatedvideo?&q=davis+dundas+blue+jeans&&mid=9C6E36DE4376CDB2E74D9C6E36DE4376CDB2E74D&&FORM=VRDGAR

#genes #dna #diabetes #eye #blind #stem cells #climate change

Renewable energy from seaweed Now there’s a thought

If we are going to get through the current climate crisis, and come out alive at the other end, we ‘ll need to consider every new idea, however outre it may sound at first sight, Which is why we want to showcase, via the Conversation,[1] the work of Mike Allen , Professor of Genomics at the University of Exeter and founder of SeaGen,[2] a company which has the courage and vision to think differently. ]For Mike thinks that by using robotics, he can harness the enormous biomass of seaweed in the sargasso sea, and other places

Now we’ve always been pro- seaweed here. Veteran readers may recall our promotion of the new Sussex kelp forest, both on this site and in articles in local newspapers and websites [3] and we certainly talked about how the stuff, especially kelp, could be a source of all kinds of useful things like food and fertiliser. But as his article and website makes clear, Mike is taking this to a whole new level. By using autonomous robotic systems, the harvesting and processing of the weeds can be done on an ergonomic and industrial scale.

We have no financial or any other connection to this man or his company. But we are massive fans of the hopeful start-up. Because we believe that progress, real progress grows form that complicated network of new companies , university departments, government agencies and anonymous little industrial estates where the real dreams of the future are born. We’ve done stories like this before, and will do more in the future. If you really need a declaration of interest it is this: they may help us to survive.

[1]https://theconversation.com/how-seaweed-is-a-powerful-yet-surprising-climate-solution-251195?utm_medium=email&utm_campaign=Latest%20from%20The%20Conversation%20for%

[2]https://www.seagen.io/

[3]https://www.sussexgreenliving.org.uk/sussex-kelp-forest-leads-the-way-by-keir-hartley-first-published-in-west-sussex-county-times/

#seagen #seaweed #sustainability #robotics #ocean #climate change

Cortical Labs: the first working Synthetic Biological Intelligence

Far back in the last century, Arthur C Clarke drew attention to a slow but steady trend in human evolution: the gradual merging of the human body with artificial technology. Like all great things it started small, so small as to be almost unremarked. Firstly were primitive artificial legs and hands, all that could be done with the technology of the time. By the time Clarke made his prediction in the novel 2001; a Space Odyssey, the scientists of the day were experimenting with artificial hearts, lungs and kidneys. Fast forward to our own age. Not only have things like prosthetic limbs and eyes greatly improved. We are starting, tentatively, to modify the genes of living cells with early techniques like CRISPR Cas-9 (LSS passim). Elsewhere, the attempts to engineer interfaces between human tissue and silicon chips seem to be showing real possibilities of success.

But we think that the efforts of Cortical Labs to create Synthetic Biological Intelligence(SBI) takes the trend to a whole new level. [1] Their CL1 computer uses laboratory grown neurons interfacing with silicon chips to create an entity that defies old -style classifications of what is biology and what is technology. Rather than offer you 18 dreary paragraphs, we will urge you to visit their website. But if we cherry-picked that: The CL 1 far more energy-efficient than a conventional computer; that it is ideal for disease modelling. drug disorder research; that it dispenses with much of the need for animal experiments; that above all it will be available for shipment at a cost of $35000, you would see why we have chosen this item for your entertainment today. Because we honestly thought that this kind of thing was decades away. Forgive us: but we have no financial, professional, personal or any other kind of relationship with this company. We never endorse; but when we report, we mean it.

And we do indeed report developments which seem to be genuinely game changing, and truly the work of the most intelligent people at the very limits of human accomplishment. We believe that this is one of them. Which is where our doubts creep in. For Arthur C Clarke also pointed out how the very act of adopting technology (stone tools at the beginning) transformed the biology of creatures that used it. So much so that they changed into new species, quite unrecognisable to their ancestors. And absolutely dependent on the new technologies to survive, with no possibility of de-inventing them . We are not the first to suggest that some engineered organism will replace us. But we do think that possibility is now very real and very near.

thanks to G Herbert

[1]https://corticallabs.com/cl1.html

#synthetic biological intelligence #cortical labs #artificial intelligence #computers #biology #evolution