AI-designed antibiotics: more good news to report

This is getting to be a habit. About a year ago we showcased a story about the redoubtable Professor de la Fuente and his team at the University of Pennsylvania who were starting to use AI for the development of new antibiotics. (LSS 6 6 2024). Since when our optimism has been justified seven fold over and seven, to coin a phrase. For today we are genuinely excited to bring you this story from James Gallagher of the BBC which takes things up to the next stage. [1]

Because another redoubtable Professor, one James Collins and his team at MIT have now used AI not only to identify potential new antibiotics, but also to synthesise them and prepare them for testing. What’s more, they’re going to try them out on MRSA and gonorrhoea, two recalcitrant old lags which have long frustrated researchers, as our long term readers will recall

The story ticks quite a few more LSS boxes with institutions like Imperial College and the Fleming Fund getting quotes. At last, things seem to be coming together. When we started our antibiotics obsession, ten long years ago, we foresaw the current civilisation collapsing under unstoppable plagues, just like the Roman one before us did. But if it does, it may not be for lack of new antibiotics: we feel we can say that much now. Plenty of lethal threats still confront us, from Global warming to the threat of nuclear war. And the recent collapse of the talks designed to limit plastic pollution is a shameful reminder of the cognitive limits of our species..[2] But: just occasionally, something can be done about something. Maybe that’s hope , for all we know.

[1]https://www.bbc.co.uk/news/articles/cgr94xxye2lo

[2]https://www.bbc.co.uk/news/articles/cvgpddpldleo

#artificial intelligence #antibiotics #antibiotic resistance #MRSA #MIT

Bacteriophages v Bacteria: this arms race offers opportunities

We’ve always hymned the praises of bacteriophages here (LSS passim): that they will be a vital second option to supplement the next generation of antibiotic drugs. But we have a confession. We didn’t understand them. We didn’t appreciate that they are biological systems (viruses) interacting with other biological systems (bacteria). And as such, will obey all the usual rules of all such systems, such as arms races between predator and prey, Now a new article by Franklin Nobrega for the Conversation puts that right. [1]

Bacteria have evolved some fascinating defence mechanisms to ward off the relentless attacks of their phage enemies. These involve cutting the nuclear material of the viruses: building up strong cell walls and cellular shutdown mechanisms which act a bit like your IT Department does when it detects a global virus attack on your building’s systems. Recently Franklin and his team have investigated an early warning system called KIWA which gives the bacteria advanced notice that an attack is imminent. To which phages have in turn responded by their own mutations, and so it goes on, etc etc.

There’s a lot to encourage us here. Firstly, human knowledge of bacteriophages and their ways is deepening all the time, always a good thing. In fact Franklin is part of the University of Southampton phage collection project which we showcased here a few weeks ago (LSS 1 7 25) More strikingly, as two systems attack each other in an arms race, they leave little gaps, tiny vulnerabilities, which outsiders can exploit. The promise of new drugs and new bioengineering techniques looks very real indeed. Especially, we suggest if information scientists and complexity theorists are brought in to work alongside the biological teams. All in all, a rather good day for those of us interested in the problems of microbial antibiotic resistance. Go boldly, gentle readers, and be of good cheer.

[1]https://theconversation.com/how-ancient-viruses-could-help-fight-antibiotic-resistance-261970?utm_medium=email&utm_campaign=Latest%20from%20The%20Conversation%20

#microbial antibiotic resistance #bacteria #bacteriophage #health #medicine #phage collection project

If you want to know the truth about cancer, ask Liz O’Riordan

Because she’s seen it from both sides, is why. First she was a doctor, who like, worked in the field? And then because, she got it herself, right? Became a patient, and experienced all the heart stopping, roller coasting, will-I -won’t-I? chain of emotions that all her own patients did. If those aren’t qualifications enough, gentle readers, we don’t know what are. And-she has one other which seals the deal as far as we’re concerned. Read on, and you will learn what that is.

We came across Dr O’Riordan in the course of listening to a series called Marianna in Conspiracyland on BBC Radio 4 [1] Not having an especially large legal department we must be careful what we say. But the programme details the activities of the types of people who disparage reason-based science and evidence-based medicine. And instead offer a dubious range of alternative theories, explanations and prescriptions to people who are scared out of their wits by a cancer diagnosis. In the nicest possible way, the programme tried to explain the consequences of choosing these paths of treatment, And Dr O’Riordan was one of the speakers they called in their support. A little bit like the prosecution in a criminal case calling an expert witness in DNA or drugs, as t’were.

Because since her own diagnosis and treatment, Dr O’Riordan has spent her days ceaselessly writing, speaking, making media appearances, all to one end. Refuting fallacies, identifying illogicalities, reasoning with the unreasonable. In books like The Cancer Roadmap [2] she tries to explain the science behind why cancers develop and grow, what the best treatments are, and why so-called “alternative systems” don’t seem to be up to much. In this undertaking she joins a great tradition of rationalists and sceptics starting with Lucian of Samosata,[3] and stretching all the way through to people like Peter Medawar, Carl Sagan and Dr Ben Goldacre.

But she goes one step further. Because she never condemns or sneers at anyone. Instead she tries to ask why people turn from rational medicine to alternatives and faith. In other words she deploys human qualities of empathy and compassion. And we could all learn from that. For years on this blog we have bemoaned the growth of fake information, conspiracies and general rubbish which grows on the interweb like the digital equivalent of a cancer. Not just in cancer theory; in matters like global warming, politics and economics. Hasn’t done much good. Somehow, the easy, comforting answer outpaces the complicated rational one each time, and by ratios of thousands. We are in danger of becoming the last generation of enlightened, rational thinkers, perhaps for thousands of years. Time to listen to Liz and her methods. Soon.

[1]https://www.bbc.co.uk/programmes/m001mssm

[2]https://liz.oriordan.co.uk/author/

[3]https://en.wikipedia.org/wiki/Lucian

[4]https://en.wikipedia.org/wiki/Ben_Goldacre

#cancer #medicine #alternative medicine #rational #empirical #science #health

The economic costs of antibiotic resistance

Down the years we’ve tended to cover the health risks of antibiotic resistance , and the various scientific and medical developments in the field. We haven’t written so much on the economic risks. And frankly, that’s been a blind spot.

Now a very clear sighted article by Anna Bawden of the Guardian[1] makes those potential costs very clear indeed. Drawing on report from the prestigious Centre for Global Development [2] Anna serves up some chilling facts Get this:

A UK government-funded study shows that without concerted action, increased rates of antimicrobial resistance (AMR) could lead to global annual GDP losses of $1.7tn over the next quarter of a century.

Breaking it down by countries:

The research calculated the economic and health burden of antibiotic resistance for 122 countries and forecast that in that in this most pessimistic scenario, by 2050, GDP losses in China could reach just under $722bn a year, the US $295.7bn, the EU $187bn, Japan $65.7bn and the UK $58.6bn.

That alone should give the thoughtful 5% of us pause for thought. But it’s Anna’s background which makes this a great article. For it comes at a time when countries like the USA and the UK are busily cutting their overseas aid budgets. Which is shows a worrying lack of self interest on their parts. For one thing, antibiotic resistance will not be confined to poorer countries: but it is much more likely to develop in them. Secondly, being at the forefront of pioneering science can spin off the most amazing business and technological opportunities for the more astute kind of entrepreneur. And thirdly, and most acutely for their voter base: if the health system in those poor contries collapses, guess where their populations will pitch up? “Stands ter reason,dunnit, mate?” as our old friend Dave Watford is fond of stating. Thanks, Dave- you’ve got it right this time.

[1]https://www.theguardian.com/society/2025/jul/20/superbugs-could-kill-millions-more-and-cost-2tn-a-year-by-2050-models-show

[2]https://www.cgdev.org/media/forecasting-fallout-amr-economic-impacts-antimicrobial-resistance-humans

#antibiotic resistance #health #medicine #economics

Could this new mRNA vaccine end cancer?

In the UK alone cancer accounts for 24% of all deaths.[1] Which means you, gentle reader have a close to one in four chance of going that way. You might hope that someone might do something about it. Today we bring you news that somebody has, via the industrious Luke Andrews of the Daily Mail [2] But before then, a tiny apology.

Because in reporting this we have no desire to disparage the heroic efforts of scientists, doctors, fund raisers and honest-to-God patients who have already done so much to ameliorate and already effect cures for this terrible disease. Luke’s story could be a game changer-but only because it comes at the ned of an enormous process of scholarship and research. That said, it is truly exciting. Firstly, because it tries to use the new mRNA vaccines which came of age during the COVID 19 pandemic. Secondl, because it offers a hope, however tentative at this stage, of a universal vaccine. Luke explains matters really well,. with all the links you need to the source journals, so we’ll leave you to him. Upbeat to say the least.

Vaccines are a contentious subject. We have talked about cancer vaccines here before(LSS 24 5 21 et al) and are aware of the mixed reactions we get. We suspect that not all anti-vaxxers are bad people: among them you will will find the stubborn types who refuse to accept any information coming down from above on whatever subject. Grit in the wheels of the machine; but one day you just might need them. But we in what might be called the empirically based community have our uses too.(we invented the computer you’re reading this on) it’s time for a dialogue, instead of hissing and growling at each other like so many cats and dogs. The patients deserve that.

[1]https://www.cancerresearchuk.org/health-professional/cancer-statistics/mortality

[2]https://www.dailymail.co.uk/health/article-14919401/immune-hack-vaccine-mrna.html

#mRNA #cancer #vaccine #medicine #health

Conversation Article gets to the heart of why people get things wrong

You know a piece of writing is good when it explains many things, not just the ostensible subject the writer has before them. Such is the case with Edward White of the prestigious Kingston University in the UK whose article in the Conversation forms the basis for today’s blog [1] Ostensibly, the subject is Evolution. Now, we’ve always liked a bit of Evolution here. But only as abit of light relief, following it the way people follow the fortunes of Leicester City FC or the doings of celebrities.

Not so in the United states of America where the subject is of neuralgic importance as Edward points out. Huge numbers of the citizens of that country still hold that God created Man exactly according to the schemata laid out the in the early chapters of Genesis in the Hebrew Bible. And he has a barrage of statistics to explain how and why. But the point for us, gentle readers is why these people think as they do. For it explains a much wider truth, which is: no species as so supremely adapted to self delusion and to believing the lies, deceits and threats of charlatans as is Homo sapiens. And this is true in all fields-politics, religion, economics, even science and medicine(remember the MMR controversy?) The fault according to Edward is motivated Reasoning, where you start with a conclusion and work back to justify it. This ensures a high chance of error, whatever cognitive powers you may possess, as astute readers will have spotted. Why do people do this? Get this killer quote from Ed:

Brain imaging studies show that people with fundamentalist beliefs seem to have reduced activity in the dorsolateral prefrontal cortex — the brain region responsible for cognitive flexibility and analytical thinking. When this area is damaged or less active, people become more prone to accepting claims without sufficient evidence and show increased resistance to changing their beliefs when presented with contradictory information. Studies of brain-injured patients show damage to prefrontal networks that normally help us question information may lead to increased fundamentalist beliefs and reduced scepticism.

As Edward concludes: for most people learning is about who gets to define truth, and own the power that flows from it thereby

And our conclusion? We seem to be drilling down to the bedrock at last and knowing why people make and hold errors, From here at last the Progressive Community may find a way forward

[1]https://theconversation.com/why-many-americans-still-think-darwin-was-wrong-yet-the-british-dont-260709?utm_medium=email&utm_campaign=Latest%20from%20The%20Conversa

More on the deadly dangers of stress (sorry, but you need to know this)

Photo by Michael Willinger on Pexels.com

A few decades ago, a friend remarked how his brother had left a stable happy marriage for a much younger woman at work. It didn’t last long- the man in question died a few years later of Crohn’s disease. The new relationship didn’t turn out very happily, as I learned from passing gossip. “Going over the side” they used to call it, back in the day. It seemed unremarkable enough -until a few years later a work acquaintance of about the same age and circumstances suffered a similar fate. Raising the question: was the knowledge of the awful decisions they had both made eating away inside, burning with stress, until their poor immune systems broke down altogether? This was the start of a trope we have followed ever since. We have alluded to it several times on these pages(LSS 2210 24; 23 8 20} to name but a few. Now we are glad to see our concerns addressed by altogether more weighty and learned persons (surely not?-ed)

For Nature and its brilliant Briefing arm have put the matter at the forefront of their latest editions Read this, Time to Take Stress seriously, if you don’t believe us:

When George Slavich’s father died suddenly, the clinical psychologist was well aware of how the stress could affect his health, but his health-care providers weren’t as interested. “The experience highlighted a paradox between what I know stress is doing to the brain and body, and how little attention it gets in clinical care,” says Slavich. He is among the researchers investigating how the body reacts to stress and how it contributes to deadly diseases.Nature | 11 min read

You see George isn’t any old George. He is a clinical psychologist at UCLA, no less. And he has launched a project with many other eminent scholars to research the link between stress and many disorders that plague us all, from heart and respiratory disorders to all kinds of psychological and psychiatric ones. Is there good stress? Is there bad? What causes each, and how to cure them? All these questions are now front and centre of George’s research. You can read more here[1] and here[2]

For the last fifty years or so, the whole psychological imperative has been to make people work ever faster for longer for ever lower wages. it is supposed to make us all more prosperous and happy, or something. What if it is doing the opposite?

[1]https://www.nature.com/articles/d41586-025-02066-z?utm_source=Live+Audience&utm_campaign=5e2c1eb595-nature-briefing-daily-20250708&utm_medium=email&utm_term=0_-33f35e09ea-

[2]https://www.frontiersin.org/journals/psychology/articles/10.3389/fpsyg.2024.1471084/full

#immune system #stress #coronary disease #psychology #chronic illness #overwork #health

Weekly Round up: Air Pollution, Gene therapy and raspberries

Air pollution is the new smoking Stopping smoking has led to massive falls in rates of lung cancer. But this fearsome disease is still lurking out there. The current cause? Air pollution ,as Ian Sample explains for the Guardian

https://www.theguardian.com/science/2025/jul/02/air-pollution-lung-cancer-dna-mutations-study

Gene therapy chalks up another win Ok,today it’s one particular form of deafness, attributable to one particular gene, as Maoli Duan explains for the Conversation. But: the more science you do the more you learn. Meaning other disabilities may one day prove susceptible as well. And the more you spend on scientific research the more you get benefits like this. A lesson rapidly being forgotten in the United States of America

https://theconversation.com/gene-therapy-restores-hearing-in-toddlers-and-teenagers-born-with-congenital-deafness-new-research-258112?utm_medium

Machines that out think humans It’s the scary nightmare of science fiction films from Blade Runner to the Terminator series. Up until recently the idea still seemed to be fiction. All that may be about to change as Nature Briefing reports

An artificial-intelligence system called Centaur can predict the decisions people will make in a wide variety of situations — often outperforming classical theories used in psychology to describe human choices. Trained on data from 160 psychology experiments in which 60,000 people made more than 10 million choices, the system can simulate human behaviour in tasks from problem-solving and gambling, and even those it hasn’t been trained on. Using Centaur, “you can basically run experimental sessions in silico instead of running them on actual human participants”, says cognitive scientist and study co-author Marcel Binz.

Nature | 4 min read
Reference: Nature paper

Friday Night Feast Raspberries and Ice cream We are not all gloom and serious stuff here. Thinking it was time for a quick Friday Fun feature, we realised that we’d done strawberries several times (LSS passim), In which case the humble raspberry can make a really pleasant alternative, especially if combined with ice cream instead of cream. After all, even if we are on a diet-you, gentle reader may not be. So- eat a bowl for us we used to love it.

#cancer #AI ~pollution #gene therapy #raspberries

Paracetamol from Plastic Bottles-this could be the start of something big

Remember how your mum always made you swallow water to wash down your headache pills? What if those pills had been made from the remains of a long discarded plastic bottle that some other child had been forced to undergo? According to the resourceful Nicola Davis of the Guardian, it’s about to happen.[1] And the implications are enormous.

A team lead by Professor Stephen Wallace of the University of Edinburgh has actually gone and turned old plastic bottles into medicine. Combining the very best in organic chemistry and genetic engineering, they have modified a strain of E. coli to make good old paracetamol, that standby of every household drugs stash the world over. [2] The details of how they do it may be read in the links supplied. But our interest today is somewhat different.

At last someone has found a use for all those mountains of ghastly plastic waste which so disfigure this once beautiful planet. It can be made into something which millions, no billions, of people can deploy every day: and to some beneficent purpose. And if paracetamol, why not other things? Meanwhile. fans of economics will note the creation of a demand., Soon people may be fighting each other in the streets to get the best plastic bottles to sell to wholesalers. Nations will go to war to gain access to those vast disgusting rafts of waste which currently drift around the oceans. There’s one sure way to modify the behaviour of the ignorant mass of humankind- Turn virtue into economics and let them make some money from it. The Professor and his team may have done just that.

[1]https://www.theguardian.com/science/2025/jun/23/scientists-use-e-coli-bacteria-to-turn-plastic-waste-into-paracetamol-painkiller

[2]https://www.nature.com/articles/s41557-025-01845-5

#genetic engineering #organic chemistry #plastic #pollution #medicine

This is what awesome intelligence looks like

No we’re not writing about ourselves as some hardened readers may have already guessed. Because we couldn’t achieve what the researchers in these two stories, both from Nature Briefing, have indeed achieved. Sorry guv- we don’t have their intellectual bandwidth . Cognitive intricacy. Brains, in good old fashioned English But we know intelligence when we see it, and we know you do too.

Algorithms design remarkable enzymes Researchers have used computer algorithms to design highly efficient synthetic enzymes from scratch, reducing the number of tedious hands-on experiments needed to perfect them. The products facilitate a chemical reaction that no known natural protein can, with an efficiency similar to that typically achieved by naturally occurring enzymes. One design was also 100 times more efficient than similar enzymes previously crafted using artificial intelligence. In comparison to enzymes that occur in nature, the algorithm’s creations are less complex and can’t grapple with multi-step chemical reactions, but they’re proof that the approach has promise.Nature | 4 min read
Reference: Nature paper

The medical potential of designer enzymes will not be lost on readers as intelligent as our own. Yet some discoveries are to be relished not for their use, but for what they tell us about the world and our real place in it Try this for size

Dragon Man was a Denisovan Ancient proteins and mitochondrial DNA extracted from the ‘Dragon Man’ fossil — a cranium found in northeastern China that is at least 146,000 years old — have confirmed that it belonged to a Denisovan, an archaic human group. The fossil is the first skull to be definitively linked to the group, which sheds light on what the ancient people looked like, putting an end to decade-long speculation.Nature | 5 min read
Reference: Cell paper & Science paper

Learning. Reason. Curiosity. Handy, aren’t they? Their absence can lead to different outcomes indeed. As the inhabitants of certain regions of the globe know only too well.

#protein #mRNA #medicine #health #evolution