Two good news blogs:#1 AI designer phages against antibiotic resistance

Its not often we bring you unabashed good news, gentle readers. Nor moreover, blow our own trumpet. But the following from Nature Briefing AI Helps design E. coli killing viruses not only unites so many of the themes we push here-(AI molecular design, multidisciplinary studies, bacteriophages etc etc)-that we think that the advance it represents it makes this one of our more significant blogs in months.

Using artificial intelligence (AI), researchers have designed novel viruses capable of killing strains of Escherichia coli. The team used the DNA of a simple bacteriophage called ΦX174 to guide AI models to generate viral genomes with the specific function of infecting antibiotic-resistant strains of E. coli. Researchers used the model’s suggested sequences to select 302 viable phages. When put to the test, 16 of these phages could infect E. coli, and combinations of them could kill three strains of the bacterium, a feat the original ΦX174 couldn’t pull off.Nature | 5 min read
Reference: bioRxiv preprint (not peer reviewed)

its certainly worth clicking on the Nature article and even the Preprint, which has a surprisingly well written summary

Old hands to this blog will recall our long standing worries about this organism. Normally Escherichia coli (named after the ingenious Dr Theodor Escherich) is a fine upstanding member of the microbiological community, being common in nature and a doyenne of experimental departments in microbiological schools. But certain strains of it are developing a profound resistance to our best antibiotics including piperacillin/tazobactam combinations. Which could have made it a very False Friend indeed. But now it seems that Dr King and his team have got ahead of the game.

Note the careful language, full admissions that peer review awaits, and generally understated claims that mark the true signs of trustworthy scholarship. How different from some situations where leaders of great nations go before the cameras and make huge unsubstantiated claims about phenomena of which they have no certain knowledge, But when you choose to believe only what you want to believe, fate has a nasty way of catching up eventually. Wait for the next blog and we’ll tell you more .

#E.coli #bacteriophages #AI #designer biochemistry #antibiotic resistance #microbiology #medicine #health

Why Net Zero threatens a wonderful land-that was

Kingston on Thames, Surrey, England. Spring 1962. A brand new Ford Zodiac pushes out from a brand-new house on a brand-new estate to begin a Sunday outing down to the south coast. Mum, Dad and their two kids on the back seat pass rows of new houses, all like theirs, all lived in by people like them. With cars like theirs at the fronts. This is Macmillan’s England, and people have never had it so good. Even, for the first time, the working classes. As the last new estates around Chessington drop behind and the real country begins at Box Hill, someone puts on the car radio. Listen! It’s the Shadows Wonderful Land,: and here, today, its dreamy tones are true. For as they head south on the A24 (soon to be massively widened) the temples of all this wonderful modernity are still visible in the brave new petrol stations and car showrooms sprouting across the sleepy countryside. The car has made people profoundly mobile and independent. People talk about them endlessly. Buy them, sell them Discuss performance. Your car is a badge of who you are, where you have arrived at, especially if you are a man. As our travellers pull into Worthing for a welcome ice cream they have indeed crossed a wonderful land.

This is the brave new world still remembered as the base line by the two children in the back of the Zodiac. Fast forward 2025 and they are well into their seventh decade. But they still remember the promise of those years with aching nostalgia. Their own lives, minus the usual vicissitudes of marital, family and work problems, have been tolerable enough: prosperous even, as their waistlines testify. But outside the narrow world of work and golf club, there have been disturbing changes. First crack in the wall came with the 1973 oil crisis, which demonstrated their country’s humiliating dependence on foreign oil. Tax cuts and North Sea Oil brought a brief sugar rush of prosperity: but now the world is a dark distrustful place hopelessly split between rich and poor where nothing ever works and everything is broken, from roads to trains to hospitals. Foreigners just keep coming and coming and coming. Above all the USA, their great patron and guarantor of all their security, is rapidly losing its ability to prosper and protect.

Now add something worse. All those grandchildren they sent off to University have come home to tell them that everything they believed in was wrong. That burning oil warms the planet to disastrous levels. [1] That vehicle emissions are a massive cause of mental and physical health disorders.[2] So are the plastics made from oils in abundance , which now pollute every imaginable stretch of sea air and land.[3] That, therefore, the whole cult of buying cars, comparing them, fiddling with them and collecting them turns out to have been as deluded as say smoking tobacco ,drinking alcohol or keeping slaves. That in effect, their whole lives have been a bit of a mistake That they now, with so little time left to enjoy , must give it all up.

It’s a big ask. Especially when incredibly rich industries run incredibly well funded political and media campaigns to tell these same baby boomers that they not only can go on burning fossil fuels, they really ought to- must. Because only that way lies the road to a better yesterday when the world was young. And straight. And white. Here is the challenge facing all of us who call ourselves progressive or educated . We have no idea if we shall succeed We know we will need swimming lessons if we do not,

[1] Burning of fossil fuels – Understanding Global Change

[2] Air pollution and health risks due to vehicle traffic – PMC

[3] 5 Harmful Effects of Plastic on Human Health

(See also LSS 9 4 24;26 9 24; 20 9 25)

https://www.bing.com/videos/riverview/relatedvideo?&q=the+shadows+wonderful+land&&mid=E99EB6B5B2B6CEBD22FBE99EB6B5B2B6CEBD22FB&&FORM=VRDGAR

Hidden Dangers: The Conversation on PFCs

Photo by u041bu044eu0441u0438 u0414u0440u0435u043cu0430u043bu043eu0432 on Pexels.com

Today we unashamedly and wholeheartedly turn over our blog to a straight lift from The Conversation. And an excellent article from Professor Patrick Byrne of Liverpool John Moore University. Who has devoted his life’s work and formidable intelligence to tracking the sources of PFCs in the River Mersey (the one the Beatles grew up near)[1]

For those who want to come up to speed here are two paragraphs from Patrick’s article

Per- and polyfluoroalkyl substances (PFAS), more commonly known as “forever chemicals”, are a large family of human-made chemicals found in everyday products like food packaging, water-repellent clothes and fire-fighting foams. They are valued for their ability to resist very high temperatures and to repel water and oil, but these same properties make them extremely persistent.

Once released, some PFAS could take thousands of years to break down. They accumulate in the environment, build up – with different compounds accumulating at different rates – inside the bodies of wildlife and people, and have been associated with harms to health. The most studied types have been linked to cancers, hormone disruption and immune system problems.

And one elegaic, personal thought.Back in the 1960s when those same Beatles were growing up, the world was a different place. All those plastics and chemicals, now in Patrick’s rubbish dumps seemed part of a bright, dynamic new landscape of progress: a brave new world. There can indeed be progress, But be very careful how you go about it

https://theconversation.com/how-i-tracked-the-biggest-hidden-sources-of-forever-chemical-pollution-in-uk-rivers-new-study-261967?utm_medium=email&

#plastics #endocrine disruptors # PFCs #pollution #environment #toxins

More on undiscovered antibiotics in Nature

Photo by Irina Babina Nature and Wildlife on Pexels.com

A few years ago we published a couple of blogs suggesting that the saliva of Komodo dragons (Varanus komodoensis) might be a possible place to look for new sources of antibiotic compounds. (LSS 27 10 20; 6 9 21) Poor dragons! It now seems that their tantalising resistance to infection may be due to other factors than miraculous antimicrobial molecules. But at least it got us thinking: might there yet be some useful aids to our antibiotic quest lurking out there, undiscovered?

The antimicrobial potential of some plants is quite well known. Garlic(Allium Sativum) turmeric Curcuma longa)and the tea tree(Malaleuca alternifolia) are classic examples. Best estimates suggest there are between 250 000 and 500 000 species of plant on out planet. Provided not too many are destroyed to make way for shopping malls, there may be hope of some more undiscovered potential among our leafy friends. [1] Turning to animals, our first candidate is the Matablele Ant (Megaponera analis) They not only produce antibiotics from their metapleural glands,(what they?-ed) but they also diagnose infected wounds in their nestmates and apply targeted treatment. Their secretions contain over 50 antimicrobial compounds, some effective against Pseudomonas aeruginosa, a notorious human pathogen When Matabele ants are wounded, their cuticular hydrocarbon profile changes, signalling infection. Nestmates detect this and apply antibiotic secretions from their thoracic glands. This is the first known example of non-human creatures performing sophisticated medical wound care [2]. Other animals such as frogs, insects, and marine life produce antimicrobial peptides (AMPs) as part of their innate immunity. These AMPs are being studied for their ability to combat resistant bacteria. And, if we were betting men, we might take a small punt on Sarcotoxin 1A and anti microbial peptide found in the saliva of flesh flies belonging, unsurprisingly, to the genus Sarcophaga [3]

Educated readers will recall how Alice met a Cheshire Cat in a wood. After imparting some words of wisdom, it vanished. But its smile remained. [4] So with our LSS dragon: it may be gone, but the smile of hope which it gave us lingers on.

[1] Plant Products as Antimicrobial Agents – PMC

[2] Ants produce life-saving antibiotics for treating infected wounds

[3] https://en.wikipedia.org/wiki/Sarcotoxin#:~:text=The%20proteins%20are%20present%20in

[4] Lewis Carroll Alice in Wonderland Chapter 6

#antibiotic molecules #ecology #habitat destruction #health #medicine #microbiology #tea tree #sarcotoxin

Mirror Organisms: the ultimate bioweapon?

Anyone who got beyond basic school science will recall the frustrating new level of complexity when the teacher first told you about stereoisometry. You recall-all biomolecules starting with the slightly complicated upwards really have two identical forms, left hand and right hand. Amino acids, proteins you name it. And life can only work with one. All amino acids in living things on this planet have left handed amino acids and right handed sugars. Of course living systems could work the other way round, It just has happened yet on this planet. Until now. Read this Debate heats up over mirror life from Nature Briefing

At a meeting this week in the United Kingdom, scientists are deliberating whether to restrict research that could eventually enable ‘mirror life’ — synthetic cells built from molecules that are mirror images of those found in the natural world. “Pretty much everybody agrees” that mirror-image cells would be “a bad thing”, says synthetic biologist John Glass. Such a cell might proliferate uncontrollably in the body or spread unchecked through the environment, because the body’s enzymes and immune system might not as readily recognize right-handed amino acids or left-handed DNA. But there are disagreements about where to set limits on research — the ability to evade degradation could also make such molecules useful as therapeutic drugs.Nature | 7 min read
Read more: Life scientist Ting Zhu, whose work explores various mirror-image molecular processes, considers how to bridge divergent views on such research. (Nature | 11 min read)

Unfortunately its the down size that worries us here, Not only the uncontrolled spread alluded to by the learned scientists above. But, as the world falls into the grip of authoritarian dictators and ever more powerful plutocrats, the potential these tools give them to get rid of surplus and redundant sections of humanity. Forever.

#isomers #biochemistry #bioweapons

If all the wealth in the world were shared out, what would happen?

Many decades ago, we often used to hear the argument “if all the money in the country were shared out, everyone would only get 20p” A tiny sum, which could not make any difference to daily life. This was the UK in 1973, Perhaps it was true then, there. Is it true of the world as a whole today?

The statement itself is a cognitive howler: because it equates wealth with money, carefully avoiding the inclusion of all the goods, capital infrastructure(IT systems, railways, etc.) and productive resources such as factories that make up the wealth of the world, which is best expressed as GDP. When we set out to find what that was, the best estimate was from the World Bank,[1] who put it at $105 trillion in 2023. Now, the population of the world is around 8 billion (8×10⁹) people. What would happen if we found a way to share that GDP among all of them? The answer is: everyone ends up with an an income of $13 125 a year. Which surprised us greatly. Instead of being insignificant, its actually quite a lot. Let us explain why.

That same world bank defines four categories of national income by GDP. Low: $1 135 or less. Lower Middle: $1 136-$4 465. Upper Middle: $4 466- $13 845. High: $13 846 and anything above. There is enough wealth in the world to raise everyone almost to the level of high income countries, certainly to the very top of the middle range.

Now there may be very good reasons why this cannot be done. Some are practical. Some are moral. But if it were done, what difference might it make to such issues as mass migration, educational attainment, and the overall level of demand in the world economy? Let alone health, security and basic nutrition. Just a thought.

[1]https://ourworldindata.org/grapher/gdp-worldbank

#wealth #GDP per capita #economics #inequality #migration #health #geography #economics

The Best time to be alive: The University of Paris in the Middle Ages

Paris. Everyone knows what that word means, even though most people have never been there. Style. Sophistication. Fashion. Learning. Power. Money. A place to be, a box that must be ticked. How did one more city in northern Europe get ahead of all its peers? What is the secret of Brand Paris?

We think the answer lies in the foundation of the University of Paris. Starting as an adjunct to the Cathedral school before 1100, it gradually expanded into a powerhouse of teaching which began to attract the best minds from all over the world. It drew the patronage of magnates such as King Phillipe Augustus and Pope Innocent 111, who recognised the value of cultural capital and soft power. While the roll call of alumni from the earliest time to the present includes such names as Peter Abelard, St Francis Xavier, John Calvin, Marie Curie, Louis de Broglie, Emmanuelle Charpentier, Simone de Beauvoir and Yann Le Cun. This was where it was at, to coin a phrase: and the network of hotels cafes, art studios, bookshops and spin-off enterprises simply grew around in a multiplying effect that would gladden the heart of any fan of Keynesian economics. (For the curious the Sorbonne started as one college of the University, but expanded so much that its name became metanymic for the whole thing)

It was one of the earliest Universities in Europe, and even today its successor institutions remain among the best. But if you had been a student there, perhaps of Abelard, you would have known yourself at the start of something big, new and world changing, that was going to last the ages. But let’s close when our own original thought When they set it up, the costs must have seemed rather large, the incomings rather small. No doubt the same argument was advanced against the Pyramids in Egypt or the monuments in Rome. But they have paid for themselves over and over again in tourist revenue alone ever since. As its greatest alumnus of all, St Thomas Aquinas said

“Sicut enim maius est illuminare quam lucere solum, ita maius est contemplata aliis tradere quam solum contemplari.”

“Just as it is better to illuminate than merely to shine, so it is better to pass on what one has contemplated than merely to contemplate.”

And we agree.

#france #middle ages #university of paris# #sorbonne #philosophy #learning

LSS at 5:A blog of all our blogs

It’s funny, we’ve been doing this blog for more than five years now. And in response to growing numbers of readers and requests, we thought it might be time to provide a round up, not of the week, but of our whole outpourings which might be interesting to those who seem to have been trawling avidly through our archives of late.

It all started back in 2020, around the time of the great COVID-19 epidemic. Our initial aim was to raise awareness of the problem of antibiotic resistance in microbes, and the health dangers that posed. The idea was a short three paragraph hit the sort of thing that informed readers could take in over a quick coffee, while giving them a few links and references if they wanted to follow up. Just to keep it interesting, we started throwing in other topics on other areas of science. And these widened to include economics, social issues like women’s safety, and of course our regular Friday cocktail night, which certain readers still recall fondly.

Antibiotics and associated matters have remained well represented. We have looked for untapped sources in nature, even including the unlikely Komodo Dragon( LSS 3 5 21) the evolutionary arms race between bacteria and antibiotics which humans have been forced to join(LSS 8 6 23) and all sorts of new discoveries and techniques including AI (LSS 6 6 24) Being who we are, and untied to the constraints of any institution, we were quick to suggest that bacteriophages might be a useful adjunct to the general theme of overcoming resistant bacteria(LSS 17 3 22, 10 9 25 et al) Ever mindful that lack of antibiotics might not be the only catastrophe waiting we have provided handy little guides to what might happen if the magnetic poles flip, sea levels rise and even more endocrine disruptors are poured out from our factories. Other scientific tropes like evolution get a look in too. We enjoyed posing you a few puzzles on things like Homo naledi (LSS 4 4 21) the tools of Socotra (LSS 17 6 22) and even the possibility of Denisovan Fine Art( LSS 9 8 23) But these last were mainly for entertainment.

Our general theme has, we think been broad but consistent. The scientific method, of gathering objective evidence and analysing it by the rules of logic are the most reliable manner to fashion a passingly decent way of life. To this end you will have noticed is praise all kinds of people from journalists like Larry Elliott and Simon Kuper to more general thinkers like John Rawls, EO Wilson and Carl Sagan. We have tried to keep away from obvious stars like Darwin, Einstein, Bach, Keynes and the others as these thinkers speak for themselves. Instead we have tried to put forward slightly overlooked figures such as Ada Lovelace, Peter Ramus or Cassiodorus. Our Heroes of Learning feature is the place to look for those.

But above all we thank you, our readers, contributors and researchers for all their good companionship. All those who posts likes, shares and comments-it shows someone out there is interested. We wish all of you well with your various blogs, careers, lives and families. As Gore Vidal observed , it is the top one or two percent who carry knowledge through and pass it from generation to generation. And you are in it.

#antibiotic resistance #bacteriophages #environment #pollution #economics #history #evolution #science #reason #cocktails

Life on Mars? Some of us have been here before

News that the latest findings from the Mars Perseverance mission may have detected the best evidence yet of life on our neighbouring planet should provide a flurry of media attention in the next few days. it’s always good for disinterested science to get a little coverage. And we take our hats firmly off to the ingenious scientists, technicians and engineers who set up these missions and study their results with such assiduity. That said, dare we inject just a tiny note of caution into these heady proceedings? We think it’s what our readers have come to expect.

First to the results themselves, Which we admit are intriguing {1] Writing in The Conversation, Sean McMahon not only gives us a really clear exposition, he has ample links to the papers you’ll need if you wish to go further. Essentially, while exploring the Cheyava Falls region of Mars, Perseverance has found strong evidence of redox reactions, the very essence of life itself. What’s more the nature of the rocks and the visual clues, a scatter of pale spots associated with organic matter, strongly resemble similar patterns created by certain living processes here on earth. Slam dunk, get out the old David Bowie records? We would still urge caution.

Firstly because we,ve been here before. Twice actually. Older readers will recall the excitement generated by the Viking missions in 1976. [2] Two of the on board detectors, the Labelled Release and the Pyrolitic Release reported positive. However the crucial GCMS did not. And despite heroic efforts to reinterpret this data, such as the ones involving perchlorates, the Viking results must remain inconclusive in any rational. evidence based system of thought. Then there was the famous Allan Hills 84001 meteorite in 1996, which contained intriguing visual and chemical hints of microorganisms. Once again other explanations were possible. And the general consensus was the scientific equivalent of a hung jury. Quite right too, we think

And secondly because final proof will not be known until NASA and the ESA can whack up the ginger and the money for a Mars Sample Return mission. Which so far hasn’t really got beyond the talked-about stage. So Perseverance sits on Mars containing 30 tubes ready for collection, including the enigmatic Cheyvara Falls samples. Back on earth people speculate, bicker and wonder when the next war will begin. Until something happens to break this impasse, we say-don’t get out ahead of your data.

[1]https://theconversation.com/signs-of-ancient-life-may-have-been-found-in-martian-rock-new-study-264960?utm_medium=email&utm_campaign=Latest%20from%20The%20Conversation%20fo

[2] https://en.wikipedia.org/wiki/Viking_program

[3]https://en.wikipedia.org/wiki/Allan_Hills_84001

#mars #astrobiology #microorganisms #evolution #life #NASA #ESA #perseverence

Bacteriophages saved the life of this woman with cystic fibrosis

In 2023 Irene Nevado lay in hospital with little hope of anything much. She had been born with Cystic fibrosis. At he age of 8 she had contracted a persistent infection of Pseudomonas aeruginosa, which had filled her lungs with fluid, making them unusable. The bacterium was antibiotic resistant. And from that day on her life was filled with misery. All sorts of things were tried,: drugs, different antibiotics, even a lung transplant All to no avail. By 2023 she had come to the end of her road.

At this point Biologist Pilar Domingo-Calap enters the story( as told by the brilliant Nuño Domínguez of El País. For Pilar is an expert in phage therapy. She had been working closely with a team at the Centre for phage therapy at Yale in the USA. Together they had evolved a bacteriophage designed to attack and destroy exactly the strain of Pseudomonas which was plaguing Irene. They put her under ten days of treatment. The result? She now walks talks and leads as busy a normal active life as any human could wish for. She even does 4000m swims to raise money for cystic fibrosis charities. Bacteriophages saved the day.

We’ve often sang their praises here. And Nuño’s article is a brilliant summary of the current state of play, with lots of juicy links to big players, latest developments and so on. A go to for any one interested, although if you don’t speak Spanish you will need your AI translator. All in all it confirms the line we have always taken. Bacteriophage therapy is going to be a vital second method if we are to overcome antibiotic resistant microorganisms. Will you, dear readers, permit us a modest instant of self-congratulation?

[1]https://elpais.com/ciencia/2025-09-10/los-fagos-salvan-a-irene-que-recibio-y-rechazo-cuatro-pulmones-trasplantados.html

#bacteriophages #antibiotic resistant microorganisms #medicine #health #cystic fibrosis