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

Heroes of Learning: Steven Rose (and why things are never simple)

No book ever tore through the calm assurances of progress through co-operation like Richard Dawkins’ The Selfish Gene. [1] It wasn’t so much the book itself. That was an attempt to popularise, albeit sometimes in colourful language, the discoveries of an important group of evolutionary theorists such as William Hamilton and EO Wilson. It was the use made of it by political activists, zealous propagandists of the Free Market, to prove that every attempt at co operation, collective action and sharing resources was against the basic laws of nature. “Out upon your Trades Unions, your Keynesian economics” they thundered in a thousand articles in places like the Daily Mail “we are nothing but animals. Your only purpose is to pass on your DNA to make copies of yourself. Look at them lions. mate! When one of them takes over a pride he kills all the cubs and mates wiv the females to make sure his genes get frough! Go and do like wise!” It was not an experiment we felt disposed to try. Compete, for the other fellow is your genetic enemy was their credo. All barriers to that competition were both evil and deluded.

It was simple, it was seductive, it was based on some facts. It played well in the broken restless zeitgeist of the 1970s when the pillars of the old prosperity- high taxes, demand management for the common good, collective institutions like the IMF and UN seemed ineffective. It sold by the million; and swept ever more voters into the booths for one Margaret Thatcher in 1979, whose own simplistic and reductionist nostrums seemed to chime so well with those of the book.

One man did not buy. His name was Steven Rose, a remarkably accomplished scientist who spent most of his work in neurobiology and biochemistry [2] This obituary summarises his work better than us. But it was his insistence on complexity and the irreducible flexibility of the human mind, that still allowed hope for a way out from the genetic prison in to which we had been so neatly incarcerated

He wrote: “It is in the nature of living systems to be radically indeterminate, to continually construct their – our – own futures, albeit in circumstances not of our own choosing.”

Look at that carefully, then leap with us to another part of the scientific forest. Where the BBC showcases a new technique to rid the world of the scourge of inherited mitochondrial disorders [3] Basically you take a fertilised ovum from a normal male-female coupling, but put it as the nucleus in the egg of a different female. Which then develops as a normal embryo until nine months later a healthy baby emerges[3] A three parent child? Sort of. Two parents get to pass on their DNA, no doubt to the blissful delight of Dawkins’ more extreme followers. And a different mother sends her mitochondrial DNA cascading down the ages, which rather complicates matters for some. Now look at the Rose quote again what was that about continually constructing?

At the time of the great Dawkins controversy the old BBC Horizon programme ran a show in which the quoted one of the wiser and more humane scholars in the Selfish Gene camp. His name was John Maynard Smith. And he ended with this thought “humans are not just animals- we are not prisoners of simple genetics” At the time it seemed a forlorn hope. It has just been proved triumphantly real.

[1]https://en.wikipedia.org/wiki/The_Selfish_Gene

[2]https://www.theguardian.com/science/2025/jul/10/steven-rose-obituary

[3]https://www.bbc.co.uk/news/articles/cn8179z199vo

#richard dawkins #sociobiology #biochemistry #medicine #DNA #mitochondria

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

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

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

Faecal Pellets: Watch the good bacteria chase out the bad

Imagine you get bad news: antibiotic resistant bacteria have set up a colony in your intestine. OK here’s some worse: they could escape and invade your blood, kidneys, whatever. In which case you have real problems. This is a very real scenario which that brilliant researcher Dr Blair Merrick of Guys and St Thomas Hospital has sought to address. [1] as reported by James Gallagher of the BBC Why not, he has reasoned, get some good non resistant bacteria to chase out all those bad ones? It is his chosen method which may raise more than one eyebrow among you, gentle readers

According to Dr Merrick, the way to get the good bacteria into his subjects is via pills made of…..well, made of faecal matter, you know,,,poo. To quote James:

Dr Merrick says there are “really promising signals” that poo pills could help tackle the rising scourge of superbugs and that donor bacteria could be going to microbial war with the superbugs as they compete over food and space on the lining of the gut and either rid the body of them completely or “reduce them down to a level that doesn’t cause problems”.

We like this for all sorts of reasons. Firstly the gut really is such a good harbour of antibiotic resistant bacteria. Secondly, as in all things ecological, making its flora more diverse can only be a good thing. Thirdly, we think it has a clever little principle behind it. Antibiotic resistant bacteria have devoted a tiny bit more of their genome to this purpose than non resistant ones. In the world of ecological competition, where tiny differences can make an enormous difference to long term survival, this could be crucial. If done correctly, the good non resistant ones should out compete the bad ones.

It’s early days yet, and the early trials have only been on 41 subjects But as seasoned veterans of the long wars of antibiotics will know, we at LSS welcome every initiative, however unusual it may at first seem. We wish every success to Dr Merrick and his team and hope that their early accomplishments continue in the bigger trials to come,

_{thanks to Ms G lynch}

[1]https://www.bbc.co.uk/news/articles/clyge290l4xo

#gut #microbiome #antibiotic resistant bacteria #health #medicine

AIDS breakthrough shows what science can do

We now live in an age when science (and the rational habits of mind it depends upon) is under attack. Heirs to the rational tradition have always had to live with religious fundamentalists who deny inconvenient truths like evolution. But nowadays attacks come thick and fast from those who wish to deny climate change, the dangers of smoking, the efficacy of vaccines and much besides. From people who nevertheless cheerfully accept other scientific findings which suit them. So, just to redress the balance we thought we’d showcase this breathtaking new advance in AIDS research which, for the first time, holds out the hope of a permanent cure.

It comes from Kat Lay of the Guardian,[1] reporting the work of the Peter Doherty Institute in Australia.[2] The background will be familiar: the great evolutionary survival trick of the HIV was to bury itself deep in certain white blood cells of the immune system, where it was immune to our attack. In the words of Kat:

In a paper published in Nature Communications, the researchers have shown for the first time that mRNA can be delivered into the cells where HIV is hiding, by encasing it in a tiny, specially formulated fat bubble. The mRNA then instructs the cells to reveal the virus. First AIDS was a death sentence: then it could be slowed with drugs. Now at last comes hope of a real cure for its 40 million or so sufferers

Science itself is a process, not a monolithic entity. It evolves, refines, and corrects itself over time. But when people selectively accept only the parts that align with their worldview, they undermine the very foundation of rational inquiry This kind of cherry-picking often stems from cognitive biases, ideological commitments, or economic incentives. Climate change denial, for example, is frequently tied to political or financial interests, while opposition to vaccines or smoking regulations can be fuelled by misinformation or personal convenience. But the deniers should remember one thing: if they do decide to overthrow the rationalists, will they put anything better in our place?

Truth is compared in Scripture to a streaming fountain; if her waters flow not in a perpetual progression, they sicken into a muddy pool of conformity and tradition.”

Milton: Areopagitica

[1]https://www.theguardian.com/global-development/2025/jun/05/breakthrough-in-search-for-hiv-cure-leaves-researchers-overwhelmed?CMP=Share_AndroidApp_Other

[2]https://www.doherty.edu.au/

#HIV #AIDS #disease #mRNA #medicine #science #climate change #smoking

Genetics: a whole new perspective on human evolution?

Every so often it pays to look at the same problem from a completely different perspective. For the past 57 years or so we have been collecting and grading reports of human fossil bones and old tools the way that cricket fans collect the records of every game their team has played. But today, with the help of one or two of our redoubtable AI chums, we present a whole new perspective on the old story. Much of it is locked in our genes and has been uncovered by the amazingly intelligent efforts of genetics researchers.

Their discoveries are so extensive that there is too much for a tiny blog: so we’ve summarised the findings below. But look at the timing of the mutation in the famous FOXP-2 gene, and the human species which were running around at the time. True humans fall naturally into two groups. One one side, big -brained essentially modern forms : Homo heidelbergensis, Denisovans, Neanderthals and Homo sapiens. On the other? Poor old Homo erectus, significantly smaller-brained and with a much more exiguous technological and cultural life. In this light, the mutation is almost eerily coincident.

Of course the time lines of the mutations are a bit open ended; but the picture from the fossils is a bit vague too. What really impresses us is the way that, give or take an Ice Age or two, the geneticists provide independent validation of the fossil finders’ picture overall. And there’s an even deeper lesson. The same truth can be seen in two completely different ways, Like those night sky apps you can get which can show the same firmament through visual light, x-rays, microwave or radio waves; whichever you choose. Next time you argue with someone ask yourself and them: are we really talking about two different things? There’s a cognitive advance for the ages.

_{all based on peer reviewed or reputable pre pubs sources (microsoft assistant)}

Time (Million Years Ago)	Key Genetic Mutation	Hominins Present
~6 MYA	ARHGAP11B (linked to brain expansion)	Sahelanthropus tchadensis (early bipedal ape-like species)
~4.4 MYA	Changes in genes affecting bipedalism	Ardipithecus ramidus (early upright walker)
~3.3 MYA	SRGAP2C (enhanced neuron connectivity)	Australopithecus afarensis (Lucy and her relatives)
~2.4 MYA	MYH16 (jaw muscle reduction, allowing brain growth)	Early Homo habilis (first tool users)
~2 MYA	SCN9A (pain sensitivity mutation)	Homo erectus (first hominin to leave Africa)
~700,000 YA	FOXP2 (language-related gene)	Homo heidelbergensis (ancestor of Neanderthals and modern humans)
~900,000 – 4.5 MYA	Chromosome 2 fusion (reduced chromosome count from 48 to 46)	Various early Homo species
~300,000 YA	Microcephalin & ASPM (brain development genes)	Early Homo sapiens (our direct ancestors)

#genteics #paleontology #tools #fossils #anthropology #human evolution

We said Base Pair editing would outshine CRISPR. This breakthrough proves we were wrong. Or not

When is CRISPR- Cas-9 Base Pair Editing, and when is Base Pair editing CRISPR Cas-9?. Readers of this blog may be forgiven for thinking Base Pair Editing was the exciting new kid in town that was going to make CRISPR look like VHS tapes ( what they?–ed) But according to reports of a recent breakthrough in medicine, they are, sort of, one and the same thing.

Perhaps we had better start with the breakthrough. Doctors in Pennsylvania in the USA have used gene editing techniques to treat a poor little boy whose liver lacked the necessary enzyme system to process ammonia. Our reports come firstly from Ian Sample of the Guardian and the New England Journal of medicine via hyperlink) , where Base Pair is very much to the fore While Nature Briefing has the following take , again with the hyperlink to the NEJM, Baby Boy Receives CRISPR for One Therapy

A baby boy with a devastating genetic disease is thriving after becoming the first known person to receive a bespoke, CRISPR therapy-for-one. KJ Muldoon, now almost 10 months old, received three doses of a gene-editing treatment designed to repair his specific disease-causing mutation, which impaired his body’s ability to process protein. While Muldoon appears healthy, it is too soon to use the word “cure”, says paediatrician Rebecca Ahrens-Nicklas. “This is still really early days.”Nature | 5 min read
Reference: New England Journal of Medicine paper

From all of which we have obtain the following Learning Points for your Edification , gentle reader:

1 It matters less what you call it, and more that it works-the kid’s OK now!

2 Maybe Base Pair Editing is a subset of CRISPR the way that Hammersmith is a region of London. OK, it’s Hammersmith. But it’s London too. What’s the big deal?

3 It would be interesting to learn if other big cities like New York or Madrid for examples, contain smaller areas with funny names. But we will leave that to another day.

4 If you educate people, teach them critical thinking skills and give them some money to buy test tubes with, things like this can happen

5 If you keep people working long hours for little money, educate them to a minimum and give them things like Fox News to watch, societal outcomes may be very different

[1]https://www.theguardian.com/science/2025/may/15/us-doctors-rewrite-dna-of-infant-with-severe-genetic-disorder-in-medical-first?CMP=Share_iOSApp_Other

also: see LSS 23 7 2022 and follow ups

#gene therapies #base pair editing #CRISPR Cas-9 #medicine #health

APPEAL: the charity that tries to mend broken lives like Peter Sullivan’s

It is November 1987. If you turn on the radio, you might hear T’Pau‘s popular ditty China in your Hand, or maybe George Michael belting out Faith. In the UK , Mrs Thatcher‘s government is reaching peaks of popularity, although last month’s financial crash is a harbinger of that there may be troubles ahead. But you don’t mind, because you’re going to see Cher in Moonstruck, and…….that’s it. Nothing else happens for 38 years. Because you are in prison. High Security prison in fact, for a murder which you did not commit. The world moves on, but you are frozen in 1987.

That’s what happened to Peter Sullivan. [1]His conviction was for the murder of a poor innocent woman called Diane Sindall, who died in tragically brutal circumstances in 1986, and whose real assailant has never been found. And despite repeated appeals to courts and organisations like the CCRC, whose ostensible purpose is to review purported miscarriages of justice, nothing was ever done, Until his case was taken up by APPEAL. They are a tiny charity, skeleton-staffed by lawyers and other professionals. Legal Davids taking on a Goliath of wrongful convictions. You can read more about their work here [2] One recent heart warming success was the release of an unfortunate man named Andy Malkinson who was wrongfully jailed for rape in 2003. Their are many other cases like his on our system; there will be in yours too, overseas readers.

We know there have been advances in Forensic Sciences. We know that Police Officers are forced to work far too hard, with dreadful lack of funds. We know that makes them vulnerable to all -too -human faults like jumping to conclusions and confirmation bias. ( we are less sympathetic to the hysterical vitriol poured out by the media when a “successful” conviction has been achieved) But we do know that the world needs an organisation that deals in the best currency of our species-second thoughts. APPEAL is one such. Hopelessly understaffed. desperately under resourced. They are there for every little person who has felt the full obdurate weight of the criminal justice system sitting right on their chests. And to help some of these victims stumble free, unbelievingly, into 2025.

[1]https://www.theguardian.com/law/2025/may/13/peter-sullivan-jail-murder-conviction-quashed-diane-sindall?CMP=Share_AndroidApp_Other

[2]https://appeal.org.uk/who-we-are/

here is their donate page, just to save you time (hint hint)

#APPEAL #CCRC #peter sullivan #diane sinda;; #andy malkinson #miscarriage of justice #court pf appeal #forensic science #dna