Evolution is happening right now in South Korea

We tend to think of Evolution as something happening over millions of years. First, all those trilobites and early fish swimming in the warm Devonian seas. Then early newts and scorpions slithering out onto land, followed by dinosaurs and pterosaurs dodging the cycads; and finally those desperate battles between humans and mammoths in the frozen wastes of the tundra. Millions of years-billions if you look at things like bacteria and red algae.

But evolution isn’t like that. The change of one species into another is a by product some something much smaller, local and more rapid. It is about the environment selecting a gene here, now, for one small purpose. Read this from Nature Briefing, No Diver is an island

A tradition of diving on the South Korean island of Jeju might have influenced the genomes of all of the islanders. The Haenyeo — meaning ‘women of the sea’ — have been cold-water diving year-round and without any breathing apparatus for centuries. A genetic analysis revealed that gene variants associated with reduced blood pressure, cold water tolerance and red blood cell count — which is related to oxygen-carrying capacity — are more common in people from Jeju, regardless of whether they dive themselves, than in other South Koreans.CNN | 7 min read
Reference: Cell Reports paper

In other words, good old fashioned Darwin-Mendel natural selection of the central DNA of the organism. Because one gene variant conveys a selective advantage which the other allele doesn’t. Textbook case: on single genetic change will transform a bacterium into an antibiotic-resistant organism, with profound consequences millions. Of course, if you have enough of these over time, you might eventually transform a tabby into a tiger, or a dinosaur into a bird. But those are second order consequences.Recent discoveries have made our understanding a little more complicated. We have to factor in epigenetics (the great Nessa Carey is good guide [1] ) and even the possibility of some environmental feedback into the genome, to which we have alluded here sometimes(LSS passim)

Every so often we come across some fool, usually a pub bore or right wing columnist, who loudly declaims” I don’t believe in evolution-why would a fish want to transform itself into a salamander?” Here is your answer. The majestic old Darwinian model still functions, Right at the heart of one of the most modern countries in the world.[2]

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

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

#natural selection #evolution #epigenetics #darwin #mendel #dna #gene #south korea

Gepotidacin marches on

Gentle readers we’re more than happy to present the next chapter in the story of Gepotidacin. Against all the gloom and doom we serve up here, it really is a wonderful new class of antibiotic We have covered it before (LSS 30 1 23 ; 17 4 23) but today Manuel Ansede of El País [1] serves up a handy little resumé, not only of where we are now, where we have come form, and all kinds of hyperlinks to bring you up to speed. We can add little but to such erudition as Manuel’s. But for the sake of long term readers will riff on these few -humbly derived- observations

Firstly, this really is a new class of antibiotic., going by the snappy name of triazaacenaphthylene bacterial topoisomerase inhibitors. Unlike traditional antibiotics that target bacterial cell walls or protein synthesis, gepotidacin disrupts bacterial DNA replication by inhibiting two essential enzymes: DNA gyrase and topoisomerase IV. Which as most readers will instantly recall, are crucial for bacterial DNA replication and cell division. Thought so.

Secondly its already showing real world efficacy against all kinds of bacteria, including antibiotic-resistant strains like methicillin-resistant Staphylococcus aureus (MRSA) and multidrug-resistant Neisseria gonorrhoeae. Get that: real science works.

Thirdly, to make our old LSS point: effective action in medicine takes time. It requires teams of intelligent people. Who do not act alone, but exist in an ecosystem of universities . research institutes and government agencies. Which in turn requires careful nurturing , funds and right to feel safe enough to make long term plans without bullying and interference from the proudly ignorant and impulsive. American readers take note.

[1]https://elpais.com/ciencia/2025-04-14/el-primer-antibiotico-descubierto-en-30-anos-llega-justo-a-tiempo-de-evitar-que-la-supergonorrea-sea-imposible-de-tratar.

#gepotidacin #antibiotics #antibiotic resistance #health #medicine

Human Genome Editing: A Frankenstein Future?

Technology always advances faster than ethics. Leaving society and individuals floundering in it wake. The printing press transformed European society in the sixteenth century. The cotton gin transformed the economy of the US South, arguably deepening Slavery, and instituting a pattern of violence and cultural wars which have lasted to this day. In the last century, the development of nuclear fission and computing have effected changes as profound as any known in History. It is with these examples in mind that we approach the subject of Human Genome Editing, which may make everything before look silly.

This has been a decade in which the effective manipulation of nucleic acids in living systems has become routine. We have covered such exciting techniques as CRISPR Cas-9 and Base Pair Editing. While all educated people stand in awe of the rapid advance of mRNA vaccine technology, which did so much to stem the COVID-19 pandemic and now offers real hope of new cancer treatments. But, without disparaging the intellectual brilliance or immense hard work of their creators, these technologies are relatively small scale in the size of the biological interventions which they entail. So now read this from Nature Briefings:

Brace for the arrival of Gene editing Modifying multiple DNA variants in human embryos at the same time, a process called polygenic genome editing, could substantially reduce the likelihood of certain diseases occurring. But it also raises concerns, say the authors of a Nature analysis — not least the renewed threat of eugenics. “This is not a hypothetical issue,” argues an accompanying Nature editorial. While such genome editing might be decades off, societies need to consider its possible benefits and risks now to avoid having to play regulatory catch-up when the technology becomes available.Nature | 4 min read
Reference: Nature paper

Imagine a society where the very richest may edit the DNA of themselves and their offspring so that they, and they alone form a race of superbeings. The future for the rest of human kind, the untermenschen if you will, looks grim, and may be very brief. Such evolutionary bottlenecks have occurred in the past; and those on the wrong side(always the majority) “fly forgotten as a dream, flies at the end of day” as the old hymn puts it. Time to consider this very seriously indeed we think. Nature thinks you may have 30 years: we suspect it to be much shorter than that.

#gene editing #dna #biology #biochemistry #CRISPR #Base pair editing #genetics

Out of Africa #2: Upsetting the Apple Cart

Fans of this blog will recall our long standing reservations about the various Out-of-Africa hypotheses which crowd the field of human paleontology. We’ve mentioned our doubts about the earlier one before (LSS 18 5 23). To be fair, the second one, involving modern Homo sapiens has stood up rather better, in view of all the archaeological, linguistic and genetic evidence which supports it.[1] [2] All of which is no reason not to be glad when someone comes along and upsets the apple cart. Today that someone is Professor Huan Shi, whose work is more than admirably reported on by Matthew Phelan for the Mail. [3]

The jumping -off point for Professor Shi is the Dali skull from Shaanxi province. Not only is it very old (260 000 BCE) for something which displays a lot of modern traits; it’s also a very long way from Africa. He goes on to suggest genetic similarities between early H sapiens in Europe and those in East Asia, distancing both from African centred populations. Finally he rests on the (slightly controversial) theory of Maximum Genetic Diversity, which suggests ancestral populations will exhibit a lower diversity, while derived ones will go higher.

Out thoughts? Since China rejoined the community of civilised nations after 1976 they have made some wonderful contributions to paleontology; so treat this with respect. However: there are even older fossils in parts of Africa, such as Jebel Irhoud at 315 000 BCE, which have modern features.. And all the all the models of linguistic complexity suggest the most complicated phoneme patterns are in African languages, and the least out in the Pacific islands, almost the last places we reached in our wanderings. What if both sides are asking the wrong question?After all, a thousand years is a long time for a powerful top predator. Such a species spreading at only ten miles a year would cover the whole landmasses of Africa and Eurasia in that time. Add a few thousand more and maybe the odd climate fluctuation and instead you would have a population endlessly marching, cross breeding and throwing up all sorts of variations. Of which a few fragments found hundreds of thousands of years later will give only the most cursory understanding. What if our species never began at all but has just carried on evolving, and always will?

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

[2]https://www.nature.com/articles/srep36645

[3]https://www.dailymail.co.uk/sciencetech/article-14236961/Scientist-challenges-Africa-theory-human-evolution.html

human evolution #china #homo sapiens #out of africa #lingiustics #genetics #microbiology

A quick round up: Plastic Pollution just got worse, Computers just got faster…and who were the Denisovans?

a few stories that caught our eye

Plastic pollution just got worse Remember those old movies where hard-pressed producers stared combining other movies? Think Godzilla and King Kong or Jesse James and Frankenstein’s daughter. The results were nearly always worse than the original. Well, it’s the same in the ocean PFAs do quite a bit of damage, So do microplastics, all things considered. But when you consider the two together, as Tom Perkins does in this Guardian article, you are in for a whole lot more trouble.

https://www.theguardian.com/environment/2024/nov/25/pfas-microplastics-toxic

Quantum Computers just got faster Just when someone comes up with the-best-thing-ever-yet, someone else supersedes it. Remember CRISPR-Cas-9 and Base pair editing? Well now it looks as if AI may be going the same way. Read this:Giant Quantum Computers built from Light, in Nature Briefings

By the end of 2027, researchers at the private quantum-computing firm PsiQuantum aim to be using light in silicon chips to build a giant, programmable quantum computer. That ambitious goal is far ahead of major rivals such as Google and IBM. PsiQuantum researchers say they hope to also show that such a computer can run commercially useful programmes. The company has raised US$1 billion but has shown relatively little compared to its competitors, leaving some scientists worried it’s promising more than it can deliver.Nature | 13 min read

Who were the Denisovans anyway? One of the most intriguing puzzles in paleontology is the nature of the Denisovans, that mysterious third cousin of the modern human family. Since their discovery through the truly remarkable achievements of Professor Paabo and his teams, their details remain sketchy. A few scraps of bone, some DNA, and a few artefacts. So-hats off Linda Ongaro of The Conversation who pulls together what is known now, in November 2024. We are sure that she shares our wish that one day this excellent article will have been superseded.

https://theconversation.com/their-dna-survives-in-diverse-populations-across-the-world-but-who-were-the-denisovans-244441?utm_medium=email&utm_campaign=Latest%

#dna #pollution #microplastics #PFA #denisovan #quantum computer

Apologies for big mistake in that last blog!

Oh God, oh God, why do we keep doing this? In last week’s blog Plastic Pollution, killed by neo liberalism and how we can’t keep up, we forgot to include anything that covered that last bit! Tiredness, information overkill, whatever the reason we apologise utterly un-reservedly. This is what we were going to say:

There has been yet another discovery in Biochemistry. A noble and intriguing discovery no doubt. But one which has left us reeling, longing for the simplicity of earlier times. Before we start, read this: The study of RNA’s strangest form, from the admirable Nature Briefings

Circular RNAs (circRNAs) — molecules in which an unusual version of the standard RNA-splicing process folds the strand back on itself — are implicated in diseases from cancer to Alzheimer’s, but exactly what they do is still a mystery. This is in part because circRNAs are so rare, and distinguishing their impact from that of their linear cousins isn’t easy. Fortunately, researchers are quickly assembling a toolbox of materials and methods to recognize, quantify and uncover the functions of these puzzling loops. The database circAtlas is helping to clarify the landscape by requiring listed circRNAs to be identified by two tools, and biotech company Arraystar is designing microarrays to hunt for circRNA in human samples.Nature | 11 min read.

Admirable indeed. But we couldn’t help an odd nostalgia for an age when RNA came in two forms. When there were only three TV channels(in the UK) There was only beer to drink. Do you sometimes, just sometimes, feel the same?

There, Happy Now?

https://en.wikipedia.org/wiki/RNA

#rna #biochemistry #information #nostalgia

Reason or Unreason: which will give you a better life?

What happens when you apply reason to solve your problems? And what happens when you give way to emotions, like fear or anger? Two stories from Nature Briefings illustrate the consequences rather nicely, we think.

Reason: New developments in RNA therapies Older readers, who remember as far back as the Covid-19 pandemic of 2020, may recall how a little thing called an RNA vaccine began to make a big difference. Since when a lot of time has passed, and RNA medical technology has come on leaps and bounds. Don’t take our word for it, read this, RNA treatments nearing reality

As early as the mid-1990s, scientists suggested editing molecules of RNA as a treatment for certain diseases, but at the time, they lacked the tools to do so. Around thirty years later, those tools are at our disposal. Editing RNA instead of DNA has several advantages. It’s a process that cells perform naturally, it doesn’t risk permanently altering a person’s genes and it doesn’t introduce bacterial enzymes to human cells as CRISPR-Cas9 gene therapies do. The field of RNA editing may be in its infancy, but pharma companies are already testing its use in some types of eye disease and cancer.Science | 13 min read

For the record, it’s worth clicking on the link, because the article is very clear, with some truly awesome graphics

Unreason: Let’s chuck foreigners out of our Universities Now try this:

A surge in far-right parties entering governments across Europe is raising concerns for science. Policy experts warn that these parties typically show no interest in research and innovation, leaving scientists vulnerable to budget cuts. In the Netherlands, researchers are bracing for €1 billion (US$1.1 billion) in cuts to the university and research budget under a coalition government including the anti-Islam Party for Freedom. The coalition also wants to limit the intake of international students and implement rules that would require universities to apply for permission to teach courses in English, which could trigger an exodus of foreign academics who don’t want to, or can’t, teach in Dutch.Nature | 5 min read

Chuck out foreigners! Don’t let those evil English speakers corrupt the purity of our language! The really odd thing about this for us is the parallel with football . The most successful Universities are like the most successful clubs(compare the Imperial College with Manchester City, if you like) The trick is to create centres of excellence, drawing in the very best talent you can find, and taking a relaxed view of things like native language, dress sense and marital customs. There is often a strong overlap between certain types of football fan and support for right wing parties. Do they really want their favourite team to send home all the foreign players?

#football #university #learning #reason #unreason

Round Up: New Brains for old, Fungal resistance, do we need growth?

Could CRISPR Cas-9 Rebuild your brain? As the brain ages, cells and circuits die off. Hence the unprecedented rise of neurodegenerative diseases in our ageing populations. Hope that this could one day be treated comes from several sources. None more so than this new development in CRISPR Cas 9 gene editing, a much touted favourite on these pages, we admit. Here’s the inimitable Nature Briefings:

Reducing the activity of one particular gene in ageing mice rejuvenates brain stem cells, allowing them to proliferate and provide a supply of fresh neurons. Researchers used CRISPR-Cas9 genome editing to systematically disrupt 23,000 genes and test the effects on neural stem cells. Messing with one such gene, Slc2a4, reduced stem cells’ glucose intake and increased their power to proliferate in old animals, but didn’t affect the cells in young mice. The results provide crucial information for the design of cell therapies that might one day treat neurodegenerative conditions, says neuroscientist Saul Villeda.Nature | 5 min read
Reference: Nature paper

Fungal resistance: a growing problem. Regular readers of these illustrious pages could be forgiven for thinking we spend too much time on antibacterial resistance among bacteria, and not enough on fungi. We hope this very prescient article from The Conversation may go some way to correcting this imbalance

https://theconversation.com/antifungal-resistance-is-not-getting-nearly-as-much-attention-as-antibiotic-resistance-yet-the-risks-to-global-health-are-just-as-serious-239677?utm

Good Growth/Bad Growth The difference in utility between having a small family car, such as a Vauxhall Corsa, and no car at all, is very great indeed. The differences between having that same Corsa and a Rolls Royce are, we humbly submit, rather marginal. Unless you count the awe-inspiring status statement which the latter brings. Growth is good for raising people out of poverty. Yet for centuries it has been based on the production and consumption of status goods rather than useful ones. The complexities of this issue are so fiendish, that we have never known where to begin to understand it. But Larry Elliott of the Guardian makes a brave first try at untying the Gordian knot:

https://www.theguardian.com/business/2024/oct/20/degrowth-image-problem-solve-planet-climate

#veblen #growth #status #antimicrobial resistance #CRISPR Cas 9 #alzheimers #medicine #health

Goodbye CRISPR and epigenetic medicine. Two genuinely exciting developments in one day

Far in the future when the current crop of elections in France, the UK, Iran and the USA are lost in the dusty pages of history books, people will remember this sunny weekend . For it was when Nature Briefings published not one but two stories (count ’em!) about learning and technologies which will still be shaping the lives of those yet unborn. And you read about them here, gentle reader!

Epigenetic Advance From one time Cinderella to starring role, the science of Epigenetics(all that stuff hanging around DNA but isn’t your honest to goodness genome)[1] has started to come of age. Proof of this lies in the fact that it’s starting to become the basis of real cures, in this case for Prion-based diseases “Epigenome Editor” blocks bad proteins

A molecular-editing tool that’s small enough to be delivered to the brain shows promise for warding off prion diseases, a rare but deadly group of neurodegenerative disorders. The system — known as coupled histone tail for autoinhibition release of methyltransferase (CHARM) — changes the ‘epigenome’, a collection of chemical tags that are attached to DNA and that affect gene activity. In mice, CHARM silenced the gene that produces the disease-causing proteins in most neurons across the brain without altering the gene sequence. This system is the first step towards developing a safe and effective ‘one and done’ treatment for reducing the levels of harmful proteins that cause prion disease, says bioengineer Madelynn Whittaker.Nature | 5 min read
Reference: Science paper

Goodbye CRISPR, welcome Bridge RNA Remember how this blog used to wax lyrical about CRISPR back in the ancient days of 2022? Well, there’s a new kid on the block “Jumping Gene” enzyme edits genomes

A technique that harnesses ‘jumping genes’ — mobile genetic sequences naturally found in bacteria that can cut, copy and paste themselves into genomes — could hold the key to redesigning DNA at will. Guided by an RNA molecule called a ‘bridge’ RNA or ‘seekRNA’, the system has been shown to edit genes in a bacterium and in test-tube reactions, but it is still unclear whether it can be adapted to work in human cells. If it can, it could be revolutionary, owing to its small size and its ability to make genetic changes that are thousands of bases long — much larger than is practical with the CRISPR — without breaking DNA.Nature | 6 min read
Reference: Nature paper 1, Nature paper 2 & Nature Communications paper

You’re a funny old species, aren’t you? When you use your inherent qualities of curiosity and intelligence you can achieve things like this. The rest of the time you divide yourselves into imaginary groups and spread destruction, holding yourselves back by centuries from a better life. Will someone pray tell us why you do it?

[1]https://www.wob.com/en-gb/books/nessa-carey/epigenetics-revolution/9781848312920?msclkid=f5800b66adbb110d62696d196c3d84a0&utm_source=bing&utm_m

#medicine #epigenetics #genetics #prions #gene editing

Nature Briefings upsets the apple cart. Big Time

What if everything you learned forty and fifty years ago was wrong? Where would you be then. Something a bit like that happened to us this week when we read this piece from Nature Briefings, Bizarre bacteria scramble workflow of life

Bacteria have stunned biologists by reversing the usual flow of information. Typically genes written in DNA serve as the template for making RNA molecules, which are then translated into proteins. Some viruses are known to have an enzyme that reverses this flow by scribing RNA into DNA. Now scientists have found bacteria with a similar enzyme that can even make completely new genes — by reading RNA as a template. These genes create protective proteins when a bacterium is infected by a virus. “It should change the way we look at the genome,” says biochemist and study co-author Samuel Sternberg.Nature | 4 min read
Reference: bioRxiv preprint (not peer reviewed)
For more coverage of the most abundant living entities on our planet — microorganisms — and the role they play in health, the environment and food systems, update your preferences to sign up to our free weekly Nature Briefing: Microbiology

When we were young, there was a central doctrine in biology. Information was stored in genes, deep in the cell nucleus. These were made of DNA. This information was turned into RNA, then used to make proteins. The DNA code was unchangeable, inviolate which made the operations of natural selection all the easier to facilitate. If a large cat suddenly developed DNA to give it stripes, then it could hide better in the jungle, and pass on more copies of the DNA. Hence tigers evolved. Job done. To think the DNA could be modified by some environmental feedback was not only Lamarckian heresy, there was no obvious mechanism by which it could come about.

Now we are Not saying that the above discoveries overthrow the central tenet. Not yet. But remember how the Michelson Morley experiment in the 1880s posed a deep, unanswerable question at the heart of physics which was not fully resolved until Einstein came along a generation or so later. And we are certainly not going to make impulsive conclusions . But our story today, combined with all the recent advances in Epigenetics, do suggest however that the old model is now awaiting a major rethink.

[1]michelson morley experiment##biology #cell biology #dna #rna #darwin #lamarck #bacteria #protein #gene