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

Is this plastic eating bacterium the ultimate in antibiotic resistance?

Bacteria that mutate to resist the strongest known antibiotics. At this blog, it’s in our DNA, if you will pardon the flippant quip. But-get this-what if the bacterium in question starts eating the walls you are trying to contain it in? Sounds fantastic, like the plot of one of those old 1950s B movies. Read this piece called Hospital Superbug eats Medical Plastic from the admirable Nature Briefings

Pseudomonas aeruginosa — a strain of bacterium that often causes antibiotic-resistant infections in hospitals — can produce an enzyme that can break down medical-grade plastic. Researchers found that the enzyme, dubbed Pap1, can break down a plastic called polycaprolactone that is commonly used in health care because of its biodegradable properties. The ability to break down plastic could explain why these microbes persist in hospital environments, says biomedical scientist and study co-author Ronan McCarthy.Nature | 4 min read
Reference: Cell Reports paper

We’ve put up the Cell Reports posting for you too here[1]in case the clicker above does not get you through

So is this it? The big one? A wave of highly infectious bacteria that not only eats us humans, but gleefully chomps its way through the very defensive systems we use use to contain it? Possibly, yes. But-let’s keep our Alans on, as they used to say in the old Guy Ritchie movies. For there are two good reasons to do so.

First, it’s only eating one type of plastic, so far. There are lots of others which could be deployed for special medical uses which will be less vulnerable.

Secondly, the fact that this plastic is indeed biodegradable, and that something has found a way to do it, offers great hope. Imagine a plastics ecosystem wherein every bottle, every carton, each piece of wrapping is open to attack by this Pap-1 enzyme. Potentially it opens the way to clean beaches, litter- free hedgerows and unblocked rivers and sewers. There is no reason that the genes to make the enzyme could not be spliced into a safer organism than Pseudomonas aeruginosa. It’s an ill wind that blows no one any good, we say.

[1]https://www.cell.com/cell-reports/fulltext/S2211-1247(25)00421-8

#plastics #antibiotics #microbial antibiotic resistance #science #ecology #pollution

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

Cortical Labs: the first working Synthetic Biological Intelligence

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

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

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

thanks to G Herbert

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

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

Deadly Fungus spreads as globe warms

Rising seas. Flooding rivers. Blankets of uncontrollable wildfires. But the latest risk from global warming is a humble fungus, which could now spread across the globe. We’ve mentioned the danger of antibiotic resistant fungi before here(LSS 21 10 24 et al) But we never thought to tie it to climate change.

Well all that’s just changed. Because according to a new study by Dr Norman van Rhijn of Manchester University, reported here by Alex Croft of the Independent, via Yahoo [1] dangerous strains of the Aspergillus family of fungi are starting to spread . If we carry on burning fossil fuels at the rate we do now, the strain A. fumigatus will probably extend its range by 77% by 2100, pushing up into polar regions such as Alaska. And the trend is worrying experts from many fields.[2] For one thing, fungi have an immense potential to damage drops. But they also pose a clear and present danger to human health, especially in those with weaker immune systems, such as the elderly and children. They may also produce substances such as aflatoxins which may cause liver damage and even cancer[3] It’s hard to get an exact figure which parses the number of deaths caused directly by fungi, and those cases where they become an opportunistic secondary infection. But about 3.5 million a year might not be a bad ball park figure. As the fungi become resistant to antibiotics and fungicides, this figure will grow and grow.

This is a bank holiday weekend in our country. People will be doing bank holiday things. A great many cars will be cleaned, tents put up, boats sailed and drinks drunk. But , we can’t help thinking, wouldn’t it be better to put all the fun on hold for a bit, until problems like this have been finally sorted out?

[1]https://uk.news.yahoo.com/killer-fungus-could-spread-parts-170653452.html#:~:text=Norman%20van%20Rhijn%2C%20the%20Wellcome%20Trust%20research%20fellow,a

[2]https://www.who.int/news/item/25-10-2022-who-releases-first-ever-list-of-health-threatening-fungi

[3]https://www.cancer.gov/about-cancer/causes-prevention/risk/substances/aflatoxins

#global warming #climate change # antibiotic resistance #aspergillus #fungi

Fish farms in Space? They might be closer than you think

One thing about Science Fiction: the food in future worlds always seems a bit dodgy. From Soylent Green through 2001: A Space Odyssey all the way to Red Dwarf, it’s all a bit artificial. Despite the ingenious efforts of valiant biochemists and microbiologists,[1] it’s not really the same. But wait, gentle readers! Almost unbelievably a brilliant French Scientist called Dr Cyrille Przybyla really believes he has a way of serving up a tasty plate of fresh real Sea Bass in the dining room of a lunar colony, assuming we all survive to construct one.

According to Kim Willsher of the Guardian, it’s not so outlandish as it sounds.[2] Apparently our finny friends have been making trips into space since the 1970s. All Dr Przybyla and his his Lunar Hatch Project are doing at this stage is sending a few up to the ISS to see how they get on. But, if it’s a success-who knows. Bass are exceptionally rich in omega 3 and B group vitamins, all of which are good for fighting muscle loss which comes with low gravity or zero gravity environments. Being fish, they’re already weightless in effect, so they won’t care anyway. The idea of putting them into enclosed, self sustaining eco systems might be very feasible on the moon. We now know there’s plenty of water up there, so that potentially exorbitant problem is largely solved.

There’s so much to like about this idea. Firstly it’s new different thinking: but not so new that bits of it haven’t been tried already. Secondly, a cautious, step-by-step approach is being applied-always a good sign of a successful project. Thirdly, it addresses a real need. No wonder the Chinese are getting interested, as Kim points out. that’s because they look to the future, instead of wasting all their time and energy trying to restore a lot of rusty old factories whose time has long since passed. We think there’s a lesson in there somewhere.

[1]https://www.bbc.co.uk/news/articles/cp34wzql2xvo

[2]https://www.theguardian.com/environment/2025/apr/28/sea-bass-in-space-lunar-hatch-fish-farms-moon-aquaculture

#space exploration #fish farms #nutrition #sea bass #ifremer

Do glaciers have political opinions? and some other mystery questions do get you thinking

Instead of all those discourses on things like microbiology or economic history, we thought we’d offer you something a little different today, gentle readers. We’ve decided to come up with one of those puzzle exercises, you know, brain teasers they call them. So here are 11 questions designed to get you thinking, to stretch the old grey matter as t’were. And the good news is: Most of the answers will be available somewhere on the Interweb, or via the websites we have so helpfully posted below.

1 How do you explain the change in the ratio of C₁₃ to C₁₂ in the atmosphere since 1850? Why did this ratio seem have fallen especially quickly after 1950?

2 Since 1750 about 2400 gigatonnes of carbon dioxide have been added to the atmosphere. If this call came from volcanoes, why is the isotopic signature of atmospheric CO₂so different from that from volcanic sources?

3 Do glaciers retreat because they share the political opinions of the Green Party, or is all this melting caused by something else?

4 Why have global surface temperatures increased by 1.2% since the late nineteenth century, but stratospheric temperatures actually fallen?

5 Why is the ocean warming faster than the land? Why would the land warm fastest first if all this were caused by the Sun?

6 Why does spring arrive earlier and earlier in the Northern hemisphere?

7 Do fish conspire with extremists,or have their migrating patterns changed for other reasons?

8 What is causing all these temperature rises anyway?

9 Why is the atmosphere of Venus so hot? And why is the atmosphere of Mars so cold?

10 Do you think rises in sea levels will drive increases in human migration?

11 If scientists are right about cures for cancer, physics, astronomy computers and many other things, why are they suddenly wrong about climate science?

[1]https://royalsociety.org/news-resources/projects/climate-change-evidence-causes/

[2]https://science.nasa.gov/climate-change/evidence/

[3]https://www.climate.gov/news-features/climate-qa/what-evidence-exists-earth-warming-and-humans-are-main-cause

#climate change #global warming #climate science #carbon dioxide #ecology #pollution

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