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

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

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