Human Evolution: More muddle in the middle?

Taking time out as ever from more serious matters, we return to our old playground of human evolution. And not just for R and R, important as that is. Also, because the methods and pronouncements of its scholars are important guides to how we should all approach any complicated and potentially controversial subject.

Until recently the origin of our own species seemed fairly clear cut. It emerged from a pack of other big-brained contenders (think Denisovans and Neanderthals among others) starting around 250 000 years ago, in Africa, and clearing the rest of the field no later than 35000 years BP. However recent work by Professor Chris Stringer of London’s prestigious Natural History Museum and colleagues have now cast this into doubt. It is even possible that the line leading to Homo sapiens may have started to go its own way before 1000 000 years BP. You can read why in these takes from Jonathan Chadwick of the Mail here [1] or a slightly extended version in the museums own PR piece here [2] It all goes back to 1990 and the discovery of a rather squashed skull called Yunxian 2 which was attributed to Homo erectus: a perfectly reasonable decision at the time. But using advanced new reconstruction techniques Stringer and his colleagues assert

……… Yunxian 2 displays a unique combination of primitive and more advanced traits. These include a large, squat braincase and a more projecting lower face, similar to Homo erectus. At the same time, derived features in the face and rear of the braincase, as well as a larger brain capacity, are closer to later species such as Homo longi (‘Dragon Man’) and Homo sapiens.

We have been following this game for for nearly six decades: so what do we think? First Chris Stringer is a fine scholar whom we have always admired. Secondly, we welcome all attempts to re evaluate data and set it in new contexts: that way real learning occurs. Our caveat is more with practice . Always and again in human evolution, new fossils found are baptised with confident new binomial Latin names in the great Linnean tradition. Then vast conclusions are drawn, which, in our experience, are substantially revised some years later. This has led not only to the muddle in the middle to which the articles allude. There are plenty more early on the story, and more than one much later on. We think the first clearing step should be to talk less about species, and more about gene frequencies populations. and ways of life. These clearly cluster at points of excavation, such as Afar, Java or Atapuerca to name but a few. But each point, however iconic, is represented by relatively few bones. There are enormous gaps in space and time between each, into which genes and populations must have been flowing all the time. Is it not possible that there has only been one human line all along, and that many of the variations are likely due to factors such as ecology, climate or isolation? The real answer is to dig, dig and dig again.

[1]https://www.dailymail.co.uk/sciencetech/article-15132633/skull-pushes-origins-400-000-years.html

[2]https://www.nhm.ac.uk/press-office/press-releases/analysis-of-reconstructed-ancient-skull-pushes-back-our-origins-.html

#paleoanthropology #human evolution #clade #species #Homo sapiens #China

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

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

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

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

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

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

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

Mirror Organisms: the ultimate bioweapon?

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

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

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

#isomers #biochemistry #bioweapons

LSS at 5:A blog of all our blogs

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

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

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

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

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

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

Life on Mars? Some of us have been here before

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

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

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

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

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

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

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

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

CRISPR gallops ahead (article contains a warning for xenophobes)

Warning: this article may make uncomfortable reading for xenophobes everywhere)

Progress in CRISPR-Cas-9 (Clustered Regularly Interspaced Short Palindromic Repeats)[1] and the associated enzyme is getting faster and faster. We started reporting on this truly innovative technique in 2020 and regular readers will recall updates ever since. Only four years ago it still felt a bit theoretical. But now radical applications are coming thick and fast Read this from Nature Briefing CRISPR horses spark debate reporting on the rather recondite world of polo pony breeding

the horses pictured above{*} are the first of their species to have been created with the help of the CRISPR–Cas9 gene-editing technique. They are clones of the prize-winning steed Polo Pureza, with a tweak to myostatin — a gene involved in regulating muscle development — that is designed to quicken their pace. Critics say that genetic manipulation has no place among polo’s traditional breeding practices — it has already been banned by some of the sport’s governing bodies. But a zoo of CRISPR-edited animals, from cows to sheep, is gaining acceptance in agriculture.Nature | 5 min read

^{{*} sorry LSS readers-we can’t show this}^-ed

In one sense there’s nothing new here. Humans have been modifying the genetics of plant and animal species since the dawn of the Neolithic. CRISPR and other base editing techniques have simply speeded the whole process up by making specific, designed changes and crucial nodes in the subject organism’s development. There is every reason to suppose that any number of new modifications to animals(and crop plants such as wheat) will be developed in the next few years. Some may even enable us the preserve the integrity of food supplies despite the ravages of things like plastics pollution and global warming. Also, as we have also reported here, gene editing is beginning to show real applications in medical fields such as sickle cell disease and certain cancer therapies. All of which leads us to an intriguing thought.

If ponies may be so easily modified, why not humans? One could start small by just modifying athletes and other small groups. Yet eventually the techniques could become ubiquitous in our species. Hang on-our species? Because the genetic differences between beings consisting entirely of CRISPR modified genes and the rest of us would then be far, far greater than those currently existing between our different races and ethnic groups. Are xenophobes everywhere already wasting their own time?

[1]https://www.yourgenome.org/theme/what-is-crispr-cas9/

#CRISPR Cas 9 #base pair #medicine #biotechnology #sickle cell #agriculture #stock breeding

The Slippery Slope fallacy: the one we’ve never got on with

“Don’t throw that rubbish there! Put it in the bin like you’re supposed to!” Many years ago we lived on a pleasant private estate in West London with trimmed lawns, walkways, security, a residents association, all those sorts of things. The only problem was some of the residents, who were either too lazy or felt culturally compelled to throw their domestic rubbish down by the rubbish chutes instead of putting in properly, as we, the decent majority did. This bad practice spread, being quickly copied across the estate and soon we all had a widespread problem with flies, rodents and an ugly disfigurement of our pristine areas. It’s called the slippery slope. Another example is when the office agrees to step out for a single drink and, three hours later, the entire company ends up blind drunk ,broke and embracing each other with varying declarations of love. Everyone copies bad behaviour, because they feel entitled, or are missing out. And so crime, disorder, drugs and violence spread quickly through communities, reducing everyone to common beggary.

And that raises a bigger problem for us here at LSS. For years we have proudly touted our Enlightenment, Whig, rational, call them what you will credentials like a badge of honour. Central to our purpose, hardened readers will recall, is the practice of reason and logic. Avidly do we follow websites like your logical fallacy which are stuffed with every classic example you could wish for: post hoc propter hoc, texas sharpshooter, all shining beacons of clear thought each one of them.. Standing out like a dead rat in a melon souffle is the slippery slope, of which the authors state

Allowing to happen will cause Z to happen: therefore we should ban A now!

Yes, we see the error. The slippery slope is a fallacy for it allows one to jump to conclusions without checking each intervening link from A to Z for both logic and empirical fact. Its the classic howler of someone like a Daily Mail columnist, carried away on tides of hysteria and dread. The trouble is: it’s how humans really behave. It’s the way most of them are.

So our problem with the slippery slope mirrors a more general problem. Reason, learning, and all the the qualities which we prize are not always good guides to how society works. (Try a Friday night out in Croydon if you don’t believe us) Yet the values we espouse are the only ones which will ensure not only the good life but also human survival in the long term. The problem we now have is how do we form a critical mass to allow those values to prevail?

[1]https://yourlogicalfallacyis.com/

#logic #fallacy #reason #slippery slope #enlightenment

How life evolved long ago is absolutely relevant today

Long suffering readers of this blog will recall our occasional sallies into the remote past. Like some latter day Doug McClure we occasionally take you into a world stuffed with dinosaurs, ape men and pterodactyls, to the detriment of more relevant stuff on antibiotics or the US Ten Year Bond. And so, although we were privately raving about this piece below called How did life get multicellular? from Nature Briefing, we thought we ‘d spare you from our private obsessions about things that took place between 800 -600 million years ago.

Until a chance encounter with one of more intelligent friends in the car park at our Spanish Conversation group produced the most inspiring thought. “All those Choanoflagellates. protometazoans. Filasterea. whatever, have to do several things if they are to succeed in living together. To glue up to each other. To signal little messages. To co-ordinate the cycles of cell division. Just like cancer cells have to, in fact. And then it hit us. These funny little organisms are the perfect way to model the behaviour of cancer cells. Not just the molecular and genetic mechanisms, but also the Information and Complexity models we must build to understand them: a cancer cell is a typical metazoan cell gone wrong.

Which confirmed a very old principle of this blog. All research however abstruse it may seem, will have a pay off somewhere one day. If it doesn’t benefit the economy, it will make us live longer; sometimes it may do both. These researchers are not just having fun on the edge of time: they may be contributing directly to the study of a disease which will kill half of us. There’s a thought for anyone who wants to cut university budgets or meddle with the findings of scientists.

To play out we shall first post the Nature Briefing paragraph. If you can get past that we’ve some supporting evidence for our basic proposition. We hope both will inform

Across all forms of life, the move from being single-celled to multicellular seems to have happened dozens of times — for animals, though, the jump was one-and-done. The unique cocktail of environmental and genetic factors that helped animal ancestors make that jump still eludes our understanding. To investigate, researchers are focussing on unicellular organisms that ‘dabble’ in multicellularity, occasionally forming colonies of many cells. By studying these organisms as they flit between the two states, scientists are hoping to illuminate how multicellularity stuck in animals — and what sparked the single successful event that gave rise to the animal kingdom.Nature | 11 min read

ASTRACT BECOMES APPLIED

This work discusses how cancer disrupts the gene regulatory networks (GRNs) that evolved to coordinate multicellular life. These networks balance genes inherited from unicellular ancestors (handling basics like metabolism and division) with newer multicellular genes (handling coordination, differentiation, and tissue integrity). https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03247-1

and this how somatic mutations in early metazoan genes specifically disrupt the regulatory links between unicellular and multicellular gene networks. The result? Tumours behave like rogue unicellular entities, ignoring the cooperative rules of multicellularity. Some of these disrupted genes even correlate with drug response, hinting at therapeutic relevance

thanks to R Muggridge

https://elifesciences.org/articles/40947

#cancer #evolution #multicellularity #medicine #health #choanoflagellates

Co-LAB-oration, or why its good news UK is back in Horizon

Science is good for economic growth. It’s theme we’ve touched on before in this blog(LSS 4 10 23; 1 3 24) So any initiative that builds on this incontrovertible fact will meet with our approval. if only because we want a higher standard of living next year. Which is why we showcase this article by Lisa O’Carroll of the Guardian [1] which reviews progress of the UK’s revived membership of the EU administered Horizon Programme, which tries to bring together the efforts of scientists technologists and scholars from across many countries.

It may soothe the objections of our more rabid eurosceptic readers, to learn that almost half the members (20:27) are not in the European Union, but are located as far afield as Canada and New Zealand (“is that Bri’ish Empoire enuff fer yer, Guv?”) But because science is a collaborative process it helps if you can recruit your teams from close neighbours, if only because it saves on things like travel costs on the day of the interview. We need not discourse long on close financial and technological links as Lisa covers them well in her article. It’s a cultural link of a different stripe which makes us think that rejoining was the right decision.

For what the UK and its fellow members have in common is that they are open societies, where information and people flow freely. The other possible partner, the USA, is showing strong signs of both damaging the free flow of information as well as launching major attacks on both the funding and the very work of scientists, as our readers well know. The Horizon programme and the countries that contribute, are the genuine heirs of both the Renaissance and Enlightenment. Societies that abandon the practice of truth and reason soon fall into cultural and economic stagnation. Just as being in UEFA is a sound bet for British Football Clubs, so is Horizon for British Universities. A good news day forr once

[1]https://www.theguardian.com/science/2025/aug/12/uk-recovers-position-horizon-europe-science-research-eu-brexit

[2]https://commission.europa.eu/funding-tenders/find-funding/eu-funding-programmes/horizon-europe_en

#science #technology #economics #EU #UK #renaissance #enlightenment #donald trump

Exclusive: We reveal the only definite finding from quantum physics(and you can be certain of it)

Always believe someone who tells you that they don’t know what’s going on. Especially when that someone is one of the best trained and most intelligent people in the world. That’s why this story from Nature Briefing caught our attention as the week-ender for this session of blogs: What Does quantum Physics Mean anyway?

First sketched out a century ago, the equations at the heart of quantum mechanics underpin technologies from computer chips to medical-imaging machines. But no one seems to agree on how best to describe the physical reality that lies behind the maths. A Nature survey of more than 1,100 researchers — the largest ever on the subject — has revealed just how widely researchers vary in their interpretations of the most fundamental features of quantum experiments, and their confidence in their answers. [1]

The survey asked questions like “is there a real quantum world behind – or does all this work we’ve done only represent what’s inside our heads? What are the most favoured explanations for quantum theory? What is a wavefunction anyway? Is there a boundary between classical objects and quantum objects (i.e ,between the table you’re sitting at and the atoms it’s made from) And the answers that came back-and remember who gave them-read more like the responses to political opinion polls or market surveys about the best brands of instant custard.

From all of which we concluded the following.

1 If the brightest and the best think like this about something they have studied for decades, it suggests the rest of us might do well to be a little less opinionated on many things

2 Above all this includes certain journalists who think they know it all on things like climate change, vaccines and global warming

3 Watch the last episode of Jacob Bronowski‘s TV spectacular The Ascent of Man on You Tube. or one of the other streamers. It’s still good after 52 years [2]

4 There is still much out there to discover-as we tried to hint with our little blogs on Euler’s number and π(LSS 14 3 22; 16 4 24)

5 All knowledge exists within certain limits, and is probable. Of this last point, you may be certain

[1]https://www.nature.com/articles/d41586-025-02342-y?utm_source=Live+Audience&utm_campaign=a8d315930b-nature-briefing-daily-20250730&utm_medium=email&utm_term=

[2]https://www.dailymotion.com/video/x20p9h4

#quantum physics #uncertainty principle #knowledge #reason #science #nature