Round up: Stem Cells, Venezuela, allergies, goodbye to Old King Coal, and the second-most-famous Austrian of all time

stories that caught our eye

Adios, Venezuela, Stage Left : It has always been a conceit on the Left that somehow, whatever bad things we do, we are still somehow the exclusive guardians of the flame of human progress. Whereas the Right, poor dears, are steeped in superstition and ignorance. But Left-wing Governments, at least extreme ones, can do just as much damage to the scientific culture of their country as any Right-wing theocracy, as this piece form Nature Briefings makes clear

Some researchers in Venezuela fear that science in the country is “going down the drain”. The country’s economy has been in crisis and national science funding is proportionally smaller than in comparable countries, leaving research institutions and universities struggling to stay open. Young scientists have left in droves seeking out high-quality education or stable career prospects. And an ‘anti-NGO’ law now requires non-governmental organizations to share information about their funding with the Venezuelan government. Researchers, who sometimes look to NGOs for support, worry that this gives the government discretion to prosecute anyone whose motives it does not agree with.Nature | 6 min read

Every Breath you take: We hear a lot about microplastics in water and food. Now it seems we are breathing them in from the very air itself. And what’s really scary is that the risks of this are quite, quite uncharted, a bit like tobacco in 1924. Here’s Michael Richardson and Meiru Wang for The Conversation:

https://theconversation.com/breathing-may-introduce-microplastics-to-the-brain-new-study-239347?utm_medium=email&utm_campaign=Latest%20from%20The%20C

Stem Cells give hope for diabetics About twenty or so years ago, we had the privilege of a few words with one of the greatest scientific entrepreneurs of this generation. And he told us that Stem Cells were going to be in the in thing for the future. Proof of this foresight comes in this second piece from Nature Briefings

A woman with type 1 diabetes started producing her own insulin less than three months after a transplant of reprogrammed stem cells. This case represents the first successful treatment for the disease using stem cells from the recipient’s own body, which could avoid the need for immunosuppressants. She was injected with the equivalent of 1.5 million stem-cell-derived islets in June 2023. While promising, the woman’s cells must continue to produce insulin for up to five years before considering her ‘cured’, cautions endocrinologist Jay Skyler.Nature | 6 min read
Reference: Cell paper

Allergies Rising? One of the few good things about the Covid-19 pandemic was the rise to prominence of Professor Devi Sridhar, that most clear-sighted of thinkers. So when she says: “allergies are really on the rise, this is not just a sampling error”, we sit up and take notice. So should you, via her article for The Guardian.

https://www.theguardian.com/commentisfree/2024/sep/30/food-allergies-children-england

Goodbye Coal and steel No one gloats at the loss of great workplaces and the terrible social changes their workers must now endure. And no one more than us, blissed-out children of the Enlightenment/Industrial Revolution can deny that coal and steel were really big steps forward in their day. But their comes a time both for individuals and societies when they really must move on, because it’s the future where reality lies. So Britain closes its last coal power station and blast furnaces. It is a brave step, and one day it will pay off.

https://www.bbc.co.uk/news/articles/ckgn4gg5y2yo

https://www.bbc.co.uk/news/articles/c8vdq6y56v0o

Mozart Rise and Fall of a genius few years ago we saw a rather nifty series called Rise of the Nazis. It was one of those drama documentaries where they mix a narrator over pictures of actors depicting real people, including such luminaries as Heinrich Himmler, Herman Goering and a certain Mr A. Hitler. It looks like the producers must have sat down and asked themselves; “Who’s the next most famous Austrian everyone’s heard of we can do?” No it wasn’t Arnold Schwarzenegger: instead they came up with this excellent series on Wolfgang Amadeus Mozart. We have always put him right up there in the top five or so musicians of All Time. So we loved it, and hope you will too Here’s a link which we hope works to the BBC i Player. Hasta la vista, baby!

https://www.bbc.co.uk/iplayer/episodes/m0021zdr/mozart-rise-of-a-genius#:~:text=Mozart:%20Rise%20of%20a%20Genius.%20Child%20prodigy,%20flawed

#allergies #microplastics #mozart #president maduro #venezuela #climate change #fossil fuels #stem cells #diabetes #medicine #health

Molecular Paleontology sheds light on our universal common ancestor

Once upon a time all we had to go on was bones. Comparing them appeared to show a tree of life stretching back to a common ancestor, at least of all animals. Disciplines like embryology helped of course. However, apart from a few woolly traces of bacteria like things in old rocks like the Gunflint Cherts, most early organisms were too small and too fragile to fossilise well. It was a nice idea but the proofs were all a bit shaky.

Enter Molecular Biology. Using the comparative analyses of proteins and nucleic acids, and the rates of change and mutation over time, we have had amazing insights into how all different living organisms are related. Plants, bacteria, fungi, archaea and animals may now be all cross related, which of course means going back in time. Read this article Meet the Parents from Nature Briefings

The shared forebearer of all life — known as the last universal common ancestor (LUCA) — lived around 4.2 billion years ago, ate carbon dioxide and hydrogen, and produced acetate that might have fed other life. Researchers inferred information about our great-great-grandblob’s genetics and biology by tracing duplicated, lost and mutated genes back up the family tree. LUCA probably possessed an early immune system, too — hinting that it lived in an established ecosystem full of microbes and pathogens.Science | 6 min read
Reference: Nature Ecology & Evolution paper

We would not dare to improve on Nature Briefings, our go-to website for science news. We would however draw your attention to two talking points, as t’were, which have accorded us some pause for considerable thought.

The molecular regression analysis suggests that these things lived about 4.2 billion years ago. Which is incredibly early, as best estimates for the age of the planet come in at around 4.5 billion years[1] That seems a vey short time for so much evolution. What was happening?

The second point is a bit more philosophical. Like one of those fiendish brain teasers about barbers and shaving that Bertrand Russell used to set his brightest students. The authors suspect the LUCA lived in an ecosystem of microbes and pathogens. So was it not ancestor to them too? If not, what was?

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

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

#LUCA #molecular biology #dna #rna #protein #precambian #origin of life #origin of earth

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

What if you could detect cancer before it was cancer?

If you want to cure a cancer, identify it as soon as possible. That’s long been a truism among medical experts. But what if your techniques were so advanced that you could identify the precursor steps to cancers before they had even started to initiate a tumour in someone’s body? According to an article by Anna Bawden and Nicola Davis of the Guardian, the first steps to do just that are now feasible, as two studies suggest.

Instead of simply rehashing their excellent prose[1] upon which we urge you to click, we’ll provide a brief summary, and raise some interesting and rather hopeful observations. The first looked at 44000 samples from the UK Biobank. 618 proteins were identified, which could then be linked to 19 different types of cancer. In a different take on the same trope, a second study using a whopping 300 000 samples came up with 40 different proteins linked to 9 different types of cancer. We dare not comment, but dare to observe:

1 It’s amazing the amount of new discoveries you can make just by crunching data. As AI comes into its own, it should be able to handle bigger and bigger numbers. Think of alpha-fold, if you don’t believe us-and that quite old hat by now!

2 Talking of hats, let’s all take ours off to Cancer Research UK, whose steady, patient work down the decades has not only provided a congenial ecosystem for researchers, but also a steady stream of reliable income for the planners and the finance people. Come on, hands in pockets, please! [2]

3 We were impressed that the results were already identifying different types and subtypes of cancers. It suggests a subtlety of technique which has probably only just got going.

and, finally:

4 The bigger the database, the better. Without belittling today’s researchers and journalists, these are still relatively small numbers. Imagine an AI supercomputer tirelessly combing the biological samples of every human on the planet. And maybe their pets. Would might it not find.

Oaks and acorns times, gentle readers. Keep donating.

[1]https://www.theguardian.com/society/article/2024/may/15/proteins-blood-cancer-warning-seven-years-study

[2]https://donate.cancerresearchuk.org/donate?gclid=cf2827b39f4311a97ff841f589e5c887&gclsrc=3p.ds&utm_source=bing&utm_medium=cpc&utm_campaign=IMP%20%

#database #cancer #medicine #AI #protein #gene #prediction

Two amazing stories from genetics that woke us up this morning

One of our great pleasures in life is to stand amazed when someone does something amazingly clever. Especially when you get that feeling that what they did was there, waiting to be done, all along. Which is why we bring you two such stories, all gift wrapped up by the admirable Nature Briefings and BBC, for you to click on at your delight.

A Cure for HIV? Anyone who lived through the 1980s will recall the terrible ravages of the AIDS pandemic, caused of course by the HIV virus. Even if you were lucky enough to be in a low-risk group, we all knew someone or a local community organisation who suffered the ravages. Sad. Sad. Sad. Now that old friend of LSS, CRISPR gene editing may actually offer some hope towards the final elimination of the virus from our genomes. It’s early days yet, as both Michelle Roberts of the BBC and the researchers themselves say. Proof of concept and all that. Good, it’s better to be cautious. But if they can “snip” the HIV virus out of your cells, what else might not be achieved?[1]

Ghost DNA made us brainy Talking of embedded DNA, many a 1980s conversation concerned all that mysterious DNA lying around our genomes that didn’t seem to do anything (no, it was mainly about EastEnders-ed) Was it some of it ancient embedded viruses that attacked our ancestors long ago, in some forgotten Permian Pandemic? Well, get this from Nature Briefings, Virus Helped Brain Evolution

Remnants of an ancient viral infection are essential for producing myelin, a protein that insulates nerve fibres, in most vertebrates. Certain viruses insert DNA into the genetic material of the cells they invade. Sometimes, these insertions become permanent and even aid evolutionary processes. Myelin helps nerves to send electrical signals faster, grow longer and thinner so they can be packed in more efficiently. “As a result of myelin, brains became more complex and vertebrates became more diverse,” says stem-cell biologist and study co-author Robin Franklin.Science News | 6 min read
Reference: Cell paper

The implications are rather profound. The idea of the single autonomous gene line, the pure selfish individual at the core of your biological identity is rather compromised, isn’t it? What if the genetic “you” isn’t just “you,” but is you+some (rather random )free riders, who may or may not be helpful? That Natural Selection is acting on several of you at once. and may force you to cooperate? What price The Selfish Gene now?

[1]https://www.bbc.co.uk/news/health-68609297

#genetics #dna #rna #hiv #aids #myelin #evolution #CRISPR #medicine

Mystery of the left-handed chimps

If you’re reading this, we can be confident of one thing. The chances are 90% that you’re right-handed. And of one other thing: they are 10% that you’re left-handed. when you think about it, this fact is so woven into our everyday lives that we take it for granted-in work, in sport, art-well, everything. And it seems to be very old. Our Neanderthal cousins showed exactly the same ratio.

So, if such a pesky thing as handedness exists at all, you’d expect our nearest relatives, chimpanzees, to show exactly the same pattern, right? Wrong. Chimps do indeed show hand preferences. But give and take a few donnish arguments among researchers, they seem to come out somewhere around 50% right and 50% left. They certainly don’t show this strong, settled right-hand bias that the human line has preserved. Counter-intuitive, isn’t it?

So, why? It’s a very big question. Any answer has to be hypothetical, as the trend must have started millions of years ago. Hannah Fry makes a good first stab it here[1] for the BBC. But there is one other possible reason. Humans spend a lot more time standing up than chimps do. And this frees the hands for several things. Carrying. Signalling. And making tools. Now, as Sverker Johannsen [2] points out, the parts of the brain that control language is on the left side of the brain. And by the simple fact of the way we’re wired up, that controls the right hand. Is it possible that this handedness thing is in some way connected to the use of tools, or language, or even both? We await new discoveries with anticipation.

[1]https://www.bbc.com/future/article/20160930-the-mystery-of-why-left-handers-are-so-much-rarer

[2]The Dawn of Language; How we came to talk by Sverker Johannsen , translated by Frank Perry Maclehouse Press 2021

#evolution #tools #language #left hand #right hand