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Reference: bioRxiv preprint (not peer reviewed)
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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