Nice article by David Krakauer and Chris Kempes about the computational view of living things. I have some initial thoughts...
aeon.co/essays/is-life… Most of all, it feels crucial to maintain a distinction between what evolution does and what living things do. I have no problem with considering organisms as problem-solving - as goal-directed entities, they *must* be. /2

"Dr Simoné said a lot of people are drinking plenty of water however that water is not the same structure as what we have at an intracellular level."
Oh hello again my old friend.
dailymail.co.uk/femail/health/… "'If we can use lemon lime cinnamon clove and Celtic unprocessed sea salt you can actually change the structure of the water so it hydrates,' she said."
God give me strength (and commas).

Reading a new biography of Jim Lovelock (of which more at a later date) has sent me back to an exchange I had with Jim in 1993 in the ecological magazine Resurgence. My God, the biography casts that in an interesting light.
A 🧵 /1
resurgence.org/magazine/issue… My piece was called Myth and Meaning in Gaia, and it set out to explain the version of Gaia theory then current. A little priggishly, I argued that the idea raised some interesting ideas but that the “strong Gaia” view – that the Earth is literally alive – was untestable. /2

Had a fun argument last night about the machine metaphor in biology. My position is that, while it's fine to use a machine metaphor to describe some parts, like a heart or a flagellar motor, it doesn't work well for a living organism as a whole. The counterargument was... ...that if a machine is an entity in which component parts work together to achieve a goal, we're machines. But my objection is that this is then no longer a metaphor but a redefinition of machines to include us (as well as all kinds of things, like books, that...

Here goes another thread on why a new paper illustrates an aspect of what I’m loosely calling “the new biology”: an emerging picture of the operational principles of our highly complex molecular and cellular basis. /1 Here’s the paper: /2
(I gather it's best now not to put the links in the first tweet of a thread, because Elon.)
nature.com/articles/s4158…

Here’s another thread dissecting an amazing but complex piece of molecular/cell biology. Again, I believe it illustrates some important general principles. (And it’s condensate-free!) Here’s the paper. /1
cell.com/cell-systems/a… It comes from the lab of Aryeh Warmflash at Rice University, who is at the forefront of decoding the molecular processes that govern the behaviour of pluripotent stem cells. The 1st author is Elena Camacho Aguilar of the Andalusian Center for Developmental Biology in Seville. /2

Ready for another long thread on why a new paper reporting some complex molecular biology touches on some important context for how life works? Then strap in. Here’s the paper. /1
pubs.rsc.org/en/content/art… First thing: it’s about one of my favourite proteins, called Hsp90. “Hsp” stands for “heat shock protein”, because when the protein was first encountered, it was in the context of being seemingly a response to – and a defence of – cells being stressed by heat. /2

Here’s another long thread on a complicated new paper that, as well as being of considerable interest in itself, illustrates some important features of today’s molecular biology. I’m reposting to clarify an earlier error. Here's the paper: /1
nature.com/articles/s4158… It is by James Lee & colleagues at the Crick Institute, and reports on efforts to understand the genetic roots of irritable bowel disease (IBD) such as Crohn’s. These are common & can be horrid, & it would be great to find new treatments. /2

I hadn't expected to be doing another thread for a while that tries to open up and contextualize a bit of complicated molecular biology. But then along came this paper. So here goes. It's another long one, but I hope it's worth persevering. /1
nature.com/articles/s4158… The paper, from James Lee & colleagues at the Crick Institute, reports on efforts to understand the genetic roots of irritable bowel disease (IBD) such as Crohn’s. These are common & can be horrid, & it would be great to find new treatments. But there’s some important context. /2

I was delighted to see such an appetite for unpacking of WTF molecular biology: the kind of acronym-stuffed paper that is never going to get within a mile of the science press and can easily leave non-specialists shaking their head at the opacity of life’s workings... /1 – but which actually reveals some deep principles. So, ready for another? Here goes.

Here’s the paper. /2
pnas.org/doi/abs/10.107…

Gonna post this again, with apologies to those who saw it earlier, as the thread seems to be getting prematurely truncated.
So: Ready for another bit of obscure WTF molecular biology that has an important broader message you’ll see discussed nowhere in the science press? /1 Of course you are! Then here goes. (Warning – long thread! But with a punchline.) It’s about this paper: /2
nature.com/articles/s4158…

Ready for another bit of obscure WTF molecular biology that has an important broader message you’ll see discussed nowhere in the science press? Of course you are! Then here goes. (Warning – long thread! But with a punchline.) It’s about this paper: /1
nature.com/articles/s4158… The general issue here is how genes are translated into proteins – yes, about the most central aspect of molecular biology there is. Protein-coding DNA sequences are first transcribed into mRNA in the cell nucleus (that is, for eukaryotes like us, which have a cell nucleus). /2

Here’s a paper that will get zero press because it looks totally specialist, not to say obscure. It’s about how an important class of transcription factors regulate genes. But I think it's worth dissecting because it raises a wider question.Bear with me...
pnas.org/doi/10.1073/pn… NFk[kappa]B transcription factors are a hugely important class, regulating hundreds of genes including those involved in the immune response. So understanding how they work is a big deal.

I was asked this question today: As a materialist, why am I sceptical that, if a simulation of the human body were possible down to the atomic scale, it would not show genuine consciousness? Articulating the answer is not easy. (1/n) It's tempting to offer the answer that simulating black holes does not produce a singularity, and simulating water does not make the circuits wet. But I'm not sure that quite works here, where we might assume that the property in question (consciousness) is not inherently...

I figured it might not be a bad idea to post a little thread on what my book How Life Works does and doesn't do...
how-life-works.philipball.co.uk Several reviews have focused (approvingly!) on the takedown of gene-centric narratives of life. That is absolutely a part of the book, but only a part (there's only one chapter directly about genes). Some might say: "But biologists don't think that way any more!"

Atoms are not mostly empty space. I'd agree with pretty much everything here - and I think its main message could be retained even if we acknowledge the need for simplifications in early learning about the atom. However!!...
aeon.co/essays/why-the… ...it remains the case that nucleons can be considered to have a well defined and finite size, and electrons can be considered point-like particles. So how do we help school kids navigate that in a pre-quantum syllabus? I'm not sure there are easy answers...

This is a great thread by Jim on current positions on the interpretation of quantum mechanics. I even agree with most of it! Inevitably, I'll add some comments... (1/n)

https://twitter.com/jimalkhalili/status/1674694255489560577

Of course, the choices of interpretation are not limited to these four. There's the coherent histories view, the relational view, QBism, and more. It can admittedly be hard sometimes to figure out how they're distinguished. But we're not spoilt for choice! (2/n)

A useful look at what some of the leading figures in AI are thinking about the dangers.

However...

newstatesman.com/long-reads/202… I'm quite taken aback at some of the simplistic comments Hinton makes. He seems to feel that the only thing separating deep-learning AI from the human mind is a matter of scale. I can't fathom this conviction that somehow all intelligence must be heading towards ours.

I'm naturally inclined to agree with this leader, but I do think it needs a bit of nuancing. The initial govt response was shambolic and slow, but *was* guided by the "herd immunity" thinking of some chief scientists - which was flawed. So the inquiry...
theguardian.com/commentisfree/… ... also needs to ask how that position came about. I don't want to exonerate the abysmal way Johnson handled it, but at first it wasn't just govt ignoring "the science". Later it was a different story, for sure.
bbc.co.uk/programmes/m00…

Interesting to look back now at the UK govt's "Living with Covid" document, last updated May 22. I have questions:
1. Is it being audited now to see how well the plans are being implemented? If so, by whom? ...
gov.uk/government/pub… 2. At a glance, I don't see any mention of long Covid; certainly it does not leap out as the big deal it now is. What are the plans here?
3. What are the future plans for vaccinations? Who gets them, and when?

Excellent as ever from @gabyhinsliff. It is both (probably) unavoidable and outrageous that the Covid inquiry will not announce its findings before 2027 at the earliest.
theguardian.com/commentisfree/… From a purely personal point of view, I'd be interested to compare the conclusions of the inquiry against the occasional complaint of a few scientists at the time that science communicators like me were being too harsh on the government.