Andrew Thorpe writing about how Stanford researchers have created a virus not found in nature using genomes designed by artificial intelligence.

US researchers have for the first time successfully synthesised brand-new viruses not found in nature, based on designs generated by artificial intelligence.

[…]

Genome language models operate in a broadly similar way to large language models (LLMs) except that they predict genetic code instead of written text, having been trained on the genomes of other viruses and bacteria, as well as more complex organisms such as plants and animals.

The two models in question were told to generate complete genomes for a viable bacteriophage — a type of virus able to infect and replicate itself inside bacteria, destroying them from the inside.

Using an existing bacteriophage as an example — ΦX174 (pronounced “fie-ex-1-7-4”), known for its ability to infect and destroy E. coli bacteria — the models generated about 700,000 potential designs, of which the researchers picked 285 that looked most promising.

The researchers then synthesised new DNA molecules using those designs and inserted them into E. coli bacteria, before waiting to see if viable bacteriophages would emerge.

Shortly afterwards, 16 of the Petri dishes in which the bacteria were growing began to show clear spots, as the viruses began to attack and replicate themselves inside the E. coli, demonstrating their viability.

Some of those viable viruses proved more effective at attacking E. coli than the original ΦX174 bacteriophage.

This is how Will Smith’s film I Am Legend starts:

News presenter (NP): The world of medicine has seen its share of miracle cures, from the polio vaccine to heart transplants, but all past achievements may pale in comparison to the work of Dr. Alice Krippin. Thank you so much for joining us this morning.

Dr. Alice Krippin: Thank you.

NP: So, Dr. Krippin, give it to me in a nutshell.

Krippin: Well, the premise is quite simple. Take something designed by nature and reprogram it to make it work for the body rather than against it.

NP: You’re talking about a virus.

Krippin: Indeed, yes. In this case, the measles virus, which has been engineered at a genetic level to be helpful rather than harmful. I find the best way to describe it is: if you can imagine your body as a highway, and you picture the virus as a very fast car being driven by a very bad man, imagine the damage that that car could cause. Then if you replace that man with a cop, the picture changes. And that’s essentially what we’ve done.

And this is what Dr. Ian Malcolm says in Jurassic Park.

Your scientists were so preoccupied with whether they could, they didn’t stop to think if they should.

To be clear here, I am only drawing parallels between fact and fiction. I am all for science. But this achievement is both amazing and scary at the same time.

This comment on Hacker News by lordnacho on why you need to understand the time in which the book was written to truly understand book.

As an old man I now think the art and humanities classes in school landed at the wrong time.

You need context to really understand a book or a work of art. You want to know what kind of environment produced it, what it’s talking to.

But when you’re in school, there isn’t time for that. You aren’t going to know a bunch of things about history to put things into context, because there simply isn’t enough time for it.

So you end up doing a bunch of weird commentary on say a book where you as a teenager have no idea where to place it. Like if you read Dickens, will you know enough about the industrial revolution, the condition of cities at the time, and such? Will you know what kind of thing the characters would care about?

How would you know what the characters in Pride and Prejudice are worried about if you don’t know how that society is?

So as a kid it just totally didn’t mean anything to me, it was just a strange torture where you are meant to comment on the motivations of the characters and how the writing style brings that out.

Linus Torvalds message post his debug session with AI.

And this was a debug session from hell, enormously helped by an AI doing much of the grunt-work.

I’d like to call it my tireless helper, but the AI several times stated flat out that this was impossible and unsolvable and that we should just write a report about it.

I suspect those things have been trained by people who may not be quite as stubborn as I am.

But while the AI was ready to give up several times, it did keep adding debug code and analyzing it faithfully when I pushed. So credit where credit is due and I let the AI write the commit message above.

This is basically a one-liner fixing a bogus “round_up()” to a “round_down()”, but there were 24 patches adding more and more debug information to this, and 18 kernel boot to finally narrow it down to this.

Nithin Kamath drawing parallels between tobacco and broking business, and the intense government scrutiny that comes to both.

The fact that ITC started diversifying away from its main tobacco business into hotels and other businesses after almost 70 years of existence was an immense feat of foresight. Especially considering ITC was never a founder-driven company.

They knew tobacco was extremely harmful to health and addictive. When something is bad for people but difficult to ban outright, governments invariably keep regulating and taxing it more.

Over time, the taxes become so high and the revenues so significant that the government itself ends up in a strange place: ban it or continue taxing it?

I can’t help but see a parallel with the broking industry.😬

F&O trading is bad for almost 99% of retail traders. It is unlikely to be banned outright, but regulation will probably keep getting tighter, and taxes like STT will probably keep going higher.

Simon Willison’s suggestion on how lowering your standards can help you to blog more.

My number one tip for blogging is to lower your standards! Aim to hit publish while you are still actively unhappy with what you have written, because the only alternative is a huge folder full of drafts and never publishing anything at all.

Nobody will ever know how perfect the thing you intended to write would have been. The flaws you see in your writing are invisible to everyone else.

Comment by geye1234 on Hacker News:

When we quantify something, we abstract away everything about that thing that is not quantifiable. So our thinking is only about a tiny aspect of that thing’s existence.

This post by Nathan Sanders and Bruce Schneier viewing AI’s technological problems separately from its socio-political problems.

Imagine an AI assistant for a doctor. We can imagine it affecting the profession in one of two ways. The AI could give a doctor more time to do the human parts of their job: to spend more time with their patients, to listen more closely to their needs, to explain things more fully. Or the managers of the medical practice could give that doctor five times the patients—and fire the other four. Which way it would go is not a question of technology. It’s a question of market incentives.

The two are related, of course. Capitalism steers technology, and technology steers markets. But holding the two separate helps us understand that we, as a society, face independent choices on both the technological and sociopolitical axes that need not be coupled.

Madeline McCurry-Schmidt talking about the new HIV vaccine’s success in preclinical study.

The new vaccine works by intervening in a process called B cell maturation. B cells make antibodies. Like many immune cells, B cells have an early “naive” stage before they are ready to make antibodies. B cells start to mature once they get the signal that a pathogen, such as a virus, is trying to attack. B cells see pieces of that pathogen’s molecular structure and start producing antibodies that can bind to that structure and halt infection.

It can take a little while for B cells to find the right “bullseye” on a pathogen. But B cells keep trying. As they mature, B cells tweak their antibody production, refining antibody structures to bind to a pathogen in just the right, vulnerable spots.

Scientists describe B cell development as a training process or bootcamp. In most cases, the body is left with a well-honed B cell army.

HIV is hard to beat because it doesn’t give B cells a chance to develop effective antibodies. The first problem is that HIV disguises itself from the immune system. The virus is wrapped in an ever-shifting cloak of sugar molecules, called glycans. This lets HIV sneak undetected past human cells, which are also covered in glycans.

The second big problem is that HIV mutates very quickly. “The worldwide diversity of HIV mutations is extraordinary. Even the diversity within one individual person living with HIV is dramatic,” says LJI Instructor Patrick Madden, Ph.D., who served as study co-first author with Jon Steichen, Ph.D., an institute investigator at Scripps Research.

The third problem is that HIV changes its shape when it infects human cells. Even if B cells get a glimpse of its viral structure—snap!—the structure changes.

Taken together, these problems rarely give B cells a chance to hone their antibody responses against HIV. Even if a B cell manages to make neutralizing antibodies, the virus can mutate or change its shape, rendering those antibodies useless.

I love it when someone explains science in a simple language that I can understand.

Rohan Rajiv talking about the difference between hard and valuable problems.

[…] there’s very little correlation between a problem being difficult and a problem being valuable.

It is easy to fall into the trap of assuming the two travel together. If something is taking all our effort and ingenuity, surely it must matter — and we take the struggle itself as proof we’re doing important work.

But difficulty and value sit on separate axes. Plenty of brutally hard problems are worth little once solved. And some of the most valuable ones are relatively simple — but executing them well is worth a lot.

Golden words by M. Pattabiraman:

“Can you suggest a good international fund—or include one in my portfolio?”

I hear some version of this question regularly in my work as a SEBI-registered investment adviser. Usually, I respond with another question:

“If I hid the last three years of returns from you, would you still want to invest internationally?”

Take a moment before answering. If the answer is still yes, there may be a genuine portfolio reason for investing abroad. If the answer suddenly becomes less certain, perhaps the attraction is not diversification but recent performance. That difference matters.