[firefoxbrower]

Late-stage capitalism didn't bring us AlphaFold, scientists did, late-stage capitalism just brought us Alphabet swooping in at literally the last minute. Socialize the innovation because that requires potential losses, privatize the profits, basically. It's reminiscent of "Heroes of CRISPR," where Doudna and Charpentier are supposedly just some middle-men, because stepping in at the last minute with more funding is really what fuels innovation.

AlphaFold wasn't some lone genius breakthrough that came out of nowhere, everything but the final steps were basically created in academia through public funding. The key insights, some combination of realizing that the importance of sequence to structure to function put analyzable constraints on sequence conservation and which ML models could be applied to this, were made in academia a long time ago. AlphaFold's training set, the PDB, is also a result of decades of publicly funded work. After that, the problem was just getting enough funding amidst funding cuts and inflation to optimize. David Baker at IPD did so relatively successfully, Jinbo Xu is less of a fundraiser but was able to keep up basically alone with one or two grad students at a time, etc. AlphaFold1 threw way more people and money to basically copy what Jinbo Xu had already done and barely beat him at that year's CASP. Academics were leading the way until very, very recently, it's not like the problem was stalled for decades.

Thankfully, the funding cuts will continue until research improves, and after decades of inflation cutting into grants, we are being rewarded by funding cuts to almost every major funding body this year. I pledge allegiance to the flag!

EDIT: Basically, if you know any scientists, you know the vast majority of us work for years with little consideration for profit because we care about the science and its social impact. It's grating for the community, after being treated worse every year, to then see all the final credit go to people or companies like Eric Lander and Google. Then everyone has to start over, pick some new niche that everyone thinks is impossible, only to worry about losing it when someone begins to get it to work.

[iknowstuff]

Why haven't the academics created a non profit foundation with open source models like this then? If alphabet doesnt provide much, then they will be supplanted by non profits. I see nothing broken here.

[j-wags]

I work at Open Force Field [1] which is the kind of nonprofit that I think you're talking about. Our sister project, OpenFold [2], is working on open source versions of AlphaFold.

We're making good progress but it's difficult to interface with fundamentally different organizational models between academia and industry. I'm hoping that this model will become normalized in the future. But it takes serious leaps of faith from all involved (professors, industry leaders, grant agencies, and - if I can flatter myself - early career scientists) to leave the "safe route" in their organizations and try something like this.

[1] https://openforcefield.org/ [2] https://openfold.io/

[firefoxbrower]

Individual labs somehow manage to do that and we're all grateful. Martin Steinegger's lab put out ColabFold, RELION is the gold standard for cryo-EM despite being academic software and the development of more recent industry competitors like cryoSPARC. Everything out of the IPD is free for academic use. Someone has to fight like hell to get all those grants, though, and from a societal perspective, it's basically needlessly redundant work.

My frustrations aren't with a lack of open source models, some poor souls make them. My disagreement is with the perception that academia has insufficient incentive to work on socially important problems. Most such problems are ONLY worked on in academia until they near the finish line. Look at Omar Yaghi's lab's work on COFs and MOFs for carbon/emission sequestration and atmospheric water harvesting. Look at all the thankless work numerous labs did on CRISPR-Cas9 before the Broad Institute even touched it. Look at Jinbo Xu's work, on David Baker's lab's and the IPD's work, etc. Look at what labs first solved critical amyloid structures, infuriatingly recently, considering the massive negative social impacts of neurodegenerative diseases.

It's only rational for companies that only care about their own profit maximization to socialize R&D costs and privatize any possible gains. This can work if companies aren't being run by absolute ghouls who aren't delaying the release of a new generation of drugs to minimize patent duration overlap or who aren't trying to push things that don't work for short-term profit. This can also work if we properly fund and credit publicly funded academic labs. This is not what's happening, however, instead public funded research is increasingly demeaned, defunded, and dismantled due to the false impression that nothing socially valuable gets done without a profit motive. It's okay, though, I guess under this kind of LSC worldview, that everything always corrects itself so preempting problems doesn't matter, we'll finally learn how much actual innovation is publicly funded when we get the Minions movie, aducanumab, and WeWork over and over again for a few decades while strangling the last bit of nature we have left.