[ramraj07]

Easier drug discovery is what they tell public and grant agencies. In a roundabout way it’s true. Maybe. Many other hurdles still exist. But what this and other similar tools really are, is significantly advancing basic science in creating our own protein designs.

Before alphafold changed this field, creating your own protein design was considered an insane task (not impossible, bakers lab and others have done it a couple times). But these tools (now we have multiple) allow you to create new proteins From scratch that can do exactly what you want (caveats galore). New enzymes that can catalyze reactions never found in nature for example.

Before this all we could do was take proteins that already exist in nature and modify them. So you can imagine how new this world is.

[famouswaffles]

Large Language models can also generate novel and working protein structures that adhere to a specified purpose https://www.nature.com/articles/s41587-022-01618-2

[westurner]

Can optical tweezers construct such proteins; or is there a more efficient way?

Optical tweezers: https://en.wikipedia.org/wiki/Optical_tweezers

"'Impossible' photonic breakthrough: scientist manipulate light at subwavelength scale" https://thedebrief.org/impossible-photonic-breakthrough-scie... :

> have successfully demonstrated that a beam of light can not only be confined to a spot that is 50 times smaller than its own wavelength but also “in a first of its kind” the spot can be moved by minuscule amounts at the point where the light is confined.

> According to that research, the key to confining light below the previous impermeable Abbe diffraction limit was accomplished by “storing a part of the electromagnetic energy in the kinetic energy of electric charges.” This clever adaptation, the researchers wrote, “opened the door to a number of groundbreaking real-world applications, which has contributed to the great success of the field of nanophotonics.”

> “Looking to the future, in principle, it could lead to the manipulation of micro and nanometre-sized objects, including biological particles,” De Liberato says, “or perhaps the sizeable enhancement of the sensitivity resolution of microscopic sensors.”

"Digging into DNA Repair with Optical Tweezer Technology" https://www.genengnews.com/topics/digging-into-dna-repair-wi...

[c1ccccc1]

It's much easier than that! Living cells already have ribosomes that construct proteins and all the other molecular machinery needed to go from DNA sequence to assembled protein. You can order a DNA sequence online and put it into e-coli or yeast cells and those cells will make that protein for you.

[ramraj07]

That’s like saying anyone who has a computer can hack into the NSA. In principle yes, but the amount of know-how and troubleshooting is being underplayed here. Not to mention the question of what you do with the protein once you produce it.

[westurner]

TIL about mail-order CRISPR kits. "Mail-Order CRISPR Kits Allow Absolutely Anyone to Hack DNA" (2017) https://www.scientificamerican.com/article/mail-order-crispr...

Protein production: https://en.wikipedia.org/wiki/Protein_production

Tissue Nanotransfection reprograms e.g. fibroblasts into neurons and endothelial cells (for ischemia) using electric charge. Are there different proteins then expressed? Which are the really useful targets?

> The delivered cargo then transforms the affected cells into a desired cell type without first transforming them to stem cells. TNT is a novel technique and has been used on mice models to successfully transfect fibroblasts into neuron-like cells along with rescue of ischemia in mice models with induced vasculature and perfusion

> [...] This chip is then connected to an electrical source capable of delivering an electrical field to drive the factors from the reservoir into the nanochannels, and onto the contacted tissue

https://en.wikipedia.org/wiki/Tissue_nanotransfection#Techni...

Are there lab safety standards for handling yeast or worse? https://en.wikipedia.org/wiki/Gene_drive

[westurner]

"Bacterial ‘Nanosyringe’ Could Deliver Gene Therapy to Human Cells" (2023) https://www.scientificamerican.com/article/bacterial-nanosyr... :

> In a paper published today in Nature, researchers report refashioning Photorhabdus’s syringe—called a contractile injection system—so that it can attach to human cells and inject large proteins into them. The work could provide a way to deliver various therapeutic proteins into any type of cell, including proteins that can “edit” the cell’s DNA. “It’s a very interesting approach,” says Mark Kay, a gene therapy researcher at Stanford University who was not involved in the study. “Where I think it could be very useful is when you want to express proteins that can do genome editing” to correct or knock out a gene that is mutated in a genetic disorder, he says.

> The nano injector could provide a critical tool for scientists interested in tweaking genes. “Delivery is probably the biggest unsolved problem for gene editing,” says study investigator Feng Zhang, a molecular biologist at the McGovern Institute for Brain Research at the Massachusetts Institute of Technology and the Broad Institute of M.I.T. and Harvard. Zhang is known for his work developing the gene editing system CRISPR-Cas9. Existing technology can insert the editing machinery “into a few tissues, blood and liver and the eye, but we don’t have a good way to get to anywhere else,” such as the brain, heart, lung or kidney, Zhang says. The syringe technology also holds promise for treating cancer because it can be engineered to attach to receptors on certain cancer cells.

[westurner]

From "New neural network architecture inspired by neural system of a worm" (2023) https://news.ycombinator.com/item?id=34715188 :

> "I’m skeptical that biological systems will ever serve as a basis for ML nets in practice"

>> First of all, ML engineers need to stop being so brainphiliacs, caring only about the 'neural networks' of the brain or brain-like systems. Lacrymaria olor has more intelligence, in terms of adapting to exploring/exploiting a given environment, than all our artificial neural networks combined and it has no neurons because it is merely a single-cell organism [1].

Which proteins code for organisms that compute?