Saturday, January 29, 2022

Enzyme Pipeline


The next twenty years are going to make changes in the first 60 years of our experience look quaint. Coming fast are AI, Robotics, IOT, radical advances in materials science and engineering, Biotech, movement into outer space (Starship) as well as innerspace (VR), CAD, networking and computing, big data, etc. It's not just the incredible advances in things individually, it is the synergy of those advances. A perfect example is something that made my friend a lot of money investing in Nvidia. Advances in monitors, CPUs, network buses, and software led to graphics cards as separate engines to run highly parallel graphics routines. Techniques enabled by advances in AI made GPUs into GPGPUs and, for instance, predicting protein folding, and beating everybody/anything anywhere in Chess followed. Protein folding is a biggy, once we can design and build the right enzymes we can re-engineer bacterial genomes to build enzyme pipelines that would do chemistry impossible otherwise. There are some useful chemical structures (explosives for instance) for which we have designs we know work because they have an activation barrier on the reverse side that renders them stable. We don't know how, or even if it is possible using conventional chemistry, but get this, I should probably find somebody to patent this:


It does not matter how you house the pipeline. I would think that it would just be easiest to house it in bacteria because the engine that builds the device and the engine that builds the engine that builds the device requires such an environment. That's likely a patentable idea itself, but there is something more:

You design and build a pipeline that takes precursor molecules, and alters them step-wise such that multiple reactions assemble something that would otherwise be essentially impossible. 

1) Precursor molecules floating about
2) Precursors bind to enzyme activation site
3) Bound precursors Red and Blue start self assemble
4) Bound precursors Red and Blue self assemble
5) Assembled Red and Blue move across second enzyme
6) Red/Blue begins self assembly with Purple
7) Final output molecule finished
8) Finished molecule released



 
Believe it or not, that's not the big trick. The big trick is this: 
You find/design a molecule you want made
You give it to a chemical building device 
Software reverse engineers intermediate steps needed
Software uses AI to figure out what proteins will fold to enzymes that will do the job
Software determines what intermediates are needed to build the pipeline
Device creates DNA that codes for the proteins and enzymes
Device builds pipelines
Device runs pipelines
Device collects and delivers released molecules. 
Fin.

A few enormous breakthroughs are required for the above, and as far as I know they have been made and are being refined for production now. 

The pipeline above has a lot of fussy bits, but it is buildable. When we were in high school it was not even conceivable that something like this was possible. Now it's conceivable and in a decade or two it will just be technology. 

A set of pipelines similar to the above might be able to assemble carbon nanotubes to make cable for a space elevator. It could also be used to productionize the building of these pipelines so the thing can bootstrap upward. 

Yes, COVID is real.

Questioning whether or not we are in a pandemic is nonsensical on its face. Questioning things like tests for COVID, betrays a fundamental lack of understanding of statistics, chemistry, sampling techniques, and titration. 

It also displays a lack of understanding of psychology, and social mores. Regardless of any technical matter, if you are refusing to vaccinate and mask, then you lack judgment. You should not be advising people on strategies for dealing with life-threatening disease.

Healthcare systems are being overwhelmed because of the spread of the virus. Advice not to mask or vaccinate exacerbates an already thus far uncontainable problem. Every single person you convince becomes a vector for disease. Even in the case of the vanishingly small likelihood that you are correct that the danger is low, and a majority of the world’s medical people are somehow mendacious or incompetent, It is bad manners to advise against simple measures that make people more comfortable that their loved ones will be safe.

I will hazard a guess that you have been wrong before in your life about something. The evidence says that you are badly mistaken in this case both as a technical matter and a social one.

You may well be correct that we are propagandized, that main stream media is often untrustworthy, that there are many conflicts of interest that make judgement difficult, and that the majority of people are ill-equipped to examine evidence. Conspiracies do exist. However, there is not a world-wide conspiracy among medical personal to fake evidence, lie about ICUs being stressed, and create elaborate false reports. 

It is easy to examine tons of material put online by me, and to verify that I am a real person with a family, a house, and a dog, as well as technical credentials and a track record of technical success. I am not involved in a conspiracy about this. I examined the data about this at the very beginning, and continued to examine data for more than a year. The evidence of which I am aware tells us that the pandemic is quite real, and that simple harmless measures like masking and getting vaccinated will save lives. 

If your belief is simply unshakeable, at least keep your physical distance from people, like me, who are at risk and who have families that care about them. Don’t be wandering about in public places spreading disease. Surely you can see that even if the disease is illusory you still make people uncomfortable if you are unvaccinated, unmasked and exposing yourself to people's loved ones. 

If you have ever, in your life, discovered that you have been incorrect and changed your mind, I highly suggest that you stand well back and re-examine, not just those things that confirm your clear biases, but also, as I have done, evidence that contradicts your point of view. I am, like everyone else, imperfect. However, it was clear to me even back in early 2020, that this was an aggressive pathogen spreading at an exponential rate. I got the data and did the numbers myself. For theories that this is a fake pandemic to be correct, nearly every agency in the world reporting numbers for more than 5 billion people is incompetent or dishonest. Anybody sufficiently numerate will realize that this is improbable to the point of being essentially impossible.

The raw data for more than 200 countries from Jan 2020 through to the present can be downloaded from github. The data supports the fact that COVID has had a severe impact

https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv?fbclid=IwAR1ofHb27OqQnXPQVmlxUNjonYhXZoBEzGPEeE8js2dgRn06uPhXJdfNf_E

Javascript webp to png converter

[Done with programmer's assistants: Gemini, DALL-E] OpenAI's DALL-E produces images, but as webp files which can be awkward to work ...