Re: [DIYbio] Re: Is BioBricks Free Genes Project still maintained and alive?

It was said moment ago...:

 

" Today's methods, BioBricks or other, are tremendously overhyped and the "design by trial & error" methods have a failure rate of near 100% when scaled beyond the trivial.  The journalists universally fail to report these facts and unfortunately are never held accountable. "

Dan says:

Regarding the blued text especially.

Huh. I suppose this is roughly a verification of what I believed and poked in here as text, unfortunately.

It's remarkable how ( hopefully its unintentional ) misleading the WWW stitched around databases is for these alleged magic rabbits-from-hats systems composed of WWW programs, fat PDF's and CSV ( or more fashionably, TSV ) files.

I worry I am rattling on about the obvious, but you might notice I am interested in numbers that create milestones in time, or other ways to estimate actual, as opposed to synthetic, progress.

One way I thought about it lately is the H.S.-tuna-fish-to-ATP benchmark. The baseline is, if I gobble back a tuna fish sandwich and a map is developed from plate to ( ATP and 10 A.A); and we assume the area under the curve is 95% the mass of the food; ( ex. exclude metabolics for the olives, maybe etc.). How many unique proteins are in that transformation ?

e1) < 100

e2) > 100 < 1000

e3) > 1000 < 5000

If you go super low and dare e2. think how reliable each transformation has to be characterised to win ? If many are 30 xforms long ... and 98% percent grokked. 30^ in that subset is in for failure in series is ... 0.98^30 = 0.55

So if either the deviation from the central dogma, errors of omission, mini-fraud, whatever is at 98% some are only 1/2 good. out of 30 of those, the chance ones important and completely obliterates the analysis is kind of well, certain.

 So beyond P.R. to get funded, get queen-kissing-ops with Nobel Prizes, etc Mother nature has made this not medium hard but really, really hard. 

I wonder if this kind of thinking has utility, or the general approach is: "Shut up and keep shoveling", that is the hard way is the only way... period. 

A.I. programs kind of allow some more deviation to allow the unknown, but expecting a lot of them seems to me more misrepresentation, maybe.

I'd suggest a lot more humility in goals, and specifically NAMING of projects etc would help slightly. To explicitly discuss hoping to get from 2% to 10%, not a vague sci-fi ready story that's some mix of wishful thinking and fraud.

Regs,
Daniel B. Kolis

my ref: BioBricks, blog, 28 Dec 2022, JonC

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