Is BioBricks Free Genes Project still maintained and alive?

[Dorif]

Last submission ( https://docs.google.com/spreadsheets/d/1j5Gc7KEfRlPCIaXMGjDhgQDfSOVx7tnbss9AksrHhzk/edit?usp=sharing ) is in year 2018. Majority of sequences listed in spreadsheet are unavailable. I've tried to submit a gene (adenovirus death protein, for malignat cell lysis), but received no reaction, just autoreply from bot.

So, is it still alive?

Thanks for help!

[Koeng]

It's still alive, just turns out handling incoming single requests takes way too much time. I pretty much only handle collections of materials now. Some of those can be had on stanford.freegenes.org (password: freegenes). 

If you have a good collection of genes (>20 genes) we can definitely talk, though. 

[Dorif]

By the way, are you working at stanford freegenes.org ? If yes: may you help me? I need pro forma invoice for my order (FreeGenes-1584). Our customs are getting mad when see things with zero price. So I need this invoice with any ridiculous value for these items just to receive them. The same will be actual for FreeGenes-1599.

Thanks in advance!

понедельник, 4 мая 2020 г. в 18:33:01 UTC+3, Koeng:

[Koeng]

Not anymore, unfortunately

[Dan Kolis]

Is this summary correct ?

" The aspiration of many people in bio sciences that electronics provides macro concepts useful for application of nucleotide sequences is essentially incorrect. "

" These notions, ( that simplify life processes ),  cannot be excised from viable life systems, including chaperones, post translation mRNA edits, long standing methylization attachments, and literally hundreds of biological effects implemented in life as built by Mother nature, in everything alive. "

Finally: "The reused terminology and desire to make VLSI like IDE's, ---may be useful in development of synthetic biology, but it appears this is almost simply a dead end. "

Is this possibly correct ? 

Regards,

Daniel B. Kolis

PS I saw paper saying the actual wet-lab attempts with BioBricks DB plopped into glassware had a success rate by the applicable goals of each project of around 2%. My belief system is that is not zero... But the notion itself needs a full scale downgrade from first principles. What replaces it is: MORE USUAL HARD WORK AND NEW IDEAS ENTIRELY.

what do you think ?

Daniel B. Kolis

[Eric]

molecular cloning in itself as a molecular biology technique is automatically regarded to some/most as 'biobricks' activity but its use far predates the synthetic biology movement

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[Dan Kolis]

I thought the biobricks 'story' is a uniform 'design' of promoters and so on, so gene expression of novel organisms includes adding protein expression with a cookie cutter uniform approach.

I'd guess this involves protocol so the urge to fulfilment is with a predefined approach; ex cut with a certain R.I. add this or that to detect which cells 'took', etc.

 Not the major contribution of them, then ?

Isn't something akin to mail order mitosis, in in itself, barely worth a yawn ?

Daniel B. Kolis

 

[Abizar Lakdawalla]

are Dan Kolis answers from a random sentence generator?

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[Jonathan Cline]

Biology is nanotechnology using nanomachines; therefore it is possible to create CAD systems which create compatible and/or replacement nanomachines to either interface with existing biology, or to simply create a New Biology.  The present limitation is that the design rules of the nanotechnology are not well understood or replicable, thus leading to a "design by trial & error approach" rather than a "design by known rules" approach, and that is the fundamental weakness in biology and biological engineering today.  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.

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## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223

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[Dan Kolis]

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

[Eric]

as the saying goes 'biology is technology,' there's even a book with such a title

but technology as a term that engineers use should refer to 1) who built it, and 2) what it's built to be used for, nothing more.  thus it seems we're caught between a technology without an application (think google glass) and something more sinister and disturbing, so i'd just leave it at the former

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[Dan Kolis]

Well, I'm more interested in making molecules listen up to human urges then worry endlessly about what those urges might be.

 I mean, is it time to yawn on this line item yet ?  Scholars heavy hitting on the invoicing-the-learned-institutions on systems for a perfect world go nowhere. Until the things do something all the way, no decisions are made on what's what. I think that sort of thing is for all practical purposes, a total waste of time. 

But even a single line item in the full flower of the 'story of biotechnology' can be pretty remarkable. For instance, tweak crops so just the right amount of nitrogen is fixed back without fertilizer, or maybe cure a couple diseases here and there.

And this moves Biotech from Sciencey fun stories to the reliability of technology. And a DIY subset is a perfect straddle of Science as fun to technology, totally. So This is a good spot to discuss how to make things work I think first, since what they do is decided by crazy uniformed processes anyway, yowling about it is a waste of attention span.

Of course, invoicing 3rd parties to dispense wisdom nobody listens to much is great work if you can get it.

Daniel B. Kolis

[Dan Kolis]

The book "DIY Scientists Hack the Software of Life" is breezy and full of DIY stories not much technology or science really.

2011 Marcus Wohlsen

Well written from an entertainment point of view. but lots of the little side projects and people stories are interesting enough. I'd say worth a lib lend for sure. I happily Borrowed a paper copy from Toronto's bizarrely well equipt public library.


Lots of San Fran, NYC and Boston in this book of course.

And so it goes,

 

Daniel B. Kolis

my ref: Jan 2023,  https://groups.google.com/g/diybio/c/X7S8oFe1CPc. nafl, DIY