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

2:12 PM |


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



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

12:01 PM |

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

On Wed, Dec 28, 2022 at 12:56 PM Dan Kolis <dankolis@gmail.com> wrote:
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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[DIYbio] Re: Is BioBricks Free Genes Project still maintained and alive?

9:56 AM |

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

8:53 AM |

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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## jcline@ieee.org
## Mobile: +1-805-617-0223
########################
 

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

5:51 PM |

are Dan Kolis answers from a random sentence generator?

On Tue, Dec 27, 2022 at 12:59 PM Dan Kolis <dankolis@gmail.com> wrote:

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



 

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

12:59 PM |


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



 

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

11:58 AM |

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

On Tue, Dec 27, 2022 at 12:13 PM Dan Kolis <dankolis@gmail.com> wrote:
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



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

9:13 AM |

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



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Re: [DIYbio] Re: "Theranos, CEO Holmes, and Former President Balwani Charged With Massive Fraud"

2:26 PM |

https://www.cnbc.com/2022/12/07/former-theranos-coo-sunny-ramesh-balwani-sentenced-for-fraud.html


https://people.com/crime/elizabeth-holmes-is-pregnant-with-her-second-baby-it-is-revealed-sentenced-to-11-years-in-jail/

https://www.cbsnews.com/news/elizabeth-holmes-prison-minimum-security-bryan-texas-theranos/


Now the leaders of Theranos are convicted of Fraud. 
On Thursday, January 27, 2022 at 12:48:15 PM UTC-8 Biology Discussions wrote:
Good Points!

On Thursday, January 27, 2022 at 12:29:00 AM UTC-8 Nathan McCorkle wrote:
I read all 3 articles you just posted... none of them commented on her
voice being same or different... which is all I wanted to know.

On Wed, Jan 26, 2022 at 12:05 PM Biology Discussions
<discussio...@gmail.com> wrote:
>
> https://www.npr.org/2022/01/24/1075364585/elizabeth-holmes-stanford-rape-sexual-assault-report
>
> https://www.nytimes.com/2022/01/24/opinion/theranos-venture-capital.html
>
> Update Elizabeth Holmes convicted of Fraud
>
> https://www.theguardian.com/technology/2022/jan/13/elizabeth-holmes-sentence-september-fraud
> On Monday, November 29, 2021 at 4:53:28 AM UTC-8 Biology Discussions wrote:
>>
>> https://www.youtube.com/watch?v=67q_1zg-fZM
>>
>> Here is the latest on the Theranos Fraud Trial. Yes this included a false HIV test.
>>
>> On Wednesday, September 1, 2021 at 10:41:08 AM UTC-7 Jonathan Cline wrote:
>>>
>>> Twisted plan to become pregnant & give birth to coincide with the
>>> start of her court trial and use motherhood as an excuse for lenient
>>> sentencing.
>>>
>>> Anyone want to bet she won't continue to use her fake "low voice"
>>> during the trial ?
>>>
>>> On 8/31/21, Biology Discussions <discussio...@gmail.com> wrote:
>>> > https://www.fiercebiotech.com/medtech/elizabeth-holmes-fraud-trial-begins-a-timeline-blood-testing-startup-theranos-downfall
>>> >
>>> > Update Elizabeth Homes on Trial.
>>> >
>>> > On Wednesday, March 17, 2021 at 9:13:19 PM UTC-7 Biology Discussions wrote:
>>> >
>>> >> https://www.youtube.com/watch?v=gtAg9Z_3cgw
>>> >>
>>> >> Here is an overview of the Theranos Scandal.
>>> >>
>>> >> On Friday, March 12, 2021 at 9:38:30 PM UTC-8 Biology Discussions wrote:
>>> >>
>>> >>>
>>> >>>
>>> >>> https://www.cnbc.com/2021/03/12/elizabeth-holmes-trial-delayed-because-shes-pregant.html
>>> >>>
>>> >>> Here we go again
>>> >>>
>>> >>> Former Theranos CEO Elizabeth Holmes, whose criminal fraud trial was
>>> >>> scheduled to start in July, is asking for a delay because she's
>>> >>> pregnant.
>>> >>>
>>> >>> In a court filing on Friday, her defense attorneys and prosecutors asked
>>> >>>
>>> >>> Judge Edward Davila to delay the start of her trial by six weeks to begin
>>> >>>
>>> >>> on August 31, 2021.
>>> >>>
>
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Re: [DIYbio] Glowing Freshwater Algae?

8:02 AM |

Folks, what's the worry about toxicity? Pyrocystis bioluminescent dinoflagellates that are widely available to hobbyists, and aren't toxic.


If you're trying to make freshwater algae, i.e. Chlamydomonas, that glow continuously the fungal luminescence system might be your best bet.

All the best,
-Tim

On Dec 13, 2022, at 7:56 AM, Dan Kolis <dankolis@gmail.com> wrote:

Disappointing you have had no support on ths. I watched that over time with some dismay.

I think though, you need much more specific info then the question you asked, too generalized. Certainly there is more to the potential work then simply if it radiates.

How to make, what you want to make is perhaps a more answerable question !

DNA is pretty generalised the last time I checked.... However every aspect of utilising it by direct human intent, --is racked with details.  Fortunately, the particular humans who know about it, like details.

Regards,
Daniel B. Kolis

my ref: nafl, 13 Dec 2022, pp, CoryG







On Monday, November 28, 2022 at 1:27:53 AM UTC-5 Cory J. Geesaman wrote:
Any ideas on how to go about splicing together glowing freshwater algae (preferably without all the toxic side-effects of naturally-biolumenescent-algae?)

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