Science

Hi everyone :) 

My name is Jiwon and I run XX, a 12-week accelerator program that invests in super early founders.

We're funding $50K in companies tackling the coronavirus and I thought many people at DIYbio must be working on projects creatively solving for the crisis. 

We also pair founders with super experienced founders who'll help build fast and grow. 

Happy to answer anyone's questions! Our deadline is this Friday, April 3rd and I hope many from DIYbio apply!

Jiwon

That's you on soundcloud? beautiful work

On Friday, March 27, 2020 at 5:48:16 AM UTC-4, Vanessa lorenzo toquero wrote:

Thank Yuriy for this information and thank you Haley and all from bringing up the topic, which is core to my interest.

I work on the media and speculative design context, specifically on the notion of hybrid media ecologies and the sign exchange between machine and biological entity for comunicating  / trigggering actions.

Any readings you would recommend around this topic, or regarding biosemiotics / cyber(bio)semiotics)?

Thank you very much in advance.

Vanessa Lorenzo

www.hybridoa.org

Le jeudi 26 mars 2020 03:30:31 UTC+1, Yuriy a écrit :

When you mention bio-bots, in my non expert opinion, they are mechanically stitched clump of cells functioning on a principle of cellular motors, having some rigid structure to flex off.

They can't be used outside the lab. They can't be used outside the liquid media. This will be useless unless as cells used can be harvested and cultured on a more immunologically and pH, salt, CO2/O2-buffering cell and media independent environment. 

The bio bot still needs an electric input to function just like most other bots.

The bio bot needs to have a 3D printed scaffold.

The bio bot needs to feed.

The bio bot needs to respire (there is now an exception to this rule in animals).

Bio bot must itself be layered to do the desired/designed range of motions.

Even to produce a jellyfish like bio bot, heart and muscle cells are used to populate the extracellular matrix.

Mammal cells are used often as they are best characterized. The media is expensive. 

They could be cultivated to produce humane meat.

This (bio bot) was done to show that it can be done. People publish on these curious fabrications to show they are not sitting on their hands in a university. 

I spoke to an engineer over a concept of planetary proportions once. He said "just because it can be done doesn't mean society will waste its resources to do it." Bio bot is a multidisciplinary cumbersome toy (for now). If you can send it to the organism from which it was sourced, for delivery, even then you might be faced with problems. If someone you know plans to release it to the environment, I have a bridge to sell them. 

Now if the thing was assembled from a clump of rotifer or other next to microscopic animal cells, I wouldn't know what to tell you. Those things are pond scum. They evolved to take on environmental beating.

On Tuesday, March 24, 2020 at 8:39:14 PM UTC-4, Haley Sales wrote:

I know absolutely nothing at all about bio-bots, crispr-cas9 or biohacking. I don't intend to build bio-bots myself.

I just want to know where the research is at so that I can be aware.

I work with blockchain technology and my research is focused on a "trust protocol" that can influence physical infrastructure. This could impact how we manage physical labs & elect/sort expert opinions on research topics.

But what I'm most interested in is propagating the "watcher infrastructure" of this protocol as efficiently as possible. I imagine that bio-bots would be less expensive than regular robots once we've perfected this research.

Feel free to be as scientific as you want. There will be a lot of terms I don't know, but at least now I can be aware of them, so that when I do research later I can figure out how far along we are.

Thank Yuriy for this information and thank you Haley and all from bringing up the topic, which is core to my interest.

I work on the media and speculative design context, specifically on the notion of hybrid media ecologies and the sign exchange between machine and biological entity for comunicating  / trigggering actions.

Any readings you would recommend around this topic, or regarding biosemiotics / cyber(bio)semiotics)?

Thank you very much in advance.

Vanessa Lorenzo

www.hybridoa.org

Le jeudi 26 mars 2020 03:30:31 UTC+1, Yuriy a écrit :

When you mention bio-bots, in my non expert opinion, they are mechanically stitched clump of cells functioning on a principle of cellular motors, having some rigid structure to flex off.

They can't be used outside the lab. They can't be used outside the liquid media. This will be useless unless as cells used can be harvested and cultured on a more immunologically and pH, salt, CO2/O2-buffering cell and media independent environment. 

The bio bot still needs an electric input to function just like most other bots.

The bio bot needs to have a 3D printed scaffold.

The bio bot needs to feed.

The bio bot needs to respire (there is now an exception to this rule in animals).

Bio bot must itself be layered to do the desired/designed range of motions.

Even to produce a jellyfish like bio bot, heart and muscle cells are used to populate the extracellular matrix.

Mammal cells are used often as they are best characterized. The media is expensive. 

They could be cultivated to produce humane meat.

This (bio bot) was done to show that it can be done. People publish on these curious fabrications to show they are not sitting on their hands in a university. 

I spoke to an engineer over a concept of planetary proportions once. He said "just because it can be done doesn't mean society will waste its resources to do it." Bio bot is a multidisciplinary cumbersome toy (for now). If you can send it to the organism from which it was sourced, for delivery, even then you might be faced with problems. If someone you know plans to release it to the environment, I have a bridge to sell them. 

Now if the thing was assembled from a clump of rotifer or other next to microscopic animal cells, I wouldn't know what to tell you. Those things are pond scum. They evolved to take on environmental beating.

On Tuesday, March 24, 2020 at 8:39:14 PM UTC-4, Haley Sales wrote:

I know absolutely nothing at all about bio-bots, crispr-cas9 or biohacking. I don't intend to build bio-bots myself.

I just want to know where the research is at so that I can be aware.

I work with blockchain technology and my research is focused on a "trust protocol" that can influence physical infrastructure. This could impact how we manage physical labs & elect/sort expert opinions on research topics.

But what I'm most interested in is propagating the "watcher infrastructure" of this protocol as efficiently as possible. I imagine that bio-bots would be less expensive than regular robots once we've perfected this research.

Feel free to be as scientific as you want. There will be a lot of terms I don't know, but at least now I can be aware of them, so that when I do research later I can figure out how far along we are.

When you mention bio-bots, in my non expert opinion, they are mechanically stitched clump of cells functioning on a principle of cellular motors, having some rigid structure to flex off.

They can't be used outside the lab. They can't be used outside the liquid media. This will be useless unless as cells used can be harvested and cultured on a more immunologically and pH, salt, CO2/O2-buffering cell and media independent environment. 

The bio bot still needs an electric input to function just like most other bots.

The bio bot needs to have a 3D printed scaffold.

The bio bot needs to feed.

The bio bot needs to respire (there is now an exception to this rule in animals).

Bio bot must itself be layered to do the desired/designed range of motions.

Even to produce a jellyfish like bio bot, heart and muscle cells are used to populate the extracellular matrix.

Mammal cells are used often as they are best characterized. The media is expensive. 

They could be cultivated to produce humane meat.

This (bio bot) was done to show that it can be done. People publish on these curious fabrications to show they are not sitting on their hands in a university. 

I spoke to an engineer over a concept of planetary proportions once. He said "just because it can be done doesn't mean society will waste its resources to do it." Bio bot is a multidisciplinary cumbersome toy (for now). If you can send it to the organism from which it was sourced, for delivery, even then you might be faced with problems. If someone you know plans to release it to the environment, I have a bridge to sell them. 

Now if the thing was assembled from a clump of rotifer or other next to microscopic animal cells, I wouldn't know what to tell you. Those things are pond scum. They evolved to take on environmental beating.

On Tuesday, March 24, 2020 at 8:39:14 PM UTC-4, Haley Sales wrote:

I know absolutely nothing at all about bio-bots, crispr-cas9 or biohacking. I don't intend to build bio-bots myself.

I just want to know where the research is at so that I can be aware.

I work with blockchain technology and my research is focused on a "trust protocol" that can influence physical infrastructure. This could impact how we manage physical labs & elect/sort expert opinions on research topics.

But what I'm most interested in is propagating the "watcher infrastructure" of this protocol as efficiently as possible. I imagine that bio-bots would be less expensive than regular robots once we've perfected this research.

Feel free to be as scientific as you want. There will be a lot of terms I don't know, but at least now I can be aware of them, so that when I do research later I can figure out how far along we are.

I know absolutely nothing at all about bio-bots, crispr-cas9 or biohacking. I don't intend to build bio-bots myself.

I just want to know where the research is at so that I can be aware.

I work with blockchain technology and my research is focused on a "trust protocol" that can influence physical infrastructure. This could impact how we manage physical labs & elect/sort expert opinions on research topics.

But what I'm most interested in is propagating the "watcher infrastructure" of this protocol as efficiently as possible. I imagine that bio-bots would be less expensive than regular robots once we've perfected this research.

Feel free to be as scientific as you want. There will be a lot of terms I don't know, but at least now I can be aware of them, so that when I do research later I can figure out how far along we are.

To be clear I am in no way advocating testing of possible infected individuals in a community lab setting.

My primary goal here is to do environmental testing. Right now there is a lot of fear around this virus and there is a high likelihood that it is not yet present in most of our communities. I fear by the time it is actually present that response fatigue will have set in and people will have become more lax in self-protection. With the long latency period, while virus is being shed, it is likely that sampling of public banisters, buses, etc. may show evidence of community spread of the virus prior to showing active cases in any particular area. This would be an indication of the need to take stronger self-protective measures or at least get an updated "go to the hospital and get tested if you're ill" message out there.

In terms of primers and evidence of their working, during the initial calibration of the test I expect will have to spread some of the positive control on surfaces in the lab and see if they can be picked up, sensitivity, etc.

In terms of safety considerations, I think that this is helpful to public safety and the safety of individuals involved in the effort. Since we are discussing sampling of public spaces that are generally presumed safe, or at least safe pending mitigation such as frequent hand washing, it would seem that no additional safety risk is presented. And the act of sampling itself increases awareness of the possible vectors for infection. If we included primers for something more common, rhinovirus for instance, that we could expect to see in many places it would further the awareness of which surfaces tend to promote contagion.

It would be great if there were a test that people could do at home if they felt that they were infected, but as noted above that could have nothing to do with infected individuals or their samples entering a community lab. One approach that is promising is the dipstick-based isothermal amplification approach coming out of the Zhang lab. https://www.broadinstitute.org/files/publications/special/COVID-19%20detection%20(updated).pdf

In terms of links, I am collecting others and will update but here are a couple of the sources I mentioned:

https://www.biobasic.com/coronavirus-covid-19-primers/

https://www.molecularcloud.org/How-to-detect-the-2019-novel-coronavirus.html

https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-detection-instructions.html

and a couple different kit approaches:

https://www.idtdna.com/pages/landing/coronavirus-research-reagents

https://www.sciencellonline.com/PS/7038.pdf

Derek

On Saturday, 29 February 2020 00:20:49 UTC-8, Thomas Landrain wrote:

I think we all agree on not transforming DIYbio labs into local diagnosis medical labs for contagious diseases. Way too dangerous and irresponsible :/

However, I'm seeing an opportunity for this community to perform "safe" research projects to develop cheap and easily implementable methodologies to detect the presence of the virus. Such as the one proposed by Derek where he uses a small piece of its DNA sequence. 

The approach would be the same as for the open insuline project, the research can be done safely, but the implementation has to be done in a controlled environment which cannot obviously be DIY labs. The goal is to obtain scientific and technological commons that can be used and improved by the global community, medical scientists and international health organizations included. 

BioCurious, OpenCell and Derek's pioneering efforts in trying to contribute to understanding and fighting Covid-19 need to be continued and this crisis is an important opportunity to mobilize safely our community around it. 

Thomas 

On 29 Feb 2020 at 08:23 +0100, Jonathan Cline <jnc...@gmail.com>, wrote:

This is a terrible idea.  No one in a DIY community should be actively going within 50' of someone who wants a covid swab test.  This is a highly contagious virus.  It is not something you want to do for the LoL's or the rep's.  The first medical doctor (and others, probably) who treated patients in China is now dead himself.  It is not something you want to do in a community environment, where, once you are infected from the DIY patient solicitations, you also infect others in the ad hoc unprotected community lab, since you may not show outward symptoms for a week or more.  Do some critical thinking, eh?   This is not the DIY project you are looking for.

On Friday, February 28, 2020 at 4:20:57 PM UTC-8, Thomas Landrain wrote:

Hi there from Paris, France,

Great initiative! 

I'd love to help organize a community of contributors aiming to design a DIY 2019-nCoV diagnosis test. I'm a biologist myself

... 

I also believe we should start organizing our DIYbio community around this very goal and research various ways to provide DIY/cheap 2019-nCoV testing abilities and methodologies that are well documented and that can be reviewed by the international community too. 

Let me know if you like this idea and if yes, we can start documenting the projects on JOGL and mobilize people around them. 

-- 

## Jonathan Cline

## jcl...@ieee.org

## Mobile: +1-805-617-0223

########################

 

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Anyone tried it?  Someone just recommended it to me.  Another Church company.  I don't understand how is this different than Veritas 2.0? 

On Thu, Feb 20, 2020 at 1:47 AM Nathan McCorkle <nmz...@gmail.com> wrote:

Starting a new thread on this.

Just heard of this, supposedly, $300 genome for 30X coverage:

https://nebula.org/

On Sun, Feb 16, 2020, 1:32 PM drewbug <dr...@drewb.ug> wrote:

https://www.dantelabs.com/

On Wednesday, February 5, 2020 at 11:31:59 PM UTC+1, Dakota Hamill wrote:

Not to hijack your thread Nathan, but since Veritas is dead or dying, is there anywhere to get your whole genome sequence for $1,000-$2,000 yet? 

On Wed, Feb 5, 2020 at 5:28 PM Dakota Hamill <dko...@gmail.com> wrote:

Anecdotal evidence which I'm not even sure is related but after I got mono-nuceleosis (Epstein-Barr Virus) and was bedridden for a month at 14-15 my parents said something changed about me forever.  Always lethargic and depressed, gained 80-100 pounds, and ended up getting GI problems and some kind of auto-immune inflammatory problem with a lot of blood in stool and many other issues.  https://www.mdmag.com/medical-news/can-epsteinbarr-virus-cause-autoimmune-illnesses

Fun times. 

On Wed, Feb 5, 2020 at 5:20 PM Jason Bobe <jaso...@gmail.com> wrote:

On Wed, Feb 5, 2020 at 5:04 PM Nathan McCorkle <nmz...@gmail.com> wrote:

It's an idea I've thought of each time this "immune amnesia" topic comes up, but I don't see any "legitimate" discussion on it.

Digging a bit into immune amnesia, it seems the existence of that idea is even argued. Though I can't tell if those claims are legitimate either, since I mostly found search hits on blogs and websites with "doctor" in the URL (which at first reaction seem 50:50 untrustable).

This is a very cool paper, using PhIPseq to characterize antibody repertoire of people pre- and post-measles infxn, as well as people pre- and post-MMR vaccine:

https://science.sciencemag.org/content/366/6465/599

and brief summary:

https://www.sciencemag.org/news/2019/10/how-measles-causes-body-forget-past-infections-other-microbes

 

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