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joshuamcginnis

1,239 karma · joined November 14, 2014

Biologist and software engineer.

Researching fungal natural products and the use of generative AI in biotech.

josh at everymanbio.com

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joshuamcginnis··on U.S. Capitol Locked Down Amid Escalating Protests
That you have to offer that sort of reassurance makes my point.
joshuamcginnis··on Ganja.js: Geometric Algebra Generator for JavaScript, C++, C#, Rust, Python
> Ganja is a Hindi name for hemp, derived from the word ganjha, from the Sanskrit gañjā, referring to a "powerful preparation from cannabis sativa". The term ganja, one of the oldest and most commonly used synonyms for marijuana in the English language, dates to before 1689.

I had hoped there would be a more direct association between the Hindi name and the underlying mathematics given Indian mathematics emerged as early as 1200 BC. Would make for a perfect reverse-psychology alibi.

joshuamcginnis··on Making Playstation 1 Modchips (2018)
I did maybe a half dozen or so - nothing crazy. A lot of people were understandably scared to entrust me with a soldering iron on their expensive toy. Then PS2 came out and modding became much more complex. I do miss the satisfaction of putting in a chip, loading a burned game and seeing it load after a long anxiety-provoking black screen.
joshuamcginnis··on Making Playstation 1 Modchips (2018)
I used to program PSX mod chips and install them 20 years ago from my door room in Jester Dormitory at UT Austin. I printed out an ad, taped it on my door and waited for the knocks to do business. Back in those days, I would burn chips with hard-to-find .bin files using generic EEPROM programmers that used a printer parallel port. And I never had to buy any chips because, at the time, I'd request samples from the big silicon distributors (e.g. DigiKey / Mouser) and they'd send me dozens for free.
joshuamcginnis··on I should have loved biology
Hi there - thanks for the thoughtful response and great list of contacts! I'm actually in talks with a few of them already. Rolando Cruz Perez, I didn't know about and will reach out to chat soon. Appreciate your support!
joshuamcginnis··on I should have loved biology
It can take me weeks if not months to fully comprehend a new paper. One paper will require that I look up a lot of new terms, watch a lot of videos explaining the terms and repeating the process for the cited references. It sounds like you need more structure so I would suggest you take notes, set goals, organize your materials and schedule time for focusing on particular topics, tasks or techniques.
joshuamcginnis··on I should have loved biology
Go to scholar.google.com, search "autoimmune disease treatment", filter by last five years, use sci-hub to read the paper. Repeat until you learn enough to find your next step forward.
joshuamcginnis··on I should have loved biology
I was depressed, yes. But 7g wasn't my first experience with psilocybin. I was just saying that generally, I would not recommend 7g for newcomers. As for being irresponsible, I don't know man. I grew a Schedule 1 drug and then consumed it on my own terms in a way that affected no one but myself in a positive manner. There were risks involved, but when weighed against how I felt at the time, I took the chance.
joshuamcginnis··on I should have loved biology
By serendipity, I discovered a few YouTubers around that time who were showing how to do synthetic biology and biotech step-by-step on the cheap. After the trip, it dawned on me that perhaps I should put my intellectual abilities to work in this new field as it might bring the connection to life and meaning that I've struggled to find in tech.
joshuamcginnis··on I should have loved biology
It was difficult and I wouldn't recommend it for newcomers.
joshuamcginnis··on I should have loved biology
I suffer from pretty bad depression and have been battling with it for a while using all available treatments. Someone recommended I try psilocybin mushrooms. I learned how to grow them, grew them and then had my wife help facilitate a safe well-intentioned trip using 7g of dried mushrooms. Happy to answer any questions about it. It was a profound experience. It isn't a cure but it's certainly a tool in my toolbox that has helped reshaped my life in a real and lasting way.
joshuamcginnis··on I should have loved biology
After 15 years in tech and a life-changing psychedelic trip, I decided to self-learn genetic engineering and share it with the world[1][2] while I look for a meaningful biotech venture to found.

What you can do today from your kitchen or home lab is remarkable. For instance, I taught myself PCR (polymerase chain reaction) and recently published my first genetic sequence at GenBank from fungi that I cultured, extracted, sequenced and aligned. I'm planning to have developed my first GMO yeast in the next 90 days.

If you're interested, I also host the EverymanBio Podcast (YouTube & iTunes) where I talk to folks doing incredible work in the biotech / startup / diybio community.

[1] http://everymanbio.com/

[2] https://www.instagram.com/everymanbio/

[3] https://www.linkedin.com/in/joshuamcginnis/

joshuamcginnis··on ‘Extremely aggressive’ internet censorship spreads in the world’s democracies
If we are going to have an honest conversation about censorship in the United States, we must call out the political left as the principal perpetuator. Whether it's college campuses violently protesting conservative speakers (e.g. Ben Shapiro), tech platforms banning and labeling speech they disagree with (e.g. Twitter, YouTube, Reddit), or corporate America demonizing those whose speak the truth and/or hold differing views from politically left ideologies (e.g. James Damore), postmodern leftist ideology, as articulated so poignantly by Dr. Jordan Peterson, is not only attacking our free speech, but drawing under question the very ideas that form the foundation of our country. I think I speak for many rational liberally-minded small-government constitutional conservatives when I say that it has become increasingly dangerous for us to even have our ideas, let alone express them. This notion that because you feel your ideas you give the moral high-ground you can justify doing horrible things to your fellow citizen with whom you disagree with must be stopped.
joshuamcginnis··on There's a Mason Jar Shortage
Not just canning - there’s been a noticeable increase in interest and activity related to mushroom growing since the pandemic began. Mason jars are commonly used to colonize spawn before fruiting or spawning to bulk.
joshuamcginnis··on When is no-code useful?
I know Fortune 500 companies using online databases like QuickBase to operate their businesses. QuickBase is a sort of web-based relational database meets excel formulas. Business owners love tools like this. I know of a handful that run $50M+ ARR online businesses using no-low-code platforms where the only technical person on payroll is the IT guy that reboots the phone system each day.
joshuamcginnis··on Why are the noses broken on Egyptian statues?
I once took an Africana Studies course at UMass Boston and the professor taught us that the noses were broken off the statues due to the hatred of black peoples by white explorers over millennia. She also taught us that the ancient Egyptians were black and that it was black people that built the pyramids. When I innocently asked her why the slides she showed us seemed to show Egyptians as having more middle eastern appearance, she scolded me on my prejudice and denial. I dropped the class shortly thereafter.
joshuamcginnis··on Open Source PCR Thermocycler
I don't believe that is entirely accurate. Positive pressure systems are designed to blow 99.999% sterile air over the work area to prevent contamination. Commercial PCR workstations will typically take dirty outside air, run it through a prefilter, through a HEPA and then over the workstation either horizontally or vertically - blowing away any contamination that might be brought towards the sample. I'm not sure I've run into anyone who do this kind of sterile work who has necessitated the need for the kind of negative pressure system you're suggesting.

Also, I'm learning how to do DNA barcoding and typically, the PCR product isn't opened but rather sent off for sequencing or analysis. Anyway, thank you! Maybe I'm wrong so I'm happy to hear your thoughts. And thanks for the support.

joshuamcginnis··on Open Source PCR Thermocycler
A thermocycler is simple: it heats up and cools down in series of programmable cycles. The thing being heated and cooled is often a tube of DNA and reagents. The strands of DNA denature, or separate into individual strands, at a specific temperature and the reverse happens (annealing) at cooler temps. Imagine peeling apart a double strand of DNA creating two single strands. Now imagine making each single strand whole again by plugging in free-floating nucleotides. You'd now have two strands of DNA when you started with one. This is a simplified explanation of DNA amplification and is quite useful for taking a small sample of DNA and making lots of copies for analysis like sequencing.
joshuamcginnis··on Open Source PCR Thermocycler
There's also PocketPCR[0] and MiniPCR[1]. $499 for OpenPCR is still pricey imo when you can buy a proper programmable thermocycler with heated top for less than half on eBay, presuming it actually works.

I'm documenting my journey in self-learning genetic engineering[2][3] and in the market for PCR and electrophoresis setup, so I'd be happy to hear what folks recommend.

[0] https://www.minipcr.com/

[1] http://gaudi.ch/PocketPCR/

[2] https://everymanbio.com/

[3] https://www.instagram.com/everymanbio/

joshuamcginnis··on Coming soon: Fedora on Lenovo laptops
How's the battery life? I dual boot ubuntu and win10 on my T450 and the battery life under win is noticeably better.
joshuamcginnis··on Stanford Student Claims to Run Bootleg Covid-19 Testing Lab
FYI, the same core equipment and supplies will also allow you to do dna-based lab work, such as crispr/cas and fingerprinting for phylogeny, at home. If you're clever, you can replicate the same cutting-edge work step-by-step from published research papers and then use that knowledge to run your own experiments.

I'm currently working on adding the gene for bioilluminescence to p. cubensis fungi. If I can successfully breed offspring with the desire genotype, I hope to sell the novel spores and use those funds to invest in a variety of altruistic research like individualized DNA-based cancer treatment.

joshuamcginnis··on Ask HN: Outreach for Covid-19 longitudinal study proposal?
Check out the OpenCovid19 Initiative[0]. They have many ongoing sub-projects and a dedicated slack channel for developers. You may find help for your project or that something similar is already in the works.

[0] https://itsfoss.com/opencovid19/

joshuamcginnis··on Ten-Minute Coronavirus Test for $1
Ready to ship and April are much different than the countries who have been, and continue to test, upwards of 10Ks+ folks a day. As of today, the CDC is reporting only N=4225 completed tests in CDC labs and N=20907 in other US labs.
joshuamcginnis··on Ten-Minute Coronavirus Test for $1
Five days ago, it was reported that a German biotech company had already produced 4 million tests.[0]

"The tests use what’s called the polymerase chain reaction, a diagnostic method recommended by the WHO that amplifies the virus’s genetic code so it can be detected before the onset of symptoms. The kit comes with two vials: a primer to help detect an infection, and a synthetically engineered piece of the virus, which labs use to produce a surefire positive match to ensure their machines are working correctly. A lab technician combines these ingredients with a patient’s mucus sample—usually from a throat or nasal swab—and results are usually available in a few hours."

Coincidentally, I recently discovered the burgeoning biohacking scene in which many folks are already using affordable PCR thermocyclers in their home labs to do DNA amplification and crispr-cas experiments. I do fungal sequencing for phylogeny myself.

Given the simplicity of the testing process using PCR, why does it seem like the US is moving so slowly with getting tests in peoples hands? Is it the primer or control virus synthesis? Is it the manufacturing process? Is it red tape? If so, which specifically? Is it poor communication? Is it a confluence of factors?

Why isn't every local university or lab working together to at the least, copy the Germans protocol and get to work on manufacturing ASAP? Why isn't there a line of people outside these labs ready to drop-off their sample and get the results online? Where is the American version of the aforementioned biotech startup?

This epidemic and the general response has only reinforced my belief in the future of citizen science and the widespread accessibility of indie biohacking tools and methodologies. There are just too many misaligned incentives in pharma research, leaving huge gaps in the ability to bring new tests and drugs to the market. Look no further than the antibiotic resistant drug problem.

[0]https://www.msn.com/en-us/finance/companies/a-berlin-biotech...

joshuamcginnis··on Find Yourself a Hobby for 2020
Grow mushrooms. It's incredibly rewarding and intellectually stimulating - even if you're like me and don't care for the taste. We are on the cusp of a cultural transformation in how we view, study and use fungi for the benefit of mankind.[0] It's so much more than psychedelics, although profound in its own right.

[0] https://fantasticfungi.com/

joshuamcginnis··on Human-Assisted Archival of Yahoo Groups
Could Mechanical Turk be used to do this? I'd be happy to make a donation to help offset the cost.
joshuamcginnis··on GNU Radio first steps: a FM receiver
I was able to read my neighborhoods unencrypted power meter data within an hour of receiving my first rtlsdr. I also live under a flight path and found it pretty fun to listen to the pilots overhead obtain their landing clearances. Building a dish and downloading satellite images from NOAA or GOES also looks fun.
joshuamcginnis··on The decline of the family has unleashed an epidemic of loneliness
Wouldn't that also contradict the biological imperative to pass on our genes? If having children had an overall and prolonged negative impact on your stress levels, it would also impede humans' ability to effectively procreate since stress has a direct impact on life expectancy and fertility. I can understand that in the short-term, that might be the case, but over a longer period (say the last 10k years) it does not appear to be true.
joshuamcginnis··on Ask HN: Who is hiring? (June 2019)
Theorem | Software Engineers, Solutions Architect, Product Managers and more. | USA, Central and South America, Europe | REMOTE | https://theorem.co/

We are a diverse team of talented engineers, designers, and product managers from 10+ countries and five continents around the world. United in our passion for creating outcome-focused software solutions, we build products for business, many Fortune 500, as if they were our own.

If you're interested in working on a variety of real-world problems from great companies all over the world, I encourage you to learn more. Ideal candidates are located within GMT-10 to GMT+2, have some consulting experience and are comfortable working remotely.

All Open Positions: https://theorem.co/careers

If you find a role that you think may be a great fit, email your resume directly to joshua.mcginnis@theorem.co and I'll make sure it is reviewed by the correct manager.

joshuamcginnis··on Amateur Radio in Space Pioneer Astronaut Owen Garriott, W5LFL, SK
Thanks to you both for the additional resources. I wish I knew about these sooner.
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