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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 Ask HN: Why are resume gaps frowned upon?
To think we punish our fellow man for pursuing all life has to offer, especially over a career spanning decades is a travesty. If I'm hiring, I don't favor someone who's never once broke away from the matrix of 9-5 employment year after year to explore something new or meaningful or to rest.

This hyper-optimization people have to go through now to beat the resume screening algorithms is dehumanizing as it leaves no opportunity for people to explain their individual life choices. I understand why it is the way it is, but I don't like it and it's not getting any better.

joshuamcginnis··on Show HN: Whataaabout.com – unique activity ideas for the holiday break
My first three recommendations: shooting guns, consuming marijuana brownies, axe throwing. Oh my.
joshuamcginnis··on An AI that learns about chemical reactions and designs a procedure to make them
The parent article isn't doing anything more than using ChatGPT as a frontend either. The API does all the _work_ (pipeline running, robot control, etc) while ChatGPT uses it's vast knowledge to interpret, analyze and iterate on future commands sent to the API.
joshuamcginnis··on An AI that learns about chemical reactions and designs a procedure to make them
As an example, asking questions like "show me which genes from my genome are related to growth regulation" requires an API call to give ChatGPT a list of annotated genes from the genome we're studying so it can then filter them into growth regulation related genes. Leveraging ChatGPT's extensive knowledge of genes lets us find new insights into our newly assembled genomes much faster.
joshuamcginnis··on An AI that learns about chemical reactions and designs a procedure to make them
We're pursuing grant-funded research at the moment. We have some hunches on some specific fungal genetic functions but they need to be better characterized before we think about commercialization.
joshuamcginnis··on An AI that learns about chemical reactions and designs a procedure to make them
This is the real-world use-case! We're using to accelerate the discovery and elucidation of novel or unknown gene function in previously unstudied fungal strains.
joshuamcginnis··on An AI that learns about chemical reactions and designs a procedure to make them
This is identical to what I've been building and using my own gpt (via ChatGPT) with API integration to automate full genome base-calling, assembly, annotation and prediction pipelines. Using this approach, me and my team can use it to debug pipeline failures, interpret the results, draw inferences and create context-dependent experiments. There's no leap in the tech beyond GPT facilitating the interaction with APIs, but it is a completely new way of working. This is what I can currently do:

User: Show me my genomes

ChatGPT: Here's a list of your genomes ... [API call to GET /genomes]

User: Annotate genome #nnnn

ChatGPT: Kicking off annotation [API call to POST /annotate]

User: Show me what genes are related to growth regulation for the genome

ChatGPT: The genome appears to have several genes related to growth regulation. Here's a list [API call to GET /genome/X/annotations] ...

User: Design an experiment to knock-out this gene using CRISPR in Aspergillus niger, include the guideRNA specific to this gene.

ChatGPT: Here you go...

joshuamcginnis··on Fly Kubernetes
If the org is going to go that far with managing and scaling their platform, why would they use fly then?
joshuamcginnis··on Fly Kubernetes
Why should one use kubernetes? Or rather, at what point of an apps growth cycle does k8s become appropriate?
joshuamcginnis··on Show HN: I scraped 25M Shopify products to build a search engine
I love your approach; you found a problem and developed a solution for it. And then you got the courage to share with the larger technical community. Good on you.

There's obviously some rough edges (multiple duplicate products, issues with product links linking to empty pages, and no results for broad terms), but don't let that stop you. I'm certain they can all be fixed.

Keep going! At the least, you'll come out of this with an excellent project in your portfolio.

joshuamcginnis··on Inside OpenAI's crisis over the future of artificial intelligence
Much of your question depends on defining "human-level" and AGI. AI is already better at humans at a number of specific tasks. That will only continue to broaden over time until it all aggregates into something that doesn't exist yet but I suspect will look a lot like a multi-modal digital super human. Attempts will be made to slow or deter the effects of technological advances but the evolutionary process will march on nonetheless.
joshuamcginnis··on New York approves the first congestion toll in the US: $15 to enter Manhattan
True and so too have the expectations of services from the public.
joshuamcginnis··on FDA approves a CRISPR-based medicine for treatment of sickle cell disease
Fetal hemoglobin has a lot of biochemical advantages for fighting sickle-cell disease on its own so this is leveraged in the CRISPR solution - e.g. create more of the cells that inhibit the disease in the first place.

https://en.wikipedia.org/wiki/Fetal_hemoglobin#Treatment_of_...

joshuamcginnis··on FDA approves a CRISPR-based medicine for treatment of sickle cell disease
Here's basically how the process works:

* Harvest stem cells from the patient.

* Prepare a DNA plasmid with the Cas9 gene, guide RNA for the desired genetic modification, and an antibiotic resistance gene.

* Electroporate the plasmid into the harvested stem cells. Grow the electroporated stem cells in antibiotic-containing nutrient media. Only cells with the plasmid (and thus antibiotic resistance) survive.

* Expand and freeze the genetically modified cells.

* Administer chemotherapy to the patient to eliminate defective bone marrow stem cells.

* Inject the modified stem cells back into the patient, where they repopulate the bone marrow with the CRISPR edits, aiming to correct the genetic mutation.

This process isn't new but one of the biggest challenges is propagating genetic modifications to all effected cells in the body. This is why it's much easier to GMO an egg / sperm because once the change is made there, it's replicated in every new cell thereafter.

Other techniques utilize harmless viruses to transfect genetic modifications to the body, but this has other trade-offs. mRNA vaccines don't propagate to every cell, but the cells which do successfully transcribe the mRNA are able to generate enough of the target protein that the body can recognize it and develop an immunity to it. Eventually, the modified cells will die and no cells will be left to produce the mRNA vaccine protein.

joshuamcginnis··on LinkedIn is laying off nearly 700 employees
I don't do any outbound messaging. Someone just read one my posts and reached out. That's sort of the ideal way to land customers; have them come to you. It's still hard, just in a different way.
joshuamcginnis··on LinkedIn is laying off nearly 700 employees
I just paid for a "Premium Career" account and it was $250 for one year or $39.99/month. I've gotten my $250 back from consulting leads through LinkedIn, but it stills seems high for the value to the average person.
joshuamcginnis··on Upcoming .com and .xyz domain price increase
How do you know they have lower costs? My local water municipality recently increased prices citing increased pricing across the entire spectrum of equipment, materials, chemicals and labor. This in addition to state-mandated improvements to waste water management that must be completed within a certain timeframe.
joshuamcginnis··on Ask HN: How do you look for jobs in 2023?
UPS is paying $170K on average per driver this year per renegotiated contracts. True, like any job, you start off on the lower side, but unlike other companies, UPS pay begins going way up after just a year and that doesn't include the incredible amount of overtime available to even new drivers.

You don't need to pull in large contracts or even be the business owner of a skilled-trade to do well. Literally every tradesman I speak with is telling me the same thing: we're desperate for bodies; we're willing to hire kids out of high school, train them and pay them > $100K and we still can't fill the seats.

My overall (unpopular point) is that a lot of people are complaining that their high-paid cushy remote job isn't available anymore, while ignoring that there is a huge need for skilled labor in other areas of the economy. This strikes me as a huge opportunity for lots of people, and I don't see it changing anytime soon.

joshuamcginnis··on Ask HN: How do you look for jobs in 2023?
UPS is paying $100-200K for drivers and I can't find a decent plumber, electrician, roofer or concrete installer without paying insane costs and/or waiting for months. Something to consider!
joshuamcginnis··on When the facts change, I change my mind. What do you do?
In addition, I'd add that "not being dogmatic" includes the potential of adopting the dogmatic belief. That's because the idea itself was evaluated for more than just the fact that it was dogmatic; though, the associated dogma can still be considered a variable in the evaluation.
joshuamcginnis··on When the facts change, I change my mind. What do you do?
It's worth noting that this form of dogmatism (e.g. ironic or paradoxical dogmatism) can lead to intellectual arrogance or self-righteousness. If taken to an extreme, an individual can become close-minded about their own beliefs regarding open-mindedness. I see this a lot in today's society, especially amongst many young people who may not have accumulated enough life experience to understand why others might have come to think differently than themselves.
joshuamcginnis··on When the facts change, I change my mind. What do you do?
What describes being dogmatic about not being dogmatic?
joshuamcginnis··on Let slime moulds do the thinking (2010)
As a collector and researcher of molds[0], I'd just like to point out that "slime molds" are not really molds. They're phylogenetically classified in Protists > Amoebozoa > Mycetozoa. No longer even in the same kingdom of Fungi!

[0] https://everymanbio.com/

joshuamcginnis··on Depression, Anxiety, and Stress Spread Through Employee Mobility (2022)
https://en.wikipedia.org/wiki/Transference
joshuamcginnis··on MIT faculty adopts “Statement on Freedom of Expression and Academic Freedom”
Two things can be true at once: you can abhor the beliefs of others and support their right to express those beliefs. This is because limiting the expression of beliefs will inevitably cause broader global harm to a society as a whole down the road.
joshuamcginnis··on Ask HN: How would you build a ChatGPT detector?
I suspect that in time, this will only accelerate the degree to which AI and human-authored text are indistinguishable from each other.
joshuamcginnis··on Twitter engineer: I thought I’d been hacked. It turned out I’d been fired
There's a mountain of evidence that companies (which by the way, often includes employee who hold equity in the companies they work) are incentivized towards increased productivity but not hours worked. That so many companies are now offering "unlimited vacation", "wellness days", and "no work Fridays" is indictive of this.

One can find fulfillment in hard work and going the extra mile without that expectation from the employer and without expectation of a tangential reward. There is often intrinsic value in hard work that can be rewarding in and of itself.

There have been times in my life where I stayed late or worked weekends on my own accord because I felt the situation warranted it. I wasn't asked to do it and I didn't get paid extra, but I felt good doing it and in the long-run, the short-term sacrifice yield wonderful long-term gains.

joshuamcginnis··on Twitter engineer: I thought I’d been hacked. It turned out I’d been fired
Generations of workers fought for the _choice_ to not work weekends. Some people, including myself, are happy to work weekends and long hours if its worth it. The point is, it should be the workers choice and if they don't like it, they should be able to leave and find something better. There are clearly still plenty of engineers at Twitter who have done the cost-benefit analysis and decided staying was right for them.
joshuamcginnis··on How many decimals of pi do we need? (2016)
Is there any relationship between pi and fractals?
joshuamcginnis··on Ask HN: YouTube Problems Today?
Official update thread: https://support.google.com/youtube/thread/159624032/known-is...
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