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jkimmel

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Quantitative biologist.

Co-founder & Head of Research at NewLimit. Previously Principal Investigator at Calico, PhD at UCSF.

If you're in town, feel free to shoot me an email to chat about how cells work, aging research, the life sciences, startups, or the local coffee shop landscape. I'm always looking to learn from interesting people.

@jacobkimmel on Twitter et. al.

jacobkimmel@gmail.com

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Notion thankfully does support LaTeX, but only in equation mode (e.g. `\[...\]`, not `\(...\)`).

Just type `/math` in a Notion document to bring it up.

even going so far as to pay a nanny

I really like this idea as a way to expand access to startup opportunities.

Have any acceleartors/incubators experimented with offering child care? I imagine that economies of scale could make that more economical than having X% of each investment go to child care with no coordination, even if it was just a group-rate contract with a local child care center.

This is definitely an Umami Burger problem. I've had it there and at Cockscomb down the block, and it's infinitely better at the latter location.

As a former Orlandoan, I would pull Orlando from that list based on public transit.

Transit in Central Florida is basically non-functional, and not likely to change anytime soon. The region is entirely car-centric, and there is a strong cultural bias against public infrastructure of any kind.

You can surely look up a map with lots of bus lines drawn across the Orlando core (Lynx), but the service is so remarkably horrific, I never met anyone who used Lynx in the 21 years I lived in the region.

Likewise for SF, their estimate is $1250/month, which will rent you a garage or a converted living room with a curtain separating it from the kitchen in the far reaches of the city.

As a grad student, this is about my budget for housing, and I promise you I'm not exaggerating.

Short of a drug that provided a permanent cure for opioid addiction itself, I'm not sure what sort of solutions can be pursued by scientific/tech research, as opposed to addressing the root social causes.

People have actually been trying vaccine approaches to opioid addiction for a while, but it's tricky since opioids are small molecules which inherently don't give you a lot to work with as far as antigen presentation.

Apparently there has been some promising evidence recently though. See Derek Lowe's blog below for details.

http://blogs.sciencemag.org/pipeline/archives/2017/06/26/a-h...

There's no reason storing information in a population of DNA molecules is fundamentally unstable.

Yes, mutations occur. Randomly. This means that if you sequence a set of DNA molecules the consensus sequence can still render the proper data string despite flaws in each individual copy.

In the context of generating organisms like this, so long as your stored information is not in a loci that could be mutated to regulate proliferation in a positive way, mutations in your storage string wouldn't propagate in a consensus manner (in some organisms, it's hard to make them grow faster. E. coli for instance have already been optimized to divide pretty darn quickly by evolution).

The same is true for populations of DNA molecules rather than organisms (are any organisms much more than DNA storage and maintenance machines :-D?). Random mutations in one molecule in a tube would be different for each neighboring molecule, but the consensus sequence is still valid.

This all makes perfect intuitive sense when you recognize that even some DNA sequences with no positive effect on growth are fairly well conserved on evolutionary timescales. https://www.wikiwand.com/en/Long_terminal_repeat https://www.wikiwand.com/en/Alu_element

There is a set of assumptions in your argument that I believe are false.

1. Unregulated water use that allows for production of export cash crops will continue

This could easily be fixed by regulating water use properly, such that farmers have economic incentive to grow crops that are less water intensive given that CA is not water rich.

2. Market prices of current export and current import crops will hold constant regardless of growth

That's not how markets work.

If there was a sudden surge in lettuce demand, farmers in Salinas would respond to increasing prices by switching some fields currently used for export crops to lettuce, which would be consumed locally.

This is aided by point (1) above, where we could push this shift with water regulations.

On the whole -- your concerns seem best addressed by sensible regulation of water in CA, which is a long term political problem. Opposing the farm lobby is well known third rail in the CA Leg.

Nativist population control programs are not the solution to a market failure of water distribution, however they might be implemented. Opposing housing construction is even a really poor way to implement a nativist population control program.

If SF housing politics has taught me anything, it's that the nastiest of human behavior is revealed by parking disagreements :(

I never understood the residential parking permit argument anyway.

Public dollars built the road, which now contains public parking spots.

Implementing residential parking permits is a transfer of value from the public domain to private land owners.

In Palo Alto (and the rest of the Bay Area, where land owners are inherently millionaires), this constitutes a transfer of wealth from the public to the wealthiest few.

CA exports a large portion of its agricultural products, including several top exports that are very water intensive to grow (again, almonds, walnuts, dairy & beef).

Moreover, current irrigation methods in the valley are not ideal for water conservation. Many farmers have water rights dating to the 19th century allowing nearly unfettered access to whatever water they can find, providing no economic incentive to invest in conservation infrastructure.

There is no Californian Malthusian crisis, just a story of poor resource management.

https://www.cdfa.ca.gov/statistics/

Only ~10% of California's water use is residential/urban (varies a little bit year to year) [0].

The majority of non-environmental water is used to grow cash crops in the central valley, like almonds, which take 1 gal/almond.

Overall, urban residents have far less impact on climate than exurban residents who drive around in SUVs. It is in the best interests of everyone on planet Earth to make our cities denser and more inviting [1, 2].

[0] http://www.ppic.org/main/publication_show.asp?i=1108

[1] http://pubs.acs.org/doi/full/10.1021/

[2] https://www.theguardian.com/environment/2009/mar/23/city-dwe...

In George Church's book Regenesis, he recounts the interesting story of resurrecting the Pyrenean Ibex by somatic cell nuclear transfer and surrogate pregnancy in a closely related species. The source article is a great read [0].

The animal that resulted died of lung complications shortly after birth, but apparently veterinarians indicated that these complications were totally within the norm of ibex ontogeny, and probably not a failing of the underlying cell biology.

So, for just a few minutes, an extinct species was brought back to life.

[0] -- https://www.ncbi.nlm.nih.gov/pubmed/19167744

Why Momentum Works 9 years ago

Likewise, I'm very impressed with the early article selection. The site itself is beautiful, and interactive figures like the one at the top of this link are incredibly helpful.

Overall -- huge fan!

Harry Reed reduced the threshold for confirming non-Supreme Court nominees to a simple majority, preventing a filibuster.

The Senate was locked 50-50, in which case the Vice President becomes the deciding vote.

I am deeply saddened to read this. I apologize, on behalf of the country.

Please know that the majority of people in the US do not support this policy. We want to see you reach your potential. We want to benefit from the talent you would bring.

Many of us will be working hard to fix this for the next several years.

I'm sorry I couldn't do more to prevent it from happening in the first place.

Quite nearly so.

You have to remember the time constraint on drug profitability (~15 years for a US patent on a new molecular entity).

A new antibiotic would be held in reserve except in exceptional circumstances. Even if it was put to use on day one for extensively drug resistant TB and the like, there are too few patients to find a functional price point. It's sort of like the situation with many rare diseases.

My favored approach for solving this problem is using some sort of prize system (Sanders had a bill to do this for all drugs last year if you want to see a model). Effectively, the government offers $X billion for a new antibiotic meeting criteria Y and Z, ensuring that the private sector has financial incentive. In most plans, the drug IP would become public, allowing for immediate low cost generics.

The situation in the clinical biotech companies I worked at was never that bad because of HIPPA compliance and more focus on networked services like lab databases but still atrocious.

I can attest that academic biotech labs are still pretty atrocious, for the reasons you mention.

Windows XP (or super old OS X installs, pre 10.5) are pretty common on non-networked machines that function as appliances. It's not uncommon to hear about a machine controlling a $X00,000 device being compromised by malware that road in on a USB drive, despite the air gapping.

Sometimes I feel that it would be better for vendors to use a super minimal Linux distribution for each of these workstations that basically function as an appliance. Not only could the vendor reduce the attack surface for any potential malware exposure, but the one-off nature of the distro and small overall number of workstations would provide a minimal incentive for malware authors to target.

If you stood up in the middle of a geology lecture and tried to start an argument about Roe v. Wade

This is a false premise. I've spent my week at a large scientific conference.

We have continually had panels re: our role and responsibility as scientists in the current political environment. Talks on hard technical issues have often included comments alluding to these roles and responsibilities.

Technologists are so deeply involved in the way that modern society perceives the world outside their immediate community that it's absurd to believe they can be apolitical.

Technologists need to discuss their roles and responsibilities as well.

So no -- you would not be thrown out of a room for bringing up politics in a Geology lecture.

HN isn't a Geology lecture at all. It's more like a quad at an engineering school. We're here because we're curious, we like to build things, we want to help create a better world. We cannot do that while insulating ourselves from the reality of our world's most powerful organizations and their leaders.

but even still, that adds only another layer of testing to ensure that your techniques for converting the raw data to structured data are sound enough to be reproduced.

That's actually not correct. What if your validation method is broken? What if that unit test you wrote has a bug in the test itself?

In science you have to keep the raw data available.

This is not only for reproduction of your particular structured metric (i.e. tail flick angle), but for other groups to design novel metrics that may add to or trivialize the published result.

You don't need to be a direct party in a contract to be affected by it.

You can insure against possible negative outcomes of someone else's contracts.

e.g.) Party A and Party B sign a contract that Party B will pay Party A $X by some date. Party A has seperately agreed to pay you $0.9X shortly afterward.

You are a savvy businessperson and realize that Party A will not have $0.9X to pay you if the Party B fails to make their payment.

Party B is on the rocks after a nasty reorg, and you think the probability they fail to pay is significantly greater than 0.

You want to protect your business against this event. To do so, you purchase a Credit Default Swap from Party C for $0.05X that ensures the full $0.9X payment.

While Michael Barry was "speculating" using CDS's, you could also argue that he was "insuring" his firm against a housing crash, which did tank most investment vehicles.

There is single large window displaying text, with lots of space between the lines. At the top, there are tabs with the names of different books. It looks like you can scroll in the large window displaying text to read a book. Also at the top, there are dropdown menus with what I assume are different application options. At the bottom, there is a sliding position indicator labeled "Document position".

It looks the way I would expect an older e-book reader application to look. It seems totally usable and intuitive. I know exactly where to click and what I might expect to happen.

There could definitely be some aesthetic improvements, but as far as "UI functionality" is concerned, this is great.

The SF transit situation is the direct consequence of a failing tax base. The wealth of the local tech industry is not "trickling down" to improve city infrastructure, in proportion to the industry's growth.

I'm not sure this is true. The city budget has grown substantially, now ~$9B [1].

The problem is we don't spend it on transit infrastructure, and when we do invest, we get financially mismanaged projects like the central subway [2].

[1] http://modernluxury.com/san-francisco/story/san-franciscos-i... [2] http://www.sfweekly.com/sanfrancisco/covering-their-tracks-t...

Not only that but power trains are engineered with a half life of ~250-300,000 before they become unusable

This makes me think of an interesting side effect.

Will there be pressure on automotive engineering teams to significantly increase drivetrain half-life in consumer vehicles due to automated-driving?

I imagine there are trade-offs made at present that limit the drivetrain half-life simply because there isn't a great deal of pressure to increase the life of a consumer car beyond 300,000 miles ( 300,000 mi * 1 yr / ~10,000 mi = 30 yr old cars).

Semi-trucks may be a nice example where a similar engineering pressure currently exists. A mechanic friend once told me semi's can drive a million+ miles.