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jkimmel

917 karma · joined June 1, 2012

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

submissionscomments
jkimmel··on A radically simple idea may open the door to a new world of antibiotics
>guarantees you won't things that can't be learned from the single, genetically uniform mouse type that is used.

This is a misrepresentation of the state of mouse biology research.

We use many different strains of inbred mice (check out the JAX Labs list of available inbreds)[1]. Inbreeding reduces the genetic variability of our mice, allowing us to control more of the variation in an experiment. This allows us to perform pilot studies with smaller samples sizes while still reaching sufficient statistical power. This is important -- mouse biology is expensive, and we try to discover as much as possible with limited funding.

If a result merits generalization to multiple backgrounds, it is often tested in multiple inbred strains and an "outbred" strain that is genetically diverse.

[1] - https://www.jax.org/jax-mice-and-services/find-and-order-jax...

jkimmel··on Sam Altman's Twitter AMA
This is true. However, you can get to any topic you want easily using the search feature. A Table of Contents is provided, making front-to-back reading by topic pretty trivial.

I've taken many university courses using this book and managed to read all the required material on NCBI without much effort.

jkimmel··on Sam Altman's Twitter AMA
Molecular Biology of the Cell (Alberts) is free through NCBI! Many investigators jokingly refer to it as 'the bible'.

http://www.ncbi.nlm.nih.gov/books/NBK21054/

jkimmel··on Theranos Trouble: A First Person Account
They take smaller blood draws from finger tip pricks that aren't large enough in volume to run on a standard machine from Siemens et al.

To get around this, they supposedly dilute the samples to a point where the concentrations of analytes are well below the machines minimum operating specifications.

jkimmel··on OS X 10.11 El Capitan: Review
Here's to hoping Bluetooth on my Macbook won't stop working every time I put the computer to sleep. Then hanging the entire system when I try to toggle it off/on.
jkimmel··on A Huge Overnight Increase in a Drug’s Price Raises Protests
It appears Martin Shkreli has tried this a couple times before.

http://blogs.sciencemag.org/pipeline/archives/2015/02/20/mor...

In the past, he actually planned to limit access to the existing drug (ie. the one he increased the price on) to prevent a competitor from creating a new generic formulation and gaining FDA approval. It appears he modeled this heinous approach on a maneuver by Celgene to prevent production of generic thalidomide.

http://blogs.sciencemag.org/pipeline/archives/2014/09/11/the...

It seems to me that the FDA needs sharper teeth in this arena to ensure access to an existing drug is not a limiting factor in the approval of generics.

jkimmel··on Tell HN: Clickable domains and other new features for story quality
I really like this idea from a historical preservation perspective.

HN comments contain a lot of a value in aggregate, and it would be a shame to lose necessary context to exploit this value due to simple link-rot.

However, I can see issues arising with paywalled links. The HN cache would likely display a rather useless paywall for many of the most popular stories. Navigating around the paywall by technical means may present an IP issue.

jkimmel··on It’s expensive to be poor
>If you've got no money, you end up having to buy eg single cans of drinks instead of large bottles...you'd end up paying a lot more for a similar amount of stuff than someone who happened to have the money for the bulk.

As an aside, this effect may be further pronounced if lower-income consumers don't have the storage space for bulk purchasing.

Even if the differences in price are within someone's budget, they may be forced to purchase smaller, more expensive per unit items because they don't have enough shelf/refrigerator/storage space. In San Francisco for example, I think many people who wouldn't necessarily be considered lower-income consumers are negatively effected by an inability to purchase in bulk.

jkimmel··on China Stock Market Drops 8.5%
Beta is a coefficient that attempts to measure an investment's likelihood to move 'with the market.' The total market has a Beta == 1 by definition, with beta ratings above 1 indicating higher volatility/sensitivity to market movements, and vice-versa. See Wikipedia for how the calculations are made.

https://en.wikipedia.org/wiki/Beta_%28finance%29

In this context, I a 'high beta investment' is likely to move with the market, ie) is dependent on some aspect of market performance. 'Beta capital' I think refers to using sources of capital that are likely to become more or less available depending on the market. I've never heard of capital sources being given beta values though, so I think this may be a finance/VC colloquialism rather than an actual calculated value.

Disclaimer: I am not a VC and may be totally wrong.

http://www.investopedia.com/terms/b/beta.asp

jkimmel··on The abandoned college campuses of Second Life
The university where I did undergrad conducted "Virtual Biology Lab" in Second Life as recently as Spring 2015. A friend of mine got stuck in one of these fake classes. His description made it sound like a terrible excuse for a learning environment, clicking a single button to magically perform dissections while constantly battling connectivity issues.

Of course, they still charge students the full lab fee, as if they were actually purchasing supplies.

jkimmel··on Grooveshark co-founder, 28, found dead in home
My step-sister dated Josh for a while when I was growing up.

My few memories of him consist mostly of Josh explaining technology to me at the dinner table in slow, careful words so that a middle school kid could understand. I remember him laughing with me about the crazy/terrible things I had done to overclock my Android Dev Phone 1 at a time when no one else I knew thought that was interesting. I remember feeling really cool when he hooked me up with free Grooveshark premium to be nice.

It's strange. I haven't seen or heard from him in nearly a decade. He stopped dating my step-sister years ago. He likely wouldn't have remembered my name if you asked him.

Still, I feel like a friend is gone.

jkimmel··on ‘Flash Boys’ Programmer in Goldman Case Prevails Second Time
In the book, Sergey says they simply rip the FOSS license off the header and replace it with a Goldman proprietary license. It's implied that the legality of this is a grey area.
jkimmel··on ‘Flash Boys’ Programmer in Goldman Case Prevails Second Time
In Flash Boys, he makes it clear that he did not take any trading strategies or in-house models.

They don't provide a ton of detail in the book, but it seems that he wanted to take some FOSS code he modified himself while at Goldman. All code ever used on a Goldman machine is licensed as proprietary, even if it was downloaded from a FOSS repository 1 µs beforehand. It's mentioned that some irrelevant infrastructure code may have been intermingled with the modified FOSS he took, though it doesn't seem Goldman was particularly incensed by any particular piece of code, simply by the fact that he took any to begin with.

Also in the book, Michael Lewis brings together a panel of HFT technologists to interview Sergey and assess whether anything he took was consequential. Their collective conclusion after meeting with him for several hours was that he took absolutely nothing of value.

jkimmel··on Fun with Magic
I think Magic could be great as a lower-price-finder for people with a more normal income.

ie.

"I found a rental car for $PRICE at SFO tomorrow. Can you find me anything cheaper?"

If Magic finds you a better deal even with their cut (they work their fee into the price they quote you), they get paid & you still save money.

jkimmel··on Science, Now Under Scrutiny Itself
>The problem with these lab books is that they're often the personal property of the scientists and, as such, almost a sort of diary

Further complicating things, individual researchers don't actually own the books. Often, an institution or the lab owns the rights to the book. This can make individuals who are otherwise keen on "open science" hesitant to place copies of this information in a publicly accessible place.

See page 4 of this manual from the NIH (National Institutes of Health) about the ownership of notebooks.

https://www.training.nih.gov/assets/Lab_Notebook_508_%28new%...

jkimmel··on Tech Startups Woo Investors with Unconventional Financial Metrics
In general, you can simply Google the title of an article and following the link in Google search results will circumvent the paywall.

Google demotes links in their search results if they don't allow "first click" access to the content.

Further discussion in this thread: https://news.ycombinator.com/item?id=9531941

jkimmel··on Twitter’s CEO Dick Costolo Is Stepping Down
> I was talking about the firehose, not the full social graph

Ah, I got a bit muddled in my diction here. I was trying to refer to the firehose. The firehose itself should inherently have some useful graph data though, as you would be able to see all the @reply relationships.

> What issue do you see here? can you expand?

I don't have a great handle on the economics here, but I can envision a scenario where:

cost to deliver firehose (engineering, infrastructure) + (marginal cost/user * users) > market value of firehose/user * users

Again, this may sound silly to someone with a better handle on the numbers behind engineering & maintaining this solution. My salient point was just that I'd be curious to find out what kind of value they could extract from the firehose by selling it directly.

jkimmel··on Twitter’s CEO Dick Costolo Is Stepping Down
Are there any examples of company selling their social graph data in this manner directly?

The other companies I can think of (FB, Google, Tumblr) utilize the social graph to provide ad-targeting services, but don't charge to access the graph itself. The live nature of Twitter's firehose is probably better suited to sale as a recurring commodity than FB or Tumblr's.

I wonder if there's a price point where they could achieve widespread API usage while still making money with standard infrastructure (no custom datacenters, &c.)

jkimmel··on How US students get a university degree for free in Germany
This isn't exactly the case.

Many training funding mechanisms (ie. NIH Training Grants, Fellowship awards, & Career Grants/"K-awards") are not allowed to fund non-residents [1]. Funding international students is a difficult problem for most PhD programs in the life sciences. I don't have direct experience in physical/social sciences, but I believe similar restrictions apply to NSF funds.

I believe most PhD programs cover international students using a mixture of direct project funds (ie. an NIH R01, the same grant that covers reagents/equipment), private fellowships, and endowment money.

1 -- http://www.niaid.nih.gov/researchfunding/sop/pages/foreignwo...

jkimmel··on A book on the persistence of elites is an unexpected guide to getting a good job
I'm not sure if it's uniquely American. I think the secondary school social system is based in the individualistic culture of American society at large, and may appear in other countries with a similar individual emphasis.

In many cases, American children (at least in my region of the country, growing up in the late 1990's & 2000's) are told that they are exceptional at a young age by their parents/mentor figures. This article sums up the environment nicely.

http://www.huffingtonpost.com/wait-but-why/generation-y-unha...

I think a desire to fulfill this expectation of individualized achievement can lead adolescents to pursue peer approval as an activity unto itself, the so called "trying to be cool," you may have observed.

jkimmel··on Legacy of Agent Orange
An example of "dehousing"

http://en.wikipedia.org/wiki/Bombing_of_Dresden_in_World_War...

jkimmel··on Twitter CFO Anthony Noto Privately Analyzes Facebook
Also it seems a bit odd to suggest Google wouldn't understand mobile advertising value vs desktop.

Google controls the #1 smartphone OS by marketshare and serves mobile ads over Google search products (& GMail now) to a large number of users.

Unless there is an inherently different value for mobile-social ads than just normal mobile/mobile-productivity ads I'm not sure how this would make sense.

jkimmel··on Ask HN: Which book are you reading these days?
Regenesis by George Church

It's an interesting primer on the potential benefits of synthetic biology to society at large from one of the field's luminaries.

He covers everything from engineering "mirror humans" (with inverted biochemical chirality) to reviving extinct species.

http://www.regenesisthebook.com/

jkimmel··on Suburban sprawl is stifling the US economy
I live in downtown Orlando, FL.

We have a perfect (pathetic) example of this phenomenon.

Most of the older buildings in the downtown core rest along brickpave streets that are awful to drive on. Horrible for the suspension, tires, the works. I believe the insistence on keeping them is an attempt to limit through traffic from a nearby East/West interchange with the notorious Interstate-4 (http://en.wikipedia.org/wiki/Interstate_4#Orlando_area).

Through traffic is still a huge issue, and in addition, the poor brickpave road is constantly riddled with pot holes from the heavy trucks and sheer number of vehicles that detour through. I can't imagine what the maintenance must cost relative to regular asphalt.

jkimmel··on Why Many Smart, Low-Income Students Don't Apply to Elite Schools
In some situations, getting the parental income information can make for an awkward conversation. If the students assume they won't get in for absolutely free, they might decide against asking their parents probing financial questions.

This is different than the FAFSA. When I last filled it out, the FAFSA had an option for you to send a link to your parents, so they could fill in their information without disclosing it to you. Unfortunately, money is a taboo topic in American families, and I don't doubt that many applicants feel more comfortable using this option.

jkimmel··on Life in New York City, Where Arrests Are Down and Tickets Are Rarities
>The USA had the most crime, and the USA has seen the biggest decrease. No one knows why.

Some have proposed that outlawing leaded gasoline has led to less lead poisoning in children, thus less aggressive behavior in adults and subsequent decreases in crime.

NBER paper - Environmental Policy as Social Policy? The Impact of Childhood Lead Exposure on Crime

[1] - http://www.nber.org/papers/w13097.pdf

MotherJones story

[2] - http://www.motherjones.com/environment/2013/01/lead-crime-li...

Links to criticism of the story above

[3] - http://www.motherjones.com/kevin-drum/2013/01/lead-and-crime...

jkimmel··on Transcriptic for YC biotech startups
We find it to be pretty competitive for our needs (PCR, genotyping, long-term storage).

PCR is something like ~$1.50/rxn with our standard genotyping protocol, which works out to ~$0.30-0.40 more than the same reaction run in house. If I recall correctly, the cost per rxn goes down if you run more in parallel, because they share the same instrument time.

Setting up that reaction might take me ~0.5 hours base, and 0.05 hours for each subsequent reaction prepared in parallel.

Grad students are cheap, but even valuing my skilled labor at minimum wage, it's cheaper to use Transcriptic.

jkimmel··on Why Math Might Be the Secret to School Success
I haven't heard of this being attempted, though I would surprised to find that it hasn't.

However, one reason it might be avoided is due to the potential negative effects tracking [1] strategies may have on some students. In my public school district, any form of tracking at the elementary level was difficult to implement due to pushback from parents, even in situations where the educators felt it was beneficial.

1 - http://en.wikipedia.org/wiki/Tracking_%28education%29

jkimmel··on Transcriptic for YC biotech startups
This is really remarkable.

I've used Transcriptic in a research setting for a while now. From a user's perspective, it's like looking into the future, and it's awesome.

From the business side, this makes YC a more attractive option for biotech startups. The life sciences are still very capital intensive. While the New YC Deal helps in this department, many businesses still need to look toward an STTR/SBIR grant from the NIH to get to the stage where they have a product to show investors.

Moves like this probably won't change that for a ton of companies, but there are a few on the margin who may be able to pursue an idea through YC with the benefit of the extra $20K in fuel.

jkimmel··on NASA’s Orion Spacecraft Splashes Down in Pacific After Test Flight
I'm bullish on SpaceX when it comes to launch systems and vehicles, but to the best of my knowledge they haven't demonstrated any expertise in Life Support Systems.

The hardest part about getting to Mars isn't flinging a metal tube off the Earth. That part we know how to do.

The hard part is keeping people alive for 6 months there, 6 months back, and providing all the equipment necessary to do meaningful science on the surface.

This isn't to say that an adequate launch system isn't essential to the mission, but I would be very surprised if SpaceX developed life support systems independently and more efficiently than NASA. More likely, I can imagine a news headline in which a SpaceX rocket sends a NASA capsule and living module to an off-world mission.

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