Addressing the Fallacy: “people must practice in their spare time to be good in a field”

i haven’t posted this response since I swore off reddit for a bit — but thought this might be interesting to other folks.

Let’s take a step back. I find it really dangerous to assume there’s a causal link or 1:1 correlation between [people who spend all their time studying a field] and [people who are extremely competent at a field].

For one, this leads to a culture of “all work, all the time.” For instance, professors are expected to work essentially all the time by default. Another example: In programming, there’s this growing trend of using contributions (often unpaid) to open-source projects as a benchmark for competency.

This becomes problematic when, for various reasons, people cannot devote their spare time to the study of a field. Maybe it is financial: they don’t have time to spare to make unpaid contributions to OSS. Maybe it is life-related: a small child or family is taking up a lot of their spare time.

The overly-simplistic thinking you outlined leads to people in positions of power / employers discriminating against or manipulating young women in the field because they might get pregnant and have less spare time to study the field for a while (there are other issues at play here, for instance maternal / significant other leave, and the expectation that women do most of the child-rearing work). Another possible result is systematic exclusion of lower-income people from the field, because they can afford less unpaid work relative to high-income people.

Secondly, I think it’s absolutely true that people (whether for nurture, e.g. previous exposure, learning styles, presence of mentors, presence with curricula that matches their learning style, enjoying studying instead of thinking about family members getting shot up, etc. or nature) will pick up a new field at different rates. Thus, it is definitely possible for motivated people new to a field to catch up very fast with people who have been studying the field for a while (not to mention bringing in fresh perspectives and new ideas). I don’t know any names off the top of my head, but I can look around for examples if you would like. [1]

This could, fortunately or unfortunately, mean there exists

  • an extremely intelligent and motivated 9 to 5 brogrammer who has officially been in the field for 10 years

who is as technically competent as

  • someone who toils night and day and has been officially in the field for 30 years

Whether this actually happens, or if so the frequency with which it happens, I have no idea.


Therefore, I find it much less problematic to assume something along the lines of

  • “people who enjoy a field so much they would study it in their spare time if they could, or who study it whenever possible, tend to be the ones who persevere and become extremely competent at it”

rather than

  • “only people who study the field in their spare time are extremely competent at it”.


[0] I apologize for the bad syntax. I meant 10x, not O(n). I think my brain went “abbreviate Order of magNitude” and shat out O(n). I find it no more rude than correcting usage of “I could care less” or “should of”, which some people may find rude, but which I tend to appreciate.

[1] Perhaps Einstein is an example of someone who caught up in a field rapidly without officially studying it full time, although now I feel obligated to pull up examples of non-dead-white-men, since someone on the Internet will make the wrong conclusion otherwise.

Sadly, so far in my life most of my curriculum has given me biopsies of white male geniuses, so I can’t say for sure as I don’t know the life history of many non-white-male people (also, I don’t know the life histories of many not-famous people).

Technical people I could try to vet to see whether they could be considered “examples”:

  • Non-male: Emmy Noether, Marie Curie, Dr. Grace Murray Hopper, Hedy Lamarr, Émilie du Châtelet, Laura Deming (living). (thanks quora). Sufiah Yusof [2], Kathleen Holtz
  • Non-white: Srinivasa Ramanujan, Kim Ung-Yong (still living), Akrit Jaswal (err… reportedly not at all humble), Jaylen Bledsoe (living)
  • Non-male non-white (black): Rochelle Ballantyne (living), Brittney Exline (living)

[2] (now that was sad to read about, but happy update:


hg19 vs hg38 in two pictures

I took these two screenshots for work recently. Shows our evolving understanding of the complexity of the human genome at the population-scale, as reflected in the changes in the reference genome between hg19 and hg38.

hg19 / GRCh37: 2009
hg38 / GRCh38: 2013


(ignore the temp folder, not part of hg19)


Note: I make no claims as to actual accuracy or completeness of these two directory listings, I haven’t taken a close look at them in a while. But they’re interesting from a big-picture perspective.

Note to self: continue uploading interesting pictures to imgur album, (reduce bandwidth consumption on orangenarwhals)

cross-posted to

Short boat update

There’s obviously lots to talk about (how I planned the Fairhaven to Boston trip, how it actually went, what it was like living on a boat, my multiple trips around the harbor, thoughts on outboards, good books I invested in, and more), but here’s a quick picture post.

fixing up the boat over the summer 2014
food, batteries, everything’s ready to be packed onto the ship before we leave Fairhaven, MA
A distant view of Boston, from out by the Graves
Home sweet home. E15 at Constitution Marina
occasional fireworks in my backyard

a gif of night-time botoring (boat motoring)

crazy ideas, crackpottery, open-source hardware, and economics

I consort with some interesting people now on the open-source-hardware mailing list.

I suspect this is how my ideas would all end up looking like if I didn’t have some awesome friends who put up with my crazy rants and criticize me and force me to make sense… (function sort of like academic reviewers, but in-person and my friends can unplug me from the internet and force me to go sailing when I get really unhinged)

Full slideshow:

Sensorica has some interesting ideas behind it, but it’s hard to access through a layer of what, for lack of a better term, I must describe as “crackpottery”. maybe genius is just refined crackpottery?

side note/pun: get it? crazy crack-tea pot? heehee

Hennie Meyer | Dancing Teapots

However, the term craze is also used to refer to minute cracks in pottery glaze, again suggesting the metaphorical connection of cracked pots with questionable mental health. (src)

Heck it appears I’m halfway there according to some made-up-indexing method…

1. Cranks insist that their alleged discoveries are urgently important.

2. Cranks love to talk about their own beliefs, often in inappropriate social situations, but they tend to be bad listeners, being uninterested in anyone else’s experience or opinions.



frictionless human blobs

Anyway, my friend’s opinion:

it’s assuming humans are frictionless spheres a bit

but I’m always down for a novel utopia

I think it’d be a terrible way to run an economy or manufacturing chain tho

there doesn’t seem to be any planning for predictability, contract, risk

in that way seems a bit Valve-like, in their ideal of their internal structure

Here’s the valve new employee PDF, which is now on my commute reading list:

Anyway, here’s my own (mostly coherent, but very long) post on the topic of open-source hardware and its relation to economics.

long post is long

I agree that our current economic system (capitalism) has inspired an amazing amount of innovation via the (greed + cash + ego –> innovation) cycle. I would much rather live in 2014 than in 1714.

However, we can definitely say that this incredible innovation / economic system has its downsides — unwillingness to confront global warming, marketing cigarettes to developing countries since advertising is heavily restricted in developed countries [1] [2] [3], marketing baby formula instead of breast milk[5], verizon/comcast [6], these are some obvious examples of how corporate systems have led to evil / “not good”, without even talking about the overall distribution of resources in the world (why does poverty still exist?).

I agree that open & closed ecosystems are not exclusive. But I sometimes wonder if as a society we are kind of like the Hollywood studio execs — “each movie is 500 million dollars, let’s not risk doing anything different like having perse female characters.”

For instance, from what I understand, the Republican point of view is that “our current economic system has led to great advances in technology that has bettered everyone’s life. This system may be unjust and rife with a whole host of issues, income inequality may be set to worsen forever, the planet may become inhospitable to humans, but we should not risk trying anything else.”

There’s actually no way to tell who will be right in the short- or long-term future. However, I strongly do want to encourage or get out of the way of people who want to experiment with these more “peer-based” models of production, where “everything is shared and people benefit from each others’ knowledge and contributions.”

I personally think this is what we should move toward in the future, and these pangs of “open source work / socially conscious work / academic research is not rewarded equivalently in cold, hard, cash” are the result of a transition between the two models, where ultimately we end up in 100% opensource land. But my personal opinion is pretty irrelevant, it’d take hundreds of years to arrive at this sort of scenario, and for all I know a mixture of the systems may be the most stable or ideal state. I recognize the human limitations to my knowledge and personal beliefs. tl;dr I don’t make for a great revolutionary ;P

Getting back to the original point, yea, cool people work for both lots of money and lots of purpose, and although working for lots of money can lead to bad things, working for lots of purpose can lead to bad things too [7] [8], so we shouldn’t unilaterally judge people either way (although, as puny humans, we invariably will stereotype in order to function in life).

Anyway, philosophy hour aside, now I’m going to go back to rabidly supporting opensource just like Apple fanboys support Apple! 😛


[1] News article summarizing recent move to expand market in developing countries

[2] Overview of scientific research

[3] (pictures!) Packaging


[4] check out how many cigarette ads were in the old Tech

FRIDAY, JANUARY 7, 1955: “Your own college-and-class pipe” ?? o___O Thanks, but no thanks.

[5]  UNICEF Formula for Disaster (Nestle, Phillipines)

[6] “it appeared that Verizon learned a valuable lesson: it can flat out lie to governments, promise 100% fiber coverage in exchange for subsidies, then not deliver, and no one will do a damn thing about it” .




other people’s emails on the thread:

“Yes, [x], you’re right.  I recently saw Linus Torvalds in Central begging.  Richard Stallman hit me up for a job washing my windshield.

Just joking of course, people make lots of money off of commons-based production.  Check out some of the economics of “free revealing” of ideas by Eric von Hipple (MIT) or Yochai Benkler (Harvard).  It’s not the zero sum game you represent.  Benkler’s book is affordable, even if you only make 90k”

Review: While some of Benkler’s arguments and examples are fascinating and easily read, they are sandwiched between portions of confusing, thick, often heavily theoretical prose. […] In spite of these attempts to make this book more accessible, it is probably best suited to an academic or technical audience; those with an interest and background in the topics discussed. (src)

“Eric von Hipple’s books are really good, too.”

Review: There is no doubt that the continued lower costs and democratization of the tools and distribution of things previously the realm of pros is reshaping our world. But this book reads like a college textbook. More academia than Malcolm Gladwell or Chris Anderson. Which I guess is good if you’re a true researcher. (src)

Heehee. Guess academics try so hard to distinguish themselves from crackpots that to laypeople they reach another dimension of incomprehensibility.

Update: Just read this thanks to Ned —

relatively flat networks can quickly generate hierarchical structures even without any attempt at a power grab by emergent leaders or by any organizational, coordinated action.

basically, for networks to remain flat, they must be engineered to stay that way, since they’ll strongly tend to un-flatten, especially thanks to social media


why the **** does everything around me assume I’m a guy (updated)

unfortunately lately i have been very angry and random passerbys have been bearing the brunt of my rage. sadly i’m also too angry to be coherent enough and calm enough that it won’t just pass over their head. oh well.

like this tv show casting company (brand removed).


sigh. the individual ad by itself isn’t sexist per se. but the cumulative weight of all these ads and tv shows and everything around me is sexist. what they say is, “you don’t exist.”

i fixed it by changing the blue to hot pink and adding in some fingernails with nail polish. not to say “since your ad was masculine instead of feminine, you’re being sexist”, but rather to point out how stereotypical they were being without even noticing or acknowledging it.


probably most guys (aka most of my friends) missed the point and just dismissed it as “oh another crazy person advocating political correctness”. oh well. but especially the people who work in media, if they’re not conscious of what they’re doing — well, basically they should at least be self-aware enough to admit they are okay with perpetuating these stereotypes and publicly admit it. basically, all I want them to do is include a little line:

“we welcome all types of people even if our ad is a little stereotypical!”

There is growing hope for the media industry, though, which makes me really happy.

MARCH 18, 2015 9:55 PM
Hollywood’s Best Will Pay You $5,000 To Help Find a Female “MacGyver”
White House supports effort to create programming highlighting women in STEM

oh here’s another angry lady (oops, when you tell women to stand up for themselves, be prepared, they might take you up on the offer!) who impressed me

Phoenix Perry – Female Game Developer Community for some classy examples, like this (i removed the brand, because *** them)


I concluded my reply email with “but in more seriousness, if you ever want to talk person-to-person instead of stereotype-to-stereotype, let me know”.

ball’s in their court now. i’ll let you all know if they follow through on talking to me.

UPDATE 3/25/15

One of my friends was able to act as a de-anger-translator and better articulate what I meant than my snarky email.



Note the lack of stereotypical white-male stock photo, and that they now ask for pictures of what you made, not pictures of your team (I didn’t even catch the words the first time around!). -^-^- I’m happy they were able to fix their poster without much effort at all, and (I’m told) that the casting company seemed entirely sincere. As suspected, the issues was simply that they “just pulled a stock photo to get it done quickly.” (who knows about the Major Cable Network they are feeding into…).

I do feel that visually the poster is less strong as a result of the lack of human interest. Ah well, so it goes — I guess the tricky thing to do, if you include “human interest” in visual design, is to not fall into stock-photo-corporate-blandness. Maybe that’s where a sincerely-worded short sentence could help.

I feel really happy about this outcome overall. It resulted in a lot of fruitful conversations with my guy friends who were previously avoiding gender issues and now reached out because they themselves felt confused or alienated, and the casting company updated their poster.

“A journey of a thousand miles begins with a single step.” Changing society is a long, slow, and frustrating process, and it’s been very gratifying to put effort in and get concrete results, however small in the grand scheme of things, out. A+ would do again.


I confused some of my friends (who perhaps haven’t thought or listended as much about gender issues) with these pictures. They corresponded privately with me, prior to the casting company releasing their updated version.

Person A: Is your problem with the image that it depicts a white male wearing a dress shirt to reflect a hobby and industry largely dominated by males. It seems the words on all these images are the same, merely the gender or presence of the hand and the color of the background, neither of which seem relevant to me with regard to stereotyping or sexism.

Me: Yes, my problem was with that image. Specifically, the context of the picture was not “here is a reflective picture in our academic article detailing the current demographics of the industry”. They were saying, “here is an image with which we are soliciting people to represent an industry to a large number of people not currently in the industry”.

Thanks for clarifying your confusion !___!

Person B: Wouldn’t it be better to congratulate them on making an ad that is not sexist? In fact, their ad seems far more gender neutral than your suggested ad.

Me: I personally don’t want to them to be gender neutral, that’s boring… I’d rather they celebrate diversity, but in an honest way, instead of a corporate-mandated hokey way. That’s why I suggest a single well-written not-canned sentence would go far.

Kitten Working Group of the Internet Engineering Task Force

Today I discovered this gem:

Kitten Working Group
Internet Draft

More info here:

The purpose of the  Common Authentication Technology Next Generation (Kitten) working group (WG) is to develop extensions/improvements to the GSS-API and to the Kerberos authentication system […]

They have a mailing list called kitten at ietf, hah.

To explain the name, apparently kitten is “the next generation of the CAT (Common Authentication Technology) working group”.

They sounded like they were having a lot of fun at work… but then I realized the more likely scenario is that defining Internet standards is so “fun” that every little bit helps.

hattip MIT’s Student Information Processing Group (SIPB)

ga4gh proposal. Beacon Versioning: Simple, Current, Future (three use cases)


I am posting this on my blog because I spent a lot of effort on this email & there’s no reason for it to be buried inside a private mailing list.

if you, dear reader, are like most of my real-life friends and call biology “bi-lol-logy” — ignore this post, save your sanity, and come back to bioinformatics in a year. i think things will be much better then. in fact, i’m not even going to attempt to explain what’s going on here except to link to ga4gh:

otherwise… down the rabbit hole we go…


Hi all,

I’d don’t want to stall momentum, since I care much more that Beacon v0.2 happens rather than a particular Beacon v0.2 happens, but as an engineer I’d also hate to see us be too hasty and make poor design choices.

Unfortunately it’s possible to describe a single variant in multiple ways in VCF

Yep, that’s concisely the problem with state-of-the-art.

From my perspective, there are three conflicting use cases and we’re trying to smush them into one Beacon/Server/Variants API spec, which may or may not be advisable.


1. Simple

You may only query for one position, limited to precise string

  • “Does AAG exist at position 1” –> implicitly asking, does an insertion of “AG” exist between positions 1 and 2 on the reference genome
  • Vision is “painless way for organizations to visibly commit to wanting to share genetic data by adopting a single standard, i.e. GA4GH”
  • Sidestep genetic data privacy and security issues by trading [usefulness to research] for [painless adoption]

2. Current


  • “Does an insertion of AG exist between reference coordinates 1 and 2”
  • Vision is “people share useful data for researching functional impact using the current industry-standard, VCF” — definitely better than silo-ed no-sharing world, but
    Source: Quote Investigator. Attribution: 1942 June 3, Florence Morning News, Mutt and Jeff Comic Strip, Page 7, Florence, South Carolina. (Newspaper Archive)
    Source: Quote Investigator. Attribution: 1942 June 3, Florence Morning News, Mutt and Jeff Comic Strip, Page 7, Florence, South Carolina. (Newspaper Archive)
    • Lamppost = current standards, which sort of support population/functional impact research if you try really hard
    • Dark = hopefully the future, where it’s painless to query for things like frame-restoring indels
    • …I hope this lamppost analogy makes sense outside the confines of my brain…

3. Future

population-based / reference-free

  • “Does an insertion of AG between query coordinates 1 and 2 exist where-ever the query ‘ATTATAGAGAG’ is best aligned on each genome in the population”
    • query string ‘ATTATAGAGAG’ used to locate position on genome
    • specific variant we’re looking for is AG, that is, we want to find genomes that say “AAGTTATAGAGAG” in the place where population-wide most genomes say “ATTATAGAGAG”
  • Vision is “future-oriented standard for developer to implement toward / iteratively develop”


My gut feeling is #3 is beyond the scope of Beacon v0.2 and we should be clear that Beacon v0.2 is meant to support the #2 use case.

My personal opinion is that Beacon v0.2 should actually be a standardization of use case #1, but it seems like I’m in the minority (if anyone else cares about #1, please speak up!).


With respect to, “+1 for consistency with other GA4GH APIs” —

My concern is that currently the GA4GH APIs are very VCF-oriented, and VCF is very reference-oriented and not very population-scale-oriented [1]. On the other-hand, Beacon is population-oriented (no sense in having a Beacon to query two genomes, that doesn’t preserve anonymity at all).

My gut instinct is that the Variants API will move toward being population-oriented (reference-free). Consistency is very important, however, I think we should be cautious about moving toward consistency with Variants API in its old state. In fact it’s already starting to reflect this shift —

“graph”, in which all variation is associated with `Allele`s which may participate in `Varaints` or be called on their own. The “graph” mode is to be preferred in new client and server implementations.

[1] people are spending months merging VCF-based datasets and then indexing them with Tabix and wormtable, then they have to reindex for something as simple as querying a subset of the population … oh, I could got on but I hope I’m preaching to the choir here. If not, I’d much appreciate knowing where I’m incorrect if you’d care to explain. I’m certainly not an expert in bioinformatics.


Thanks Mark Fiume for taking the lead and Stephen Keenan for organizing Beacon work.


I think more lists (specifically ga4gh schema, & ga4gh server) needed to be included in this discussion, or we need an “Issues” for all of GA4GH, or something, but it’s getting very hard to keep tabs on Issues, some of which are closed, in three repositories at once. Or maybe I just need to “watch” and get email notifications on all three repos? How are people handling this crazy explosion of GA4GH work?


I also would note that I strongly prefer all ga4gh mailing lists be made public going forward. It’s really ridiculous to have people forward me emails from 3 different private mailing lists and link me to 10 issues on 3 repositories.

Although ga4gh-dwb-beacon is private mailing list :/ I’m still emailing instead of opening a public Issue on Github because it keeps feeling like “my calls are dropping” and no one is hears me…

other links

wow, the more i poke around on ga4gh github the more related links I see… here are some I need to read

godaddy email forward to yahoo fails due to 550 error, forward to gmail works fine

there is no fix for this, unless yahoo changes their server settings. try using gmail instead.

after some debugging, because godaddy kept complaining about mx records, i followed this to the letter:

still didn’t work. when i checked the  bounce message, it was actually due to yahoo.

Google tried to deliver your message, but it was rejected by the server for the recipient domain by [].

The error that the other server returned was:
550 relaying denied for <>

Tues Startup: Social Media Network of Pigeons,

Recently I asked someone who shared a link with me where he found it. He told me “from the internet”.

Well, yes, almost all hyperlinks are found and shared on the internet as a matter of fact.


You extended the pigeon protocol to the concept of social media.

Say you want to share an article, youtube video, or other link with a friend.

  1. you install the app and hit “ave it!”
  2. a robot prints the link out and attaches it to a Certified Pigeon. that pigeon finds you, poops on your head to get your attention, and gives you the link
  3. if you “like” the link,
  4. you feed the pigeon some crackers so that when it returns to the sender
  5. the sender then knows how much you appreciate the link based on how much the pigeon poops on him/her 30 minutes later

This Tuesday Terrible Startup Idea post brought to you by “it’s still Tuesday in Hawaii”.

Oh, check this out, someone was paid to write this article, and it wasn’t even April Fools: They came up with a “coo-ing” Twitter-like startup name called Coo-ee , haha.