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I'm an immunologist, microbiologist and computational biologist. I research cheese microbes, I'm creating an online biochemistry course and I have a podcast about the immune system.


The limits of tolerance

3 min read

I have a very strong memory of a moment, I think it was in middleschool, when durring some argument with my dad, my mom said "the only thing that I'm intolerant of is intolerance." I don't know where she heard it, but it's a nice turn of phrase. According to wikipedia, there's a fairly robust intellectual history for this idea - this paradox of tolerance.

Less well known is the paradox of tolerance: Unlimited tolerance must lead to the disappearance of tolerance. If we extend unlimited tolerance even to those who are intolerant, if we are not prepared to defend a tolerant society against the onslaught of the intolerant, then the tolerant will be destroyed, and tolerance with them.

I find myelf wanting to find common ground with Trump supporters, or at least to try to understand them. I suspect there are a great many of them that I would agree with on some issues. I suspect there are a great many of them that love their children, that just want a better life for themselves, that don't have a hateful bone in their body. I've heard them on the radio - they don't like some of what Trump has said, or some of what he's done, but they still think he's our best bet.

The trouble is, I just can't fight the feeling that they're wrong. I don't mean I disagree with them, I mean that they are objectively wrong. 

I believe that there are things in the world that are true, and other things that are false. I thought some of these things could be widely agreed upon, but given the last year of campaigning, it's sometimes hard to remember this. 

There's a great list at pressthink of things the media will need to grapple with in the coming years if they are to remain relevant. The one that most concerns me now is:

4. Re-imagining how journalism can operate in a low-trust environment where most information that conflicts with identity is rejected, no matter how solid it is.

How do we have empathy for people that hold beliefs that are so contrary to our own without embracing moral relativism? How can we have conversations when we don't accept the same reality? 

And how can we tolerate people whose attitudes come from that separate reality? We have to avoid being smug about the truth, but we must still assert it. We need not be tolerant of wrong ideas or bad ideas, though it's worth remembering that people with bad ideas aren't necessarily bad people.

If we are not prepared to defend a tolerant society against the onslaught of the intolerant, then the tolerant will be destroyed, and tolerance with them.


The limits of privilege

7 min read

I must admit, I think I've been spending too much time on Facebook in the days since the election. There's some solace in the fact that most of the people I'm connected with (or at least most of what the algorithm decides to show me) feel as hurt, as angry, as saddened as I do. Sometimes, the filter bubble is a comfort.

In the hours I've spent reading people's personal posts, clicking on links, and generally trying to forget the world, a few themes have emerged.

The first is anger at the "racists, bigots, mysoginists, and xenophobes" that voted for Trump. I've seen that exact phrase multiple times, though I don't know where it originated. There's backward looking anger ("how could they not know?"). There's anger at the present (largely concerning reports of hate crimes, graffiti etc, though it's unclear how much of this is real). And there's anger and fear about what's coming (Trump is apparently planning to fill his cabinet with some real winners, not to mention fear over the courts).

The second theme is hope and resilience. Not a lot of news articles here, mostly heartfelt and well-meaning posts about using the anger in positive ways. Vows to fight against bigotry. Safety pins and solidarity. This urge is strong for me - I want to find ways to help. Ways to get involved in the community. Ways to prevent or slow down the collapse of society that feels certain to come. Mostly, I want to gird myself against the apathy that I know is likely to follow in the wake of such a momentous challenge. 

And then there's the theme that's hardest to grapple with, but feels the most true: Confusion. How did this happen? What did we miss? Who are these people that felt that the solution to their problems was a man that eschews facts, lies without shame, and flaunts his disdain for everyone and everything? The hard truth is that most of the people voting for Trump were not "racists, bigots, mysoginists and xenophobes," though it would be much simpler if they were. I do not understand these people.

Some people do. I did not see their writing before the election, but it was there. The hardest piece I've read this week was by Emmett Rensin on Vox. The whole piece is quite long, but worth every minute of reading:

"Suffice it to say, by the 1990s the better part of the working class wanted nothing to do with the word liberal. What remained of the American progressive elite was left to puzzle: What happened to our coalition?

Why did they abandon us?

What's the matter with Kansas?

The smug style arose to answer these questions. It provided an answer so simple and so emotionally satisfying that its success was perhaps inevitable: the theory that conservatism, and particularly the kind embraced by those out there in the country, was not a political ideology at all."


"Privilege" has become a more important part of my lexicon in the past few years. Roxane Gay has a wonderful essay about priviliege. It's the sort of thing that's hard to wrap your head around if you have it.

"Privilege is a right or immunity granted as a peculiar benefit, advantage, or favor.  There is racial privilege, gender (and identity) privilege, heterosexual privilege, economic privilege, able-bodied privilege, educational privilege, religious privilege and the list goes on and on. At some point, you have to surrender to the kinds of privilege you hold because everyone has something someone else doesn’t.

The problem is, we talk about privilege with such alarming frequency and in such empty ways, we have diluted the word’s meaning.When people wield the word privilege it tends to fall on deaf ears because we hear that word so damn much the word it has become white noise."

As a white, straight, upper-middle class male, I have just about every privilege. I've spent a fair amount of time trying to understand my race and gender privilege - those things percolate through the culture that I'm imersed in. When people in facebook comments under the "Racists, bigots, mysoginists, and xenophobes" posts point out that many Trump supporters are working class, and have been ignored, a typical response goes, "Whatever, they're white men, they have it better than most."

The whole Roxane Gay essay is also worth reading, but this section really speaks to this moment:

We tend to believe that accusations of privilege imply we have it easy and because life is hard for nearly everyone, we resent hearing that. Of course we do. Look at white men when they are accused of having privilege. They tend to be immediately defensive (and, at times, understandably so). They say, “It’s not my fault I am a white man.” They say, “I’m working class,” or “I’m [insert other condition that discounts their privilege],” instead of simply accepting that, in this regard, yes, they benefit from certain privileges others do not[...]

When we talk about privilege, some people start to play a very pointless and dangerous game where they try to mix and match various demographic characteristics to determine who wins at the Game of Privilege. Who would win in a privilege battle between a wealthy black woman and a wealthy white man? Who would win a privilege battle between a queer white man and a queer Asian woman? Who would win in a privilege battle between a working class white man and a wealthy, differently abled, Mexican woman? We can play this game all day. We will never find a winner. Playing the Game of Privilege is mental masturbation—it only feels good to the players.

Privilege is relative and contextual. Few people in this world, and particularly in the United States, have no privilege at all. Among those of us who participate in intellectual communities, privilege runs rampant. We have disposable time and the ability to access the Internet regularly. We have the freedom to express our opinions without the threat of retaliation. We have smart phones and iProducts and desktops and laptops. If you are reading this essay, you have some kind of privilege. It may be hard to hear that, I know, but if you cannot recognize your privilege, you have a lot of work to do; get started.

In all of the (necessary and important) focus on gay rights, women's rights and minority rights, I think we may have forgetten about the rights of people who are poor. Or maybe not even poor - just less well off than they could be. The Democratic party ignored the screams of the working class too long. Ignored labor unions in favor of big banks, ignored the steel worker and autoworker and focused on marriage equality. When we tell white men that can't afford a house that they have privilege, and elect a black man president while saying that black men have less privilege, I can see how that might rankle.

But what the hell do I know? I definitely lose the game of privilege. 


“Defenseless under the night
Our world in stupor lies;
Yet, dotted everywhere,
Ironic points of light
Flash out wherever the Just
Exchange their messages:
May I, composed like them
Of Eros and of dust,
Beleaguered by the same
Negation and despair,
Show an affirming flame.”

- W.H. Auden


Good Bones by Maggie Smith | Poetry Foundation

I want to believe America has good bones.

Good Bones
Life is short, though I keep this from my children.
Life is short, and I’ve shortened mine
in a thousand delicious, ill-advised ways,
a thousand deliciously ill-advised ways
I’ll keep from my children. The world is at least
fifty percent terrible, and that’s a conservative
estimate, though I keep this from my children.
For every bird there is a stone thrown at a bird.
For every loved child, a child broken, bagged,
sunk in a lake. Life is short and the world
is at least half terrible, and for every kind
stranger, there is one who would break you,
though I keep this from my children. I am trying
to sell them the world. Any decent realtor,
walking you through a real shithole, chirps on
about good bones: This place could be beautiful,
right? You could make this place beautiful.

Jass at the Lake

Converting the inlaws


Women in Biology, Computer Science and Computational Biology

2 min read

My colleague Melanie Stefan and I have just submitted a manuscript for review (you can see the preprint here) about the representation of women as authors on scholarly publications. 

The bare outline of our procedure is not revolutionary:

  1. We downloaded the information for a bunch (over 200,000) papers indexed in pubmed
  2. We computationally inferred the gender of the authors based on their first names (this process is somewhat complicated - you can find the code and some more explanation here)
  3. We analyzed the results, splitting the data a couple of different ways, bootstrapping statisticts etc

No surprise, women are under represented in computational biology, like they are everywhere else:

 Figure 1A - proportion of female authorship by author position.

There are a couple of points that I think are particularly interesting though. The first is that, if the senior author of the paper is female, women are much better represented at all other positions. Computational biology is still worse than biology as a whole, but the bio representation jumps to nearly 50%, and the computational biology jumps to 40%.

Paradoxically, I think that the most encouraging news comes from a graph that shows the lowest female representation. Pubmed data only allowed us to compare biology and computational biology, but what about computer science? For this, we turned to the arXiv - a preprint server for quantitative fields. We can't really compare this directly to the data from pubmed, but they do have a "quatitative biology" section. 

There, quantitative biology has better representation than computer science. It's still abysmal, don't get me wrong, but it suggests that maybe, just maybe, biology might be used as an inroads to get more women into computational and quantitative techniques. 

This gets at the question I'm most interested in - we know represenation is bad, but is there a way to improve it? These data aren't conclussive by any means, but they suggest there's a reason to try. 

Now I just need to get a job where someone will let me experiment on (with?) undergrads...


Submitted! Gender disparity in computational biology research publications | bioRxiv