Jeff Kaufman


Software engineer at the Nucleic Acid Observatory in Boston.

Full list of EA posts:


I think it's "mostly avoidable" in the sense that you can avoid the majority of it, but for most parents and kids not in the sense that you can get it down to nothing?

If you are not thoughtful about it you can end up in a place where both parents have sleep that is massively disrupted, at which point it becomes pretty hard to actually address the problem because you're so tired and thinking so poorly.

Important components in avoiding sleep deprivation:

Jeff Kaufman, do you have kids of your own that makes you more confident in your statement?

Three kids: 8y, 6y, and 15m

I don't know if it is possible to tag someone in a comment to notify them they have been mentioned

Happened to see it ;)

do you think there is a good pronatalist argument to be made that an EA that doesn't feel like they want kids should still regardless have kids?

I don't think anyone who doesn't want to have kids should have them. It's a huge amount of work, and if you're not excited about it it seems likely to make you miserable.

One confounding factor here is that the children that you might potentially adopt are pretty different from the children you might have biologically. Most adoptees have gone through some form of trauma, they are rarely newborns, they often had worse prenatal environments, their biological parents probably wouldn't enjoy the forum, etc.

I think if somehow one of my children had been swapped at birth with a child from similar parents it probably wouldn't have much of an impact on what raising them would be like, but that's not really what we're talking about?

(I do also think it's cute the various more specific ways our kids resemble us, but I agree this is not a major contribution to the experience of parenting.)

On (1), another consideration you don't mention is that having kids earlier means more years of overlap with your kids and, potentially, grandkids: you'd get to see more of their lives, which is something people usually find pretty rewarding.

Do you think never celebrating holidays such as Christmas or birthdays would have a strong effect on the psychological development of our children? My partner and I intend to avoid celebrating any conventional holidays, except for Halloween, and to celebrate the Solstices and Equinoxes instead.

Would you be up for saying more about why you don't want to celebrate the conventional holidays? Your kids are likely going to want to celebrate the things their friends and extended family are celebrating, and unless you have a strong reason not to, might as well make them happy?

For example, despite being atheists we celebrate Christmas, Easter, Hanukkah, and Passover. Not in an especially religious way, just things like dying eggs and looking for them are fun.

For men reading this and thinking "I want to be an equal partner in raising kids, but I know a lot of men who intellectually want this don't end up doing their share; what should I do", you might be interested in my Equal Parenting Advice for Dads

Finally got a chance to finish reading the paper! I don't entirely understand it, though:

  • I think they're modeling prevalence as initially constant and then sharply transitioning to an increase of 5% per year. In thinking about infections in the cases I'm familiar with (people and wild populations) this sounds very unlike real spread, which is exponential initially (or the sum of an exponential and a constant if you're observing something new growing to exceed some background). Is their model more realistic for farmed animals, or is this just highly simplified?

  • It looks to me like maybe the statistical method they're using relies on this clear transition between a linear constant regime and a (very nearly) linear increasing regime, and so if the model is overly simplified (above) then their results will be too optimistic about detection. (See Figure 2 on p4 of the supplementary materials.)

  • They talk about being able to detect entirely novel antibiotic resistance genes (scenario 3), but I don't see anything in the paper about how they know to track a particular novel gene to see if it's an antibiotic resistance one? Is the idea that once you do realize you care about a gene you can go back and re-analyze the sequencing data you've been collecting to learn how quickly it has been spreading?

how you could identify a novel pathogen

I've been working on simulating exponential growth detection: count how many times each k-mer (I've been using 40-mers) occurs on each day, and then run Poisson regression to see whether this looks like an exponential increase and how good the fit is. It works, though as discussed in this post the signal for novel viruses is likely to be extremely weak and so enough sequencing gets expensive.

and know it's a pathogen

Yes, that's also an important part of the problem. In some cases I think it would be clear how much of a problem it was simply from looking at it and seeing how close various parts are to matching known things (which could be automated if we're getting lots of them). But yes, in others it would be pretty hard to judge how seriously to take it.

if you don't know if something is a human pathogen

That one seems manageable: once we recognize that something is spreading in particular areas we could use more targeted and cheaper methods, like random sampling of hospital arrivals and qPCR.

how it spreads

I think how it spreads is probably smaller than the other concerns. Yes, if we had more details we could make a more targeted response, but general responses like lowering thresholds for wearing PPE, ramping up PPE production, ramping up testing ability and developing cheap targeted tests, reducing some forms of non-essential activity, etc would still make sense.

wait to see if clinical cases start showing up in hospitals, it's not much of an early warning system.

As above, I think there are a bunch of things you can do aside from waiting to see if people show up in hospitals, but even then it's much cheaper to check for in hospitals if you know specifically what you're looking for.

An alternative is to look at airplane waste...

Yes, I think airplane waste is very promising, though the statistics are likely much trickier because of the small numbers (small numbers of fliers, small number of fliers using the in-flight toilets). I'd like to see exploration of both (and also sentinel populations) to see how they compare.

Plus, depending on your sampling system, you may not have plane-level data.

(Writing for myself, not the NAO)

where people talked at normal volume

Why are you modeling people on the flight as, on average, talking? On flights I've been on most people are watching videos, reading, sleeping, eating, etc and only a few people traveling together talk.

Microcovid gives more details on how they're modeling airplanes:

Load More