Improving Commuting

As a follow up to yesterday, I just want to say that having a thing I look forward to that I can only do on the bus is working out brilliantly as a device for making commuting less miserable and it was totally worth buying the Kindle Fire to make it happen.  If you want to try for yourself, I recommend getting the 16gb, the 8gb could barely hold three HD episodes. I also recommend an anti-glare screen, because its glare is awful and the screen picks up fingerprints like woah.

The next recommendation is a little weirder.  I bike to the bus, which means I’m in biking clothes and have to maneuver my bike onto the cow catcher.  This makes waiting for the bus a little tricky- anything I have in my hands will have to be put away really quickly so I can rack my bike and get on, but I have no pockets.  And for reasons that may not be entirely rational, the time it takes to unsling my backpack and put a toy away makes me really stressed out.  But if I don’t use a toy the time at the bus stop is wasted, and that’s stressful too.  What I wanted was a way to make the whole of commuting feel either productive or like an indulgence.

So I made myself a shirt, out of two shirts and some fabric glue.

Two shirts enter, one shirt leaves
I believe my cat may have been getting high off the fabric glue.


  1. Place desired toy on shirt, cut patch around it.  Leave space for depth.
  2. Put fabric glue on single edge of patch and apply to surviving shirt.
  3. Lock cat in other room.
  4. Reapply patch to surviving shirt.  Once you have it aligned, apply glue to other two edges and apply (you leave the top open so it’s a pocket).  Remember to apply it less than completely flat, so the pocket will have depth.
  5. I don’t know if this is a property of the fabric glue, my shirt, or this project in general, but some of the glue filtered down such that the base shirt was glued to itself and the patch ran free.  If you catch this early enough you can separate and try again.

This shirt is not aesthetically pleasing and is weirdly stiff where I overapplied fabric glue, but it gets the job done.

Making Hannibal Make Sense

[explicit spoilers for episode 1 of Hannibal, implied spoilers for 2 and 3.  I haven’t seen past that  but I am making predictions about what will happen]

My need to make movies make sense is most obvious when it comes to animal behavior*, but that’s not its only manifestation.  Take police procedurals.  I made Bones tolerable by saying la la la science fiction.  I’m now watching Hannibal because it’s one of the best shows available on Amazon Prime Streaming, which is the only streaming service that allows offline viewing, which is important because I have a bus commute again.**

Hannibal… does not make a ton of sense.  The premise is that an ex homicide detective is a brilliant criminal profiler but unable to get into the FBI because he couldn’t pass the psych screening, so they just hire him as a “special agent” that does everything a normal agent does, including field work.  You would think that was Hannibal Lecter, but it is not.  Lecter is the psychiatrist the FBI hires to babysit the unstable profiler (who I can only imagine will one day regret copying Lecter’s answers off a psych test).  Lecter also accompanies the agent on field work, which I don’t think even regular FBI agent’s counselors are normally allowed to do.  The actual profiler (Will Graham) comes up with theories more or less out of thin air and they always turn out to be correct.  He insists the evidence makes it obvious.

On the face of it, this makes no sense.  But what if Hannibal is set in a just slightly alternate universe, where psychic powers exist but are considered shameful because they make people mentally unstable?  The FBI can’t officially hire them, and they in fact test for powers before hiring to make sure they don’t hire any psychics.  But if there just happens to be a profiler who makes totally evidence based leaps, enabling them to catch really gruesome serial killers they otherwise couldn’t, well surely you can hire them on a contract basis.***

Why doesn’t the psychic Graham notice Hannibal is murdering and eating people? I’m glad you asked.  Hiring a babysitter for a psychic is tricky business.  You wouldn’t want someone they could manipulate or even read, that would defeat the purpose.  So you hire someone who’s a null field to psychics, or at least your psychic.  As a bonus, this person can lie to them when need be.  Note that Graham says he hates going to psychiatrists- presumably every one he’s been to has been unreadable to him, and he hates that.

And that’s how I learned to enjoy Hannibal.

*Ask my brother about watching the King Kong with me.

**”So you’re coping with your motion sickness by watching a show about food and gore?” “Yes”

***The same way my team at Microsoft rehired the same contractor for our Apple version over and over again.

Review: Inside Out

First, it’s great, and totally reverses Pixar’s downward slide.  Second, they did an amazing job of making everything work as a character/story and a metaphor for how the brain works and an Aesop.  A good chunk of the time kids’ shows teach lessons I consider abhorrent (looking at you, My Little Friendship Means Never Having Boundaries) , and at the beginning it looked like they were setting up one of those, but in the end in became clear they considered it exactly as problematic as I did.

Also I need to see it at home so I can cry harder. That is all.

Link 6/26/15

Another argument for remote work.  Pixar once accidentally deleted the entirety of Toy Story 2.  When I read the headline I assumed this was some sort of really complicated RAID failure, but no, someone “rm –rf”ed from the wrong directory and the backup’s overflow mode was “overwrite old data.” Translation: someone typed “delete all” from the wrong directory, the backup system didn’t have half the space it needed, and it didn’t tell anyone when it ran out.  The movie was saved because an employee was working from home after giving birth, and she had a two week old copy at her house.

Then Pixar decided they didn’t like the movie and redid the whole thing.  But it was a great story up till then.

How do you think family income predicts children’s college attendance?  This article gives you a chance to predict it before you see the actual results (along with other people’s guesses).  Keep in mind the x-axis is income percentile, not income.  I was unable to find a graph that went by income.

Attempted chlamydia vaccine in the 1960s made people more likely to get the infection (and this was not just because they had riskier sex- they saw the same effects in mice).  New research suggests this is because the vaccine somehow stimulated the part of the immune system that is supposed to recognize your own cells and prevent your immune system from attacking it.  The vaccine taught your immune system to ignore chlamydia infection.  They think they’ve found a way to correct for that.  Bonus: Vaccine works better as a nasal spray than a skin injection because the uterine lining is more like the sinuses.

Putting the bed net problem in perspective.

Diet, Skeptics, and Getting It Wrong:  “Mocking people for wanting to absorb their food and avoid intestinal cancer isn’t going to teach anyone anything except that they should stop listening to you.”

It always makes me happy to see researchers studying who a drug helps, rather than looking at the population average.  This week it’s a suspected link between blood pressure and the efficacy of a particular PTSD treatment.

Many software teams operate on “you were the last person to touch it, you own it.”  Sometimes this makes sense (it prevents people from checking in cheap hacks and leaving others to deal with the consequences), but it also engenders a learned helplessness, because you can’t make one change without becoming responsible for every bug and feature request until someone gets desperate enough to make one little check in, at which they become responsible for every bug and feature.  It engenders a kind of learned helplessness that encourages hacks rather than digging in a fixing a problem.  The Copenhagen Interpretation of Ethics is this problem, but for altruism..

When genes fight

For those of you just tuning in: on a genetic level, all parental investments in their offspring are equally valuable.  From the offspring’s perspective investing in them is two to four times as good as investing in their sibling (depending on if they’re half or full siblings).  The fight to get the amount of resources they think they deserve is parent-offspring conflict

One manifestation of parent offspring conflict is weaning conflict, where offspring would like to keep getting nutrients with no effort and their mom would really like them to go out and get a job.

But it can start before then.  Conflict over exactly how much nutrition a fetus should get may contribute to preeclampsia (high blood pressure during pregnancy) and insulin resistance (PDF).  This is not just about mothers not wanting to give up nutrients- more nutrition leads to larger babies, which is almost always good for the baby but kind of hard on the person forcing it out through their vagina.  There is even speculation that the human custom of making a thick uterine lining (nutritionally expensive) only to flush it away each month evolved as self defense against a placenta that would otherwise invade your uterus like ivy invades bricks.

This is your uterus on babies.
This is your uterus on babies.

Creepy, yes.  Abhorrent, at the level of individuals.  But totally logical and predictable from the level of a gene.

Kin Selection

The idea of kin selection was implicit in my post on haplodiploidy but let’s make it explicit.  The unit of selection is the gene, not the individual.  The individual is a co-operative venture by many genes to reproduce themselves [I attempted to explain why this was and it became 4 paragraphs on the origin of DNA, so let’s just take it as a given].  There’s no reason for genes to prefer directly reproducing themselves: if you can get more copies of yourself by helping someone else’s co-operative venture than your own, that’s a better investment.  Doing so is known as kin selection.

The most obvious example of this is parental investment in offspring.  Offspring aren’t you, but they have your genes.  For a diploid sexually reproducing organism, a given allele of yours has a 50% chance of being in your offspring via common descent (sharing an allele via coincidence doesn’t count for reasons we will get to).  But a full sibling is just as related to you as your child, so raising them is just as good.  The technical term for this is helpers at the nest*.  It’s especially likely when raising offspring is exceptionally costly and resources (e.g. territory) are very limited, so the choice is between raising siblings or nothing, rather than raise siblings or raise your own offspring.

As you might guess from the name, helping at the nest is most common in birds, but you do see it elsewhere. Golden Lion Tamarins live in groups of 2-8, but will usually have one, with a maximum of two, breeding females.  Females are unable to provide sufficiently for their offspring on their own.  They’re helped out by other group members, which are likely to be their own children, siblings, or sibling’s children.

Honestly I have no idea if that's a helper or the parent but it's adorable.
Honestly I have no idea if that’s a helper or a parent but it’s adorable.

Nest-helping may be at intermediate step between the “good luck, fuckers” school of parenting (technical term: r-strategist) and eusociality.  For example Carpenter Bees (carpenter is a genus, there are 500+ species within it) are usually solitary, but some build nests near each other in trypophobia-inducing pattern,. show specialization and cooperation between nesting adults (e.g. one guards all nests while others forage) , and daughters sometimes share a single nest with their mothers.

Don't trust pictures in nature articles.  I couldn't find a picture of cooperation so I used one of fighting.
Don’t trust pictures in nature articles. I couldn’t find a picture of cooperation so I used one of fighting.

One way to help your own siblings is to raise them, like helpers at the nest do.  Another is to free up parental energy by taking less for yourself.  From a genetic perspective, you should stop asking for things from your parents if the energy would benefit a full sibling twice as much, or a half sibling four times as much.  But from the parents perspective children are all equally valuable, so they will want to switch giving as soon as resources benefit one child more than another.  This is parent offspring conflict, as explained by noted evolutionary biologist Dylan Moran at 30:00 in this lecture:

More on parent offspring conflict tomorrow.

*Note: kin selection is not necessarily the only reward for helping to raise siblings; individuals may also learn parenting skills or give themselves a leg up claiming their parents’ stuff when they die.


Let’s start way at the beginning.  All eukaryotic cells (which includes any multicellular organism) carry their DNA wrapped up in a chromosome


In any given species the chromosomes are numbered, and chromsome N contains predictable information.  For example, the human chromosome 16 contains the DNA to alpha-globin, a component of hemoglobin, the thing that lets your red blood cells carry oxygen.  Some people have a variant in their alpha-globin genes that leads to sickle cell anemia.  It’s still chromosome 16.  The general location and form of the DNA that produces a protein is the gene, different variations are called alleles.  So technically it’s wrong to say “the gene for sickle cell”, you need to say “allele for sickle cell”, but everyone knows what you mean.

Many organisms contain more than one version of their chromosomes: the second (or more) chromosome has the same genes but different alleles (unless something goes weird, which does happen but we don’t have time to get into).  You are probably most familiar with the human chromosomes: 2 versions of 22 normal chromosomes, an X chromosome, and either an X or a Y chromosome, with Y chromosomes conferring maleness.    Having two versions of each chromosome is referred to as being diploid, and it’s not the only choice.  Certain sugar cane hybrids have as many as 12 copies of the same chromosome.  Some species show variation in ploidy between individuals.  This is more common in plants, which can self-fertilize, but is also seen in insects.  In humans individual chromosomes are occasionally doubled when they shouldn’t be: this causes death if it’s a big chromosome and things like Down’s Syndrome if it’s not.

Note that the Y chromosome does not contain all the information you need to be male: it releases the signals to be male, and numerous genes on multiple chromosomes respond accordingly.*   That’s not the only way to determine sex.  Birds, some fish, some reptiles, and a few others species use the ZW system, which is the same as XY except females are the one with the Y chromosome.  Many reptiles sex depends on the temperatures their egg experienced (and not every species responds to temperatures the same way).   We don’t know how sex is determined in the platypus, which, yeah, that’s about what I expect from the platypus.

Then it gets weird.  Fruit flies, and have the equivalent of X and Y chromosomes- but they have anywhere from one to four versons of sex chromosomes, and 2-4 versions of each non-sex chromosome (autosome). All autosomes have the same number of versions, but there may be a different number of sex chromosomes.  The sex of a fruit fly depends on the ratio between the # of autosome copies and sex chrosomsome copies.

But what I really want to talk about (600 words in) is haplodiploidy.  A haploid cell has only one version of each chromosome, a diploid two.  In haplodiploidy, females are diploid, and both male and female produce haploid gametes (egg and sperm).  Unfertilized eggs grown into males, and fertilized eggs grown into females- so females have twice as many chromosomes as their brothers.  Males have one grandfather and no father at all.

This has a couple of implications.  One, most deleterious recessive genes get weeded out right quick, because no male will produce them.  On the other hand, such a gene could persist if it boosted female reproduction sufficiently.  Second, females can reproduce without males, although they will produce only sons.  Which they can then mate with (and inbreeding isn’t nearly as dangerous as it is in diploid animals, because of the aforementioned filter on negative recessive genes), and produce daughters, so a single female can repopulate the planet.

Then there’s relatedness.  A human is 25% related to a half sibling (for any given gene there’s a 50% chance it came from the shared parent, and a 50% chance the parent passed it on to the sibling).  But a haplodiploid father passes on the same genes to every child, so each sibling is 50% related to each other through him.  If the siblings also share the same mother, they are 75% related to each other.  That is more related than they could be to their own offspring (50%).**

It was initially thought that this was why/how eusociality developed: it was literally more advantageous to raise sisters than daughters.  That’s not strictly true:  There are haplodiploids without eusociality, and strict diploids with eusociality.  Some  eusocial haplodiploid queens breed with multiple males, so their daughters are raising sisters only 25% related to them.  But eusociality is heavily overrepresented in haplodiploid animals, so it clearly affects the math.

*Fun fact: the signal for male development in utero is not exactly the same as the signal for male development at puberty, and it’s possible to be unable to produce the fetal signal but successfully produce the puberty signal, producing babies that are born with female external genitalia but grow a penis and testicles at puberty (nearly all of these children identify as men as adults).  This was common enough in certain villages in the Dominican Republic that they have a name for it, which translates to “penis at 12.”  It’s considered a joyous thing because sons are more valued than daughters.

**But aren’t their sons 100% related to them?  Yes.  But relatedness is not necessarily reciprocal.  A gene in a female has only a 50% chance of being in a given son, so she is only 50% related to him.