Gas station without pumps

2018 March 29

Regrowth: a return to normal

Filed under: Uncategorized — gasstationwithoutpumps @ 17:04
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As those who’ve been reading my blog for the past five months know, in October I had my head shaved as part of a fundraiser for pediatric cancer research, including my beard and my eyebrows.  (I believe that it is still possible to donate at https://www.stbaldricks.org/participants/Karplus2017.)

Since then, I’ve had a photograph taken about every two weeks, to record the regrowth of my beard and head hair, and my gradual return to a normal (for me) appearance.

Before getting shaved, this is what I looked like.

This is what I looked like right after the shaving, wearing the silly medal they gave me for the most funds raised at UCSC for St. Baldrick’s.

After 2 weeks there was some grey stubble on my chin and shorter brown stubble on top of my head.

After 4 weeks the grey beard began to look like an unsuccessful attempt at growing a beard, rather than just stubble.

After 6 weeks, the beard looked deliberate, but the hair on top of my head still looked like it had just been shorn off.

At nine weeks the beard looked more or less normal, though about as short as I’ve ever trimmed it. The pattern of white and dark hair in the beard stands in strong contrast to the uniformly dark hair on top of my head.

At eleven weeks, I dyed the beard to make the color contrast less, shaved my cheeks, and trimmed my mustache.

At thirteen weeks the beard looked ok, if a little scruffy and the head hair was starting to come back, though the “reverse Mohawk” stripe from front to back where they had shaved closer was still visible.

At fifteen weeks the beard dye was fading out (I use a dye that gradually washes out).

At seventeen weeks I had re-dyed the beard to match my head hair.

At 20 weeks the beard was pretty much back to normal (though still substantially shorter than what I started with), and the head hair was getting close to where I have it cut to at the beginning of a summer.

At twenty two weeks after the shaving, I re-dyed my beard yet again, in anticipation of the start of a new quarter. I expect to dye the beard about every 8–12 weeks, to keep it more or less coordinated with the hair on top of my head, instead of the white with darker stripes that can be seen in weeks 4–9.

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2018 March 28

Personal genome sequencing

Filed under: Uncategorized — gasstationwithoutpumps @ 12:41
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I have just ordered whole-genome sequencing (WGS) for myself from Dante Labs, as I suggested I would do in Direct-to-consumer genome sequencing.

Dante Labs has the cheapest WGS service I could find at $499.  They say that they ship the data in 3 forms: FASTQ, BAM , and gVCF.  The FASTQ format is basically the raw read information from the sequencing machine, BAM is the alignment of the reads to a reference genome, and gVCF is a variant-call file based on the alignment of the reads to the genome.

Many other sequencing services charge extra for sending you the data, as they want to hang onto it and charge ridiculously large amounts to run little software genetic tests on it.  You can get essentially all the standard tests run on the data by Promethease for about $10.  The Promethease analysis is limited to what is in the SNPedia database, which is a fairly large database of published information about genomic variation, with pointers to the original literature.

I’m interested in finding out what my inherited bradycardia (resting heartbeat lower than 60bpm) stems from. The inheritance of this condition has not been studied much as it has little medical consequence by itself (an increased need for pacemakers in old age, perhaps).  Most bradycardia is caused by heart damage and old age, so that is what gets studied.

I found a good open-access survey article on the subject,

Inherited bradyarrhythmia: A diverse genetic background
Taisuke Ishikawa, DVM, PhD, Yukiomi Tsuji, MD, PhD, Naomasa Makita, MD, PhD
Journal of Arrhythmia 32 (2016) 352–358

in which 16 genes are linked with bradycardia (though often with serious other conditions, which our family does not have).  SNPedia only mentions bradycardia 8 times (talking about only 3 genes), and there is no overlap between SNPedia’s entries and the genes in the survey article, so it is clear that SNPedia is not going to be very useful here.

I believe that Dante Labs uses SNPeff to do its annotation, a free tool that seems to be even older and less up to date than Promethease’s use of SNPedia.  But I don’t think that any of the commercial services will be any better for the analysis I’m interested in, as it is quite likely that my family has an idiosyncratic mutation that has not been published.

I’ve communicated with Dante Labs, and they say that the $500 produce is for 30X sequencing with BGI sequencers (not Illumina).  I was worried that the price was too low to be real, as even wholesale sequencing for large numbers of genomes is $600 each from BGI, but a couple of people in Europe that I communicated with were pretty sure that Dante Labs was a reputable lab, and one said that he’d run 10 genome samples through them.  I was reassured enough to risk the $500 on testing my own genome, but I’ll wait until that data comes back before testing anyone else in the family.

I expect that it will take 3 or 4 months before I have any data from them, as they are not paying for quick turnaround from the sequencing labs, and even quick turnaround would be a couple of weeks with the low-cost sequencing methods.

2018 March 13

Cabrillo College Robotics

Filed under: Robotics — gasstationwithoutpumps @ 13:56
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I just donated to the Cabrillo College Robotics Club, to help them send students to the NASA Swarmathon this year:

https://www.gofundme.com/cabrillo-college-robotics-club/

I am not affiliated with Cabrillo College in any way (except as a resident of the county which they serve), but I’ve been impressed with their recent attempts to better serve the community, with an extensive Extension program of non-credit courses and a new Makerspace. So I look for small ways to support Cabrillo College.

The Cabrillo College Robotics Club looks like a good opportunity.They are trying to raise $7000 in a month, which may be difficult, given the resources available to community-college students.  The goal is to send the team to the NASA Swarmathon in April.  They won the 2016 NASA Swarmathon Virtual Challenge, and they are hoping to win the 2018 in-person competition this year, but first they need the funds to go there.

2018 March 2

Long-term care insurance

Filed under: Uncategorized — gasstationwithoutpumps @ 20:59
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Every year, I get a letter from the State of California’s Department of Health Care Services urging me to get long-term care insurance, but the reasoning in the letter never makes sense to me.  They say

Most of us have fire insurance on our homes, even though only 1 out of 1,000 home owners will ever have a serious fire. Consider that 700 out of 1,000 of us over the age of 65 will need some type of long-term care.

OK, I’ve considered it, and their argument makes no sense at all. Insurance is a trade-off—you pay somewhat more than the expected cost of something, in order to reduce the variance.  So for fire insurance, if you have a 1/1000 chance in 40 years of a $1 million loss, then the expected cost per year is about $250, but people are willing to pay about $1000 a year to reduce that loss to a few thousand if it does occur.  The variance is now quite small (almost constant cost whether or not there is a fire), rather than high probability of no cost with a low probability of enormous cost.

But it long-term care is almost always needed, then insurance is not the right vehicle for dealing with it—savings is.  The cost of the insurance would be more than you would need to save (otherwise the insurance company would make no profit), and if you turn out not to need the long-term care, you would still have the savings, but insurance premiums would be gone.

The only justifications I could see for long-term care insurance are

  • if there is a very small probability of needing very expensive care, so the insurance reduces the probability of a disastrous outcome, or
  • as a forced savings plan, because people can’t be trusted not to spend the money that they have set aside for the possibility of long-term care.

Whole-life insurance used to be used as a form of forced savings, which turned out to be very profitable for insurance companies, but very bad deals for consumers. (Separate term insurance and other forms of savings were much better financially.)  So I don’t trust insurance companies to devise good forced-savings plans.

That only leaves the very small probability of needing very expensive care as a possible justification, and the letter sent out each year implies just the opposite—that there is a very high probability of needing long-term care.  I wish that they provided real information—like the probability distribution of cost of long-term care for the population, so that I could figure out how much risk was really being covered by the insurance.

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