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2019 April 17

Running hiatus

Filed under: Uncategorized — gasstationwithoutpumps @ 10:48
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I am going to stop running for a few weeks and reassess my goals.  What triggered this change was my annual physical, where I got some of my various aches diagnosed.  There were three main outcomes:

  • It is worth trying ezetimibe in addition to my current rosuvastatin to see if that controls my cholesterol better—it is probably less of a risk than increasing the statin dose.  Interestingly, my insurance requires prior authorization for ezetimibe (a $9/month generic), which makes no sense at all.  I’ll probably be paying for the prescription without insurance, since the full price will be less than the insurance co-pay would be.  (They don’t pay for the $6/month rosuvastatin either.)
  • My elbow injury is probably tennis elbow (lateral epicondylitis), for which I’ve been prescribed stretching and strengthening exercises.  I’ll also start wearing one of the tennis-elbow braces that wraps around the forearm.  I’ve had elbow inflammation before (due mainly to bad keyboarding posture), so I know more or less what to do about it.
  • The ache in my hip that I’ve had since last August is osteoarthritis, as I suspected (confirmed by X-ray). This is bad luck, but not unusually bad luck—the incidence of hip arthritis among men my age is about 12%, if I’m reading the literature correctly.  Experts seem to disagree about whether running is safe for people with hip arthritis, but even those who recommend running agree that one needs to change to low-impact running styles and do other exercises to stretch and strengthen muscles to avoid further injury to the joint.  Almost all recommend working with a sports medicine specialist and physical therapist trained in running and arthritis to determine exactly what is reasonable.  I’ll probably be doing that when I have some spare time (this summer?).

I was just feeling good about having done a 5km run last weekend, albeit at a slow pace (8:35 mile pace), and now it looks like I won’t be increasing my distance to 15km this summer as I had planned.  I may never run a marathon—I should have tried 20 years ago, when my body was better able to tolerate abuse and recover from it.

2019 April 13

Thinking about charity

Filed under: Uncategorized — gasstationwithoutpumps @ 21:39
As I enter what university-development people optimistically call the “wealth-distributing years”, I’ve been thinking about increasing the amount I give to charity.  Currently, the amount I give is modest (about 2.5% of gross household income), but I’ve determined that I now have more than enough retirement savings and income, and my son is finished with college, so I can up my giving substantially, without much risk of running out of money in my lifetime.
My wife and I will be discussing who we want to give to and at what level over the summer (when we time to think about something other than work).  I mentioned my intention to up my level of giving to charity to my son,  and we had a discussion about the philosophy of charity. He suggested a long reading list that has shaped his own approach to charity (he plans to be more generous than me, initially giving 10% of his gross income to charity).
Here is what my son sent me:
Here are some of the essays that shaped my views on charity and philosophy. I don’t expect you to fully agree with them (I certainly don’t), but most of the arguments that I was making are derived from these essays. If you’re only going to read a few, they are organized in roughly decreasing order of importance.
A good FAQ about giving, specifically giving 10% of income:
About political activism and what it means to be a good person:
About animal welfare and local giving:
About existential risk:
About political giving:
About classifying good and bad:
About spreading donations over multiple charities:
Anecdotes about the weirder aspects of the movement:
And, finally, some feel-good news:
I don’t have time right now to read everything here—certainly not and think about it carefully, which is what I need to do—so I’m putting the list up on my blog so that I can find it again easily.  I’ve not started on the reading yet.
I expect to write future blog posts as I work my way through the list.  I suspect that I’ll find things that I agree with, things that sound good but I’m not convinced by, and things I disagree with.  I’ll probably be asking readers for help thinking about the things I’m not convinced by or that I disagree with.

2019 April 12

MS > PhD

Filed under: Uncategorized — gasstationwithoutpumps @ 11:46
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I have once again seen that in engineering fields, a Master of Science is a more valuable degree than a Doctor of Philosophy.  My son (who just finished his M.S .in computer science) has been on the job market for a few weeks and has just gotten his first job offer.  The salary is larger than the salary offered to a new engineering faculty member at UCSC who has a Ph.D. and 3 or 4 years of postdoc training (in fairness, his is a 12-month salary offer while the faculty member’s is a 9-month salary, which could be supplemented another 22% if the faculty member gets grants to fund it).

For that matter, his starting salary would be over three-quarters of my salary as a full professor with a Ph.D. in computer science and 37 years of experience.  It is easy to see why academia has a hard time hanging onto engineering faculty, when industry is willing to pay so much more for shorter hours.

I’ve no idea whether my son will accept the job offer. He has had serious interviews at 4 companies, so may be getting more offers soon—he is down in Santa Barbara for a 2-day interview right now.

2019 March 31

Thirty-fifth weight progress report

Filed under: Uncategorized — gasstationwithoutpumps @ 14:21
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This post is yet another weight progress report, continuing the previous one, part of a long series since I started in January 2015.

I have found it harder than I expected to keep my weight within my target range.

My weight continues to drop (slowly), and I’m back to the weight I was a year ago. I hope to be able to pull the weight down a little further this spring, and I really want to avoid the big summer&fall weight gains I had last year.

My exercise for March included about 3.67 miles/day of cycling, which is a drop from February—probably attributable to exam week and Spring break, during which I was not commuting to work every day, but grading from home.

I’m now doing 2.5km runs two–three times a week. That’s not going to get me to my goal of eventually running a marathon, but I’ve not injured myself again, and it helps keep me in shape so that I can try upping the distance over the summer.  I’m going to try again for a 15km run in August or September.  There seems to be about 1 pay-to-enter run a month in Santa Cruz (starting around March), so I shouldn’t have any trouble finding something to enter.


I’m maintaining about an 8:20 mile pace (3.2 m/s, 11.6 k/hr) at the current distance.


2019 March 27

Comparing 23andme and Dante Labs data

Filed under: Uncategorized — gasstationwithoutpumps @ 06:22
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I got the grading for the last lab of winter quarter done yesterday (I took me several days longer than I expected, even allowing for an hour per paper—they took me more like 2 hours each). I have to turn in grades today, and I just found out last night that the graders had not finished grading homework 11, so I need to grade that also.

Before I found out that I have unexpectedly even more grading to do, I had taken an hour to write a short Python program to compare my data from 23andme with my data from Dante Labs. The two seem very concordant, and so I now believe I have gotten good data from Dante Labs:

23_and_me                              | vcf from Dante Labs
638531 genotype_sites                  | 3499617 genotype_sites
  chr   no-call haploid diploid matches|   chr   no-call haploid diploid mismatches
  chrM    306    3995       0      0   |   chrM      0      21       0      2   
  chr1   1177       0   48337  11756   |   chr1      0       0  267787     65   
  chr2   1121       0   50654  12303   |   chr2      0       0  287274     59   
  chr3   1013       0   42011  10184   |   chr3      0       0  240607     43   
  chr4   1006       0   38468   9719   |   chr4      0       0  261070     56   
  chr5    885       0   36147   8733   |   chr5      0       0  212325     41   
  chr6    956       0   43067   8505   |   chr6      0       0  204102     53   
  chr7    857       0   33500   8348   |   chr7      0       0  203647     44   
  chr8    626       0   31057   7690   |   chr8      0       0  183159     21   
  chr9    700       0   25746   6431   |   chr9      0       0  148637     65   
  chr10   656       0   29869   7494   |   chr10     0       0  177729     35   
  chr11   605       0   30337   7523   |   chr11     0       0  174926     28   
  chr12   677       0   28755   7366   |   chr12     0       0  165987     26   
  chr13   392       0   21688   5571   |   chr13     0       0  133928     30   
  chr14   472       0   19489   4871   |   chr14     0       0  111553     23   
  chr15   452       0   18554   4757   |   chr15     0       0  103635     16   
  chr16   504       0   19893   5019   |   chr16     0       0  107064     20   
  chr17   510       0   18891   4370   |   chr17     0       0   89744     24   
  chr18   307       0   17368   4591   |   chr18     0       0  100640     12   
  chr19   551       0   14366   3554   |   chr19     0       0   75073     29   
  chr20   295       0   14486   3603   |   chr20     0       0   73566     19   
  chr21   227       0    8380   2261   |   chr21     0       0   52060     18   
  chr22   244       0    8671   2073   |   chr22     0       0   45153     12   
  chrX   1033   14970     527   3663   |   chrX      0   74099    1801     36   
  chrY    506    3226       1    161   |   chrY      0    1393    2637      2   

  total 16078   22191  600262 150546   |   total     0   75513 3424104    779                     

Count of types of genotype
   CT   41086                          |    CT  696904
   AG   40444                          |    AG  696669
   CC  142899                          |    CC  358678
   GG  142411                          |    GG  358891
   TT  104122                          |    TT  320081
   AA  104648                          |    AA  319335
   GT    9760                          |    GT  173342
   AC    9810                          |    AC  172678
   CG     321                          |    CG  178718
   AT     215                          |    AT  148808
   C     5797                          |    C    18824
   G     5495                          |    G    19064
   T     5343                          |    T    18873
   A     5272                          |    A    18752
   --   16078                          |    --       0
   II    3245                          |    II       0
   DD    1259                          |    DD       0
   I      195                          |    I        0
   D       89                          |    D        0
   DI      42                          |    DI       0

There are only 779 sites where both 23andme and DanteLabs call a variant and disagree about what it is—a 0.5% disagreement, which is lower than I would have expected given the differences in the technology and the error rates of DNA chips. I think that 23andme is being fairly conservative and not calling many of the low-quality hybridization reads.

The biggest difference seems to be that Dante Labs does not cover the mitochondrion—the very small number of variant calls there could be mismapping of reads from homologous regions of the nuclear genome. Of course, 23andme does extremely thorough coverage of the mitochondrion, in order to get as much maternal haplotype data as feasible. If you are looking for maternal ancestry information or mitochondrial variants related to disease, the Dante Labs whole-genome sequencing is not the way to go.

The 23andme data also has a lot of coverage of the Y chromosome, in an attempt to get as much paternal haplotype information as possible, but the VCF file has few calls on the Y chromosome, and many of them are diploid calls, probably from homology to the X chromosome (the 23andme sites appear to be carefully chosen to avoid the homologous regions of the X and Y chromosomes, which may or may not be reasonable, depending on what is going on in those regions). Again, if you are mainly interested in ancestry information, the Dante Labs whole-genome sequencing is probably not the way to go.

The Dante Labs vcf file does not include deletion and insertion genotypes (the I and D codes in the 23andme data), but I think that the full data Dante Labs sent me on disk may have that information in a different VCF file. It may be a while before I have time to examine that more detailed data.

There are about 5.5 times as many SNPs in the VCF file as in the 23andme file, but only about a quarter of the 23andme sites are matched by the Dante Labs variants—the rest may be places where I am homozygous for the reference allele, which the VCF file does not report, or they may be places where Dante Labs had insufficient coverage to do a variant call. It will take a lot more work for me to analyze the Dante Labs data to figure out which is correct. The 23andme genotype data has a lot more homozygous calls than heterozygous ones, so I suspect that the bulk of the differences will be just that I am homozygous for the reference allele.

The most common SNP variants in the Dante Labs VCF file are CT (or the equivalent on the other strand AG), which is to be expected, as C⇒T conversion is common in DNA, because of C⇒U deamination and subsequent treatment of U as T in replication.

The Dante Labs data shows a lot higher proportion of CG and AT variants than the 23andme data—I don’t know how to interpret that. Perhaps when I get the fullgenomes data, which uses a different sequencing technology, I’ll be able to compare VCF files and see if there is technology effect here.

I clearly have a lot more work to do to interpret the data, but this preliminary look convinces me that I have good data from Dante Labs.

I retract my former claim that Dante Labs is a scam with apologies to them—it appears that they just had very bad delivery times and poor customer service. If they are now delivering data, they may actually be a good deal, as their prices are much lower than other whole-genome sequencing services. (Of course, it is still possible that they are only delivering data to a fraction of their customers, but I have no information about that—only that the data they eventually sent me seems to be good.)

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