Gas station without pumps

2018 February 28

Twenty-eighth weight progress report

Filed under: Uncategorized — gasstationwithoutpumps @ 22:43
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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.

My weight has fluctuated a lot in the last year, but I’ve stayed pretty much in my target range for February.

It is probably about time for me to pick new breakpoints for long-term trend lines. I can’t really pretend that my “maintain” period is really modeled well as a single straight line.

My goal is to stay in the middle of my target range (~158 lbs), but this may be harder to achieve than I had originally envisioned three years ago when I started on the weight-control effort.  I’ve been skipping lunch entirely lately, which makes me a bit hungry on the days when it is 14 hours between breakfast and dinner (mostly Tuesdays and Thursdays when I have late lab classes to teach).

February had me riding an average of 4.78 miles a day—about normal for a 5-day-a-week commute with a tiny bit of weekend errand-running.  I have had huge grading loads most weekends, so sometimes I don’t even get time to do a short errand like biking down to Trader Joe’s for soy milk and cereal.

I’m still thinking that I’ll try doing some running this summer, not for weight control but to start training for running a marathon when I retire.  The longest distance I’ve ever run was 15km, and that was about 47 years ago.  I was recently told that Bike Santa Cruz County (that is the renaming of the “People Power” group that used to meet in my living room, back when I was a bike activist) sponsors a 12km run on 26 August 2018, mostly on flat dirt trails at Wilder Ranch.

If I plan on building up to longer runs by increasing length by 1km each week, then I’ll have to start training around Memorial Day. My initial training will be very easy, perhaps on the UCSC 800m track or the Santa Cruz High 400m track (both approximate measurements on Google maps).  Later in the summer I will probably alternate long days (leading up to 12km by the end of August) and short days (1–2km).  On short days, I should probably do some cycling to maintain some cardiovascular fitness—cycling up to the UCSC track to do two laps would probably make a decent short day.




2018 February 25

Weekend off!

Filed under: Uncategorized — gasstationwithoutpumps @ 15:43
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I had only 2 hours of grading to do this weekend (but next weekend will make up for that, with more than 30 hours of grading), so I got a chance to do some other things for a change:

  • Buy groceries at Trader Joe’s.  (“Groceries” is misleading here, as I generally view Trader Joe’s as a beverage store—I bought soy milk, mineral water, hard cider, beer, port, and whiskey, plus cereal, chocolate, and prunes.  I don’t drink whiskey or mineral water and my wife doesn’t drink port or soy milk, but the cider and beer are for both of us.)
  • Do a protein structure prediction for a microbiology colleague.  I no longer use my own tools for protein-structure prediction, as they have succumbed to the changes in C++ and operating systems, so that they can no longer be compiled or run.  I’ve also not maintained the template library for several years.  Because the only predictions I get asked to make these days are ones for which there are good templates, I just use HHpred and Modeller on-line.  For that sort of prediction, they are quick and do an adequate job.  The goal of this prediction was to get a good guess of binding-site residues for a chemosensor, to guide site-directed mutagenesis.  Unfortunately, the available structures did not have ligands bound, and for most of them no one knows what the real ligand is anyway, so I had to make guesses based on the structure without solid evidence for how ligands bind to them.
  • Check whether the nFET and pFET we’ll be using next quarter have small enough gate capacitances to be driven directly from a comparator, or whether we’ll still need to use 74AC04 inverters as digital amplifiers.  We could probably just barely get away with using the comparators, but the chips end up running rather warm, so I’m still going to recommend using the digital amplifier.   One inverter for both the nFET and pFET gate seems to be fine, though—the rise and fall time is short enough that we don’t need to use a separate inverter for each gate.
  • Review courses for the Committee on Courses of Instruction meeting tomorrow—I only had 13 courses to review this time, and I’d already looked at half of them.

I still have this evening—maybe I’ll repot the free live Christmas tree my wife picked up yesterday.  We gave our old one away in January, because it was getting pot bound and we did not want to transfer it to a larger pot—the current one was as heavy as we could haul up the steps.  The new one is tiny, but should last us several years before it gets to be too big.  Today might also be a good day to put the Christmas ornaments back in the attic—we’ll probably have to rebox some of them, as Marcus (our kitten) has shredded some of the boxes.)

2018 February 24

Direct-to-consumer genome sequencing

Filed under: Uncategorized — gasstationwithoutpumps @ 10:31
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I’ve been thinking of getting my whole genome sequenced, along with my father’s and perhaps my siblings and my son’s (assuming I get consent on their part).  I’m primarily interested in seeing if I can determine what causes my Dad and me to have low resting heart rates (mine is around 50bpm).

The condition is known as bradycardia, which just means slow heart rate, and is applied to any resting heart rate under 60bpm.  It is not a dangerous condition, unless it gets extreme, in which case it can lead to passing out or falling asleep at inappropriate times. Most bradycardia is due to aging (collagen buildup in the heart or scarring from heart attacks), some is due to extreme exercise, but for a small fraction of cases it is inherited.  Since it affects me, my Dad, and some other relatives, despite very different diets and exercise levels, and I’ve had it since becoming an adult, it is almost certainly genetic, not environmental.

Treatment, if needed, is to use a pacemaker to maintain a minimum heart rate. I expect that I will need to get a pacemaker sometime in next 10–20 years, but with that support, I don’t expect any shortening of my lifespan.

My dad had to get a pacemaker installed in his 70s or 80s, but he is still going strong with it at 92.  There are debates about whether to set his minimum level at what his resting heart rate was for decades (around 50, as mine is) or around 70 (more typical for adults)—there may be some tradeoff between more alertness at the higher heart rate and better sleep at the lower heart rate.  Pacemakers have already gotten fairly sophisticated and try to distinguish between sleeping, resting, and active states.  I suspect that they will continue to get better, borrowing techniques from exercise-tracking wearables.

A survey article published last year, “Inherited bradyarrhythmia: A diverse genetic background” Journal of Arrhythmia 32 (2016) 352–358 by Taisuke Ishikawa, Yukiomi Tsuji, and Naomasa Makita, lists sixteen genes that have been associated with bradycardia, with most of the variants being autosomal dominant loss-of-function mutations.  Many of them are ion channels or calcium-handling genes.

I’d like to check my own genome to see whether I have variants in or near any of these genes known to be involved in heart-rate regulation.  There are several different sorts of genetic tests available:

  • Clinical tests for specific genetic variants (like the BRCA breast-cancer genes or Tay Sachs). These are generally old technology and provide small amounts of information.  They are often quite expensive.
  • DNA microarray panels. These look for a large set of known genetic variants, generally ones that are either fairly common or have been associated with genetic diseases.  This is what 23andme offers, as it is the cheapest technology.  Because inherited bradycardia is not common, and because it can have many different causes, there are no individual markers common enough to appear in standard SNP panels like the tests used by 23andme.
  • Transcriptome sequencing.  These sequence only the messenger RNA currently being produced for translation to proteins.  This method tells a lot about the state of the cells, but misses regulatory regions (which don’t code for the proteins) and any protein not currently being made.  The results are very different depending on what tissue is being sampled.  It is commonly done in research (including cancer/normal cell comparisons), but I don’t know any direct-to-consumer companies offering it, as the results are difficult to interpret outside the scope of specific experiments.
  • Exome sequencing.  This is targeted DNA sequencing that tries to sequence all the protein-coding portions of the genome.  It is probably the most common approach for direct-to-consumer sequencing, and is offered by several companies (including Helix, Novogene, …).  Some regulatory regions may be included in the sequencing, but most of the data is for protein-coding regions.  Helix has brought the cost of exome sequencing well below $1000, but they have a business model that makes the sequencing cheap and sells analysis apps for very high prices.  It is possible to buy the variant call data (though not the raw sequence data) from them and run standard analysis pipelines on Amazon Cloud, but you need to be a bioinformatician to figure out how to run the analyses—and interpretation is still a problem. The best price on whole-exome sequencing that includes getting all the data is probably from Dante Labs: $495
  • Whole genome sequencing.  This is currently the most expensive approach, and it tries to cover most of the genome (highly repetitive regions like the centromeres and telomeres produce data, but the reads can’t be mapped to a reference genome, because of the repetitions). It is also the only approach that can uncover novel variants in regulatory regions.  So far, the best price I’ve seen on whole genome sequencing is from Dante Labs: $695

Because I don’t know whether the variants are in the genes or in regulatory regions nearby, I’m considering getting whole-genome sequencing.  The Dante Labs website provides the most technical data of any of the direct-to-consumer sites I’ve seen:  they do 30X sequencing and return the raw data (FASTQ format), alignment to a reference genome (BAM format), and variant calls (gVCF format).  They don’t document what pipelines they use for mapping and variant calling (information needed for publication these days). They also don’t provide much interpretation of the variants, so far as I can tell from their website, just running through SNPeff, which is a reasonable first cut.  They do provide all the data in their price (many sites charge extra for you to get the data), and point to third-party websites like for interpretation.

With the gVCF file, I could do standard searches against variant databases such as dbSNP and OMIM (though I believe that SNPeff already does that), to get information about known variants, and I can also use a genome browser to look for variants that are near the genes known to be involved in bradycardia.  If I get the data for n very closely related genomes (me, my Dad, my siblings, my son, …), rather than just mine, I should be able to reduce the number of variants that are candidates by a factor of 2n (from an expected 3 million to about 190,000 for 4 genomes).  Proximity to the known cardiac pacemaker genes should reduce the candidates to around 240 with a single genome and around 25 with 4 or more genomes, even if the mutation is idiosyncratic to our family and not one of the already known variants related to bradycardia.

Note: more that 4 genomes will reduce the overall pool of candidate variants, but not the number near known genes, because variants near each other on the genome will be genetically linked—either both variants will be inherited or neither will be.  With 4 or 5 genomes, I can probably narrow down the candidates to just one of the 16 known cardiac pacemaker genes, but not to a specific variation near that gene, unless I get lucky and there is either an already known variant or there is a mutation in the coding region that would obviously disrupt function.  Of course, if I’m that lucky, I might be able to guess the relevant variant from my genome alone.

I think that my process will probably be to get my own genome sequenced and see what I can do with the data, then ask for my Dad’s genome.  After that, I can ask my siblings and my son (and perhaps my nephews and nieces) for more data, to see whether we can pin down the variant.  I find it interesting that this sort of analysis, which used to require million-dollar grants, is now accessible to citizen scientists at a price less than many spend on their hobbies.  The software has to be made more user-friendly and more easily accessible, but I think that is coming.

2018 February 19

Retirement planning

Filed under: Uncategorized — gasstationwithoutpumps @ 09:45
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One of the academic blogs I read recently posted a question about long-term money goals, listing their 6 main goals:

  1. Make sure that we’re ok if DH loses his job.
  2. Continue maxing out our retirement.
  3. Be ready to replace one or both of our cars. [Update:  better be just one!]
  4. Be ready for smaller emergencies and expected home maintenance.
  5. Pay 100% for the kids’ colleges.
  6. (MAYBE):  Save up enough money to move to Paradise permanently(?)

Of the 6 goals listed, I’m not interested in #3 (I have no car), and I’ve already made the other five:

  1. We have enough in savings that we would not have financial worries even if neither of us worked.
  2. I’ve been maxing out retirement savings for decades, so I could retire on my savings even if I didn’t have a defined-benefit retirement plan.
  3. I could replace my bike out of my current checking account—bikes are much cheaper than cars.
  4. I have enough non-retirement savings for replacing all the appliances in the house and for doing small remodeling projects. We’ve been doing major maintenance all along, so the only big thing coming up is replacing the water heater sometime in the next 5 years.
  5. My son will finish his BS this year and his MS in another year, and we’ll still have money in his 529 plan despite paying full tuition—I need to think about what to do about that. He’s the youngest of his generation on both sides of the family, and all of his cousins have had about as much college education as they can stand. I have too many great-nephews and great-nieces for it to make sense to make any of them beneficiaries. I could save the money for eventual grandchildren, but I fear it will be a long wait.
  6. Not only is my house in one of the most desirable neighborhoods in one of the most desirable cities in the country, but I paid off the mortgage years ago.

Retirement is not far off—I’m committed for another year of teaching, and I’ll probably do one more after that.  My most recent plan (see Sabbaticals until retirement) had me working until June 2021, and I considered working until the group health insurance would no longer cover my son (2024), but the 30-hour grading weekends are very hard for me to deal with this year, and I don’t see them getting easier. I could use up my sabbatical credit a year earlier and retire in June 2020.  I’m afraid that my Applied Electronics course would simply disappear at that point, though, and I really would like for there to be at least the seed of a market for my book.

I plan this year to make an estimate of how much our family spends each year, so I can see whether we’ll be living on just the defined-benefit pension or will have to dip into retirement savings when I retire. Since my pension will be 2.5% * years of service * highest-3-year-average-gross-pay *85.7%(for 100% survivor benefit), I’ll be getting about 70% of my current gross pay. Because I won’t be putting any of that into retirement savings or the defined-benefit plan, the taxable pay will be about 80% of the current, and so the take-home should be also. I think that comes to about what we spend in a year, but I’m not sure—when you are consistently spending less than take-home pay, even after maxing out retirement savings, there is not much incentive to keep track.

I also need to figure out whether it makes financial sense to “buy back” the service credit for the times I took sabbatical at 2/3 pay instead of full pay. The computation gets complicated, because it trades off cash now for an annuity in the future, and annuity pricing is pretty murky, being based on weird assumptions about the future of investments and the chance of dying. My wife and I will also need to decide whether to opt for 100% survivor benefit or get more per month with a reduced survivor benefit—she’s convinced I’ll outlive her (based on parent and grandparent ages at death), and we do have enough savings that even the minimum 25% survivor benefit would not put her in financial difficulty.

My wife has suggested a few things to do with our retirement savings:

  • Give more to charity (especially local theater and music groups, but also increasing our charitable giving to Planned Parenthood, 2nd Harvest Foodbank, Southern Poverty Law Center, ACLU, …). I need to figure out whether a donor-advised fund is the best way to do this, as I’ll no longer have payroll deduction as an automatic mechanism.  Some of the donations are also not tax-deductible, so I need a mechanism for keeping track of that also.
  • Travel more. We have done very little travel for the past couple of decades, in part because of work demands, in part because we have very different tastes in travel.  I think that we can resolve the differences in taste (I mainly have to give up on some of my frugality), and we can arrange some separate trips (I’ve not done a bike tour in decades, and she’ll want an opera tour).
  • Go to more theater and concerts.  We go to almost all the local theater, so this would mean long public transit trips, or travel to theater festivals.  I think I can convince her to make the long trip to Ashland for the Oregon Shakespeare Festival, particularly if we go with the Santa Cruz Shakespeare bus group—we can’t do that group trip this year, because it is scheduled when both of us have job commitments.  I have no interest in concerts, being not very musical to begin with and going deaf on top of that, but I’d be glad to subsidize some of her concert and opera excursions.
  • Replace our furniture, most of which is either grad-student specials (futon sofas with worn-out covers) or cherrywood antiques that I bought 34 years ago.  My wife prefers light modern furniture (1950s styles), which I don’t care for, so we’ve rarely agreed on a furniture purchase. I think that our custom-built armoire for storing towels is the last piece of furniture we both really liked—maybe we need to commission more new pieces, rather than trying to find stuff that already exists.  Custom furniture can burn through money fast!
  • Take community college courses and do volunteer work (those are more ways of using time than of using money).

I’m also thinking that I should get the house remodeled for ADA compliance before I retire. With any luck, we’ll never need ramps and grab bars, but it is better to put them in without needing them than to need them and have to wait months for construction work without them.

Other things we’ve thought about but not to the point of having even vague plans:

  • eat out more. I’d like to, but my wife finds once a week about right for her—that may change when she retires and needs more incentive to leave the house.
  • remodel the kitchen.  The laminate countertops are wearing out (they’re 40–50 years old) and my wife would prefer lighter colors for the cabinetry, but there is not a lot we can do about the shape of the kitchen, which is long and narrow, so a corridor kitchen layout is all that is possible.
  • sell off a lot of our books, to make room for new ones—we ran out of bookshelf space years ago, and the boxes and piles of books are beginning to make it hard to move around.  There are a few more walls we could add shelves to, but retirement would be a good time to start weeding the collection (particularly since I have another 40 shelf feet or so of books that would come home from my office).  Selling books is harder now that the great used bookstore Logos has closed (on the flip side, we’re also buying fewer books without their stock to browse).
  • exercise more deliberately. Right now we both rely entirely on our human-powered transportation for exercise, but if we stop going to work our exercise levels will plummet.  I’ve been thinking that I’d like to run a marathon sometime in my life, which would mean soon after I retire.  It’d probably take me about 3 years of training to build up the fitness—I’ve never run more than 15k in my life, and that was when I was 16.  I haven’t done any running (other than when I’m late for class or a meeting) in decades.

One of my biggest retirement planning concerns is figuring out how to keep myself physically, mentally, and socially active.  Almost all my activity revolves around my job in one way or another, and I don’t see any of the hobbies I’ve had in the past 3 decades growing to fill that space.  My summer and fall will be spent, in part, on looking for activities that will hold my interest for the next five years.

2018 February 9

Marcus under the table

Filed under: Uncategorized — gasstationwithoutpumps @ 19:18
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Our kitten Marcus continues to grow—at his current weight and age, we expect him to get as big as our older cat, Georgie.  That will cause a problem at feeding time, because we currently feed Marcus in a cardboard box that he is thin enough to get into, but Georgie is not.  If we didn’t do that, Georgie would eat all Marcus’s food—Georgie eats like a dog, that is, until all the food is gone, then asks for more.

It is possible that Marcus will remain thin, even if he gets big, because he is very, very active.  Unfortunately, that means the he has shredded every cardboard box in the house, broken one of my favorite mugs by pulling the tablecloth off the table, and left shredded newspaper over half the house.

Here he is in an unusually quiet moment, sitting still long enough for me to take a photo (only one though, as he raced away at high speed after one shot).

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