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2015 January 23

Dress like it’s 1965 Winner

In Dress Like It’s 1965, I showed the clothes that I wore for UCSC’s “Dress Like It’s 1965″ Day on Thursday, 15 Jan 2015, to help celebrate the 50th birthday of UCSC (including the marvelous shoes my wife painted). Today I found out that I won 1st place in the men’s category! Pictures of the other winners can be found at

Here is the picture they took of me, which was used for the judging:

Copied from Sorry, I can't find the photographer's name on the 50th anniversary website to give proper photo credit.

Copied from
Sorry, I can’t find the photographer’s name on the 50th anniversary website to give proper photo credit.

I feel like I cheated a bit, as I was reproducing what I wore in 1969–1971, not 1965. Also I’m wearing a modern digital watch, since I no longer own any analog ones and forgot to take the watch off. But the judges obviously weren’t too fussy.

2015 January 17

How big is a course?

Filed under: Circuits course,freshman design seminar — gasstationwithoutpumps @ 10:42
Tags: , , ,

One of the questions that comes up when designing a course is how much work the course should be. When deciding whether to include a particular topic, exercise, reading assignment, project, test, paper, or whatever, there is always the question whether there is enough time for it, and whether it is important enough to be worth the time.  So how much time is there to allocate for a course?

In the UC system, most of the campus are on a quarter system (UCB and UC Merced are on semesters), with approximately 10 weeks of instruction followed by one week of exams. The exact number of instructional hours varies a bit from quarter to quarter, and between MWF and TTh classes, thanks to almost all holidays now being scheduled for Mondays.  All the quarter-based campuses have a 180-unit graduation requirement, where a unit is supposed to represent 3 hours of work a week for the 11 weeks of the quarter, so the 180-unit graduation requirement is supposed to mean 5940 hours of work (about 1485 a year).

UCSC is different from the other campuses, in that our courses are by default 5 units, while the other campuses generally have 3-unit or 4-unit courses. What I was not aware of until recently, however, is that UCSC also differs from the other campuses in terms of how many contact hours the students get with the professors per unit. UCSC 5-unit courses meet for 210 minutes per week. A full course, including exam, is 2100+180=2280 minutes, or 456 minutes per credit. Not counting the exam, there are 420 minutes per credit.  (In actual schedules, there may be up to 105 minutes of lecture missing due to holidays, reducing the time to as little as 399 minutes of lecture per credit.)

According to a proposal about changing class scheduling at UCSC, written in 2011, the other quarter-based campuses have at most 375 lecture minutes per credit, which lets them pack more class credits per classroom seat than UCSC does. (UCSC suffers a double whammy here, as it has the fewest classroom seats per student, thanks to former chancellors who grew the student population rapidly, on the theory that this would force the state to provide the needed infrastructure—the administrators who made this bone-headed prediction have since gone elsewhere, while the faculty are left with too many students and too few classroom seats.)

Of course, some classes involve far more contact hours. I’m a great believer in high-contact courses, where the students spend time with the faculty. For example, my Applied Circuits class in the spring has me in the classroom with the students for 3.5 hours a week, and in lab with them for another 6 hours a week, for 5700 minutes—at 7 credits that’s 814 minutes per credit,  80–90% more than the usual course. The senior design seminar I’m teaching this quarter has 1155 minutes of class for 2 credits plus 180 minutes per student of one-on-one meetings, or 668 minutes per credit—50–60% more than normal.  (Note: my time for 19 students is 76.25 hours for that class—over 5 times the usual contact hours for a 2-unit course, and that’s not counting the grading time for reading 4 drafts each of 19 theses, nor prep time.)  The freshman design seminar I’m also teaching  this quarter has 2030 contact minutes, for a 2-unit course, or 1015 minutes per credit (2.2–2.4 times normal contact hours). Those are just the scheduled contact hours—I also generally have 2–3 hours a week of office hours, and during the circuits course, I often have to stay late in the lab to help students finish.

So when I’m deciding how much homework to assign in, say, the freshman design seminar, I have to start with the 66 hours that the students are supposed to work for a 2-unit course, then subtract off the 33.83 hours of class time, and divide by 10 weeks to get about 3.2 hours of homework a week (or 3 hours a week, if some is done during exam week).  That is not a lot of homework, particularly if I want students to do some web searching and reading on their own, or do design tasks, which tend to be rather open-ended. It’s a good thing that the freshman design course doesn’t have any specifically mandated content—I can take the classes wherever student interests and abilities lead, without having to worry about whether I’ve covered everything.

Note that engineering students typically take a 17–18-unit load at UCSC (3 5-unit classes, plus labs), which comes to a 51–54-hour week, if they are doing what they are supposed to for all their classes. This workload does not allow much time for students to do a part-time job, and certainly not a full-time one. Some students, forced by the legislature’s defunding of the University to work to pay their tuition, end up with 20-hour work weeks on top of the 54 hours they are (or should be) putting in as students. The legislators may have partied their way through school and think that all students do, but the engineering students I see don’t have that luxury—being a full-time engineering student is not compatible with more than 5–10 hours a week of non-class-related work.

Engineering students at UCSC are usually advised to take two technical courses and one non-technical one. The justification is not that the students need the humanities for intellectual balance (even if it is true, students wouldn’t buy into that justification). Instead, the justification that the students accept is that grade inflation has gotten so extreme in the humanities that they can get an A– doing only half as much work as a 5-unit class should require, so that they have enough time to work on their technical courses or hold a part-time job to pay for college.


2015 January 16

Dress like it’s 1965

UCSC had a “Dress Like It’s 1965″ Day on Thursday, 15 Jan 2015, to help celebrate the 50th birthday of UCSC.  I participated in the festivities by dressing as I did in high school, with bright red pants, orange shirt, white belt, and Campbell soup tie.  The tie, tie bar, and glasses were the ones I wore in high school, but the rest of the clothes I had to reconstruct, as I weigh about 60lbs more now than I did in high school. My head is also wider, which means my old glasses don’t fit very well.  (They’re less than 1 diopter off in the prescription, though—good enough to get around in, but headache-inducing.)

The red pants should have been denim, but I couldn’t find any red denim pants—the red polyester from MoonZooom was the best I could do. The pants were the only purchase—everything else I wore we already had in the house. I was also cheating a bit, as the clothes I wore reflected 1969 or 1970, rather than 1965.  I was in 6th and 7th grade in 1965, and I did not wear anything interesting then.

Here are some photos of what I wore:

The woman is the manager of the engineering advising office—she normally has short hair and dresses very professionally—but she looks good in the 1965 styles also!

The woman is the manager of the engineering advising office—she normally has short hair and dresses very professionally—but she looks good in the 1965 styles also!

The most distinctive part of my outfit was the shoes, which my wife painted (the color is mostly Sharpie, though as she didn't have time for paint to dry).

The most distinctive part of my outfit was the shoes, which my wife painted (the color is mostly Sharpie, though, as she didn’t have time for paint to dry).

shoes_heels shoes_instep

These shoes are not like anything I wore in the 60s, but I would have, if they'd been available!

These shoes are not like anything I wore in the 60s, but I would have, if they’d been available!

The festivities were interrupted by a student protest:

One of the protestors with a cardboard sign saying "COPS OFF CAMPUS   CAMERAS OFF CAMPUS" A larger banner calling for firing the President of UC can be seen on the stage in back.

One of the protestors with a cardboard sign saying “COPS OFF CAMPUS CAMERAS OFF CAMPUS”
A larger banner calling for firing the President of UC can be seen on the stage in back.

The front of the protestors' parade, with a cowbell.

The front of the protestors’ parade, with a cowbell.

I was quoted in the Santa Cruz Sentinel:

Kevin Karplus, biomolecular engineering professor, wore his old high school 1960s tie and taped glasses. He said he was glad the event was interrupted by a student demonstration.“It wouldn’t be the 60s without one,” said Karplus, who said in his 28 years at UCSC, he’s watched enrollment and fees grow and student resources and state funding drop.

I actually said a good deal more than that to the reporter—I’m actually in agreement with the students that raising tuition is the wrong solution to the continued reduction in state funding for the University of California, and that the game of chicken that Janet Napolitano has decided to play with Jerry Brown is not in UC’s best interests. But I don’t expect anything to change as long as we have such a dysfunctional legislature—I don’t expect to see UC’s financial situation to improve before I retire in a few years. I also gave more specific instances: that the enrollment has grown threefold while the number of librarians has been cut in half.  (I now think that the actual numbers may be slightly more extreme than that.)

I doubt that firing Napolitano would do any good, though, as she is pretty much following exactly the same script as her predecessor. It would take an wholesale turnover of just about all the senior executives in the UC Office of the President (or firing and not replacing them) to get any significant change in policy there. It might also take replacing most of the Board of Regents, who seem hell-bent on privatizing the University—I don’t know if that originates with them, or whether they are just rubber-stamps for UCOP, but I suspect that the Regents and UCOP are in close agreement.

2015 January 7

Bait and switch health insurance

Filed under: Uncategorized — gasstationwithoutpumps @ 21:49
Tags: , , , , ,

I just started a new health insurance plan at UCSC this month, one that costs me $549.67 a month in premiums, that I selected specifically because it would let me continue with the family doctor we’ve had for years. Note that this plan is essentially the same as the one that was free 10 years ago—they keep raising the prices to the faculty without improving the product.

Today, I was very surprised and distressed to get the following message:

January 7, 2015

To:  UCSC Academic and Staff Employees
From:  Lori Castro, Interim Assistant Vice Chancellor, Staff Human Resources; Pamela Peterson, Assistant Vice Chancellor, Academic Personnel
Re:  Blue Shield of California and Sutter Health Provider Negotiations – Contract Termination and Transition Period

As you may have heard, Blue Shield of California and Sutter Health were unable to agree on a contract for 2015, which affects many UCSC employees using the Palo Alto Medical Foundation.  On January 5th, 2015, Blue Sheild of California sent letters to more than 140,000 members state-wide who are users of Sutter Health in Northern California, informing them that the Blue Shield/Sutter Health contract was terminated, effective Dec. 31, 2014.  However, there will be a six-month transition period for UC Blue Shield plan members.

University of California employees (and retirees) are affected by this development if they use Sutter providers, including Palo Alto Medical Foundation (PAMF), and if they are enrolled in the following UC health plans:

  • Blue Shield Health Savings PPO
  • Core Medical PPO
  • UC Care PPO

Blue Shield has directly contacted members in the aforementioned plans, but we would like the campus community to be aware of the situation.

From January 1, 2015 thru June 30, 2015 there will be a six-month transition period to allow UC Blue Shield plan members time to find an alternative provider.  During the transition period UC plan members will continue to receive services at the UC Select level at the Palo Alto Medical Foundation.  Blue Shield Health Saving Plan and Core Plan members will continue to have the preferred 80% coverage at the Palo Alto Medical Foundation but can anticipate a higher cost due to the fact the 80% coverage will now be on a non-contracted rate.

Contract negotiations are ongoing, and it is our hope that Sutter Health and Blue Shield will come to an agreement before the transition period ends. If the parties do not come to an agreement, we anticipate the University of California will announce a plan but for now there is no additional information. The UC is not authorizing a special opportunity for employees to change medical plans at this time.

Last year I used a different insurance plan (UC Core instead of UC Care—a confusingly similar pare of names) that cost me nothing, but that had high deductible and co-pays. Because I’m overdue for a colonoscopy, I decided to switch plans this year, though the premiums may still be higher than the expected medical expenses for the year.

Both the plan I was on last year and the plan I switched to this year are saying that I can’t keep my family doctor—when I selected those plans specifically because they would cover that doctor!  UC should be suing Blue Shield for bait-and-switch tactics and refunding the health insurance premiums collected under false pretenses from the faculty and staff.  But I don’t expect UCOP to do a damned thing about it—they’ve taken the attitude that as long as they have their Kaiser plan in Oakland, the rest of the University can pay through the nose for inadequate health insurance.  UCSB got screwed last year, so it is UCSC’s turn this year.

Perhaps the faculty union (the Santa Cruz Faculty Association) could protest the change? No—they have a memorandum of understanding that they will remain toothless about anything UC does to the faculty.  They might write a politely worded note expressing their dismay.

Of course, this game of chicken between Blue Shield and Sutter Health doesn’t affect just the UCSC employees. A Santa Cruz Sentinel article points out

In Santa Cruz County, an estimated 4,500 policyholders who signed up with Covered California last year and picked Blue Shield are affected along with many more who purchased an unsubsidized Blue Shield policy on the open market.

UPDATE January 30, 2015:

To: UCSC Academic and Staff EmployeesFrom: Lori Castro, Interim Assistant Vice Chancellor, Staff Human Resources; Pamela Peterson, Assistant Vice Chancellor, Academic Personnel

Re: Blue Shield of California and Sutter Health Provider Negotiations

The University is pleased to announce that as of late last night, Blue Shield and Sutter Health have settled on a two-year contract.

Blue Shield of California today, January 30, 2015, announced the signing of a new, two-year contract with Sutter Health. Blue Shield is pleased to offer members access to Sutter Health providers and facilities as participating providers through December 31, 2016. Blue Shield apologizes that the contract negotiation took longer than expected and that customers and members experienced uncertainty or disruption. We also regret the worry that this has caused the campus community.

Blue Shield will be notifying all of its members of the development.

Thanks for all of your patience on this matter.

 I’m very relieved.

2014 October 22

Banana Slug genome crowd funding

Filed under: Uncategorized — gasstationwithoutpumps @ 21:20
Tags: , , , , ,
T-shirt design from the first offering of the class.

T-shirt design from the first offering of the class. (click for high-res image)

A few years ago, I taught a Banana Slug Genomics course, based on some sequencing done for free as a training exercise for new technician.  I’ve mentioned the course occasionally on this blog:

The initial, donated sequencing runs did not produce enough date or high enough quality data to assemble the genome to an annotatable state, though we did get a lot of snippets and a reasonable estimate of the genome size (about 2.3GB total and about 1.2GB unique, so a lot of repeats).  All the class notes are in a wiki at and the genome size estimates are at

I did manage to assemble the mitochondrion after the class ended (notes at, but I now think I made a serious error in doing the assembly, treating variants due to a heterogeneous mitochondrial population as repeats instead.  The mitochondrion was relatively easy, because it is much shorter than the nuclear genome (probably in the range 23kB to 36kB, depending on whether the repeats are real) and has many more copies in the DNA library, so coverage was high enough to assemble it—the hard part was just selecting the relevant reads out of the sea of nuclear reads.

Ariolimax dolichophallus at UCSC

Ariolimax dolichophallus at UCSC, from larger image at

The banana slug genomics class has not been taught since Spring 2011, because there was no new data, and we’d milked the small amount of sequence data we had for all that we could get for it.  I’ve played with the idea of trying to get more sequence data, but Ariolimax dolichophallus is not the sort of organism that funding agencies love: it isn’t a pathogen, it isn’t a crop, it isn’t an agricultural pest, and it isn’t a popular model organism for studying basic biology. Although it has some cool biology (only capable of moving forward, genital opening on the side of its head, penis as long as its body, sex for up to 24 hours, sometimes will gnaw off penis to separate after sex, …), funding agencies just don’t see why anyone should care about the UCSC mascot.

Obviously, if anyone is ever going to determine the genome of this terrestrial mollusk, it will UCSC, and the sequencing will be done because it is a cool thing to do, not for monetary gain.  Of course, there is a lot of teaching value in having new data on an organism that is not closely related to any of the already sequenced organisms—the students will have to do almost everything from scratch, for real, as there is no back-of-the-book to look up answers in.

At one point I considered asking alumni for donations to fund more sequence data, but our dean at the time didn’t like the idea (or perhaps the course) and squelched the plan, not allowing us to send any requests to alumni. When the University started getting interested in crowd funding, I started tentative feelers with development about getting the project going, but the development people I talked with all left the University, so the project fizzled.  I had a full teaching load, so did not push for adding starting a crowd-funding campaign and teaching a course based on it to my workload.

This fall, seemingly out of nowhere (but perhaps prompted by the DNA Day celebrations last spring or by the upcoming 50-year anniversary of UCSC), I was asked what it would take to actually get a complete draft genome of the slug—someone else was interested in pushing it forward!  I talked with other faculty, and we decided that we could make some progress for about $5k–10k, and that for $20k in sequencing we could probably create a draft genome with most of the genes annotated.  This is a lot cheaper than 5 years ago, when we did the first banana slug sequencing.

Although the top tentacles of the banana slug are called eyestalks and are light sensing, they do not have vertebrate-style eyes as shown in this cartoon.  Nor do they stick out quite that much.

Although the top tentacles of the banana slug are called eyestalks and are light sensing, they do not have vertebrate-style eyes as shown in this cartoon. Nor do they stick out quite that much.

And now there is a crowd funding campaign at to raise $20k to do the project right!  They even put together this silly video to advertise the project:

Nader Pourmand will supervise students building the DNA library for sequencing during the winter, and Ed Green and I will teach the grad students in the spring how to assemble and annotate the genome.  Ed has much more experience at that than me, having worked with Neanderthal, Denisovan, polar bear, allligator, and other eukaryotic genomes, while I’ve only worked on tiny prokaryotic ones. (He’s also more famous and more photogenic, which is why he is in the advertising video.) We’re both taking on this class as overload this year (it will make my 6th course, in addition to my over-300-student advising load and administrative jobs), because we really like the project. Assuming that we get good data and can assemble the slug genome into big enough pieces to find genes, we’ll put up a genome browser for the slug.

I’m hoping that this time the class can do a better job of the Wiki, so that it is easier to find things on it and there is more background information.  I’d like to make the site be a comprehensive overview of banana-slug facts and research, as well as detailed lab notebook of the process we follow for constructing the genome.

Everyone, watch the video, visit the crowd funding site, read the info there (and as much of the Wiki as you can stomach), and tell your friends about the banana-slug-sequencing effort.  (Oh, and if you feel like donating, we’ll put the money to very good use.)

Update 30 Oct 2014: UCSC has put out a press release about the project.

Update 31 Oct 2014: It looks like they’ve made a better URL for the crowd-funding project:

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