Adventures with the iPhone music app

My wife and I like to joke that stores do their market research by figuring out what we like a lot and then discontinuing those items. That’s how I feel about Apple’s decision a couple of iOS upgrades ago to decouple Podcasts and iTunes U from Music.

I like to listen to podcasts. I listen to podcasts much more often than I listen to actual music. I often listen to podcasts using my iPhone hooked to the USB connector in my Honda Civic hybrid. Before Apple separated the apps, my phone would play the next podcast when it finished the episode I was listening to. Because I have a very short commute, I usually have a bunch of episodes to catch up on.

After the apps were separated, my phone tended to default to the music app instead of continuing to play podcasts. This was annoying but I tried to avoid the safety hazard of fumbling with my phone while driving (at least until a stoplight). It wasn’t so bad… the song that came up was usually Miles Davis’ All Blues, one of the greatest jazz standards of all time.

But that was before the most recent iOS update, which seemed to have turned on some kind of cloud sync with my iTunes account, even though I had it set to “Sync selected playlists, artists, albums and genres”. A couple of years ago I downloaded the free Apple Christmas music compendium, which included the incredibly insipid and annoying Above the Northern Lights by Mannheim Steamroller… and until just now I couldn’t delete it.

  • I deleted it from my laptop and resynced. It was still there
  • I swiped left and got the delete button on my phone. I hit delete. It came back
  • I tried the above with many different permutations of settings on the phone and the iTunes app on my laptop. It was still there.

Many of these attempts were based on Finally, I found this thread on the Apple forums. The solution involves deleting all of your music and then resyncing with a computer.

  • On the phone:
    • Settings > Music: make sure Show All Music is Off
    • Settings > General > Usage > Music: use the edit button to delete all the data from the music app
  • Connect to the computer and resync to copy music from iTunes to the phone

Note that this doesn’t work in the untethered world that Apple aspires to for iOS devices. Also, when I turn Show All Music back on, the damned song comes back. I never subscribed to iTunes match, btw.

As an Apple stockholder, I usually just let my proxy default to the current directors. But I would consider voting for an alternative board whose platform was to fire whoever at Apple is responsible for splitting podcasts out of Music (deleting the annoying song was not a priority for me until the stupid cloud song became the default) and whoever made it so freaking hard to delete songs.

Human subjects and education research

At Retraction Watch, there’s a story of a paper about ethics training retracted due to IRB human subjects protocol problems. We tend to think of human subjects research as involving things like drug trials, but a lot of it is things like this:

This was an IRB-approved paper-pencil study investigating how certain features of ethics case studies influence knowledge and application of case study principles to new ethical scenarios.

In other words, if I’m understanding the post and the excerpts, the investigators were studying what works and what doesn’t work for how to teach higher levels in Bloom’s taxonomy in the field of teaching about ethics. So what went wrong?

Several administrative issues influenced our Institutional Review Board’s decision to not allow the data from this study to be used for research purposes. One of these had to do with the fact that some of the course instructors were not listed as key study personnel and they handed out and collected the study materials and informed consent forms. Even though they did not have any other involvement in the study, we recognized this oversight. Additionally, we implemented two minor changes to study materials, including dropping two items and renumbering 8 items, and did not obtain re-approval for these changes. Lastly, through this review process, we became aware that roughly half of the informed consent forms (ICFs) were not on file. Although we kept a clear record of who consented and who did not through the use of a training checklist, we recognized this was a data storage lapse. We worked with our IRB to fix these problems and have better processes in place to prevent similar issues from occurring in the future. Although the senior editor for the journal did not think that these issues warranted retraction of our paper, our university’s decision that we could not share the data publicly influenced our decision to voluntarily retract the article.

I understand the basis for the IRB/Human subjects rules, but this case illustrates a problem for all of us as educators. Every time I teach any course, I am doing an experiment in what works. It’s usually an uncontrolled experiment with unconscionably bad record-keeping, but it’s still an experiment and my students are subjects. As there is an increased emphasis on doing more rigorous assessment of student learning outcomes, we will try to be more rigorous about gathering and analyzing data from assessment instruments, which can be done without IRB approval as long as it’s not for publication. Consider how different that is from a drug trial!

As I understand it, doing a proper human subjects protocol for assessment of teaching requires outlining ahead of time all the interactions the assessor will have with the students/subjects. Deviation from that protocol (analogous to changing an FDA approved drug manufacturing protocol) is a no-no – as in the case above. This makes it almost impossible for the actual instructors to also do the assessment… and creates a barrier to dissemination of interesting STEM teaching methods being tried by scientists who don’t have the right collaborators for assessment.

Genomes and phenomes

Via Jonathan Eisen, NSF is using a wiki to get input on genomes and phenomes

BIO seeks community input on Genomes-Phenomes research frontiersJohn Wingfield, Assistant Director of the National Science Foundation Directorate for Biological Sciences (BIO), is pleased to announce the posting of a Wiki to seek community input on the grand challenge of understanding the complex relationship between genomes and phenomes.  The Wiki is intended to facilitate discussion among researchers in diverse disciplines that intersect with biology, such as computation, mathematics, engineering, physics, and chemistry.The Wiki format encourages open communication, captures new viewpoints, and promotes free exchange of ideas about the bottlenecks that impede progress on the genomes-phenomes grand challenge and approaches or strategies to overcome these challenges. Information provided through the Wiki will help inform BIO’s future research investments and activities relevant to understanding genomes-phenomes relationships.To provide comments, ask questions and view input from and interact with other community members, first-time users should sign up for an account via this link:Sign-up.  Once registered, users will be directed to the main page of the NSF Wiki to accept the terms and conditions before proceeding.  Additional guidance and subsequent visits can be accessed via this link: Genomes-Phenomes Wiki.Community members should feel free to forward notice of this to anyone they think might be interested in contributing to the discussion. Questions regarding the Wiki should be sent to bio-gen-phen@nsf.gov.

I agree withthat phenome is a #badomics term but not with this:

How exactly is this different from “phenotype”?

Phenotype is singular.  Phenomes, for lack of a better term, are collections of all phenotypes. Part of what makes it a #badomics term, IMO, is that the good omics terms like genome, transcriptome and proteome describe sets where completeness makes sense. Phenotypes, as observable manifestations of genotypes in environments, depend on the capabilities of the observer. New technology can create new phenotypes. While new technology can improve our ability to detect genes or transcripts or proteins, they did not come into existence by virtue of our being able to see them.

Incidentally, I’m wondering why I didn’t get the email. Perhaps it’s because I don’t currently have an NSF grant. However, I’ve reviewed for NSF a lot, I participated in the NSF-funded Phenotype Research Coordination Network workshop in Arizona earlier this year. And I work on the NIH-funded Ontology for Microbial Phenotypes. We have to get OMP into better shape and publish for our renewal application this summer, but we’ve talked about it at Biocurator meetings.

Updating to Mavericks Server

We have a mini that we got to support a program to train undergrads in bioinformatics. Over the past week or so I’ve been working on updating it to run Mavericks and Mavericks Server.  I first decided to go with OSX servers back when I had a G5 blade running Panther Server for the user-friendly GUI management system. But since then OSX server has gotten to be steadily more annoying in that:

  • The Server and Server Admin apps have never been backward compatible with earlier versions. This means I have to do remote administration of older machines – some of which cannot be updated to the latest OK – through either ssh or vnc. The former defeats the purpose of having the GUI. The latter is sluggish.
  • The amount of control the admin gets over things has been steadily declining. In the first versions of Server, there that gave you pretty fine-grained control over configuration. That’s all gone.

So, as with Lion Server, which is what I’m upgrading from, I think I’m going to end up running everything via MacPorts, and not use the Server.app. Or look into converting it to a Linux Box.

Open source communities are different

Via Althouse, Farhad Manjoo argues in the NYT that Brendan Eich had to resign because:

Mozilla is not a normal company. It is an activist organization. Mozilla’s primary mission isn’t to make money but to spread open-source code across the globe in the eventual hope of promoting “the development of the Internet as a public resource.”

As such, Mozilla operates according to a different calculus from most of the rest of corporate America.

Like all software companies, Mozilla competes in two markets. First, obviously, it wants people to use its products instead of its rivals’ stuff. But its second market is arguably more challenging — the tight labor pool of engineers, designers, and other tech workers who make software.

When you consider the importance of that market, Mr. Eich’s position on gay marriage wasn’t some outré personal stance unrelated to his job; it was a potentially hazardous bit of negative branding in the labor pool, one that was making life difficult for current employees and plausibly reducing Mozilla’s draw to prospective workers.

A commenter or Manjoo’s piece adds:

I wonder why this man was given this position in the first place if his views are so counter cultural at Mozilla. Or, if the views were unknown, what does that say about management of the company?

A reply points out that Brendan Eich, as a cofounder of Mozilla, might be in a better position to be familiar with the culture of Mozilla than Eleanor from Augusta Maine. There’s a basic problem with this argument: it presumes that the labor pool is contains more talented people who object to Mr. Eich’s private political activity than talented people who now will avoid working for Mozilla due to concerns about working for a project where outside activities are a litmus test. The idea that programmers and engineers are homogeneously enlightened progressives is… let’s just say counterintuitive. Eich is himself the counterexample to political homogeneity of talent. He’s not a John Scully from Pepsi going to Apple. The man invented Javascript, which runs a large fraction of the current web.

In my view Manjoo and Mozilla’s management have it exactly backwards. Depending on a community makes it even more important to defend the right of people you disagree with on extracurricular matters to participate. Importantly to this question, as far as I can tell, there have been no reports that Eich’s political beliefs manifested as creating a hostile work environment beyond those who are sensitive to the existence of those beliefs per se. It’s not like I’m seeing reports that Eich did anything like the infamous Larry Summers talk about women in science (I find this story interesting in part because of parallel issues in academia and science).

Shrimp and grits for Christmas Dinner

Basing in on this recipe from Anson Mills, although we didn’t see their grits at HEB, so I’m using a yellow grits/polenta corn product.

Grits:

Presoak in water starting at 1:45. Cook with lots of stirring and adding more water. Add salt about halfway through.Add butter and black pepper at the end. Is this grits or polenta?

Shrimp

IMG_0917I have some frozen shrimp from HEB. Thaw these in the Nomiku set to 32F. Tap water started at about 65… dropped to the mid 50s pretty quickly.  A problem with irregularly shaped things like shrimp and vegetables has been getting things to stay submerged.  Here, I’m using a bowl and the lid of the Cambro box to hold the shrimp under.

The main use of time in this recipe is making a tasty shrimp stock.

  • Sautee celery, onions, garlic, shrimp shells
  • Add thyme, lemon peel, a couple of spoons of tomato paste, water, a bit of chicken stock, bay leaf, thyme, peppercorns.  Bring to boil, reduce to simmer for more than an hour to reduce
  • Sautee chopped bacon in the large frying pan on low heat
  • Increase heat. Add shrimp. Recipe says to cook in a monolayer, but I had too many and didn’t feel like doing batches, so I dumped them all in and tossed/stir fried them in the bacon.  Added chopped scallions (light part), since I didn’t have shallots, and red pepper flakes. SaltIMG_0922ed too.
  • Dumped shrimp on a plate.
  • Added the strained shrimp stock to the pan. Boil some more to reduce, add beurre manie, from about 1.5 Tb flour in 2 Tb butter to thicken a bit
  • Dump shrimp back in, toss, turn off heat.  Serve on grits with chopped scallions (green part)

 

Sous vide beets

Partly this is because these pictures look so good, and partly because I want to try sealing with liquids in the ThriftyVac.

  • Preheat Nomiku to 82°C (=179.6°F, close enough to 180 for other root veg recipes)
  • I peeled and cut the beets in half so they would fit better in the 1 qt ziploc bags. I need to get a larger exterior bag for the ThriftyVac if I want to use larger bags for the food
  • Added minced ginger, brown sugar, salt, balsamic vinegar, and oil. One bag was sealed in the ThrifyVac, the other by water displacement.

IMG_0910 IMG_0911

In the left picture, the bag on the left was done by water displacement, while the one on the right was done on the ThriftyVac. The spoons (2 tsp/bag) are to provide weights to make the bags sink. The good news is that doing the ThriftyVac with the liquid present wasn’t that hard. In the pic on the right, the vacuumed bag is on the bottom. The bad news is that there seems to be as much trapped gas, if not more, as in the water displacement bag. After a few minutes in the hot bath, both bags are like portuguese man of war jellyfish – a floating air sac on the surface with the food submerged by the weight of the spoons.

It could be that I need more practice with the ThriftyVac; it’s acting like the only thing that happened was that the bag got flattened by the exterior bag in the same way you would see with the water displacement, and then air got back into the spaces between the irregularly shaped beet chunks.  I also didn’t oil the seal this time, thinking that the liquid in the bag would serve that purpose.

In at ~3:30 PM. Pulled at ~6:20…the beets were flavorful and al dente.  The spoons eventually led the bags to leak, fortunately after the food was out of the bath… with beets I think I would be able to tell if it had leaked in the bath.  I think the idea of weights is good, but I need something less likely to puncture the plastic. Or better bags.

For the protein for dinner, I did sous vide chicken breast (hoping to not kill anyone). 140°F chicken breast is recommended to cook for at least 95 minutes, and can go for up to 10 hours, so I probably should have done the chicken first, chilled it, and then reheated.  Starting with partially frozen chicken, I should go longer.  Turned down the bath to 140 and added some cold water until it got to around 160.  Meanwhile, seasoned a bag of skinless chicken that Debby had taken out of the freezer earlier, put it back in the bag and used water displacement to reseal. The bath was still > 150 °F but the chicken should cool it, I hope.  In at 6:30. Bath reached 140 at 6:40.  The outside surface of the meat looks cooked already, but I suspect the interior is still cold.  Used my thermapen to check at about 6:50… internal temp was about 90°F. So, target 8:30 for dinner, while we watched The Shop Around the Corner.  The chicken was moist, but I think I prefer the white meat from a properly roasted chicken, which isn’t a fair comparison, since I started with boneless chicken breasts, which pretty much define blandness. The sous vide is essentially a way of poaching things in their own juices.

Meanwhile, I’m making roasted potatoes. Cut into chunks. Bring to boil, reduce to simmer in water with salt and vinegar. Tossed with bacon fat mixed with olive oil. Put on a rimmed cookie sheet in a 500 F oven. Cooked for a total of about 45 minutes, turning a couple of times. These came out really well.