Not Amsterdam. It's Düsseldorf.

The lady and I got into Essen with flexible plans. They looked much like this:

• Visit friends
• Visit Düsseldorf
• Find sushi
• Visit Ochtrup* 

The first step was in progress by Friday so we started in on the second. That's the easy part - it's just a short train ride from Essen. The third may seem surprising if you're unaware of Düsseldorf's large Japanese population and selection of all-you-can-eat sushi places. They're high-quality and quite inexpensive. They're also quite popular as our first choice was far too busy to ever have a table ready. Luckily, there was a great alternative not far away (the rain had finally caught up with us, so we didn't feel like searching for long). It's an atmospheric, classically German city, especially if you don't mind Nordrhein-Westphalia serving as the representative of the whole country.

In Essen, waiting for the right train.

In Düsseldorf. You can tell because they sell gazpacho in bottles (don't believe me about that - it's a novel thing to do in most places).

There's that rain again.

"What's Beef Burgers". There isn't a question mark so I don't think it's interrogative.

This building may be competing with Philadelphia's Comcast Center for the title of Most Sinister-Looking Tower.

We made it to the Rhein and had some Spaghetti-Eis (not shown, but it looks like this).

The trees by the river had managed to survive all the recent volatile weather.

The Oberkasseler Brücke. It's technically the oldest bridge in the city if you ignore how it was rebuilt in the 1970's.

Looking out at the river to see where it's going today.

Back to Essen and to this wonderful place. 

Next time: To Ochtrup.

*What's an Ochtrup, you ask? It's a small town. It's right here. They make ceramic whistles there called "nightingales". They don't look like birds but they sound like them (the ceramics, not the people of Ochtrup).

Amsterdam - Day Three. Also a bit of Essen.

One wall at the de Hoek is papered with exotic foreign currencies.

We began at the Koffehuis de Hoek and pancakes. Pancakes with raisins, apple, and bacon, to be specific. It's quite cozy and supposedly very Dutch in a difficult-to-define way.

The proprietor is also named Harry. He's had the place for 50 years, at least according to these photos.

Not shown: boat captains who may or may not have been drunk, an entire tour group, and the nearby Heineken Experience.

We followed this Authentic Experience with the requisite Amsterdam canal tour. I'm usually skeptical of guided tours as they can seem hackneyed. This tour was enjoyable, especially as it's the only way to see a number of local fixtures (oddly-angled buildings, concrete houseboats, and the inner workings of the lock system) without renting a boat or illegally swimming around in the canals.

My Heineken Experience is usually disappointment and regret about ordering a Heineken.

Theft-proofing, I presume.

An exemplary façade.

Out on the IJ. The wavy building is the EYE Film Institute. It's called that because IJ and Eye are phonetically similar. The nearby tower was once owned by Royal Dutch Shell but is now being redeveloped into offices and entertainment space.

The top of the NEMO science museum, looming.

The Montelbaanstoren. The prerecorded tour stated that the tower's bells don't ring on an exact schedule.

Have I mentioned how nice the Amsterdam city logo is? Here it is on the side of a tram platform. It's ubiquitous yet simple and recognizable.

We went shopping for some lunch - Marks and Spencer sandwiches - and made our way up to the train station.*

An ICE to Germany.

The atmospheric platform in Essen.

The eventual destination: Essen, or more specifically some friends' apartment. They're great people.

The next day: rain and the fight for sushi.


*We had left our luggage in station lockers, a precious commodity. Don't count on their availability should you plan a visit.

A recent piece on Medium compared e-mail to cockroaches in an effort to explain its longevity:

Email is a way to bypass the crowded room for something more intimate. When everything else is parading naked through the living room of your mind, email is politely waiting outside for a personal invitation. This is both good and bad when you’re trying to connect with the person on the other side of the door. They open it, or they don’t.

I'm not going to muse about how accurate this comparison might be, but I am going to use it as justification for one of my most prominent pet peeves: email without humanity. If email is truly best when it's a personal message, the worst offense a sender can commit is to fail to identify themselves. Here's an example: I recently got an email from my local recycling organization containing only the following text.

Good Afternoon

Which apt do you live in @ [my street address, spelled incorrectly]

I had requested some additional recycling bins, so this wasn't totally unexpected. The greeting is nice, but still, where's all the context? I can only suspect this message was written by a real, living human because the email address had the usual first initial plus last name format.

Even worse, some senders work under the pretense of a single organizational identity. This means they sign their emails with phrases like "Office Assistant" rather than any useful identifier. In short, they dehumanize themselves.

Email may offer convenient intimacy (at least, far more than whatever modern social networking provides) but this implied intimacy highlights situations where it's completely disregarded. Yes, I'm complaining about a decades-old form of communication. Yes, I'm venting. Even so, there's a lesson to be learned here: any medium of communication can lose its unique benefits without the right context.

Amsterdam - Day two, part two

There's that museum again.

The Rijksmuseum contains all manner of Dutch treasures, collections of artifacts which just happened to show up in the Netherlands, and an interpretive series titled Art Is Therapy. The last of these took the form of Post-it-styled notes stuck near some of the exhibits. Rather than just offering more information about the piece, each note asked probing questions about the feelings the piece may evoke or the relationship between art and a balanced life. This is a seethingly negative review from The Guardian. Invert that opinion and you have mine.*

This is where they keep the Rembrants, the Vermeers, and the like. That's the Night Watch at the end of the hall.

Pieces by the Golden Age Dutch painters often make me think of the group scenes used to promote TV shows with ensemble casts. Compare:

The cast of Law and Order: SVU.

The Meagre Company by Frans Hals and Pieter Codde, finished 1636.

Neither of those assemblages is Rembrandt's Night Watch, seen below.

It's difficult to get close.

Most museum patrons were busily attempting to photograph the whole thing. It's a challenge.

It's easy to understand the painting's popularity. It's rich in personality and fancy dress. It evokes an age and an aesthetic while leaving most contextual details (namely, whether this citizens' militia ever really had to post like that during their nightly patrols**) to the imagination.

The remainder of the Rijksmuseum contains items like 17th century dollhouses and exotic firearms.

Above the atrium of the Rijksmuseum.

The entranceway of the Rijksmuseum.

We followed the museum visit with a traditional Dutch dinner at The Pantry. It was quite respectable for its location in the middle of a tourist district (that is, just a block or so from both a McDonald's and a Hard Rock Cafe). In this context, "traditional Dutch" means meatballs and mashed potatoes, also known as stamppot. It goes nicely with a tasty Tripel.

Searching for dinner. Many choice's were available so we weighed our option's. 

Finally: a visit to the BeerTemple! D. was here on a previous Amsterdam visit and enjoyed its extensive variety of beer offerings, especially as she prefers sour Belgian styles over the ales commonly found in the US. On this visit, the Temple featured a multitude of the palest ales. That isn't D.'s cup of tea so she had an UWE cider instead. I had a Mikkeller Peter, Pale and Mary and a Brewdog Clown King. The former is a calm pale ale but the latter is a bare-fisted punch in the nose (in a good way, I think).

Not shown - several empty cases of Weyerbacher Blithering Idiot.

The lady considers the cider.

A bonus church panorama courtesy of Google. Their photo-stitching algorithms do not account for passing streetcars.

Next time: breakfast, boats, and trains.

*I'd like to think there's room for banality in an institution based around placing objects on pedestals, often literally.
**Let's imagine that they did spend the bulk of each night in dramatic poses but found it embarrassing to be painted while doing anything other than standing or banqueting.

The music for today is
El Ten Eleven - Tiger Tiger

Amsterdam - Day two, part one

Amsterdam supposedly contains more specialty museums than any other city on the planet. It's a believable claim, if only because the city has a long history of global trade. It's a natural place for strange collections to accumulate and there's no shortage of room to display it all. Specialty museums in Amsterdam include:

• The Museum of Bags and Purses
• The Funeral Museum
• The Cheese Museum
• The Cat Cabinet

Of these, we only visited the last. I'll get to that one later. 

Amsterdam is certainly more famous for its art museums, including the modern collection of the Stedelijk Museum and the definitively Dutch Rijksmuseum.

The Stedelijk is smooth and white, like a seafaring Apple store.

The Opera House peeks over a nearby wall. There's a supermarket under all that (the black structure, not the Opera House, at least as far as I can tell).

I don't generally take many photographs in museums as it leaves me feeling a bit silly. It's like recording the sound of someone eating soup.* This stairwell at the Stedelijk contains a neon installation by Dan Flavin.

We took a museum break to picnic in the Vondelpark. That's an artificial swan.

Picnic fixin's.

The cheese is from goats. The berry is from straw.

The lady D. enjoying the park.

The Museumplein, the Rijksmuseum, and a kid in a bike lane. Get away from there, kid!

Next time: Dutch Masters. No, really, you'll see them.

*Or maybe dancing about architecture. 

Amsterdam - Day one

The wife* and I arrived in Amsterdam on the second Tuesday of this month. Why Amsterdam? It may be the easiest city to visit across all of Western Europe. We didn't know that when we were first making travel plans, but we did know we had friends in nearby areas of Germany and could visit them easily in the same trip.**

We stayed at the Qbic. It's almost unbelievably convenient, sitting right at the end of an 8 minute ride from the airport. The rooms aren't easy to take photos of.

Perhaps we could have opened the curtains.

It's a bit like staying in a compact RV parked in a new neighborhood brunch place you've been willing to visit for a week or two but you've just been too intimidated by the colored neon and eclectic decor. That's a good thing here - it's a fun place to stay!

Plane delays left us with limited time for museum visits so we explored the local neighborhood. South Amsterdam (Zuid) is bucolic and distant from the noisy attractions of the central city neighborhoods. We found some parks to explore instead.

These stone lions guard the Beatrixpark.

The lions aren't very vigilant.

Yarn-bombed canals. They aren't all like that yet.

Not far away from the last photo, two stately balconies overlook the canal.

Having successfully explored the South, we found noodles at Wagamama.***

The next day and the next post: Masters of the Dutch Arts!

*She doesn't really like being referred to as "the wife." I just asked her and she expressed a preference for the phrase "my lady." I'll refer to her as D instead.

**Many of the times when I would mention traveling to Amsterdam to colleagues and acquaintances, they'd ask me if I was going there for the marijuana. I wasn't and we didn't. The popular connection between Amsterdam and weed is a unique one, though it will be interesting to see how that changes as more areas legalize consuming the stuff.

***There are US locations of this noodle-centric establishment but they are all in Massachusetts.

I am back from Europe and will be discussing my trip over the next week or so! This will include photos, my opinions on how Dutch sounds to the naïve American ear, and possibly a few thoughts about the Robocop remake.

In lieu of any of that, here is the music for today (Loscil - Dub for Cascadia).

I am in Europe (specifically Amsterdam, at the moment) for the time being. Photos will be posted either soon or upon my return to the States.

The Rosetta probe mission is an exciting one. It was launched in 2004 with the intention to orbit and land on a comet (specifically, 67P/Churyumov-Gerasimenko). In the meantime, it's passed by Mars and a few of the stranger asteroids we've studied, grabbing some great photos in the process. It's orbiting the comet now. Take a look at the new photos. For reference, the comet is only about two and a half miles long.

See also: the entire trip.

This is the music for today. August in Virginia makes one feel like an escaping cave ghost.

Today, I learned that much of the success of polio eradication in the Western hemisphere could be attributed to a vaccine delivery strategy employed throughout Central and South America. Between the 1960's-80's, a number of countries throughout the region started campaigns to immunize every child. Brazil specifically held a series of national immunization days, a strategy later adopted by other countries in the region. I'm not sure how many countries still actively maintain national immunization days or how effective they've been for diseases besides poliomyelitis. It's a bit disheartening to imagine the opposition such an approach would receive here in the US.

Today I learned about Merisopedia, a genus of cyanobacteria. Species in this genus grow in rectangular grids. They look like this:

Well-regimented. From Photomicrographs of the freshwater algae Vol. 2 by Yamagishi and Akiyama, 1984.

Merisopedia species can be found all over the planet, including the Amazon, China, and Nigeria.

Who nose why skin's the way it is

Today I read about an interaction between two occupants of the human microbiome. The authors really do their findings a disservice by repeatedly referring to them in the context of the "nostril microbiome". What they really discuss is Staphylococcus aureus and various species of Propionibacterium. Both can be found in a variety of skin locations and especially on the face. Propionibacterium - and especially P. acne - is famous for causing the inflammation associated with all manner of nasty skin conditions. S. aureus is famous for causing many similar but often more medically worrisome infections. This paper shows how they might work together.*

Long story short: it's coproporphyrin III. Propionibacterium produces it and S. aureus uses it as a sign to start making biofilms.  A biofilm phenotype can improve survival in the face of the immune system, antibiotics, or even just physical stress.

Citation:
Wollenberg, M. S., Claesen, J., Escapa, I. F., Aldridge, K. L., Fischbach, M. A., and Lemon, K. P. (2014). Propionibacterium-Produced Coproporphyrin III Induces Staphylococcus aureus Aggregation and Biofilm Formation. mBio 5, e01286-14-.

*Anthropomorphism is to be avoided when discussing microbes. The English language, unfortunately, offers many opportunities for anthropomorphism-based rhetoric. In this case, "work together" is a bit misleading as this may not be a coordinated biological phenomenon. It may simply result from one species releasing a molecule and another species noticing it.

I just found out about the BioFabric project today. It claims to offer a networking visualization method superior to traditional node and edge graphs. Nearly anything is preferable to a hairball network so I'm fairly intrigued, plus their quick demonstration looks neat. I'm starting to work with some very large networks (approaching 50,000 edges, at least) so it's nice to have visualization options.

A post I came across on the StackExchange English Language and Usage forum today asked the following question:

Is there a word or phrase that means to plant my idea in someone else’s mind so they think it is their own idea?

This is immediately followed by a mention of Inception, of course. I'm wondering if the verb incept couldn't be used for such a task. Transitively, it's an occasional synonym for ingest, though I haven't heard it used that way in recent memory.

Others on the forum suggested insinuate, brainwash, inculate, and suggest. Most of these don't seem quite right as they only include one half of the exchange of ideas; I might suggest or insinuate something without successfully landing the idea in your mind. Inculate is a historical euphemism in English and a current one in Italian, so that one's not ideal either.

The limiting factor is, as usual, mutual intelligibility.

Today, I learned that ImageMagick will do about 90% of routine image editing tasks in 10% of the time they usually take.

Here's the music for today. Yes, all seven hours of it. (No, don't listen to seven hours of this unless you're planning to sleep like a highly relaxed log.)

Here's a neat little thing, and an example of Twitter being used well for once: @congressedits. It sends out a tweet every time an anonymous English Wikipedia editor with an IP corresponding to any Congress office makes any edits. Thus far, it mostly just shows that some Congress staffers likely have obscenely dull jobs.

The code behind it, a script called anon, is here. It's in CoffeeScript, with which I'm not terribly familiar, potentially due to my general suspicion of Javascript. It may be worth exploring further for small coding tasks in the future.

Confusingly-named and located universities include:

• Miami University of Oxford, OH
• Indiana University of Pennsylvania
• American World University - OK, it's just an online-only unaccredited school

I'm sure there are additional examples.

Update: Cal U.

This is today's music. This entire album sounds like it should be the soundtrack to an alternative version of the Cosmos TV series completely lacking Sagan, Neil Degrasse Tyson, or any other human at all.

Today, I learned that the anaerobic gut microbiome occupant Bifidobacterium longum has been explored as a potential vector for treating cancer with gene therapy. B. longum is generally considered non-pathogenic and beneficial: it helps to balance pH in the gut, in part through production of lactic acid. A gut with the wrong pH can become susceptible to infection by bacterial pathogens. B. longum is added to some foods and supplements as a probiotic for this reason.

So what's going on with that gene therapy? A paper in 2000 by Yazawa et al. used a mouse model for an initial feasibility study. Though it doesn't appear that they actually used the method for tumor reduction, they did show that B. longum into mice with lung tumors could only be found in tumor tissue after 168 hours. That's presumably because the bacteria require an anaerobic (or, at least a hypoxic) environment to survice. Ideally, this means that B. longum bearing some kind of anti-tumor factor could be injected into or near a tumor with no pathogenic effect on any other tissues. B. longum can be killed off using common antibiotics; Yazawa et al. used ampicillin, though they only tried it in vitro. I'd be worried about long-term use with immunocompromised patients, though the exact anti-tumor material in play may be another critical factor.

The same research group was apparently still working on the idea as of 2010, when they published this review. A 2013 study by a different group looks like it had some success in using Bifidobacterium longum subsp. infantis as part of a method for treating bladder cancer in a mouse model.* This 2014 study just coated their Bifidobacterium in selenium, an elemental micronutrient which may have anti-tumor properties.


*I don't have access to the article so I'm not sure how well the method worked. The authors claim their treatment "exhibited the highest level of apoptosis" compared to controls so that could just mean they had a statistically-significant but limited effect on tumors. Cancer therapy isn't really my field so I'll give them the benefit of the doubt.

Sea stars. (Or, picoplankton from the Pacific.) Photo from Daniel Vaulot on Wikimedia Commons.

The oceans of our planet are so immense that it's often difficult to accurately determine what their occupants are up to. A recent paper in Science focuses on picoplankton, the tiniest ocean occupants but also the most widespread. It's a segment of life driven by photosynthesis (in the photo above, all the small orange dots are photosynthetic cyanobacteria). The new study found that the day-light cycle has an effect on more than just the dominant photosynthetic species, however. Non-photosynthetic, heterotrophic microbes also appeared to exhibit differences as a result of available sunlight.

This summary offers a more detailed breakdown.

I read a review article about phage therapy today (citation below*) with the following opening sentence:

The human gut contains approximately 10¹⁵ bacteriophages (the ‘phageome’), probably the richest concentration of biological entities on earth.

Is that claim actually true? They cite this Lepage et al. Gut paper; those folks estimate that 10¹⁴ microorganisms (that is, distinct cells) live in any single human gut. We usually guess that an environment contains at least 10 times as many individual bacteriophage as potential host cells, so 10¹⁵ bacteriophages doesn't seem like a bad estimate. That being said, could there be a more densely-populated reservoir out there? I've seen population counts for chickens as high as 19 billion but I wasn't able to find any estimates of their gut microbiome diversity. We know they're a potential reservoir of pathogens and their population exceeds that of humanity.

Update: I've been thinking about this and realized that the phrase "richest concentration of biological entities" likely refers to a single human gut rather than the sum of all human gut microbiomes and viriomes. I like to think about ecological niches on a grand scale; the total number of different variations in phage genomes is higher when we include every similar environment in the total rather than the contents of just one human gut. My qualms about the superlative remain. I'd suspect that some sewer systems may contain richer, more diverse arrays of phages, and that's without employing much creativity. Could other species on this planet maintain more diverse microbiomes and/or viriomes?



*Dalmasso M, Hill C, Ross RP (2014) Exploiting gut bacteriophages for human health. Trends in microbiology 22: 399–405.

This is the kind of music I listen to while in the lab:

When I'm feeling rushed, I listen to the same thing, just faster. 
(Yes, I made that. My inspiration was several hours of staring at protein interaction networks.)

Power couples

I read about mutualism today. There has been - and continues to be - a long-running debate regarding the evolution of mutualism. The problem has often come down to a lack of evidence: we can be fairly confident that symbiotic mutualism is a real phenomenon but it's not always easy to demonstrate. We also know that many of the best examples of mutualism, such as chloroplasts, are the result of extensive evolution. Can mutualism emerge mutation, given the right circumstances for symbiotic partnerships to emerge?

A recent paper by Horn and Murray and accompanying summary article in Science show how it can happen. It's a neat, simple demonstration which would make a great elementary science class project.

Citation:
Horn EFY, Murray AW (2014) Niche engineering demonstrates a latent capacity for fungal-algal mutualism. Science 345: 94–98.

Gotta keep it clean.

This is what my desktop looked like on December 8, 2003. Yes, I used Kazaa, the Uber of the early 00's (see previous blog entry). Other items of note:

• Matching GUI and Winamp skin. Looks like I was listening to Hybrid - If I Survive. It was probably this remix, actually.
• Fruity Loops Studio 4, the perfect software package for the young, enterprising electronic musician on a severely limited budget.
• A Temporary Desktop Folder. Nothing temporary about it. That's where every document goes.
• Both AIM and Trillian. This version of Trillian crashed every 10 minutes or so.
• I was not as cyberpunk in real life as this desktop may imply.

Remember Napster? How about Kazaa? Do you remember how popular they were and how blatantly illegal they were? The illegality was blatant but revolutionary. It was emblematic of a myopic but resolute spirit still actively pervasive among new companies, especially those providing new mechanisms for old grey markets.

The ongoing fracas about Uber and Lyft always brings that spirit to mind. Some folks in my city are excited about its possibilities. I'm conflicted about it, honestly. Just as Napster, Kazaa, and all the other early file-sharing methods rendered music sharing painless, these new companies are simplifying ride sharing. People could and did share music before the internet made it easy and they certainly still do so. They also continue to share cars, even on an unofficial paid basis.

Here's why I'm conflicted, though:

1. Taxis are terrible but I'm glad they're regulated. I'm generally in favor of regulating services: there's always some liability issue should something go wrong during a business transaction. Uber and Lyft really need some very specific safety regulations before I'm convinced they should supplant the existing taxi system.
2. I'm increasingly worried about the distancing effect of turning human interactions into apps. Is that old-fashioned?*
3. Uber and Lyft frame their business concepts as creative destruction. I don't see anything terribly creative about it. They're organizing existing systems in a patently illegal way and discarding every logical reason why the laws exist. If that's the only way this system can be improved, then I suppose I'll get used to it. In the meantime, I'll continue to be suspicious. 

*I do really like knowing how much a taxi ride will cost up-front, though. That's a clear advantage of these new services and it's obscene that the old taxi companies couldn't provide it.

This clickbait-headlined Bloomberg article makes the claim that "The Villages", a proliferant retirement community in Florida, is the most rapidly-growing metropolitan area in the US. Something seems vaguely cyberpunk about the place, possibly because it is obscenely large and chock-full of people at the tail ends of their rich lives. That's the traditional "overbearing dystopian future society" part, at least. 

So how is The Villages different from a university of equivalent size? Ohio State (er, The Ohio State University) has about 57,000 students on one campus, making it one of the most populous universities in the nation. It's not quite the 110,000 headcount claimed for The Villages, but I'm assuming that number includes resident employees as well. If we include OSU's non-student employees, their total "resident" population is closer to 87,000, not counting commuter students. 

This is my point: the population size isn't what intrigues me about The Villages. It's not the monolithic overlord problem, either. It's having that many affluent, elderly people in one place. It's a recipe for highly-concentrated success.

Unlabeled, but not forgotten.

Today I learned about Positive-Unlabeled learning, a type of semisupervised machine learning approach. This is the general problem: if you want a machine learning method to do binary classification, you need to start with examples of items which fit into one classification or the other. This is much easier and more efficient when you can safely say that everything in Column A is not in Column B and vice-versa. That isn't the case with some data. Rather, it's either labeled (Column A) or unlabeled (maybe Column B, or maybe Column A but just unlabeled).

PU learning can be used to define negative examples for protein function prediction.  Citation below:
Youngs N, Penfold-Brown D, Bonneau R, Shasha D (2014) Negative Example Selection for Protein Function Prediction: The NoGO Database. PLoS Comput Biol 10(6): e1003644. doi:10.1371/journal.pcbi.1003644.

I had a brief look at Google's Material Design guide today after seeing it linked by Andy Baio. It's essentially a series of guidelines about how to make an interface or product look Google-y. Much of it is good design advice for other projects. The color palettes are one such example.

When future historians want to know what 2014 looked like, this will be a fairly accurate record. I hope we (or just Google, at least) can improve on a few things; their cascading menus have always looked messy and non-intuitive to me. They just pop up all over the screen.

If I had to choose the most insulting sentence currently available in the English language, it would likely be the following:

Those people are mistaken, for reasons I explained in a series of tweets.

The source is here. For more immediate context, it's in reference to people who are in favor of the Oxford comma. The referenced Twitter arguments are of the usual Twitter caliber: glib, poorly organized, and myopic. The source organization, Poynter, is intimately concerned with journalism so I can forgive their editor's concern over generally trivial grammatical squabbles. I have more difficulty with the general concept of "you're wrong because of arguments I've previously made in the worst possible format."

I got married this past Saturday! Married to a lady. Photographs available on request. There's also a video on the way. Stay tuned for that.*

In other news, mice can eat a diet of bacteriophage T7 with few ill effects. Who says negative data never gets published?

*"Stay tuned", beyond being a culturally antiquated idiom, is an interesting bit of skeuomorphic language. It's a relic of a time when viewers could be asked to stay on a particular radio or TV station. Most modern radios and TVs aren't manually tuned. The audience also can and will change stations at their own volition. Asking them to remain in place is like asking them to wear the same pants for a week.

This song has been stuck in my head all morning.

I've been trying out the Android beta of Swell Radio - it's really quite nice. The basic idea is that it treats podcasts as radio shows, so you can just start the app up and it'll just keep on streaming. I had tried it on iOS a year or so ago and was disappointed to see that Android development was lagging. It looks like they're making progress now.

Its recommendation engine still needs regular maintenance. An average User Experience goes like this:

1. Swell plays hourly NPR news update
2. Swell plays a few more NPR clips
3. Swell plays a Wall Street Journal business update, or at least all of its ads 
4. User skips to next item in playlist out of irritation
5. Swell plays another NPR clip
6. Swell plays a set of Comedy Central standup clips

The issue is transitions. It wouldn't hurt for the app to announce the next item in the list so I'm not left wondering why Paul F. Tompkins is on Morning Edition. I mean, the guy loves NPR so it's not too far-fetched.

Slate apparently hasn't heard of metonymy.

In related links, @SavedYouAClick is just great. It's instant answers to all those unnecessary questions in internet news headlines. I wonder if the process could be automated.

I've been working with some very large protein-protein interaction networks lately. Many of them come out like this in Cytoscape:

An artistic re-interpretation. Not actual data. As if there was anything to find in there, anyway.

They're ominously big but still appear to be scale-free. Strict adherence to power law distributions makes me a bit suspicious even though it shows up everywhere.

Today I learned about the Girvan–Newman algorithm. It's a fairly quick way to break up networks of interacting components into clustered communities. It doesn't really join components in any way they aren't already connected. It just removes connections which don't meet betweenness requirements. If the starting network is a hairball, the final product is either distinct clusters or just a bunch of smaller hairballs (I seem to be getting the latter, for the most part, but my current networks are several thousand nodes with more than 40 thousand edges).

The clusterMaker2 plugin for Cytoscape has an implementation of this kind of community clustering. It uses GLay. The plugin hasn't been quite as fast for me as the GLay authors report but I'm content to blame that on my old* Core2 Quad 2.4GHz and/or the massive changes in Cytoscape over the last few years.


*This one came with the lab and was originally used for working with sequencing data. I'm going to use it until it dies and/or catches on fire.

I read this Nature news piece about phage therapy today. It's great that phage might finally be taken seriously as an alternative to carpet-bombing bacterial infections with antibiotics.

This sentence caught my eye: "Nature provides an almost inexhaustible supply: no two identical phages have ever been found." That claim isn't entirely true. While bacteriophage genomes are staggeringly diverse, many contain very similar conserved sequences. If we're only considering two phages to be identical if each nucleotide in one genome is present in the other, then it's very close to true. We could, of course, pick two phage out of the same culture and have a good chance of their genomes being 100% identical. Depending on the phage, we may only be talking about few thousand nucleotides (ΦX174 is only about 5 thousand base pairs, for example!). 

Let's not even start on the issue of how frequently we isolate genetically identical bacteria. We'd like to think that a culture of any one bacterial species is a monoculture, but how many cells in that culture are completely genetically identical at any one time? How about their transcriptomes? I suppose that the original idea remains true: bacteria can produce great genetic variation, so bacteriophage can do so just as well.

Bar none

"Kick the bar chart habit", they say. "Use box plots instead and you can show a distribution of your data points", they claim. They're right, of course. I suspect that most people, whether they're scientists or just members of the 24-hour-TV-news audience (there's some overlap between the two groups, of course) prefer bar charts because they're so straightforward. Higher bars are greater in value. What could be easier?

Besides scientific papers and TV news, the biggest influence on chart type is likely Excel. Hell, the newer versions let users create tiny, almost-unreadable sparkline bar charts. The only worse option may be pie charts. My introductory statistics professor was always wary of using the wrong chart at the wrong time, but he constantly warned us that there was never a right time for a pie chart. I'm usually inclined to agree.

So, bottom line: avoid using the default chart options in Excel and/or chart types which sound like desserts.

Nothing feels less productive than fighting with Git. The official documentation is the real problem: it's roughly as arcane as Norse runes.* I managed to find a few tutorials today, at least:

• Atlassian Git tutorial - just a basic rundown of the common commands.
• Try Git - I find that the Github documentation is just as bad as the Git docs: it makes the basics sound easy but doesn't provide enough detail to know what to do when things go totally wrong. This does the same thing in an interactive way. It's great for the basics but not much more than that.

*They all read like this.

An overly-compressed Sierpinski gasket. Say that fast enough and you sound like an irate plumber.

Fractals generally make good desktop wallpaper but viewing them as compressed bitmaps is a bit existentially disappointing. It's like going to the zoo: you know the animals you're seeing are just stand-ins for the authentic complexity of nature.

I've been awfully busy lately between planning for a wedding (well, my own wedding), trying to finish one paper in lab and analyzing the results for another, and a show I'm in this week (see below).

I get to make funny voices on-stage. It's convenient since I'd be making funny voices anyway.

It's still fun to sacrifice life-snippets to the Blog Gods (blods?) so I'll start posting some short bits more frequently. Here's one such item.

A rich stew.

This is what happens when you store rich nutrient agar in a recycling bin for a week or so. It was meant to be a temporary location for some poorly-melted yeast growth media but was forgotten. Now we have a survey of the organisms present in laboratory waste receptacles (at least, we would have if I hadn't just scraped it all out into a biohaz bag).

Today I learned about acetoin, a chemical found in many foods and fragrances. It tastes buttery.

Acetoin can be produced by some strains of bacteria, especially if they've been engineered to do so. (That's true about many, but certainly not all chemicals.) It's especially convenient to do so if you're trying to control the flavor of a fermented product like wine or soymilk.

Just don't do it.

If you're going to lie to someone about your work, don't do it in science.
If you're going to lie to someone about your scientific work, don't do it in biomedical research and especially not when researching potential gene therapies.
If you're going to lie about your gene therapy findings, don't do it repeatedly and egregiously for almost a decade and never do it to the source of your funding.

Dr. Li Chen did all that. The NIH (and by extension, the US Dept. of Health and Human Services) is not pleased with him. It's bad enough that his former lab had six retractions all around the same time in 2010. Dr. Chen was intimately involved in the whole mess.

His punishment is essentially a 3-year ban from federal funding and involvement. I'm inclined to think that the investigations and retractions are damning enough. This guy now has a smoldering crater in his CV. Even once he's eligible for federal funding again, I suspect he'll have some trouble getting his grant applications approved. That's a life-threatening condition in any field of science.

Let's see what happens when we add an extra letter to some popular web addresses.

You'd think they'd all be trying to ride on the fiber optic coattails of their more popular brethren. You may be correct in many cases.* Here are a few exceptions.**

• dreddit.com

It's an archive of the FAQ from the Usenet group alt.magic, a group for magicians to discuss their craft. The most recent updates to the FAQ are from 1998 and they're mostly listings of brick-and-mortar magic equipment suppliers. I wonder how many of them are still in business.

A choice quote from one of the supplier descriptions: "He uses a tremendous amount of hyperbola in his advertising..." Are these people magicians or mathematicians?

• twikipedia.org

An Amsterdam-based web design studio. They seem like they made a good choice.

• etwitter.com

Redirects to a site for some manner of art-printing business. The images are largely uncredited, leading me to suspect they were hijacked from Flickr. They also offer a sizable collection of Licensed Artwork From Star Wars, so if you're still looking for that finishing addition to your Boba Fett-themed living room, try Amazon because there isn't a retail frontend on this site.

*Most single-letter modifications to google.com appear to lead straight to Redirect City by way of the Download This Surreptitious Software Bypass.

**atwitter.com is for sale!

Today, I learned about the existence of RoMEO, a database used to answer a very specific but often problematic question about peer-reviewed journals. The question is "Can I store and share the work I've published in this journal with people who want to read it?" and the answer is often "No, nope, never, probably not, you don't have that right, this is ours now, bwahaha, etc. etc." RoMEO lists which publishers feel that way and which publishers have more open attitudes toward self-archiving.

StackExchange is so nice, I don't even mind spelling its name with CamelCaps. It has specialized niches like Reddit, an expert community like Quora has in its better moments, and a genuinely effective user-moderated reply system. The best part is finding new subforums: I just found one for German language questions and one for sound design. Whenever I find forums like these on Reddit, they're usually ghost towns or full of users with far more questions than answers.

I found some new tools for protein interaction alignment today. My PI forwarded me this paper:


Clark, C. & Kalita, J. A Comparison of Algorithms for the Pairwise Alignment of Biological Networks. Bioinformatics btu307- (2014). doi:10.1093/bioinformatics/btu307

Clark and Kalita seem to really like NATALIE, a tool which ignores parts of the network which don't appear to align well (Lagrangian relaxation!). It's part of the LiSA software collection and looks like it was last updated in 2012. I'll have to see how easy it is to implement - some of these kinds of tools may work really well but are just painful to get working, especially if their documentation is sparse.

Here's a quick Excel trick for averaging duplicate values. It's the kind of simple command that I probably should have learned years ago, but it's only been available since Excel 2007 so at least there's that excuse.

Anyway, it's the AVERAGEIF function, used as follows:

=AVERAGEIF(the column with the duplicate values, a single value to get the corresponding average for, the column with the values to be averaged)

formatted so the first and last columns are static, like this:

=AVERAGEIF($A$1:$A:$1234,A1,$B$1:$B$1234)

I'm certain that something very similar can be done in a shell script based around uniq.

I’ve been taking a personal development class for the past few months (GRAD611 at Virginia Commonwealth University, part of the nascent BEST program). The class had some broad objectives: to “develop leadership and professional development opportunities for professional, graduate and post-doctoral students that will enable them to thrive in today's professional environment and empower them to make meaningful contributions to society as they realize their potential as future leaders” and to “build a network of internal and external partnerships and identify resources to support and guide leadership and professional development initiatives for professional, graduate and post-doctoral students”. Those are the course goals as they’re written on the syllabus. They’re very ambitious. When the course started a few months ago, I was very skeptical as to whether I’d gain anything from it. I tend to take most personal development strategies with a sizable grain of salt. Too often, these concepts are rife with one-size-fits-all solutions and silver-bullet problem solving strategies.

In the end, I was pleasantly surprised! I suspect that it will be difficult to tell if any new opportunities are now available to me until I can apply what I’ve learned. The second goal listed above is even trickier to address. Have I been able to access a new network of “internal and external partnerships”? Will I know when I see such opportunities in the future?

More importantly, what have I learned about myself? Let’s list a few changes:

•          I’ve noticed lately that I’m much more tolerant of how people portray themselves. I used to find it irritating that any individual would be so myopic as to define themselves in terms of an occupation or an interest. Everyone has a multifaceted personality – no exceptions. The trouble arises from trying to communicate that diverse set of personality traits to others. I can’t just introduce myself to someone and expect them to understand who I am, nor can I try to describe every aspect of my identity to them in a brief meeting. These things require time and solid relationships. It also isn’t fair for me to find others short-sighted when they try to put their identity on display. They’re human, they’re complex, and they have their own sets of strengths. These traits may be immediately obvious or they may require communication.

•          I’m not sure if I’ve identified my authentic purpose. I’m not sure if “authentic purpose” is an authentic concept. It was frequently addressed on the periphery of the class materials but rarely discussed directly. It sounds questionable to me because I don’t believe in a discrete, guiding force. Everything happens for numerous reasons but these reasons may not conspire to guide me toward a purpose. They are natural forces as much as gravity is. That force doesn’t press me to the ground because it wants me to study geology. It has that effect because I’m conveniently made out of matter. That being said, perhaps “authentic purpose” is less of a force in itself and more of a general description of how I react to forces. I have many options in life but some options do feel more “authentic” than others.

•         I’ve become more accepting of the strengths of others. It’s easy to dismiss ideas when they don’t fit into your perspective and it’s easy to dismiss others when they don’t approach problems the same way you do. I tend to approach the world in a broad but systematic way. There’s so much interesting material out there for me to absorb, but I also need to make logical sense of it all. That’s less of a priority for some people. They may be more focused on winning people over or placing information in historic context. I like to do those things as well but they’re certainly not my first impulses.

•          I’ve also become more accepting of my own strengths. It’s quite easy to lose sight of personal strengths when there’s so much to lose from having weaknesses. Spending so much time in science and academia may contribute to that phenomenon: I tend to spend a lot of time each day worrying about what could go wrong with my plans (or, even worse, if anything has already gone wrong but I haven’t noticed). It’s a habit that extends to my own self-conception. Over the last few months, I’ve been increasingly able to see my own shortcomings as lesser strengths and my more obvious strengths as foundations to build upon.

•          I’ve been attempting to use more filters when it comes to gathering sources of input. It’s quite difficult for me to separate signal from noise when I’m searching for interesting information, whether it’s research or just the daily news. The problem really comes down to how I tend to find everything interesting: even when the metaphorical signal-to-noise ratio isn’t so great, I can still get lost in the noise. Reducing the amount of input I attempt to tackle at any one point has helped with that issue.

There are changes that I’ll continue to work on:

•          I'll try to meditate more regularly, though I don't think I'll set any numerical goal on the number of times to do so. I just know that I get more done when I'm aware of my own happiness. Being productive adds to the contentedness and completes the cycle. It’s not even a matter of sitting in once place for a while and focusing on one thing. I’m glad just to notice a momentary, beautiful detail in the world around me.

•          I’ll think more critically about what I consider failure. In a world without failure, I would become very confused and suspicious as to why I wasn’t failing at anything. Failure is a natural part of life and an educational one. Much of what people refer to as failure may just be evidence of authentic challenge.

The GRAD611 course was genuinely one of the more unusual yet useful courses I’ve taken during my graduate career. It’s provided me with a wealth of material to think about. I've listed some fairly abstract observations, but the lessons about time management and conflict resolution have already proved valuable as well. I’ll have to see what kind of lasting effect all this material may have in six months or a year from now.