Clockmakers and temptation

It's tempting to write people off as crazy.

I was following the story of Ahmed Mohamed's clock and arrest this past week. It was hard to avoid the news, especially as more questions emerged from the situation. The context didn't make the school administrators' actions any more comprehensible. There wasn't a hidden side to the story and no logical justifications were revealed. It was all just wrong without reason.

It's tempting to write people off as racist.

Just like everyone else, people in positions of power have reasons for their actions. Those reasons may not be supported with evidence or even a clear plan, but they don't emerge spontaneously. Everyone operates within the context of their own culture. If that culture is a high school, the context may preclude justification of any action, even an outright administrative mistake. It's the context in play but it's just one of many factors contributing to an environment hostile to humanity, most potently for humans who don't match the local mean skintone.*

It's tempting to write people off as backwards.

The mentality of failing to admit to mistakes usually appears stubborn and pigheaded. It looks distinctly like a failure to learn from one's errors, or at least a blatant unwillingness to try. What did the school adminstrators hope to accomplish? They clearly knew there wasn't a bomb in play. What were the police trying to do? They couldn't even get this student his necessary legal representation.

These kinds of situations happen every day. This was a neat. concise, useful example with a favorable conclusion for its victim. Even so, we won't understand situations like this any better by dismissing their antagonists as insane racists. They make mistakes and those mistakes may be rooted in racism, but a failure to learn from those mistakes is the core issue.

Schools need to be able to encourage creation, even if it doesn't occur in the traditional educational context. Students can create some amazing material on their own. We need to trust them.

* In this case, depending on how we define local, Ahmed may be closer to the local average. (Racism isn't just about skin color.)

Update (Sep. 24) - more than a few of the more conservative-leaning news outlets (and Richard Dawkins, for some reason) have been decrying the whole situation as a hoax, claiming that the makeshift clock wasn't a new invention but rather a hacked-together bit of existing electronics parts. None of that matters. If a student walks into school with a functioning piece of electronics, they shouldn't get arrested by default, and certainly not on the assumption that they're willfully terrorizing their fellow students. I'm not sure how the above scenario could be interpreted as a hoax.

Followers, following, and false fellows

I've been running my Music Suggestron twitter bot for more than a month now. That didn't take much effort as bots tend to do most of the work on their own. This bot doesn't require much user input, either: it just spits out randomized tracks and genres available on Spotify. It was born out of my desire to listen to something new every day. Spotify claims to have 30 million tracks in its database, or enough for more than 171 years of continuous listening (assuming an average track length of 3 minutes, a value based on Conventional Wisdom but increasingly untrue), so there are numerous options.

The project became a kind of metagame for me (at least, if writing the bot itself was already a game and the Twitter component provides the meta). I've never had to promote anything besides myself on a social network. My bot didn't have any identity or purpose outside Twitter, so how could I increase its visibility? It's not designed to spread marketing buzz or sell products so, again, promotion was just for my own entertainment.

I set my initial goal at attaining 1,000 followers. I started having the bot follow other accounts, starting with anyone in the music industry but later focusing on musical artists, DJs, producers, songwriters, vocalists, and instrumentalists. In theory, these would be the people most likely to see the bot's tweets anyway should it post a link to their work. Here's what I learned.

It's not easy! Twitter limits the number of "followings" for any one account to 2,000, give or take a bit depending on your following/follower ratio. I hit that limit with a follower count of ~850. Without the ability to follow new accounts, my follower count slowly atrophied. 

A noticeable proportion of Twitter users exist for promotion only. They could be called fake; about 10 percent of users may be fake. "Fake" is an ambiguous term when we consider that a fake Twitter user could be masquerading as a real person, could be a real person solely posting links to counterfeit sunglass stores, or could just be a bot. Musicians actively promote themselves and others on Twitter so it can be difficult to distinguish a real human from an automated marketing machine. Two non-musical examples:

I'm going to assume that the fictional Sheldon Cooper isn't posting context-free quotes (are they even quotes? I don't watch Big Bang Theory) several times a day, but this account isn't posting horse_ebooks-style spam links either. It's benign.

This account may have a real person in there somewhere and the associated tweets include some authentic-looking text (e.g., quotes from Winston Churchill). Recently, it's just promotional retweets. The activity isn't harmful but it's pure advertising. 

So why am I focusing on fake Twitter accounts? Isn't every social network profile an exercise in brand building? Does it even matter if the "self" in self-promotion isn't a single human being?

It's not difficult to automate social network activity. It's certainly much easier than automating other social interactions. This is exactly why I have difficulty taking Twitter seriously as a venue for useful, productive communication. Too much of the noise in the system is automated, devoid of content, and impossible to trace back to a message other than "your voice was heard".

Promotion lacking human input may not be worrisome when the product is music or art, but other fields require more personal communication. Science is one such field and Twitter is increasingly gaining acceptance among scientists as a medium for professional communication. This is a new phenomenon. Should I start setting up bots to re-tweet my new publications if I want to widen their audience? All the open access policies in the world won't help broaden my work's reach if the loudest voice wins anyway. Or, perhaps louder isn't always better.

Twitter analytics could be more helpful. I was excited to find out that Twitter offers a full buffet of metrics for how users interact with your account. They're what turned it all into a game for me. So many numbers to track!

It's difficult to complain about the service as it's free and I haven't paid Twitter a fee to promote anything for me, but I'll complain anyway. The Analytics interface lacks obvious options like accessing individual tweets or even seeing who has retweeted a particular message. It's all presented as averages and summaries, potentially to reduce database stress, but I'm just speculating. 

Here's my impression trend. Twitter defines an impression as any single view of a tweet, even if it's just scrolled past.

The blue values on top are impressions and the lower values are total tweets. New impressions from tweets made on previous days count toward the day they're made. My bot usually tweets about 140 times a day. Twitter insists on double-counting that total sometimes so there's a spike near the far right. More importantly, the bot's total impressions tapered off immediately after it hit the follow limit of 2,000 users. This suggests that most impressions are from new followers, as following users encourages them to follow back.

I won't bother showing the graph of followers as it's either massively inaccurate or includes unexplained values. It may not properly account for lost followers.

This bot is a fun programming project so I'm going to try taking it in some new directions. Perhaps it should have moods. Perhaps it should provide lyric samples. Perhaps it should violate copyright and generate mashups on demand. We'll see what happens.

In the meantime, check out some of these bots:

@everyadage

@ClipArtBot

@max_kompressor

A debugging note about Mendeley

More of a note-to-self than anything, but potentially useful if you use Mendeley:

Mendeley searches were becoming quite slow for me, even with a database of just over a thousand items. It would take more than 30 seconds for a simple query.

I fixed this problem by having Mendeley rebuild its database. That database can be found by opening up the software, pressing Ctrl+Shift+D to open the debug console, then clicking the Open Data Directory button. I opened the folder "www.mendeley.com" and the folder inside it named with my email address. That's where the sqlite database resides. Close Mendeley, remove the database files (mine had ballooned to more than a gigabyte - not sure if that's normal for this software) and start up Mendeley again.

June 20, 2019 edit: This is also a good solution if Mendeley crashes upon attempting to sync. Apparently its usual response to database corruption of any kind is to crash.

Three strange but colorful things to see

Without more detail than necessary, here are three things I saw in the last few days.

1. Subway Adventure

It's a game by Stephen Lavelle, AKA increpare games. It's classically surreal. Avoid it if you don't enjoy transit systems, open spaces, or falling into the silent void.

Yes, that's a crab. It's a fellow passenger.

2. The Japanese Tattoo exhibition at the VMFA.

That's the Virginia Museum of Fine Arts. According to a Today Show piece which may not exist anymore, Richmond, VA is the 3rd most tattooed city in the US, or at least it has more tattoo shops per capita than most US cities. That means we see an impressive variety of skin-based art around here but it's rarely as intricate as the Japanese and Japanese-derived pieces in this exhibition. The presentation is noticeably minimal and focuses on the tattoo artists and their work but avoids the pitfall of dehumanizing their living canvases. It unfortunately also provides little historical context for most of the tattoo designs. That's unfortunate as many of them are based on rich stories and shouldn't just be summarized as "traditional".   

3. That new Google logo.

The jaunty 'e' is bothersome, if only because it's now so obvious.

Bacteria with missing pieces: three papers

Here are a few papers I've read lately:

It's Caulobacter crescentus, named for everyone's favorite shape of roll.

• Gonzalez D, Collier J (2015) Genomic Adaptations to the Loss of a Conserved Bacterial DNA Methyltransferase. MBio 6: e00952–15 – .
  

A particular DNA methyltransferase, CcrM, is conserved throughout most Alphaproteobacteria, including Caulobacter crescentus. The methyltransferase isn't strictly essential but mutant strains without ccrM have difficulties with cell division. Gonzales et al. put C. crescentus mutants lacking ccrM through more than 300 generations of experimental evolution and found that they compensated by modifying expression of ftsZ, a gene coding for a product critical to cell division. This suggests that, at least in C. crescentus, CcrM acts to promote cell division through its effect on FtsZ levels.

• Shen T-CD, Albenberg L, Bittinger K, Chehoud C, Chen Y-Y, et al. (2015) Engineering the gut microbiota to treat hyperammonemia. J Clin Invest 125: 2841–2850.

This isn't open access, unfortunately, but the general idea is that bacteria living in the mammalian gut naturally produce ammonia and it isn't usually a problem unless the liver can't handle all that ammonia, at which point ammonia builds up in the blood. Hyperammonemia can cause neurological disease, coma, or death. Using a mouse model and a pre-designed gut microbiome culture, Shen et al. show that hyperammonemia could be avoided by replacing the usual gut microbiome with one able to produce less ammonia. Conveniently, the engineered microbiome they employ has been in use since the 1970's so there's extensive evidence that it isn't harmful (in mice, at least).

• Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, et al. (2015) Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523: 208–211.
  

Also not open access but there's a press release with some nice, clear graphics. This group is making excellent progress in exploring unculturable bacteria. Notably, most of the isolates they obtained are from an aquifer next to the Colorado River that luckily is well upstream of the recent mine wastewater spill.