Adam Retchless, Ph. D.

Throughout our history, we’ve cherished the freedom to share information and opinions but often felt that “freedom of the press belongs only to those who own one”. The Internet changed this by providing inexpensive publishing options — first webpages and blogs, then social media. Social media is now central to how news spreads in our society, including health-related science and the rallying cries of politicians.

But instead of guaranteeing a voice for everyone, the social media revolution resulted in a handful of big tech companies acting as publisher for the entire nation (and world), while disrupting the traditional newspaper industry. Many important public discussions now take place within walled gardens, where each social media service not only provides the technical means of communicating with others, but also controls access to the audience they have gathered. These service provider can bury or amplify our messages as they see fit, for whatever purpose, and typically without explanation.

The power of these opaque and monopolistic companies threatens our ability to act as informed citizens and consumers. By tying the community of users to a specific platform, the dominant companies severely limit our ability to choose better service providers. This allows them to act as middlemen for our social interactions online and consequently reap monopoly-like profits while wielding immense political influence. Despite much hand-wringing about “social media bias” from politicians and billionaires, their proposals don’t promote fairness, freedom, or honesty on social media; instead, they’d simply amplify the voices of their own allies and increase their own power. The only real proposal for letting regular people shape their own social media has been in the form of federated social networks like Mastodon. Mastodon is a micro-blogging platform (like Twitter) that is built according to an open standard managed by the World Wide Web Consortium, called ActivityPub. This open standard not only empowers anyone to set up their own Mastodon server, but to build any type of software for sharing messages with Mastodon accounts.

ActivityPub is already being used to share media (writing, photos, videos) and organize discussion boards. This collection of interoperable services is known as the “fediverse” (a portmanteau of “federated” and “universe”) and even includes Meta’s new “Threads” service and the Ghost publishing platform. BlueSky is another micro-blogging platform that likewise embraces federation, but it only works with ActivityPub platforms indirectly. Federation opens up countless opportunities for innovation, letting software developers create new services that work with the existing social network rather than needing to build a critical mass of users before the software has any value.

Many organizations and individuals have established Mastodon servers for their own communities, but all of them work together to connect users from different communities. Some servers aim to be general-interest services, but most are focused on specific communities, such as the Atlanta region (theATL.social), the medical profession (med-mastodon.com), or art lovers (Mastodon.ART). These servers may be hosted by community nonprofits, by membership-based clubs, by start-up businesses, or by large established institutions such as universities, corporations, or government agencies. Despite all this variety, they can all interact and share information, like websites and email servers do.

This variety of organizations and motivations is essential for establishing integrity in social media, just as it is for journalism. We must support a variety of media groups, who act independently and have real connections to the communities they serve, rather than relying on a few giant corporations and billionaires to spoon-feed us information. Social media is now part of our society, with all its advantages and disadvantages. Mastodon does not automatically solve the problems with present-day social media, but it creates choice that is currently missing from social media and creates the option for continual improvement of social media in which everyone can participate.

Tim Chambers established a list of journalists on Mastodon. It currently has 1400 names on it, added between 11/4/2022 and 12/27/2023. Many of these accounts are dormant, so I filtered them down using standard Mastodon tools — I loaded the list, removed ‘dormant’ accounts (no posts in the past month), and was left with 303 active journalists on Mastodon. I then exported that list in case anyone wants to play with it:

This could probably be done more elegantly with the API, but I have not worked with it. The original list is below.

If you care about Atlanta (The ATL) and want to participate in the Fediverse using Mastodon, sign up at theatl.social. ‘TheATL.social’ is an LLC run by volunteers (including myself) who want to improve the ability of Atlanta residents to connect and talk about their city. In addition to the primary Mastodon instance, theATL.social runs a Lemmy instance called “Y’all” for more in-depth discussions of topics and the news.

I’ve confirmed that I can send comments from my Mastodon account to this blog by responding to the blog post. That’s cool. The comments still go into the same moderation system.

The main limitation is that only public comments show up from the WordPress side. That makes sense, because WordPress doesn’t have a way to receive private messages. However, no feedback is given to the sender… so they send you any non-public message and it will just disappear into the void (unlisted, followers only, tagged only)

Also, I tried tagging my Mastodon account from here, and it did not work.

I’ve been participating in the fediverse for about the past year with the Mastodon community at mstdn.science. Microblogging has it’s benefits, but it’s not really my favorite way to write out my thoughts… the full blog is really more my style. So I think I’m going to write out at least a few posts here to organize my thoughts regarding the fediverse. Conveniently, WordPress recently released their v1 ActivityPub plugin, so I’ve activated that and confirmed that I can follow this blog from my mstdn.science account. It’s a start!

In describing a new HIV evolution paper in Science, Dan Graur (aka “Judge Starling”) writes:

“The only thing “novel” about the analysis was the use of a Bayesian method for phylogeographic inference. Interestingly, as in all examples of its use that I have seen so far, the method tells you nothing you do not know or cannot infer by much simpler means.”

I haven’t looked at the paper in question, but I have noticed this common infatuation with pointlessly (even recklessly) complex statistical methods.

As if there weren’t enough reasons to abandon the penny in the USA, I just learned of a new reason to ban the penny from my home — they are poisonous. The problem is that when pennies are swallowed (by an infant, for instance), the zinc innards can be dissolved by the stomach acid. This can lead to two medical issues: the dissolved zinc can create an ulcer, and the copper shell can cut through internal organs. This issue was brought to my attention  by the first-hand story of a health-care provider whose patient died from internal lacerations caused by a penny. I cannot find anything online about incidents like this, so it is apparently extremely rare. The problem of zinc poisoning is better documented. There’s a chance that my source was confused about the mechanism by which the  penny killed the child, but given his proximity to the case and the details he provided, I’m pretty confident that he knew what he was talking about.

The risks may be pretty low, but given that pennies are nothing more than clutter in my house anyway*, I’ve decided to ban them from my house. I’ve been leaving them behind in stores, but I should just start telling cashiers to keep them (consider it a tip, if you’d like). One of the local stores has a policy of rounding to the nearest nickel, which I wish more stores would adopt. Frankly, I’d be happy if they rounded to the nearest dime or quarter.

Having completed my rant, let’s see a  demonstration of the chemical reaction — you can dissolve the zinc core of a penny at home if you’d like:

I did this using salt and vinegar, as suggested here.
Another neat trick to plate the penny with zinc, and then turn that plating into brass:

p.s. My web-search for pro/con penny arguments came across an essay at Forbes called Don’t You Dare Eliminate the Penny, as one of the first hits. The argument is so ridiculous that it actually strengthened my confidence that the penny should be eliminated, on the grounds that penny advocates have absolutely no basis for their position. However, I was able to find some better arguments by going to Wikipedia, though even some of these were very weak. As is usual with debates, Wikipedia has a decent distillation of the major arguments.

*pennies are worth 5 seconds of minimum-wage work. It’s hardly worth taking the time to pick one up from the floor if you have a full time job.

**p.p.s. This post gave me a few good ideas for educational science projects…once my kids are old enough to not put the pennies in their mouths. So maybe pennies have value after all!

Previously, I griped about the business practices of Research Gate and swore that I would not participate in their community.

Like many online communities, RG sends out plenty of spam, but this is particularly annoying spam — the “from” lines shows the names of colleagues on Research Gate who have attempted to create links to me on RG. In contrast, LinkedIn clearly identifies itself when sending updates and connection requests. Since I have a LinkedIn account (which controls the frequency of these emails), those emails aren’t even spam.

So, if you participate in Research Gate, that company will use your name to spam your colleagues. Classy.

There are many reasons to use Linux, but the main drawback is a lack of support for third-party software. When I set up my new Fedora Desktop, I was caught off guard by the fact that Box.com does not provide sync software (there is a hack, but it’s not really a solution) — I hadn’t realized how dependent I had become on Box.com to backup my work and synchronize my computers. UC Berkeley contracts with both Box.com and Google to provide cloud storage, but neither of them come through in this situation.

However, by free Dropbox account has come to the rescue! The Dropbox client had one minor glitch, and otherwise works perfectly. Now I’m shifting to using them for my day-to-day backup, and limiting my use of Box and Drive to sharing large files.

Thanks Dropbox!

Here is some “advice” on how NOT to be a bioinformatician (i.e. how to make bad software for biology). This makes me ask the question: “Why be a bioinformatician?”

Much of the advice in here makes me think that a lot of “bioinformaticists” don’t really have a good reason for doing what they do. I have to say that I’ve seen a lot of bad biology-focused software. I’ve even heard respected biologists declare that the entire field of bioinformatics is worthless (at least, the stuff published in bioinformatic-focused journals is worthless).

So what is a bioinformaticist trying to achieve?

One approach to bioinformatics is to create software that addresses one’s own research interest. The funny thing is, these typically are not the programs that are published in bioinformatics journals — they are published in biology journals. When I look at the software tools that have been most useful to me, they are not made by people I consider bioinformaticists — they are made by biologists, who are programming computers as a tool to solve problems that they are interested in. Even when these scientists are trained in statistics and CS, they are still tightly connected to a particular biological community and they are designing software that answers research questions that this community cares about. This often allows them to answer questions that nobody has been able to answer before.

The other approach to bioinformatics is to build a tool that others will use. This seems to be the focus of the linked SCFBM article.

All too often, these software/algorithm development projects aim only to produce incremental improvements in existing methods (e.g. making them more accurate or faster or user-friendly). These typically don’t lead anywhere, and I don’t consider these to be appropriate academic projects — this type of optimization should be performed within teams that are interested in some sort of mass-production and have real accountability for the performance of their software (e.g. at commercial firms). Publishing this type of work is an invitation for BS.

There is still space for applying serious CS to improving bioinformatic tools, but these should focus on radically different approaches to the analysis, so that they enable order-of-magnitude improvements in the efficiency of the algorithm.

This same problem of misguided motivation is seen in the plethora of web services that have emerged during the mass-sequencing era. I have been very frustrated by these, since the vast majority of them simply waste my time by promising things that they cannot deliver. Many of them are not maintained — which makes perfect sense given their limited utility to begin with.

If you are going to make a software tool “for biologists”, you need to ask yourself whether it will be useful enough to be worth making properly and maintaining it. If your service is very narrowly focused, are you going to bother maintaining it just to serve the one user per month? Are biologists going to bother discovering your service if it nearly duplicates an existing service that they are already familiar with (e.g. NCBI)? Will they ever hear about it if it provides a single narrowly focused service? Does the service actually provide useful information, or does it simply make predictions that a biologist will need to test anyway if the prediction really matters?

So before trying to figure out how to properly develop bioinformatics software, figure out why you want to make these tools at all.