The moral efficiency of clinical trials in anti-cancer drug development

Testing with some Riker Ipsum

Mr. Crusher, ready a collision course with the Borg ship. Fear is the true enemy, the only enemy. Well, I’ll say this for him – he’s sure of himself. I guess it’s better to be lucky than good. and attack the Romulans. Maybe we better talk out here; the observation lounge has turned into a swamp. This should be interesting. I recommend you don’t fire until you’re within 40,000 kilometers. But the probability of making a six is no greater than that of rolling a seven. And blowing into maximum warp speed, you appeared for an instant to be in two places at once. The game’s not big enough unless it scares you a little. The Enterprise computer system is controlled by three primary main processor cores, cross-linked with a redundant melacortz ramistat, fourteen kiloquad interface modules. We finished our first sensor sweep of the neutral zone. The unexpected is our normal routine. That might’ve been one of the shortest assignments in the history of Starfleet. Computer, lights up! I’m afraid I still don’t understand, sir. When has justice ever been as simple as a rule book? I suggest you drop it, Mr. Data. You enjoyed that. Travel time to the nearest starbase? What’s a knock-out like you doing in a computer-generated gin joint like this? Congratulations – you just destroyed the Enterprise.

Why don’t we just give everybody a promotion and call it a night – ‘Commander’? I’ll be sure to note that in my log. Some days you get the bear, and some days the bear gets you. I think you’ve let your personal feelings cloud your judgement. Your head is not an artifact! Captain, why are we out here chasing comets? Commander William Riker of the Starship Enterprise. We know you’re dealing in stolen ore. But I wanna talk about the assassination attempt on Lieutenant Worf. I am your worst nightmare! You’re going to be an interesting companion, Mr. Data. I’d like to think that I haven’t changed those things, sir. Smooth as an android’s bottom, eh, Data? Yes, absolutely, I do indeed concur, wholeheartedly! Fate. It protects fools, little children, and ships named “Enterprise.” About four years. I got tired of hearing how young I looked. Then maybe you should consider this: if anything happens to them, Starfleet is going to want a full investigation. You did exactly what you had to do. You considered all your options, you tried every alternative and then you made the hard choice. Now we know what they mean by ‘advanced’ tactical training. Wouldn’t that bring about chaos? Maybe if we felt any human loss as keenly as we feel one of those close to us, human history would be far less bloody. Could someone survive inside a transporter buffer for 75 years? Not if I weaken first. What? We’re not at all alike! Damage report! Now, how the hell do we defeat an enemy that knows us better than we know ourselves? The look in your eyes, I recognize it. You used to have it for me. How long can two people talk about nothing? Well, that’s certainly good to know. This is not about revenge. This is about justice. A surprise party? Mr. Worf, I hate surprise parties. I would *never* do that to you. Talk about going nowhere fast. The Federation’s gone; the Borg is everywhere! Shields up! Rrrrred alert! Sure. You’d be surprised how far a hug goes with Geordi, or Worf. I’ve had twelve years to think about it. And if I had it to do over again, I would have grabbed the phaser and pointed it at you instead of them. We have a saboteur aboard.

Riker Ipsum courtesy of: http://www.rikeripsum.com/

“Doctor”

According to Stephen Leacock, the meaning of a doctoral degree from McGill is that “the recipient of instruction is examined for the last time in his life, and is pronounced completely full. After this, no new ideas can be imparted to him.”

I was soon appointed to a Fellowship in political economy, and by means of this and some temporary employment by McGill University, I survived until I took the degree of Doctor of Philosophy in 1903. The meaning of this degree, is that the recipient of instruction is examined for the last time in his life, and is pronounced completely full. After this, no new ideas can be imparted to him.
Stephen Leacock on the degree of Doctor of Philosophy from McGill

And so, for your sake, I am sorry to inform you that on 2019 April 2, I successfully defended my doctoral thesis, The moral efficiency of clinical trials in anti-cancer drug development.

I will be absolutely insufferable about having those new letters after my name for at least another week.

The nuclear option for blocking Facebook and Google

I took the list of domains from the following pages:

  • https://qz.com/1234502/how-to-block-facebook-all-the-urls-you-need-to-block-to-actually-stop-using-facebook/
  • https://superuser.com/questions/1135339/cant-block-connections-to-google-via-hosts-file

And then I edited my computer’s /etc/hosts file to include the following lines.

This blocks my computer from contacting Google and Facebook, and now a lot of sites load way faster. It still allows Youtube, but you can un-comment those lines out too, if you like.

Put it on your computer too!

(To view the big block of text that you need to copy into your /etc/hosts, click the following button. It’s hidden by default because it’s BIG.)

Introducing “Actually the singular is …”, a Mastobot

Good news for pedantic academics who like to correct others’ use of Latin-derived plurals!

I have automated that task for you with a bot on Mastodon:

Actually, the singular is …

I wrote it using Mastodon.py and BeautifulSoup and it’s a very simple little bot. (Only 42 lines of code!)

It takes all the posts currently visible to the bot on its Public Timeline, strips out the HTML formatting, makes a list of all the words that are alphabetic and end in -i or -a (so “plaza” would make it in, but “@plaza” wouldn’t) and then posts (for example): “plaza?” actually the singular is: plazum (if it had ended with an -i, it would have changed the ending to -us).

Then it adds the original word to a list of words not to post again and a cron job makes it repeat every 10 mins.

I had this idea a while back, but I got stuck on the idea that I’d need a pre-made dictionary of words that end in -i or -a. Then it occurred to me that I could just populate that list on the fly from the bot’s perspective on the Timeline. That also has the added benefit that there’s the possibility that the words it chooses may be topical, and not just random.

Enjoy!

The risks and harms of 3rd party tech platforms in academia

CW: some strong language, description of abuse

Apologies for the rambly nature of this post. I wrote it in airports, partly out of frustration, and I may come back and make it more readable later.

In this post, I’m going to highlight some of the problems that come along with using 3rd party tech companies’ platforms on an institutional level in academia. Tech companies have agendas that are not always compatible with academia, and we have mostly ignored that. Briefly, the core problem with the use of these technologies, and entrenching them into academic life, is that it is an abdication of certain kinds of responsibility. We are giving up control over many of the structures that are necessary to participation in academic work and life, and the people we’re handing the keys to are often hostile to certain members of the academic community, and in a way that is often difficult to see.

I have included a short “too long; didn’t read” at the end of each section, and some potential alternatives.

Using a tech company’s services is risky

There’s an old saying: “There’s no such thing as the cloud; it’s just someone else’s computer.” And it’s true, with all the risks that come associated with using someone else’s computer. The usual response to this is something along the lines of “I don’t care, I have nothing to hide.” But even if that’s true, that isn’t the only reason someone might have for avoiding the use of 3rd party tech companies’ services.

For starters, sometimes tech companies fail on a major scale that could endanger entire projects. Do you remember in 2017 when a bug in Google Docs locked thousands of people out of their own files because they were flagged as a violation of the terms of use?

Or more recently, here’s an example of a guy who got his entire company banned by Google by accident, proving that you can lose everything because of someone else’s actions:

TIFU by getting Google to ban our entire company while on the toilet from tifu

And of course, this gets worse for members of certain kinds of minorities. Google and Facebook for example, both have a real-names policy, which is hostile to people who are trans, and people from our country’s First Nations:

Facebook tells Native Americans that their names aren’t “real”

There are other risks beyond just data loss—for example, if your research involves confidential data, you may even be overstepping the consent of your research subjects, and potentially violating the terms under which your institutional review board granted approval of your study by putting it on a 3rd party server where others can access it. This may also be the case of web apps that include Google Analytics.

tl;dr—If your academic work depends on a 3rd party tech company’s services, you risk: losing your work at a critical time for reasons that have nothing to do with your own conduct; violating research subject consent; and you may be excluding certain kinds of minorities.

Alternatives—In this section, I have mostly focused on data sharing risks. You can avoid using Google Docs and Dropbox by sharing files on a local computer through Syncthing, or by installing an encrypted Nextcloud on a server. If distribution of data sets is your use case, you could use the Dat Project / Beaker Browser.

Tech companies’ agendas are often designed to encourage abuse against certain minorities

I have touched on this already a bit, but it deserves its own section. Tech companies have agendas and biases that do not affect everyone equally. For emphasis: technology is not neutral. It is always a product of the people who built it.

For example, I have been on Twitter since 2011. I have even written Twitter bots. I have been active tweeting for most of that time both personally and about my research. And because I am a queer academic, I have been the target of homophobic trolls nearly constantly.

I have received direct messages and public replies to my tweets in which I was told to kill myself, called a “fag,” and in which a user told me he hopes I get AIDS. Twitter also closed my account for a short period of time because someone reported me for using a “slur”—you see, I used the word “queer.” To describe myself. And for this, there was a short period of time in which I was locked out, and it took some negotiation with Twitter support, and the deletion of some of my tweets to get back on.

I was off Twitter for a number of months because of this and out of a reluctance to continue to provide free content to a website that’s run by a guy who periodically retweets content that is sympathetic to white supremacists:

Twitter CEO slammed for retweeting man who is pro-racial profiling

And this isn’t something that’s incidental to Twitter / Facebook that could be fixed. It is a part of their core business model, which is about maximising engagement. And the main way they do that is by keeping people angry and yelling at each other. These platforms exist to encourage abuse, and they are run by people who will never have to endure it. That’s their meal-ticket, so to speak. And most of that is directed at women, minorities and queers.

I have been told that if I keep my Twitter account “professional” and avoid disclosing my sexuality that I wouldn’t have problems with abuse. I think the trolls would find me again if I did open a new account, but even if it were the case that I could go back into the closet, at least for professional purposes, there are four reasons why I wouldn’t want to:

  • My experience as a queer academic medical ethicist gives me a perspective that is relevant. I can see things that straight people miss, and I have standing to speak about those issues because of my personal experiences.
  • Younger queers in academia shouldn’t have to wonder if they’re the only one in their discipline.
  • As a good friend of mine recently noted, it’s unfair to make me hide who I am, while all the straight men all have “professor, father and husband” or the like in their Twitter bio’s.
  • I shouldn’t have to carefully avoid any mention of my boyfriend or my identity in order to participate in academic discussions, on pain of receiving a barrage of abuse from online trolls.

I’m not saying that everyone who uses Twitter or Facebook is bad. But I am extremely uncomfortable about the institutional use of platforms like Google/Facebook/Twitter for academic communications. When universities, journals, academic departments, etc. use them, they are telling us all that this kind of abuse is the price of entry into academic discussions.

tl;dr—Using 3rd-party tech company platforms for academic communications, etc. excludes certain people or puts them in the way of harm, and this disproportionately affects women, minorities and queers.

Alternatives—In this section, I have mostly focused on academic communications. For micro-blogging, there is Mastodon, for example (there are even instances for science communication and for academics generally). If you are an institution like an academic journal, a working RSS feed (or several, depending on your volume of publications) is better than a lively Twitter account.

Tech companies are not transparent in their decisions, which often cannot be appealed

Some of the problems with using 3rd party tech company platforms go beyond just the inherent risks in using someone else’s computer, or abuse by other users—in many cases, the use of their services is subject to the whims of their support personnel, who may make poor decisions out of carelessness, a discriminatory policy, or for entirely inscrutable or undisclosed reasons. And because these are private companies, there may be nothing that compels them to explain themselves, and no way to appeal such a decision, leaving anyone caught in a situation like this unable to participate in some aspect of academic life.

For example, in the late 00’s, I tried to make a purchase with Paypal and received an error message. I hadn’t used my account for years, and I thought it was just that my credit card needed to be updated. On visiting the Paypal website, I found that my account had been closed permanently. I assumed this was a mistake that could be resolved, so I contacted Paypal support. They informed me that I had somehow violated their terms of use, and that this decision could not be appealed under any circumstance. The best explanation for this situation that I could ever get from them was, to paraphrase, “You know what you did.”

This was baffling to me, as I hadn’t used Paypal in years and I had no idea what I could have possibly done. I tried making a new account with a new email address. When I connected my financial details to this account, it was also automatically closed. I’ve tried to make a new account a few times since, but never with success. As far as I can tell, there is no way for me to ever have a Paypal account again.

And that wasn’t a problem for me until a few months ago when I tried to register for some optional sessions at an academic conference that my department nominated me to attend. In order to confirm my place, I needed to pay a deposit, and the organizers only provided Paypal (not cash or credit card) as a payment option.

And this sort of thing is not unique to my situation either. Paypal has a long, terrible and well-documented history of arbitrarily closing accounts (and appropriating any money involved). This is usually in connexion with Paypal’s bizarre and sometimes contradictory policies around charities, but this also affects people involved in sex work (reminder: being a sex worker is perfectly legal in Canada).

Everything worked out for me in my particular situation at this conference, but it took work. After several emails, I was eventually able to convince them to make an exception and allow me to pay by cash on arrival, but I still had to go through the process of explaining to them why I have no Paypal account, why I could try making a new one, but it wouldn’t work, and that I wasn’t just being a technophobe or difficult to work with on purpose. I was tempted to just opt out of the sessions because I didn’t want to go through the embarrassment of explaining my situation.

And my problem with Paypal was a “respectable” one—it’s just some weird mistake that I’ve never been able to resolve with Paypal. Now imagine trying to navigate a barrier to academic participation like that if you were a person whose Paypal account was closed because you got caught using it for sex work. Do you think you’d even try to explain that to a conference organizer? Or would you just sit those sessions out?

tl;dr—When you use services provided by tech companies, you may be putting up barriers to entry for others that you are unaware of.

Alternatives—This section was about money, and there aren’t that many good solutions. Accept cash. And when someone asks for special accommodation, don’t ask them to justify it.

Conclusion

Technology isn’t neutral. It’s built by people, who have their own biases, agendas and blind-spots. If  we really value academic freedom, and we want to encourage diversity in academic thought, we need to be very critical about the technology that we adopt at the institutional level.

Levels of queer representation in media franchises

Warning: spoilers for Star Trek Discovery season 1 in the table.

A few days ago, I wrote a short post about “steps” that media franchises take toward queer representation in media. I got a few requests for clarification, so I have expanded it into a table with examples and explanations.

The impulse behind the post was that resistance to representation of queers in media franchises is very predictable, falling into well-known and discrete categories, and that those categories can be ordered from worst to best. I absolutely do not take credit for being the first observer of these dynamics, as many people much smarter than me have commented on them all before. But this is how I see them, on a sort of a continuum.

I originally phrased it in terms of “steps,” although now I don’t think that’s the best way to think about it, so I call them “levels” here. There’s certainly a gradation from 1-7, but of course, not every media franchise goes one by one. Each successive step is better in some sense than the one previous (although you could probably haggle over the ordering in some cases). Levels 1-3 are refusals to represent queers and levels 5-7 are (decreasingly begrudging) attempts at queer representation. Level 4 is, or is not queer representation, depending on your reading of it.

1. Refusal without any attempt at justification

“No queers because writers hate them”

Naked hate for queers, while surprisingly common, is the least interesting case, and nobody needs help identifying it. But most people are more sophisticated because they know they’ll (rightly) get in trouble if they’re openly hateful toward queers, so usually they dress up their hate by progressing to one of the subsequent steps.

I’ve included this one because you do still see it from time to time, and it’s interesting to note how often as a sort of proxy measure for how friendly our culture is to queers.

2. Refusal with some ostensibly principled reason given

“No queers, but it’s for your own good or something”

A justification that is often given for refusal to include queer characters in a story, TV show, movie or whatever is that it would be “pandering,” and that this would be bad somehow. Straight people love to project onto queers a very strong desire that we not be included in something if it is just for the sake of inclusion, and that doing so would be much worse than the default, namely, pretending that queers don’t exist.

This is of course nonsense. The only people who don’t like queers being included just for the sake of including queers are straight people, and this is a feeble excuse for bigotry. But there’s nothing conservative people like better than telling someone No, and having it be For Their Own Good.

3. Refusal, but with a vague promise of future representation

“No queers, but just because we haven’t had a story that demands a queer”

Star Wars is at this point right now. They know there have been calls for queer characters, and they know they can’t just say “No we hate queers,” so they’re kicking the can down the road by saying “not now, but we’re not opposed to the idea,” and trusting we’ll take them at their word when they claim that it’s just “artistic reasons” that have kept them from doing so already.

It’s disingenuous and a double-standard of course. When these writers come up with characters to put into their stories, nobody demands that there be a compelling reason demanded by the plot for why some character is straight. And if they think they can get away with it, they will continue forever to promise to include queers someday, but no sooner than the story absolutely demands it.

4. Strongly implied but ultimately deniable queer representation

“Okay maybe this secondary character is queer? We didn’t say they’re not!”

Harry Potter is an excellent example of this level. JK Rowling famously made Dumbledore gay retroactively after all the book sales were in the bag, and justified it with the condescending Twitter one-liner that gay people just look like … people! So why write them any differently or provide any explicit representation?

The problem with the JK Rowling-type response is the extremely “everything is already perfect so stop complaining” vibe here. The line that we queers are supposed to believe is that the writer is just so progressive that queer representation is unnecessary.

The Star Trek reboot films are also at this level. Everyone got excited about Sulu being gay in Star Trek Beyond (2016), but what we got was 2.5 seconds of Sulu side-hugging some guy, who we’re supposed to take as his civilian husband or partner or something. No kiss. No dialogue. It’s so casual that a straight viewer could miss it entirely or see it and argue that Sulu is meeting his brother or something. And truthfully, there isn’t enough on-screen to settle the matter conclusively.

Reboot Sulu

It is both erasure of queers and it is a not-so-subtle assertion of control that can be read as a disapproval of any queer who isn’t indistinguishable from straights. Also, because this generally flies under their radar, this is a cowardly concession to the sensibilities of outright bigots.

Many Disney villains are also in this category. Ursula from The Little Mermaid (1989) was even based on a drag queen. Straight people love to include queer-coded villains, because they love queer aesthetics, but they refuse to actually provide representation, because they hate queers.

5. Tragic queer representation

“Okay there’s a queer but oops we killed it lol oops”

“Bury your gays” is a well-known and troubling mode of queer representation that has a long history, and it can be summed up as the trope that queers are not allowed a happy ending.

Sometimes, this is done to send a very specific “you get what you deserve, you dirty queers” message. Read Goldfinger if you want a really clear example of that. (Click the Project Gutenberg link and control-F for “Poor little bitch” to read about what happened to Tilly Masterton because she was a capital-L lesbian.)

Goldfinger is an extreme case and most of the time, it’s not an attempt to send an “if you’re gay you deserve a violent death” message. Usually, this happens just because the main character Has To Be Straight, and so if there’s going to be a character who dies, it’s going to be the queer one, and so we end up with a preponderance of media representation in which queers are killed just to raise the stakes for the main characters, just because we’re less important.

We saw this with Lt Stamets in the most recent episode of Star Trek Discovery (S01E09). I thought Discovery was at level 6, but actually it’s looking like it’s here. Maybe they’ll save him? Reserving judgement on this one.

6. Queer representation designed for straight comfort

“Okay there’s a queer but you can’t really tell they’re queer—Super respectable! Very comfortable for straights!”

Often queer representation that is designed for the comfort of straight people is done with the justification that it’s an attempt to “move past bad gay stereotypes.” Again, this is a more subtle example of straight people denying us actual representation and doing it For Our Own Good.

The idea is that there are, according to the straights, way too many flamboyant or promiscuous gay characters perpetuating bad stereotypes and what the world really needs is to see queer people being “good” and that will make all those bigots understand that you can be a good person even if you’re gay. What a progressive message, and who could be upset about that? Right?

The problem is that this has built into it the not-so-subtle assertion of a) control of straight people over queer lives and lifestyles, and b) implied inferiority of queers to straights.

When straights insist that queer representation include only the “good kind” of queer, there’s an implication that there’s a bad kind, and that our acceptance and inclusion hinges on which kind we are. It is tacitly agreeing that queers should be ashamed of who they are and doing their best to hide it.

This often goes hand-in-hand with a denial of the very existence of queer culture. For anything that isn’t literally gay sex, a Respectable-Gays-Only advocate can say “well, that’s not gay per se, so it’s non-homophobic for me to continue to hate it.”

7. Actual queer representation

This does actually happen sometimes. Here’s a couple examples:

Pretty much everyone in Sense8 counts. Even the straight dude is not all that straight.

Orphan Black also started at this level. Felix is an excellent example of queer representation. Felix is a nuanced and well-developed character that is undeniably gay, and also unambiguously morally good despite him having a number of the traits that Respectable-Gays-Only advocates would probably categorise as being gay stereotypes.

How to get any medical journal into your RSS reader even if they don’t provide an RSS feed

What is RSS?

For the non-initiate, RSS is a very useful protocol that is used all over the web. You can think of it as a way of separating a stream of content from the website where it’s normally viewed. Nearly every blog has an RSS feed, as do news sources, web comics, and even academic journals. Podcasts are like a specialised version of RSS for audio files only.

What makes RSS great is that I can take all the RSS links from all the news sites, blogs, webcomics and journals that I’m interested in and put them together into a single aggregator (I use Feedly). In this way, I don’t have to be constantly checking all these websites to see if there’s new stuff posted.

But what about medical journals that don’t provide RSS?

Unfortunately, there are some medical journals that do not have an RSS feed. For example, the JNCI (the Journal of the National Cancer Institute) does not have one. (If I’m wrong, please put the link in the comments.) So if I want to know what’s been published recently in the JNCI, I have to visit their site, or look on their Twitter. This is annoying, since the whole point of RSS is to have all the content you want to consume (or as much of it as possible) in the same place.

Pubmed allows users to save any search as RSS feeds

Pubmed provides a wonderful and open, standards-compliant service, but almost no one seems to know about it! This is great for people who are actively researching a subject, and also for people who just want to keep up with a particular journal or subject area.

Some of you have probably figured out where I’m going with this by now, but if you haven’t, I’ll spell it out. Let’s continue with the example of JNCI.

How to put new articles from any journal into Feedly

This assumes you already have an account on Feedly, but you can do this with any RSS reader, of course.

  1. Visit Pubmed in your browser
  2. Click “Advanced” under the search field
  3. Under “Builder,” click “All fields” and choose “Journal”
  4. In the text field beside the box where you selected “Journal,” enter the name of the journal you’re interested in (it will autocomplete, if you have done this correctly, you should see something like “Journal of the National Cancer Institute”[Journal] in the uneditable text field at the top)
  5. Click “Search”
  6. Under the search field at the top of the page, click the “Create RSS” link
  7. Choose how far back you want your search to go (I chose 20)
  8. Click the “Create RSS” button
  9. Right-click the orange “XML” button and click “Copy link”
  10. Go to Feedly, and paste the link into the “Search” field at the top right
  11. There should be one result, click “Follow” and choose which collection you want to keep it in

You’re done! Now whenever Pubmed indexes a new entry for that journal, it will appear in your RSS reader!

You can also make RSS feeds for any search you want on Pubmed

Of course, you may not be interested in everything a journal has to say, so you can refine the search to only include “breast cancer” or you can drop the journal identity part of the search entirely. The world is your oyster!

Introducing Serlingbot

My boyfriend and I were watching an episode of The Twilight Zone this week, in which a newly-minted revolutionary dictator is told by a departing member of the overthrown government that a particular mirror would show him his assassins. Of course, this leads him to kill his closest friends.

Sorry, should have said “spoilers” or something. Although really, you’ve had 56 years to see this episode. If you’re not caught up, that’s on you.

At the end of the episode, my first thought was: Trump would probably have fallen for that line too.

Inspired by that episode and of course by a Scottish newspaper immediately prior to Trump’s inauguration, I had an idea: A Twitter bot that downloads photos tweeted by the White House, turns them greyscale, overlays them with Rod Serling and tweets them again.

On my first Google search, I found a transparent PNG of Rod Serling. The Internet had also prepared a repository of json-formatted Rod Serling monologues. All I had to do was find a PHP library to connect to the Twitter API, and I was good to go!

You can follow @serlingbot on Twitter, and it will regularly send you photos from a few selected Twitter accounts that have been Serling-ed.

But that’s not all!

If you tweet a photo to @serling on Twitter, it will reply to you—with your photo Serling-ed.

And if you don’t have Twitter, I have made a non-Twitter web version of Serlingbot, where you can enter a link to an image on the web, and it will Serling your photo for your own private use.

I like to think that Rod Serling himself would have appreciated the idea of being resurrected as a post-apocalyptic robot, doomed to condemn a totalitarian government from beyond the grave. It’s something that might have happened … in the Twilight Zone.