The blog commenting universe

BoraZ has done another of his magisterial overviews of the blogosphere, this time focusing on the state of blog commenting. It’s an interesting picture that I mostly agree with, but some of it not — partly because he’s making a general survey, and Pharyngula is a weird beast. This bit I’d like to tattoo on a few people’s foreheads (backwards, so they could read it every time they looked in a mirror.)

Free Speech is a very American concept. Most of the other 200 nations on the planet do not provide constitutional protection of free speech. And Internet is global.

And even within the USA, the concept of free speech does not mean everyone has the right to say everything everywhere. It does not mean you have the right to say your stuff on my blog. It means you have the right to start your own blog. Just because I have commenting functionality on my site, does not mean you have the right to post whatever you want on it. Every host of every site has the right to delete, edit, or modify any comment in any way, to ban users, and to implement whatever moderation norms and techniques one wants.

Commenting is a privilege, not a right. You have to earn it.

That should be easy to understand, right? Yet there are so many people who wax indignant at the thought that I might actually tell them to go away.

But there are other things that I found odd. He claims blog commenting is down overall; I haven’t seen that at all. Commenting keeps sliding upwards here.

There’s also this, again a generality that may not apply everywhere.

While early bloggers were generous, giving their rare online spaces up to public discussion, there is no need to feel so generous any more. Starting one’s own blog is easy these days, and ranting on social media is even easier. There is plenty of space for people to discuss stuff, and that does not have to happen on your site – the era of such generosity is mostly over, and most veteran bloggers have severely tightened their commenting rules over the years.

I’m a veteran blogger, I think, and my rules haven’t changed substantially over time. I’m not banning more people or editing more comments; if anything, as a proportion of comments made, I’m doing less of that.

I also don’t think that tightening up commenting rules is detrimental to the quantity of comments. One thing I’ve done that complicates his analysis is that Pharyngula has evolved to have one social thread that is more heavily moderated (and just the existence of dedicated social threads may confound some of his interpretations), and another that isn’t moderated at all, that I actually encourage annoying pests to infest. I think those contribute to overall activity that spills over into other threads, and vice versa.

A relevant datum here, though, is that the moderated thread is much, much more active than the openly unmoderated thread, usually. Sometimes the jerks are just wearing, and having a thread where they’re excluded can be enabling to more discussion.

Also, one obvious point: science posts get fewer comments than other kinds of articles. I think that’s because they require more specialized knowledge to assess; maybe Bora is seeing a decline in the science blogs he reads because the ecosystem is shaking out, and people are specializing more — many blogs are less widely discursive now, and that’s another area where Pharyngula is weird. I’m just as scattershot and flibbertigibberty as ever.

The threads that go on the longest are the ones where some obtuse nitwit comes in and stubbornly sticks to some stupid point, and everyone has to show up and take a whack. I’m often told that controversy draws in more traffic; I disagree there, I think good writing and provocative thinking contribute far more, but I know that controversy definitely stirs up more community engagement, which can lead to the formation of a solid base of readers. And yes, that’s another place where Pharyngula is deviant relative to other science blogs out there. Kids nowadays just seem reluctant to pick a fight.

What I’m also going to teach today: a little image processing

My development class also has a lab. The last few weeks have all been teaching them how to get good optics on a research scope, and how to take photomicrographs with my PixeLink camera system. Today I’m going to show them how to appropriately process an image for publication, so they’ll learn a few digital enhancement tricks and a few ethical rules. I lay down a few laws about using image processing on scientific data:

What you must do to your image:

  • You must archive the original data and work with a copy. If I ask to see the original after you’ve enhanced the image up the wazoo, you better be able to show it.

  • You must document every step and every modification you make. You’re going to describe everything either on the image itself or in a figure legend; if this were to be published, you’d probably include it in the Methods section.

  • You must explain the scale and orientation of the image. The scale is usually shown by including a scale bar; orientation may be shown either by including annotations (text describing landmarks in the image) or an explanation in the figure legend, such as that it is a sagittal or horizontal section.

  • You must save the image in a lossless format, such as .png or .psd or .tiff. Do not save it in a lossy format like .jpeg, which can add compression artifacts.

What you may do to your image:

  • You may crop and rotate the image.

  • You may adjust the contrast and brightness for the whole image.

  • You may carry out simple enhancements, like applying a sharpening filter or unsharp masking, to the whole image…but remember, document everything!

  • You may splice multiple images together to produce a photomontage; you can also insert panels with enlarged or otherwise enhanced regions of the image, as long as it is absolutely clear what you’ve done.

What you may not do to your image:

  • You must not carry out selective modifications of portions of the image; you cannot sharpen the cell you care about and then reduce the contrast for other regions, for instance. You should not burn or dodge regions of the image.

  • No pixel operations or retouching: you are not allowed to go into the image and paint your data into existence!

We do a lot of this preliminary basic stuff because I run the course out of my research lab, rather than a student lab. I want to make sure they’re not going to break anything, and also that they know how to do good imaging, a skill they’ll find useful in other courses and in research (years ago when I taught this stuff, we’d also do black&white darkroom work — nobody does that any more, so now it’s all photoshop). The goal is to get them all able to churn out lovely photographic data, so later I can just hand them some nematodes or fruit fly embryos and tell them to do their own experiments and observations, just show me the pretty pictures when they’re done.

It’s a good life, being able to sit back and let students bring me gifts of biological beauty. I think they’ll also be posting some of these to their blogs.

What I taught today: gene regulation and signaling

Today was more context and a bit of a caution for my developmental biology course. I warned them that we’d be primarily talking about animals and plants (and mostly animals at that), but that actually, all of the general processes we’re describing are found in bacteria and other single-celled organisms — that in a lot of ways, microbiology is actually another developmental biology course. Yes, I went there: developmental biologists tend to be imperialists who see all the other sciences as mere subsets of the one true science. Of course, you could also take that as developmental biology being a synthetic discipline that steals bits and pieces from everywhere…

So the primary lessons today were reviews of stuff these students should have gotten in cell and molecular biology, with bits of biochemistry and microbiology thrown in. We talked about genes getting switched on and off, and the example I used was the classic: the lac operon in E. coli. What? You don’t know about it? It’s a beautiful system, in which the bacterium switches on the genes needed for digesting the sugar lactose only when the sugar is available in the environment. I showed this nice little 3 minute video:

Switching genes on and off? That’s development! It gets a little more intricate in multicellular animals, but all of the fundamental logic is right there in E. coli: activators and repressors, positive and negative feedback, the boolean logic of gene regulation. I also mentioned that when we’re reading Carroll’s Endless Forms Most Beautiful, he’s going to make a big deal out of exactly this kind of regulation, but I want them to remember that it’s not unique to butterflies or fruit flies or frogs, it’s a common theme in all kinds of diverse cells.

We then talked about cell signaling. How does a cell know which genes are supposed to be off and on? It interacts with its environment (as in the lac operon) or its neighbors to make decisions about activity. To illustrate that, we went through quorum sensing and biofilms — again, cell signaling is not unique to animal development, it was all worked out in principle in single-celled organisms. I gave them a little foreshadowing and mentioned that we’d be discussing Sonic Hedgehog and Notch and Delta later in the course, classic examples of signaling in multicellular systems, but in bacteria we have things like hapR and AHL signaling.

Finally, I raised the issue of a phenomenon we’ll be talking about on Wednesday: patterning. Why aren’t your arms growing from your hips, why don’t you have fingers on your feet instead of toes, why are your eyes paired and on the front of your head? Because there is positional information in the embryo that can be read by cells and tissues and lead to development of appropriate structures in their proper places. But once more, this is not unique to multicellular animals. A paramecium, for instance, is not a generic blob, but has a definite shape and orientation; it has organelles in predictable places, and is covered with a nearly crystalline lattice of cilia with specific axes of orientation. I showed them choanoflagellates and pointed out that these protists, representing a multicellular precursor, had a specific shape and a collar organ in a specific functional location: how do they know how to do that?

That’s the question we’ll be asking next. I warned them too that I won’t be lecturing at them on Wednesday, so they’d better have their morning coffee. I’m expecting them to read a review paper on positional information in embryos (pdf), and I’m going to make them explain it all to me for a change.

Slides for this talk (pdf)

For Wednesday:

Kerszberg M, Wolpert L (2007) Specifying Positional Information in the Embryo: Looking Beyond Morphogens. Cell 130(2):205–209.

More TV tonight!

Maybe for you, maybe not for me. PBS is supposed to show the documentary The Revisionaries tonight, a show about the Texas Board of Education and it’s horrendous abuse of the educational system, but looking at my local television schedule, I can’t see it. We’re in a conservative rural area with a rather chickenshit public broadcasting channel that often either disappears these ‘controversial’ shows or schedules them at bizarre early morning hours. I’ve been cursed over this show; the makers were going to send me a screener, and assured me multiple times that it would be mailed to me, and it somehow never arrived.

At least I can see the trailer. Maybe my blood pressure can be thankful that I may not get to see the rest of it.

Grrrr. Don McLeroy. The personification of the banality and jovial stupidity of evil.

Good news! Errm, or is it bad news? It is being shown here in the Morris area tonight. The trick is that the stations aren’t advertising it as “revisionaries”, and they aren’t mentioning creation/evolution. Look for “Independent Lens”, a documentary about textbooks.

Morris people: it’s on channel 10 at 9pm tonight. The makers did write to me, though, and say that the PBS version had a half hour cut from it to make it fit the time slot — we’ll see what gets on.

#giantsquid time!

I’ve fired up the television and am tuned to the Discovery Channel. What is this godawful crap about rednecks and moonshine leading in to the documentary on the giant squid? It does not bode well.

Ooh, they’re teasing us with short clips right at the very beginning. Good start. Less “monster” talk would be welcome, and more biology and ecology would be welcome.

Boy, they really threw money at this project: multiple submersibles, multiple film crews, cameras all over the place. Also infrared lighting, which accounts for the appearance of some of the video previews.

I would like to know what the recipe for that gloppy squid lure Steve O’Shea is mixing up. He calls it a squid “aphrodisiac”…and he tasted it. Squid breath!

Ah, the aphrodisiac is squid bits run through a blender, a squid milkshake. Do not try something analogous if you are looking for a human aphrodisiac.

Hmm. They’re kind of setting this up as a conflict between the three scientists involved — Widder, O’Shea, and Kubodera, and portraying O’Shea as ‘controversial’. Really? We’ll see if there’s any real drama or if this is exaggerated and contrived (I suspect the latter).

Real science is often tedious. This show is just giving us the highlights — O’Shea just went on a 7 hour dive in a submersible, we got to see a couple of brief shots of some lovely jellyfish and a couple of small squid (which were nice!)

I guess this is build up. 45 minutes in, we’ve seen all three scientists do a dive, and all three fail. That’s OK, I think they’re illustrating how science is done about as effectively as you can with a television entertainment.

This so reminds me of going fishing, trying different lures semi-randomly to find out what they’re biting.

Oh, wait, they are fishing!

I’ve been watching for an hour and ten minutes, and they finally flash a glimpse of a large squid at us. Need…more…data. Getting a little thin here.

It figures. All the people hanging about underwater in submersibles…nada. Unmanned probe left to record unmonitored for 30 consecutive hours…success!

It is now sinking in that that 30 seconds of a giant squid lunging at a robot probe has been padded out to an hour and a half. It’s spectacular footage, but there really isn’t that much of it.

OK, stop this. Last 15 minutes seem to be solid commercials interlaced with one minute segments of documentary. This is getting ridiculous.

Finally! A giant squid just hangs onto some bait while brightly lit for 23 minutes…and they show us about a minute of it. Why not just drop that fluff and have the last half hour be nothing but continuous footage of the 26 foot long beast hanging there? That’s what I want!

My final assessment: mixed. They got some really, really good video, but apparently they didn’t think it was enough, and so they padded it out way too much. There were some half-assed attempts at the beginning to play up conflict and drama between the researchers, but they didn’t pan out and weren’t at all relevant; the stuff about “monsters” was distracting; the occasional attempts to compare this search to bigfoot, UFOs, and the Loch Ness monster — only real — was just annoying. There was some promising set up of the methodology, but not enough about the biology.

The people who made the show clearly didn’t think just the video footage of the squid was sufficiently engaging. They were wrong. They also clearly felt a need to milk it for every penny of commercial time they could get.

I look forward to when just the raw footage of the squid is released. That’s what I want to see.

But I thought he was going to argue with me!

The other day Paul Fidalgo asked permission to quote something I said on our super-secret backchannel (there is no backchannel, no, we do not talk to each other on FtB; it’s all a lie, pretend no one said anything about it), and I got the distinct impression that he was going to pick a fight with me over it. So I said yes, because I enjoy a good argument. Imagine my disappointment, though, because he ends up agreeing with me, mostly.

So now what do I do? I’m disarmed, I’m helpless, I’ve got nothing to lash out against. Now I’m very uncomfortable. What a devious move!

A certain philosopher who will not be named has taken exception to Fidalgo’s post (he’s “very angry”!), calling him a “bully enabler” who has “written a piece justifying bullying” which makes the “situation much worse”.

What? Telling people they should shut up and listen to other people’s arguments, especially when they have more experience in the subject than you do, is now “bullying”? That makes no sense at all. So now if someone yells at me that I’m totally wrong, and I sit back and think about it and listen to their case rather than instantly barking out a rebuttal, I am engaging in bullying?

I don’t get it. I really don’t.

I’m also baffled by what “the situation” might be. I fear the situation might be something as awful as someone sometime listening to that asshole Meyers again.

Can you see through this ploy, Arizona?

A group of Republican legislators have proposed a new anti-science bill in Arizona. It doesn’t come right out and say that it’s anti-science, of course: they know better than that. They claim instead that the purpose of the bill is to promote “critical thinking skills,” which we certainly all endorse. But they give the game away with the details.

The targets of the bill are explicitly listed in a section that presents as legislative findings that "1. An important purpose of science education is to inform students about scientific evidence and to help students develop critical thinking skills necessary to become intelligent, productive and scientifically informed citizens. 2. The teaching of some scientific subjects, including biological evolution, the chemical origins of life, global warming and human cloning, can cause controversy. 3. Some teachers may be unsure of the expectations concerning how they should present information on such topics."

Somewhat redundantly, SB 1213 provides both that "teachers shall be allowed to help pupils understand, analyze, critique and review in an objective manner the scientific strengths and scientific weaknesses of existing scientific theories covered in the course being taught" and that state and local education administrators "shall not prohibit any teacher in this state" from doing so. The bill also insists that it "protects only the teaching of scientific information and does not promote any religious or nonreligious doctrine, promote discrimination for or against a particular set of religious beliefs or nonbeliefs or promote discrimination for or against religion or nonreligion."

Wow. These people have no imagination at all, no creativity in the slightest. This is essentially boilerplate taken from every goddamn creationist bill proposed in every legislature for the last decade or so. Singling out a few specific ‘controversies’, like evolution and climate change (which actually aren’t controversial at all); “strengths and weaknesses”; the denial that this is promoting a particular religious doctrine; these are such a familiar drone that my brain falls asleep reading them anymore.

Time for the residents of Arizona to rouse themselves — it’s not as if you’ve been suffering from a barrage of lunacy and bigotry lately, right? — and write to your representatives and yell at them to kill this stupid Senate Bill 1213.