18 April 2018

Teaching online and inclusion

"Do you expect me to talk, Goldfinger?" "No Mr. Bond, I expect you to make this online course ADA compliant!"

 I’ve been teaching a completely online class this semester. I’ve done partly online classes, and practically live online anyway, so I thought this would be a fairly simple thing for me to do.

It has not. It has been a real eye-opener for thinking about student needs.

One of the biggest challenges I’ve been working with is making the class compliant with the rules for students with disabilities. The rules are that whether there are students in the class who have declared disabilities or not, you must make every item in the class as readily available and accessible as if there were students with disabilities.

This means video lectures need closed captioning. There is voice recognition software that does closed captioning automatically, which is great, but it never does it perfectly. Every time I say, “Doctor Zen,” the software puts in, “doctors in.” This means you have to go in, listen to the entire lecture, and proofread the captioning for entire lecture.

Similarly, every image needs a description so that someone who is blind or otherwise visually impaired can understand the material. And many scientific diagrams are complex and challenging. Today, I was forced with trying to write a complete description of this:

Human genome influences traits. Human genome has 2 copies in every cell. 1 copy is made of 3 billion base pairs. Cell makes up tissue. In cell, genome divided into nuclear genome and mitochondrial genome. Cells manifest traits. Tissues make up organs. Tissues manifest traits. Organs make up body. Body manifests traits. Traits leads back to Lesson 1. Mitochondrial genome has 1 circular chromosome. Mitochondrial genome is many per cell. Circular chromosome is many per cell. Circular chromosome made of nucleic acid and histone proteins. Nuclear genome is one per cell. Nuclear genome is 23 pairs of linear chromosomes. 23 pairs of linear chromosomes has 22 pairs called autosomes. 23 pairs of linear chromosomes has 1 pair called sex chromosomes. Sex chromosomes are XX for female. Sex chromosomes are XY for male. 23 pairs of linear chromosomes are made of nucleic acid and histone proteins. Nucleic acid wraps around histone proteins. Nucleic acid has two types, DNA and RNA. RNA leads to lesson 3. DNA is composed on deoxynucleotides. DNA is double stranded. DNA composed of deoxynucleotides. Double stranded leads to helical shape. Double stranded by base pairs. Deoxynucleotides are 4 types of nitrogenous bases. Nitrogenous bases can form base pairs. Nitrogenous base connects to A, T, C, G. A base pairs with T and vice versa. G base pairs with C and vice versa.

Here’s what I came up with for the concept map above:

Human genome influences traits. Human genome has 2 copies in every cell. 1 copy is made of 3 billion base pairs. Cell makes up tissue. In cell, genome divided into nuclear genome and mitochondrial genome. Cells manifest traits. Tissues make up organs. Tissues manifest traits. Organs make up body. Body manifests traits. Traits leads back to Lesson 1. Mitochondrial genome has 1 circular chromosome. Mitochondrial genome is many per cell. Circular chromosome is many per cell. Circular chromosome made of nucleic acid and histone proteins. Nuclear genome is one per cell. Nuclear genome is 23 pairs of linear chromosomes. 23 pairs of linear chromosomes has 22 pairs called autosomes. 23 pairs of linear chromosomes has 1 pair called sex chromosomes. Sex chromosomes are XX for female. Sex chromosomes are XY for male. 23 pairs of linear chromosomes are made of nucleic acid and histone proteins. Nucleic acid wraps around histone proteins. Nucleic acid has two types, DNA and RNA. RNA leads to lesson 3. DNA is composed on deoxynucleotides. DNA is double stranded. DNA composed of deoxynucleotides. Double stranded leads to helical shape. Double stranded by base pairs. Deoxynucleotides are 4 types of nitrogenous bases. Nitrogenous bases can form base pairs. Nitrogenous base connects to A, T, C, G. A base pairs with T and vice versa. G base pairs with C and vice versa.

Writing that description... took time.

Anyone who think that online teaching is going to be some sort of big time saver that will allow instructors to reach a lot more students has never prepared an online class. It’s long. It’s hard. It’s often bordering on tortuous (hence the “No Mr. Bond” gag at the top of the post).

These things take time, but I don’t begrudge the time spent. It’s the right thing to do. It’s forced me to think more deeply about how I can provide more resources that are more helpful to more students. It’s not just deaf students who can benefit from closed captions, for instance. Someone who can hear could benefit from seeing words spelled out, or maybe use them when they are listening in a noisy environment, or one where sound would be distracting.

And I keep thinking that if I think it takes a lot of work to put these it, it’s nothing compared to students who need these materials who have to navigate through courses every day.

External links

Flowcharts and concept maps

16 April 2018

“It makes no sense!” versus history

There’s no channel 1 on televisions in North America.

It makes no sense.

That is, it makes no sense from the point of view of an engineer that had to design a channel system today, starting from scratch.

It makes sense from the point of view of a historian examining how broadcasting developed in North America.

Sometimes, discussions about academic systems of various sorts feel like people complaining mightily about how stupid it is that there is no channel 1, and proposing fix after fix after fix to correct it. And they do so in an environment where lots of people aren’t bothered by the lack of channel 1. And they do so even if the proposed fixes will mean some people’s televisions won’t work any more.

“Sure, but they’ll be better televisions!” Maybe, but it misses that a consistent channel numbering system is not what most people want out of a television.

03 April 2018

The NSF GRFP problem continues

This morning, a fine scientist congratulated two undergraduates in her lab about winning National Science Foundation (NSF) Graduate Research Fellowship Program (GRFP) awards. I thought, “Huh. They’re out? And two seems like a lot from one lab.”

A few years ago, Terry McGlynn wrote an important blog post about how tilted the playing field is for the NSF GRFP awards. He compared awards to Harvard students (with about 7,000 undergraduates) to the more than 20 campuses in the California State University system (over 400,000, according to a check of Wikipedia).

The NSF is good about making it easy to find a list of all 2,000 awards in this program. I went looking for the same comparison of one Ivy League university to an entire state’s system. Embarrassingly, I screwed up the calculation on the first pass, not realizing that several California State universities don’t say “California State” in their name, unlike the University of Texas institutions.

Harvard got 43, and all of California State get 50 (thanks to Terry for counting here and here).

Cal Poly Pomona 4
Cal Poly SLO 5
CSUCI 1
CSUDH 1
CSU Fresno 1
CSU Fullerton 8
CSULB 2
CSULA 1
Sac State 1
CSUSB 1
CSUN 5
CSUSM 3
SDSU 6
SFSU 6
SJSU 3
Humboldt State 2

So one lab in Harvard alone equaled the entire combined output of eight different California State universities (separately, not combined).

If this sort of pattern intrigues you, you must for to Natalie Telis’s post where she digs down into the numbers. Not just this year’s, but over 28,000 awardees worth of data, from 2011 to 2017. It’s bloody brilliant. One of her first points is, “The most expensive undergraduate schools have an extreme excess of (NSF GRFP) recipients.” She also makes some comments on Twitter about this.

I can’t wait to see what she finds for 2018 data.

Matt Cover did some similar things the previous year, and found no relationship between institutional enrollment and number of grants.

External links

NSF Graduate Fellowships are a part of the problem
The price of a GRFP, part 1
Matt Cover thread from 2017

28 March 2018

Innovation must be accompanied by education


When Apple launched the iPod, the company had to put a lot of effort into educating people about digital music.

Mr. Jobs pulled the white, rectangular device out of the front pocket of his jeans and held it up for the audience. Polite applause. Many looked like they didn't get it.

That was just fine with Mr. Jobs. They'd understand soon enough.

Apple had to inform the mass market that digital downloads could be legal (remember Napster?). They had to let people know how much music you could have with you. They had to let people know about the iTunes store. Without all those pieces of the puzzle, the iPod would have tanked.

I was reminded of these scene when Timothy Verstynan asked:

Why can’t we have a scientific journal where, instead of PDFs, papers are published as @ProjectJupyter notebooks (say using Binders), with full access to the data & code used to generate the figures/main results? What current barriers are preventing that?

I follow scientific publishing at a moderate level. I write about it. I’m generally interested in it. And I have no idea what Jupyter notebooks and binders are. If I don’t know about it, I can guarantee that nobody else in my department will have the foggiest idea.

This is a recurring problem with discussions around reforming or innovating in scientific publishing. The level of interest and innovation and passion around new publication ideas just doesn’t reach a wide community.

I think that this is because those people interested might undervalue the importance of educating other scientists about their ideas. Randy Olson talks a lot about how scientists are cheapskates with their communications budgets. They just don’t think it¤s important, and sassume the superiority of the ideas will carry the day.

I’ve talked with colleagues about open access many times, and discover over and over that people have huge misconceptions about what open access is and how it works. And open access is something that has been around for a decade and has been written about a lot.

Publishing reformers drop the iPod, but don’t do the legwork to tell people how the iPod works.

So to answer Timothy’s initial question: the current barrier is ignorance.

27 March 2018

What defines a brain?

A side effect of my bafflement yesterday over how lobsters became some sort of strange right-wing analogy for the rightness of there being winners and losers (or something) was getting into a discussion about whether lobsters have brains.

That decapod crustaceans are brainless is a claim I have seen repeated many times, often in the service of the claim that lobsters cannot feel pain. This article, refuting Jordan Peterson, said:

(L)obsters don’t even have a brain, just an aglomerate of nerve endings called ganglia.

This is a bad description of ganglia. It makes it sound like there are no cell bodies in ganglia, where there usually are. Here are some. This is from the abdominal ganglion of Louisiana red swamp crayfish (Procambarus clarkii):


These show cell bodies of leg motor neurons from several species (sand crabs and crayfish, I think; these pics go back to my doctoral work).


These are neurons in a ganglion from a slipper lobster (Ibacus peronii), where those big black cell bodies are very easy to see:


And these are leg motor neurons in slipper lobster:


And there is substantial structure within that alleged “not a brain” in the front:



And we’re know this for well over a century, as this drawing from 1890 by master neuroanatomist Gustav Retzius shows:



So ganglia are more than “nerve endings.” So putting that aside, are there other features that make brains, brains?

Intuitively, when I think about brains, I think of a few main features. Two anatomical, and one functional:

  1. Brains are big, single cluster of neurons. Even though there may be many neurons in, say, the digestive system (and there are not as many as some people claim), it’s so diffuse that nobody would call it a brain.
  2. It’s in the head, near lots of sensory organs. In humans, our brain is right next door to our eyes, ears, nose, and mouth, which covers a lot of the old-fashioned senses.
  3. It’s a major coordinating center for behaviour.

Decapod crustaceans (not to mention many other invertebrates) meet all those criteria. Sure, the proportion of neurons in the decapod crustacean brain may be smaller than vertebrates, but I have never seen a generally agreed upon amount of neural tissue that something must have to be a brain instead of a “ganglion in the front of the animal.”

I have a sneaking suspicion that some people will argue that only vertebrates can have brains because we are vertebrates, and vertebrates must be special, because we are vertebrates. That is, people will define brains in a way to stroke human egos.
 And, as I implied above, some people make the “no brains” claim out of self-interest. I don’t think it’s any accident that I see “lobsters don’t have brains” coming from institutes that have close ties to commercial lobster fisheries.

I suppose that some could argue that limiting the word “brain” to vertebrates is a way of bringing recognizing that vertebrate and invertebrate nervous systems are structured very differently. They are, but why only do this for one part of the nervous system? This is a little bit like saying “invertebrates don’t have eyes,” because they have compound eyes instead of our camera-style eyes. We routinely give things in invertebrates and vertebrates the same names if they have the same functions.

And in practice, I see people referring to octopus brains all the time. They do so even though, like other invertebrates, a large proportion of the nervous system sits outside the brain. From memory, roughly half the neurons in an octopus reside in its arms.

In practice, I am far from the only person that calls the clump of neurons at the front end of decapod crustaceans, “brains.” From this page:


So, fellow neuroscientists, if you don’t think invertebrates can have brains, why not? What is your dividing line?

Hat tip to Hilary Gerstein.

26 March 2018

I was unaware of how lobsters got sucked into an all-encopassing conspiracy theory

Miriam Goldstein and Bethany Brookshire burst my cosy bubble of ignorance. Today I learned  Jordan Peterson, a current darling of conservatives, drags lobsters into his mish-mash of writings to make white dudes feel good about themselves. Allow me an extended quote from this Vox article:

The book is a kind of bridge connecting his academic research on personality and his political punditry. In it, Peterson argues that the problem with society today is that too many people blame their lot in life on forces outside their control — the patriarchy, for example. By taking responsibility for yourself, and following his rules, he says, you can make your own life better.

The first chapter, about posture, begins with an extended discussion of lobsters. Lobster society, inasmuch as it exists, is characterized by territoriality and displays of dominance. Lobsters that dominate these hierarchies have more authoritative body language; weaker ones try to make themselves look smaller and less threatening to more dominant ones.

Peterson argues that humans are very much like lobsters: Our hierarchies are determined by our behaviors. If you want to be happy and powerful, he says, you need to stand up straight:

If your posture is poor, for example — if you slump, shoulders forward and rounded, chest tucked in, head down, looking small, defeated and ineffectual (protected, in theory, against attack from behind) — then you will feel small, defeated, and ineffectual. The reactions of others will amplify that. People, like lobsters, size each other up, partly in consequence of stance. If you present yourself as defeated, then people will react to you as if you are losing. If you start to straighten up, then people will look at and treat you differently.

“Look for your inspiration to the victorious lobster, with its 350 million years of practical wisdom. Stand up straight, with your shoulders back,” he concludes, in one of the book’s most popular passages.

The lobster has become a sort of symbol of his; the tens of thousands of Peterson fans on his dedicated subreddit even refer to themselves as “lobsters.”

This is classic Peterson: He loves to take stylized facts about the animal kingdom and draw a one-to-one analogy to human behavior. It also has political implications: He argues that because we evolved from lower creatures like lobsters, we inherited dominance structures from them. Inequalities of various kinds aren’t wrong; they’re natural.

“We were struggling for position before we had skin, or hands, or lungs, or bones,” he writes. “There is little more natural than culture. Dominance hierarchies are older than trees.”

Foul!


The logical fallacy is appeal to nature.

As analogies go, comparing humans to lobsters is... not a good analogy. This article provides a pretty good response, so I don’t have to. (Though I say lobsters have brains. But that doesn’t detract from the main points.)

External links


Psychologist Jordan Peterson says lobsters help to explain why human hierarchies exist – do they?

20 March 2018

The impossibility of species definitions


Sad news about the death of Sudan, the last northern male white rhino, prompted some discussion about whether the northern white rhino is a species or a subspecies. The TetZoo blog has a nice look at this specific issue. I’d like to take a broader look at the whole problem of why defining species is so hard.

Arguing over what defines a species is a long-running argument in biology. It’s practically its own cottage industry. There is much effort to define species precisely, for all sorts of good reasons. And that desire for clear, precise definitions often appears on websites like Quora. Questions come up like, “If Neanderthals bred with us, doesn’t that mean, by definition, they are the same species?”

But as much as we want clear definitions in science, there is a problem. You can’t always draw sharp dividing lines on anything that is gradual. (Philosphers know this as the continuum fallacy.)
To demand a precise definition of species is like demanding to know the precise moment that a man is considered to have a beard. For instance, I think we can agree that Will Smith, in this pic from in After Earth (2013), does not have a beard:


And that in Suicide Squad (2016), Smith pretty clearly does have a beard:


But does Smith have a beard in this pic? Er... there’s definitely some facial hair there.


What is the exact average hair length that qualifies a man to be “bearded”?There isn’t one. But that doesn’t mean that you can’t meaningfully distinguish After Earth Smith from Suicide Squad Smith.

It’s a problem that Charles Darwin recognized. In Darwin’s view, speciation was going to result from the slow, gradual accumulation of tiny, near imperceptible changes. Darwin recognized that speciation was a gradual process, and he  frequently made the point that “varieties” could be considered “incipient species.” At any given point in time, some groups would be early in that process of divergence, and some would be further along.

That’s why we shouldn’t expect there to be clear, consistent species definitions that apply across the board and are helpful in every case.
External links

The last male northern white rhino has died
How Many White Rhino Species Are There? The Conversation Continues