Monday, March 3, 2014

High-Minded Scientific Discourse

Do you think scientists debate carefully and cautiously, deferential to the opinions of others and always sensitive to the possibilities of shortcomings in their own reasoning?


Below are some samples from an argument over (get ready) one journal deciding to have a (still) murkily-defined open data policy.  Have a read of the original post from DrugMonkey's place.  Of course, when you start a debate/discussion with a post with "PLoS is letting the inmates run the asylum" in the title and proceed to call them "waccaloons" who employ "idiot humanities majors" you're bound to provoke inflammatory responses:

"you continually return to talking about YOUR teeny little bunny patch. It’s not your interlocutors who fail the imagination test here." (Bill)
"You are just deaf to it, is all. Theology is like that sometimes." (DM)
"Because you are not listening. Rather, because you refuse to get this.
This turns you from being a merely blinded and deluded true belieber acolyte into an actively denialist asshole." (DM)
"It’s not as though the rat-diddling that you call science is worth archiving anyway." (Bill)
"If you could put as much effort into thinking about sharing as you did into constructing this moany teenage diatribe then we’ll be fine." (Chris)
"In conclusion, Chris, and everyone else saying PLOS is being reasonable, you are either inexperienced or stupid, and either way you can go fuck yourselves." (anonymous postdoc)

I'll remind you that this is happening literally over one journal's open data policy (which they already had) and which they have yet to fully define how it will apply to each subfield.  I mean this is as academic as an academic argument can get and yet... humans be humans.

Saturday, February 8, 2014

Stop Telling Us We Can Do Anything with a PhD


Take a sample of undergrad neuroscience majors with similarly high GPAs and GREs such that they could all get into grad school.  Send half of them (Group A) to grad school, and let the other half (Group B) do whatever they want.  Five years later, put half of each group (Group A1, Group B1) into a research postdoc, and the other half (Group A2, Group B2) at a position with a consulting company.  Now assess their job performance one year after that.

My prediction? A1 >>> B1 ; A2 = B2

And that's why reading stuff like this is so frustrating:

Doing a PhD mostly prepares you for a career in academia.  Stop telling us we can do anything with a PhD if we could have done anything without one.

Friday, January 24, 2014

eLearnIn The Human Brain

Next neuro video from eLearnIn:

Views: 44,571
Like/dislike: 168/15
Comments: Disabled

Okay folks I'm not going to go through this one in as much detail as I did their last.  It's basically the same critiques: weird writing, weird visuals, content errors.  But I do need to highlight a few things:

1) There's a faded version of their logo that DVD-screensavers its way across the screen during the entire video...

2) This quote is awesome:

The forebrain contains information related to human intelligence, memory, personality, emotions, speech, and the ability to feel the mood.

Do you have the ability feel the mood?????

3) This quote is not-so-awesome:

The left hemisphere is considered to be logical, analytical, and objective and the right hemisphere is thought to be more intuitive, creative, and subjective.




My line-by-line of this one:

eLearnIn The Neuroscience

Next up in my series on educational neuroscience youtube videos:

Views: 63000+
Like/dislike: 235/21
Comments: "like if  you had to see this for school"; "where was this video 2 years ago when I took Cell Biology!?"; "How is an impulse carried across the synapse?"


This one is simply odd.  It doesn't get too much THAT wrong, but it also doesn't really do a good job explaining things correctly or connecting concepts into a broader framework.  Let's see how it does on my five areas of eduvideo quality:


There are some content errors.  For instance:

Neurons are responsive in nature, by which we imply that Neurons respond to feelings and communicate the presence of that feeling to the central nervous system which in-turn is processed and is sent to the other parts of the body for action.

Sensory neurons respond to stimuli which they can detect.  Photoreceptors can detect light, for example.  "Feelings" is simply the wrong term here.  Also, I'm not really sure what is meant by "neurons are responsive in nature".  It's more or less true but in context doesn't make a whole lot of sense.

Full line-by-line edit:

Level of Detail

The level of detail covered is too superficial to be useful.  This video basically says "Here are some facts.  Enjoy."


The organization occasionally makes little to no sense.  For instance:

Every neuron is surrounded by a plasma membrane, which is a bilayer of lipid molecules that are comprised of various protein structures. A lipid bilayer is a powerful electrical insulator, but in neurons, many of the protein structures embedded in the membrane are electrically active. 
Cell division cannot take place in neurons as they lack one of the two cylindrical cellular structures that aid in cell division. This is consistent with a simple cell division nature of the cell.
Dendrites are extensions of the cell with many branches, whose structure can be called as a "dendritic tree".

What is the fact on cell division doing there? Also note the content errors in red: lipids are not comprised of proteins (the membrane is comprised of lipids and proteins) and "electrically active" makes no sense and is wrong. There are some electrically-activated proteins, but it is more correct to say that there are proteins in the membrane that render it capable of electrical activity.

Topics are also introduced and dismissed with no warning, and are not connected. This is literally how the video ends:

There is only one axon that projects from each cell body, which is a finer cable-like projector. It is usually elongated and it carries impulses away from the cell body, that is, away from the 'soma'. It is called a efferent process. 
Many axons are surrounded by a segmented white fatty substance called myelin sheaths.

...and what does myelin do?


I'm convinced this was written by someone for whom English is not their first language, and then read off by someone else. There are some seriously funky grammatical decisions made here:

[...] these also affect the gland secretion.
The neurons connect to each other using a synapse (which is a structure that acts like a pathway connection that transmits the signals to the other cells) to form the nervous system.
[...] whose structure can be called as a "dendritic tree".

Despite being spoken slowly and deliberately, the language just doesn't make sense at times.


There are numerous visual oddities.  One theme common to neurovisualization (hell yeah I just made that up) is present: not very dense networks with pulses of light moving around the cells.  I swear people must think that the inside of the brain actually looks something like this:

In reality, things are much denser of course (one would not be able to see through it), although this is rarely mentioned in neuro videos or animations.  And it's never fully explained that the pulses of light aren't actually there - those are just meant to represent electrical signals.

Here's a visual content error from this video:

The nucleus is mislabeled as the soma.  Also this is the strangest looking neuron I've ever seen.  The dendrites are all way too thin and the soma has a crazy structure and color texture going on.  And why is the nucleus sitting on top of instead of inside it?


This video is simply strange.  The visuals are weird, the script is poor, and errors are made.  Basically, I can't wait to see what happens when I tackle another eLearnIn video: the human brain and its parts.

Thursday, January 23, 2014

When Instructional Video Goes Bad

***Post updated with addendum at the end***

Let's say you're a high school biology teacher looking to do a segment on the nervous system for your class.  Maybe you run a flipped class, and so you head to youtube to find a good video to assign.  Or maybe you just want to brush up on the material so that you can teach it effectively.  Either way, you might find this video, entitled "The Nervous System" by Bozeman Science:

Presented by Paul Andersen, who was the 2011 Montana Teacher of the Year, the video has 150,000+ views and a 50:1 like/dislike ratio.  If you peruse the comments (looking past mine...) you'll see things like "You explained it better than my teacher", "This helped me so much", "way better than reading expensive textbook or any lecture in college", "You have such a knack for making a complex subject understandable", et cetera.

Seems like a great teaching tool, yes?

The problem is that the video gets many things wrong.  Here are five areas for improvement, detailing some of the errors along the way:

Getting the content right

Numerous factual errors are made, ranging from simple, easily-correctable mistakes:

Remember [the membrane potential] used to be -70 millivolts. And now it's going to be less that that. So maybe it's going to be -50 millivolts. [-50 > -70]
What happens is that you're going to get an influx of something called calcium. [The error here is that calcium is drawn as Ca+ instead of Ca2+]

to claiming things that are highly misleading, confusing, and often just untrue:

[discussing nodes of Ranvier] the message actually, it doesn't go all the way through the axon, it's able to jump from spot to spot. Because we put all the ion channels right here. [this is drawn with arrows suggesting that the "message" is literally leaping outside the axon and coming back in at the nodes. And the action potential does of course traverse the entirety of the axon, but is only regenerated at the nodes.]
Now what happens next, well we have to reestablish that gradient. And to do that we use something called the sodium-potassium pump. And so when you see light, you're sending literally thousands of action potentials down a neuron. Between each of those action potentials, the sodium-potassium pump is going to reestablish that gradient. [...] And then we have what's called the undershoot as it resets itself with the sodium-potassium pump. [This is profoundly wrong - the number of ions that flux during a single action potential is minuscule compared to the number of ions on either side of the membrane. Sodium/potassium pumps have nothing to do with the undershoot of the action potential].
All told, I went through the transcript of the video and found roughly 36 incorrect sentences, 25 misleading sentences, and 19 potentially confusing sentences.  (There were 94 correct sentences, and 138 filler sentences.  I probably missed a few too, so don't gotcha me if the numbers don't add up.)  You can view the whole transcript with my line-by-line annotations here:

Getting the level of detail right

The nature of the content that Mr. Andersen is trying to cover here makes the video trickier than it seems.  The meat of this video was on the neuron, the action potential, and the synapse.  The problem is that to fully understand, say, the action potential, the teacher must explain material from cell biology (neuronal membranes, protein channels), chemistry (ions, gradients, charge), and physics (voltage, current, etc).  It is, simply put, too much to explain the underlying concepts and link everything together in a single 17 minute video.

So what about a purely descriptive, superficial account?  After all, the learning doesn't begin and end with a single video.  Perhaps this can be used just to give people a "sense" for the material, an accurate portrayal of what happens without really delving into why and how.

I think such a video would be excellent.  Don't bother to explaining the detailed mechanisms of how things works.  A neuron, in such a video, is just a cell that receives little inputs in its dendrites that spread to the neuron's cell body and can trigger there the production of a big output we call a spike, which then travels down the axon and triggers neurotransmitter release at a synapse.  The neurotransmitters released by the presynaptic neuron causes the postsynaptic neuron to generate little inputs which spread to its cell body, etc.

But this particular video falls into a weird middle-ground.  It does the superficial, but then tries to go a little farther and explain some how and why questions.  But because there isn't time to fully build up everything from a firm understanding of the fundamentals, shortcuts are taken that inevitably lead to errors and likely generate misconceptions in the minds of the student viewer.  For example:

Now if you've ever heard me talk about neurons before you've heard this. I always like to say that nerves or neurons, a nerve is just a bunch of neurons together, that a neuron is simply a salty banana. And that allows you to remember where the ions are. And so what do you know about a salty banana? So this visual over here on the left side is super important to remember. We've got a salt grinder up here. It's going to put salt on the surface of the banana. Well what do you know about salt? Salt's going to be high in sodium. And what do you know about a banana? It's going to be high in potassium.

A clever mnemonic!  But wrong.  On a trivial level, potassium chloride is just as much a salt as sodium chloride.  But more importantly, this leaves the viewer with the impression that there's only salt outside a neuron and only potassium inside of one.  Wrong!!  It's a shortcut that bypasses a fuller discussion of concentration gradients.  There will be no deeper understanding imparted here in the minds of the student viewers, only a misconception.

Getting the organization right

One problem with this video in particular is its strange organization.  What purpose did the brief lesson on split-brain patients serve in relation to the rest of the material?  This quote particularly bothered me:

But I want to start with the big picture. And nothing gets more big picture in the nervous system than the brain.

Okay, so the brain is the largest portion of the nervous system, measured by number of cells it contains.  But that doesn't make it "big picture".  The big picture - which is never explicitly stated here - is usually expressed as something like, "The nervous system is like the command center for the body.  The nervous system is responsible for sensing the environment, both inside our bodies and outside of it, for integrating and processing that information, and for generating behaviors both mental and physical in response to it.  Everything you experience, think, or do is mediated by the nervous system."

Getting the script right

Many of the errors made in this video stem from simple language mistakes.  Stylistically Mr. Andersen speaks in a very easy-going and accessible manner.  However, he is often imprecise.  This avoidable imprecision leads to muddles like the following:

Action potentials work by polarizing a cell. In this case it's the neuron. They set up this polarization through sodium-potassium pump. If you remember that's a form of active transport. And then when they depolarize it by opening up these ion channels then we can send a message down the neuron.

Here he simply is unclear about what the antecedent for all the "they's" are, and it makes it seem like the action potentials are doing all of this stuff.  Content-wise, that makes all the statements in red incorrect (see my correction in the Google doc).

Getting the visuals right

Content errors in the visual cartoons and diagrams video producers make are common.  Here, for instance, Mr. Andersen compounds the content error he made earlier with Na+ and K+ ions by imprecisely animating what happens to them during an action potential:

This is a screengrab of when he gets to the end of the action potential.  My issue with it (and many animations like it) is that there's no mention that the actual number of ions that flux across a membrane in a single action potential is tiny compared to the total concentration.  But because he draws it this way, he feels compelled to explain how things get back to the starting state!  See this screengrab:

Now, he makes the content error that the sodium-potassium pump has to (via magic sparkles) reset all the ions.  If the animation were clearly drawn, if the concentrations were clearly explained, if the resting membrane potential had been taught first, if equilibrium potentials had been taught before that... none of this would have happened (this is also a prime example of how there's not a happy medium between complex and simple).

Takeaway Thoughts

  • Making a good quality instructional video requires careful consideration to the level of detail, the organization of the content, the accuracy of the content, the polish of the script, and the quality and accuracy of the visuals.
  • Students, teachers, and all viewers are not necessarily going to be able to tell accurate content from inaccurate.  People love this video, so feedback is not always going to be useful, especially since feedback will tend to only come from those who enjoyed the video enough to say so (those who didn't like it already clicked away to another page).



I emailed this blog to Mr. Andersen so that he would be aware of this feedback.  He has acknowledged in his reply to me that he has misconceptions about some of the concepts he presents in this video, and he is looking into re-doing the video when he has time.  (Understandably, he is doing a lot of videos and also teaching!)

I will publish his response here if he allows it, but for now I think you should all know that it was very heartening.  He clearly cares about his students and getting the material right and I have no doubt he can make a corrected video.

Saturday, January 11, 2014

La Jollans Who Chose to Live in Oceanside Tourist Destination Annoyed that Tourists and Ocean Animals Keep Showing Up

Please read this not-The-Onion excerpt from a letter-to-the-editor penned by Melinda Merryweather, La Jollan:
Every day we have to put up with more than 2,000 cars with no parking, so we are short 2,000 parking spaces almost every day.  We have two polluted beaches and smells that no other city would ever have to put up with. 
I am not interested in La Jolla being the free SeaWorld for the city.  I want the quiet back.  I want my beaches back.  I want this nightmare over.  We have to stand up and say, "I am not taking it any more!"
(You can find the editorial in full by flipping to the back of this: )



My neighborhood of La Jolla (Mitt Romney's, too!) has some interesting quirks, one of which is that a subset of the locals really dislike the seals and sea lions who live in the ocean and on the beaches.  The seals because they took over a tiny beach that they used to go to (and that divers used to use) and now the sea lions who apparently have smelly poop.  Here's the lowdown on the sea lion issue:

  • At the La Jolla cove, there are sea lions.  Tourists (and at least this local) love them!  Arf arf arf, et cetera.
  • Also on the cliffs above where the sea lions haul out, there are lots of birds (pelicans, cormorants, gulls), who pooped on the cliffs.  People weren't allowed to walk on the cliffs, and it doesn't rain much, so the poop built up.
  • Above the cliffs are several swank restaurants with ocean views who don't like the smell of all that poop because then the rich people who would dine there won't come.
  • Well everyone assumed the smell was the bird poop, and after much legal wrangling (coastal commissions and cities and neighborhoods and yaddayadda) they powerwashed off all the poop.  Then they added a gate to the fence to the cliffs, so now people can go down there, preventing birds from roosting there and pooping.  Problem solved?
  • Apparently not, because I guess there's still some smell (it's not nearly as bad, but it's noticeable if you sniff for it).  This is blamed on the sea lions and their poop.
  • Now the restaurants have had enough, and they're suing the City of San Diego because they're sick of the smell.


1.  It is hilarious that Melinda Merryweather thinks that the actual ocean is just a "free SeaWorld" responsible for parking problems and smelliness.

2. Opening the gate is going to cause some problems...

 The cliffs where the poop used to be, now with humans getting as close as they can to the sea lions. 2013/01/11

An example of humans being stupid. 2013/01/11


If that's not enough for you, here are some other great links to classic La Jolla Light opinion moments:

Seals are Yahoos akin to termites, people who like them are The Despoilers:
Many of The Despoilers are not even residents of La Jolla and should have no say in how our city and its resources are maintained. They are INVADERS of the rights of citizens of La Jolla. 
When termites move into The Despoilers’ domiciles, let us prohibit any form of extermination of the creatures. Demand that The Despoilers vacate their homes and allow the poor creatures to fester and thrive.

The seals are bringing the Sharkpocalypse:
Within the next 20 years this place will be considered a dangerous place to swim and surf. The people who pushed having what will by then be a full-blown seal colony will have serious blood on their hands. Families will be devastated by the loss of their loved ones who will die the most horrible deaths imaginable. Generations of families will suffer. 

Google it, dummy:

Don’t sea lions poop in the water? If they do that, this would leave pelicans and cormorants as the only culprits. 
With all of the marine biologists here in La Jolla, could someone ask the right person so that we attack the right problem? 
Art Cooley, La Jolla 
La Jolla Light Editor’s note: Search for “sea lions pooping” on YouTube and you can view videos that show the sea lions defecate both in water and on land.

Friday, January 3, 2014

Khan Academy and Evolution

A slightly more egregious example of Khan Academy creating a misconception (3:40, and referenced later and throughout the series):

I discovered that their website has a feature to suggest mistakes (a good thing!).  Here's what I wrote:

3:40 Sal says "What evolution is - and I prefer this word - is natural selection." 
This is flatly incorrect!! Evolution is more properly defined as the change in a phenotype expressed/displayed in a given population of organisms as measured over multiple generations. Natural selection is ONE and only ONE of multiple paths to achieve such a change. Even if Sal does not want to discuss them in detail, the fact that other forces besides natural selection exist should be mentioned. These include drift, horizontal gene transfer, and others (really just look at wikipedia!).
Summary: Khan Academy is leaving its viewers with the misconception that evolution = natural selection when, in fact, natural selection is merely one of several classes of mechanisms by which evolution can occur.

Will the video get re-done?  I doubt it.**  But this is really a fundamental error.  No introductory biology course would neglect A) clearly defining evolution or B) mentioning that natural selection is only one of several ways evolution can occur.

Food for thought - what percentage of high school teachers who might be using Khan Academy software/videos in their classroom would notice this mistake?

**The strikethrough text is there because the day after my last post catching an error discussing the purpose of myelination, they took down the video with the error and reuploaded a new video that corrects their mistake.  So there's hope!