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

16 March 2018

The last round of the year

Reason I love the AFLW competition, number 2,749:

Going into this last round of the home and away season, five out of eight teams had a shot at the grand final. And no team was guaranteed a slot in the grand final.

And the mighty Demons are well placed to be one of the two teams in the final. Go the Dees!

It's going to be a series of nail-biting games, and I love it.

13 March 2018

“Mind uploading” company will kill you for a US$10,000 deposit, and it’s as crazy as it sounds

Max Headroom was an 1980s television series that billed itself as taking place “20 minutes into the future.” In 1987, its second episode was titled, “Dieties”. It concerned a new religion, the Vu-Age church, that promised to scan your brain and store it for resurrection.

Vanna Smith: “Your church has been at the forefront of resurrection research. But resurrection is a very costly process and requires your donations. Without your generosity, we may have a long, long wait... until that glorious day... that rapturous day... when the Vu-Age laboratories perfect cloning, and reverse transfer.”

That episode suddenly feels relevant now, although it took a little longer tan 20 minutes.

On Quora, which I frequent, I often see people asking about mind uploading. My usual response is:

So I am stunned to read this article about Nectome, which, for the low deposit price of US$10,000, will kill you and promise to upload your mind somewhere, sometime, by a process that hasn’t been invented yet.

If your initial reaction was, “I can’t have read that right, because that’s crazy,” you did ready it right, and yes, it is crazy.

In fairness, it is not as crazy as it first sounds. They don’t want to kill you when you’re healthy. They are envisioning an “end of life” service when you are just at the brink of death. This makes it moderately more palatable, but introduces more problems. It’s entirely possible that people near the end of life may have tons of cognitive and neurological problems that you really wouldn’t want to preserve.

How do they propose to do this? Essentially, this company has bought into the idea that everything interesting about human personality is contained in the connectime:

(T)he idea is to retrieve information that’s present in the brain’s anatomical layout and molecular details.

As I’ve written about before, the “I am my connectome” idea is probably badly, badly wrong. It completely ignores neurophysiology. It’s a selling point for people to get grants about brain mapping, and it’s a good selling point for basic research. But as a business model, it’s an epic fail.

And what grinds my gears even more is that this horrible idea is getting more backing that many scientists have ever received in their entire careers:

Nectome has received substantial support for its technology, however. It has raised $1 million in funding so far, including the $120,000 that Y Combinator provides to all the companies it accepts. It has also won a $960,000 federal grant from the U.S. National Institute of Mental Health for “whole-brain nanoscale preservation and imaging,” the text of which foresees a “commercial opportunity in offering brain preservation” for purposes including drug research.

I think it is good to fund research of high speed analysis of imaging of synaptic connections. But why does this have to be tied to a business? Especially one as batshit crazy as Nectome?

Co-founder Robert McIntyre says:

Right now, when a generation of people die, we lose all their collective wisdom.

If only there was some way that people could preserve what they thought about things... then we could know what Artistotle thought about stuff. Oh, wait, we do, it’s called, “writing.”

I can’t remember the last time I saw a business so exploitative and vile. And in this day and age, that’s saying something.

Related posts

Overselling the connectome
Brainbrawl! The Connectome review
Brainbrawl round-up

External links

A startup is pitching a mind-uploading service that is “100 percent fatal”

How many learning objectives?

I am teaching an online course this semester, and I had to undergo training and review of the class before it ran. In preparing it, one of the key things that the instructions stressed was the importance of having learning objectives.

All that material gave me good insight into how to write a single leaning objective, there was almost nothing about how to put them all together.
And right now I’m struggling with what a good number of learning objectives is. But so far, the only direct answer I’ve seen to that is:

How many learning outcomes should I have?
This is tied to the length and weight of the course
How many learning objectives should I have?
This is tied to the number of learning outcomes.

You’re not helping.

Most courses track lessons in some standard unit of time. A day. A week. Surely there has to be some sort of thinking about what a reasonable number of learning objectives is for a given unit of time. It’s probably not out of line for me to guess that one hundred learning objectives in a single day would be too much. On the other hand, a single learning objective for a week might be too low.

Right now, I have some weeks that have ten or more learning objectives. I’m wondering if that’s too much. And I’m just lost. I have no way of knowing.

It might sound it’s just a matter of looking at student performance and adjusting as you go. But in a completely online course, it is so hard to adjust. You have to prepare almost everything in advance, and you can’t easily go faster or slower in the way that you can when you meet students in person.

I’m not sure how much student feedback will help, because everyone’s tendency is probably to say, “Yes, give me fewer objectives so I have more time to master each one.” And sometimes students aren’t good at assessing what they need to learn.

Maybe this is a gap in the education literature that needs filling.

Picture from here.

12 March 2018

How anonymous is “anonymous” in peer review?

Last time, I was musing about the consequences of signing or not signing reviews of journal articles. But I got wondering just how often people sabotage their own anonymity.

As journals have moved to online submission and review management systems, it’s become standard for people to be able to download Word or PDF versions of the article they are reviewing.

The last article I reviewed was something like 50 manuscript pages. There was no way I was going to write out each comment as "Page 30, paragraph 2, line 3," and make a comment. I made comments using the Word review feature. And all my comments had my initials.

As more software uses cloud storage for automatic saving features, more software packages are asking people to create accounts, and saving that identifying information along with documents. Word alerts you with your initials, but Acrobat Reader's comment balloons are little more subtle.

Ross Mounce and Mike Fowler confirmed that this happens:

Yep. Metadata tags are great. 😀 Even simply the language setting can be a giveaway: Austrian English is a huge clue in a small field [real, recent example!]. "Blind" peer review is not always effective...

Having wondered how often authors do this, I wonder if editorial staff ever check to make sure reviewers don’t accidentally out themselves.

Picture from here.

03 March 2018

Signing reviews, 2018

Seen on Twitter, two days apart.

First, Kay Tye:

Dear everyone! You don’t need to wonder if I reviewed your paper anymore. I now sign ALL of my reviews.
Inspired by @pollyp1 who does this and I asked her why and she said “I decided to be ethical.” I do it to promote transparency, accountability and fairness. #openscience

I particularly noted this reply from Leslie Vosshall: (the “@pollyp1” mentioned in the prior tweet).

Open peer review would instantly end the dangerous game of “guess the reviewer.” This happens all the time with senior people guessing that some junior person trashed their paper and then holding grudges. But usually they guess wrong and inadvertently damage innocents.

Second, one day later, Tim Mosca:

Since becoming an assistant prof, I’ve reviewed ~ 12 papers. Signed one. Received a phone call from the senior (tenured) author asking, “Who do you think you are to make anything less than glowing comments?” So there are still dangers for young, non-tenured profs when reviewing.

The threads arising from these tweets are well worth perusing.

I’ve signed many reviews for a long time, and nothing bad has happened. I used to be much more in favour of everyone signing reviews, but long discussions about the value of pseudonyms on blogs, plus the ample opportunity to see people behaving badly on social media, significantly altered my views. But the problem is that everyone will remember a single bad story, and not pay attention to the many times where someone signed a review and everything was fine. Or cases where something positive came out of signing peer reviews.

How can we weigh the pros of transparency with the cons of abuse? I don’t know where that balance is, but I think there has to a some kind of balance. But the underlying issue here is not signing reviews, but that people feel they can be vindictive assholes. Univeristies do not do enough to address that kind of poor professional behaviour.

19 February 2018

Once around the earth

Gordon Pennycook asked how far people have moved in pursuit of their academic careers. I’d never added it up before. I found an online distance calculator, and off I went.

From my high school town of Pincher Creek, Alberta to the University of Lethbridge for my bachelor’s degree: 100 km

From Lethbridge to the University of Victoria for my graduate work: 1,268 km (driving)

From Victoria to Montreal for my first post-doc: 4,732 km (driving)

From Montreal to Melbourne, Australia for my second post-doc: 16,755 km

From Melbourne to Pincher Creek, for a brief period of unemployment: 13,874 km

From Pincher Creek to Edinburg, Texas to start my tenure-track position: 3,476 km

And from Edinburg to an undisclosed location, where I am on leave: 3,090 km

Grand total: 45,295 km! For comparison, the circumference of the Earth is 40,075 km.

You may now judge me on my carbon footprint. I would hate to start adding in the miles for conferences on top of that.

06 February 2018

Tuesday Crustie: Know your Lamingtons

Canada has butter tarts. Australia has lamingtons.

But because Autralia is the lucky country, it not only has lamingtons as dessert, but Lamington as a bad ass crayfish:

I loved this description (my emphasis):

One of Australia's most unusual creatures, the Lamington spiny crayfish, lives there and has been known to startle bushwalkers by confronting them in battle stance, clicking claws and warning hiss.

It’s like this crayfish is trying to live up to this description of Australia from Douglas Adams:

Australia is like Jack Nicholson. It comes right up to you and laughs very hard in your face in a highly threatening and engaging manner.

External links

Feisty crayfish surprise in rainforest

Dessert pic from here; crayfish pic from here.