Podcasting lectures works

New Scientist reports that students who listen to lecture podcasts can do better than those who actually sit their butts in seats for class. But there's an important qualifier...

Students who downloaded the podcast averaged a C (71 out of 100) on the test – substantially better than those who attended the lecture, who on average mustered only a D (62).

But that difference vanished among students who watched the podcast but did not take notes. Students who listened to the podcast one or more times and took notes had an average score of 77, McKinney says.

As always, much replies on the students. The authors note that with the podcasts alone, some -- in fact, most -- of the students listened to the podcast more than once. So what may be going on here is, in part, a simple repetition effect. You have more opportunities to learn something if you are exposed to it more thane once.

The original paper is here.

NSF's on Twitter!?

I didn't expect this. A Twitter feed from a government research agency? Seriously? I had been reading about how some companies were trying to use Twitter and mostly failing with Twitter as they had with almost all social networking, so this caught me off-guard.

Do male crickets shorten the lives of female crickets?

One of the deep insights from evolutionary thinking in the fields of ethology, animal behaviour, behavioural ecology, and sociobiology is that males and females often have distinctly different best interests when in comes to reproduction. Now, it’s very easy to made wild extrapolations about this, particularly regarding humans, but there are many examples of the general principle. Of course, when you're looking at any individual case, the devil is always in the details.

This paper, by Green and Tregenza, looks at whether male crickets (Gryllus bimiculatus; sometimes known as “bimac” in cricket labs) manipulate female crickets by transferring special seminal proteins along with sperm when the copulate. The underlying idea is that it is in the best interest of the male for the female not to mate with other males, because this would cut into the first male’s reproductive success. Thus, a male that can change a female’s behaviour or attractiveness or what have you so that she is less likely to mate would have an evolutionary advantage.

Green and Tregenza test this idea by taking spermatophores from several male crickets and making a liquid that they injected into the females. As a control, they injected a different group of females using a physiological saline (water and a few salts that are similar to that inside the cricket).

One of the potential shortcomings of this study is that these were not delivered into the reproductive tract, which obviously would be the case with actual mating, but into the abdomen directly. On the one hand, this is clearly not a natural situation. On the other hand, it does help test whether any effects are due to the physical act of mating rather than actual chemical signals.

The authors find that there are two main effects. Females injected with the mix of seminal proteins walk forward less, and they have shorter lives. The females in both conditions lay about the same number of eggs. Green and Tregenza also looked at other factors, like responses to male song, but found no significant differences. From this, they conclude that the seminal proteins are having manipulative effects on the females.

The discussion does talk about the suggestion that the injection of chemicals is causing a general immune response, but they downplay this, saying that they would have expected to see a greater decline in female’s orientation if there was a general immune response. But it seems a fairly frail argument. This experiment could have made its case much more strongly by adding one more control group.

Imagine that you have the hypothesis that the secret ingredient in a particular cola flavoured soft drink – let’s call that secret ingredient, say, 7X – causes burping. So you give one group of people glasses of water to drink, and one group the one brand of soft drink. The latter burps more. You thus conclude that 7X causes burping, right? Not so fast!

A soft drink is a complex concoction of carbonation, sugars, and flavourings. Water is not. What you would really want as a control is a soft drink with everything but 7X, either instead of, or in addition to, water.

In this paper, a complex protein mixture is being compared to a physiological saline. The implication is that the effects are due to particular proteins generated by the males that function to manipulate the females. But it may be that this is simply an effect of injecting a complex mixture of proteins, and there is no protein specific to males that is having this effect. A second control containing proteins unrelated to crickets, like bovine serum albumin (BSA), would help to sort this out this possibility. Or, use seminal proteins from a distantly related cricket species. If this was really a case of sexual manipulation, you would predict that only the proteins from the same species would have a significant effect.

Reference

Kelly Green, Tom Tregenza (2009). The influence of male ejaculates on female mate search behaviour, oviposition and longevity in crickets Animal Behaviour DOI: 10.1016/j.anbehav.2008.12.017

Which companion are you?

Dagnabit, I just can't resist quizzes like this one...

Connectome comment

PLoS Biology has published a comment from me about the paper, "The Interscutularis Muscle Connectome." This is the same paper I recently discussed here.

Shadow life and "less than inevitable"

This story in The Age predicts that we'll have evidence of life on other planets within four years. But, the argument goes, we probably won't find anyone to talk to, according to Alan Boss:

"Whether the life we find is intelligent is, however, less than inevitable. Intelligent life seems to be fleeting. In terms of the universe it only exists for a fraction of time."

Boss was apparently speaking at AAAS, as was Paul Davies, who coins the interesting term "shadow life" (analogous to a shadow cabinet, I suppose). Davies suggests that that there may be life here on Earth that evolved independently of all the life we already know. Certainly we've seen life living in places nobody expected, but so far, it all seems related. It'll be a tough haul to look. I wouldn't want to be the one writing the grant proposal.

"I seek funding to travel to the most extreme reaches of the planet to look for something that might not exist and that we might not recognize even if it does."

If shadow life exists, it would, like life on Mars, weaken the prospects for the search for extraterrestrial intelligence (SETI), since it either would show that the origin of life does not inevitable lead to the formation of a highly intelligence species capable of using advanced technology.

How geeky am I?

+++ Total Geek......................................≥25%

I scored 33.72781... very close to a major geek.

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Geek Test Results
You are 60% geeky.

Not bad. Maybe you spend a little too much time with your computer, but at least you have friends. You do have friends, right?

The current average score is: 32.15%

Fact: 20.15% of people who took this test claim to have attempted to build a robot.

---

68% Geek

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Your result for The How Geeky Are You? Test...

The Geekiest

Congratulations! You scored 82% on dorkpoints, higher than 95% of your peers.!

You're the nerdliest of the nerdy. The dorkiest of the dorky! You make other geeks tremble in your prescence! See you at the next convention!

Take The How Geeky Are You? Test

What would Darwin think?

There's been a tremendous amount of good stuff about Charles Darwin this week in honor of the 200^th anniversary of his birth. That said, there's been one frequent question interviewers have been posing that I want to take on.

"What would Darwin think about... the interest in his birthday / his theory / the current state of biology / etc.?"

This is always a question I've disliked, because the whole point of deep thinkers is that they came up with answers that surprise you. Plus, almost every answer I've heard has said something like, "Oooh, I'm sure he'd be very pleased / excited / interested." Frankly, those answers seem just a bit too pat and easy.

Since nobody really knows what Darwin would have thought about current biology, let me suggest some alternate ideas...

Darwin, a naturalist to the core, would be horrified by how few biologists are engaged in observing the natural world. He might be highly critical of biologists working in labs with, say, cell lines who no appreciation of the organisms they originated from.

Darwin, fortunate to be independently wealthy, would be shocked at how contemporary scientists are forced to work on a thousand tasks at once. Darwin could speak about the importance of uninterrupted time in developing ideas, and might be convinced this would be a superior method of inquiry over doing grant writing, teaching, grant writing, revising manuscripts, sitting on administrative committees, and grant writing.

Darwin, by all accounts quite shy, would be embarrassed by the amount of attention he is receiving. He probably be the first to give credit to the many other researchers who have contributed to evolutionary biology.

Finally, Darwin might well be saddened that arguments he had during his lifetime, and which, in many cases, he correctly answered in his own writing, are still viewed as serious problems, instead of being matters that have been settled ten times over.

Setting the bar low

Gail Patricelli is quoted in New Scientist as saying:

The males are trying to copulate with cow pies all day.

This from an article about courting birds.

And on that thought, happy Valentine's Day.

Muscle innervation is not a connectome

Since the word "genome" entered the lexicon, mainly on the heels of the Human Genome Project, there has been no shortage of people trying to cash in on the idea of "-omes." The idea is that an "-ome" is a complete catalogue of all... something. So we have budding fields like proteomics (all the proteins in an organism), and, in my own field, neuromics (all the neurons in an organism) and now, connectomics (all the neural connections in an organism).

Lu and colleagues purport to have a connectome. That's what the title says, after all. This is, unfortunately, misleading. This is innervation of one muscle. It's detailed, yes, but it's no more a "connectome" than sequencing one gene is a "genome." I suppose, though, that "Motor innervation patterns of the interscutularis muscle" is less likely to land you a spot in a high-profile journal than a title using, "connectome."

Putting my irritation with the unwarranted title aside... what's to learn here?

The authors used a genetically modified mouse that expressed a fluorescent protein in all its motor neurons. Then, they used confocal microscopy techniques to reconstruct the paths of multiple motor neurons leading to a small muscle in the head. Neither of these techniques are particularly groundbreaking in principle, but there's no doubt that achieving this level of high detail would have required a lot of patience. From there, there's lots of math and models, but it boils down just to looking closely at what they saw.

The authors summarize their main findings as these.

The more muscle fibres a neuron innervates, the bigger the twitch. Although this is presented as a conclusion, the authors didn't actually measure twitch generated by muscles in this paper, so there is still more physiology.

The bigger the neuron, the more muscle fibres it innervates. Not a huge surprise, considering that there will be more demands to create and transport chemicals to the tips of the nerves if there are more synapse.

Every motor neuron follows its own unique path, and it's often a path loaded with detours. This speaks to the development of muscle innervation being quite loosely controlled. Again, no big surprises, as there'd been a reasonable amount of evidence showing that axon guidance is something that tracks (say) chemical gradients, rather than any sort of precise pathfinding or lock and key mechanism.

Perhaps surprisingly, it's probably going to take a long time before these methods are successfully applied to many invertebrate species, particularly arthropods. Although invertebrates have fewer neurons, the way they connect to muscles is much more complicated.

Reference

Ju Lu, Juan Carlos Tapia, Olivia L. White, Jeff W. Lichtman (2009). The Interscutularis Muscle Connectome PLoS Biology, 7 (2) DOI: 10.1371/journal.pbio.1000032

361

Scientific American reports on a recent paper estimating the number of stable extraterrestrial civilizations in our galaxy.

361.

More or less.

I previously wrote about the probability of intelligence evolving. On this and related biological points, Forgan says, "The model now enters the realm of essentially pure conjecture..." Which is typical research publication speak for, "We have no idea. None whatsoever."

Trying to make the Texas State Board of Education accountable

In the Houston Chronicle, two Texas state representatives describe legislation intended to put in some periodic reviews of the Texas State Board of Education.

As scientists and educators across Texas and the nation mark the 200th birthday of Charles Darwin with calls for a renewed commitment to science education, the State Board of Education continues to engage in narrow theological debate about the validity of evolution. ...

To ensure that the SBOE works as it should, we have filed legislation to place the board under periodic review by the Sunset Advisory Commission and hold them accountable for their performance, just as we do the Texas Education Agency and other state agencies.

The decisions of the SBOE not only impact millions of young lives on a daily basis, but impact the economic progress of our state as well.

For these reasons and many others, the public has a right to full disclosure and oversight.

The board has escaped such scrutiny for far too long. The disregard for educators, instructional experts and scientists can’t continue.

Good luck, then. You'll need it.

In praise of evolutionary trees: a personal gallery

Charles Darwin's On the Origin of Species By Means of Natural Selection contains exactly one picture (here).

It's an evolutionary tree, a visual depiction of relationships between organisms. Such a relationship is now known a phylogeny, a word that Darwin coined. The point Darwin is trying to make with it is not the one that most people associate with evolutionary trees; Darwin was trying to emphasize what he called his Principle of Divergence. Nevertheless, trees have become more broadly representative of the entire evolutionary enterprise.

In that vein, and because variation is a key theme of evolution, I thought I would present the trees I've published in my research papers, with some commentary, for Darwin Day. I don't pretend that my trees are anywhere near as impressive as, say, David Hillis's massive, beautiful supertrees, but I present them here nonetheless.

There are two scientific stories being told here. One is about digging (figures 1, 2, 3, 4 and 6), and the other is about escape responses (figures 5, 7, and 8). I've grouped them in chronological order, however.

Figure 1.


This figure represents, well, bafflement. Not on my part, but on the part of the taxonomists. At the time, carcinologist Fred Schram memorably described the phylogeny of this group (Reptantia) as a "morass." Nobody had much of an idea of who was related to what, so instead of nice two way splits... a five way free-for-all. Original dissertation here (be warned, it's big!).

Figure 2.


This tree is nice and simple, and lends itself to using diagonal lines. Original paper here.

Figure 3.


This tree is considerably more complex. I'm trying not only to show the taxonomic groupings, but key features. The angle of the diagonal lines isn't terribly aesthetically pleasing to me, but I was trying to make the figure as compact as possible. Original paper here.

Figure 4.


Getting featured on the cover is always a nice ego boost. On this one, there's an ancestor nestled at the bottom of the tree, the earliest known decapod crustacean. Original paper here.

When I showed this figure to the editor, Glenn Northcutt, when he was visiting our campus, he asked, "Why are the animals pointing to the right?" He explained that in vertebrate anatomy, there was a long tradition of the anterior always being to the left. I'm pleased he published the figure anyway. Still...

Figure 5.


You'll notice everything facing left from here on in.

This one has even more species, with various traits in the branches. It was just easier to make straight lines instead of diagonals. Original paper here.

Figure 6.


That this one is back to diagonals is indicative of how long that paper sat waiting for me to revise and put it into the hands of editors! It was actually created well before the one above. Original paper here.

Figure 7.


Similar to the one before last, I think this one offers a few improvements in presentation. More of the taxa names are properly aligned, for starters. This and the cover are probably my two best looking trees. Original paper here.

Figure 8.


These two trees were the most complicated I've had to make yet. I was trying to show more groups of animals and more features. The size of this thing meant that I had to "chop the tree down" and show it horizontally, and that I couldn't show little icons of the animals, as I had done before. I really like putting in the pictures, because in some of my papers, they're about the only indication of what the organism looks like! But there was no possibility to do that and have any hope that the thing would fit on the page.

The other thing I like about this is that it shows that a tree is really an hypothesis. There are two trees, because there are two major competing hypotheses. There are similarities between them, and it turns out that both of them give the same "punch line" for my story anyway, which is multiple, repeated losses of certain neurons. Original paper here.

One thing I'm rather pleased with is that I've never re-used a tree. I've always redrawn them, always trying to look at each one afresh and make decisions appropriate for that tree. I hope these trees give a glimpse of the importance of evolutionary thinking in the research that I do.

Charles Darwin's first evolutionary tree (pictured) was not the first -- that honour lies with Jean-Baptiste Lamarck. nor was he the first to make the creation of trees rigorous and following explicit, testable rules -- that distinction lies with Willi Hennig. Nevertheless, I think we should celebrate evolutionary trees as part of Darwin Day because they represent one of the most important elements that Darwin brought to biology: history. Or maybe "deep time" is a better term.

Organisms have a past, and that past matters. That ancestry helps explain features of organisms that may otherwise be inexplicable, and it gives us a way to make predictions about organisms that we have not yet studied.

Perhaps more importantly, trees remind us that life is ancient. Organisms have been engaged in the struggle for existence on this planet a long, long time. Even the two centuries since Darwin's birth is a paltry handful of heartbeats in evolutionary time.

Before I go, I have one last tree. I did not create this one; I am grateful to Neurotree for this information. Since today is Darwin Day, an event that bills itself as a celebration of science and humanity, let me add in some personal connections. It's a reminder that the scientific community is, from a certain point of view, very small.

Figure 9.

8 Steps:

Zen Faulkes (The University of Texas-Pan American)
was a post-doc for

|

David L. Macmillan (University of Melbourne)
who was a grad student for

|

Graham Hoyle (University of Oregon)
who was a research assistant for

|

Bernard Katz (University College London)
who was a post-doc for

|

John Carew Eccles (Australian National University)
who was a grad student for

|

Charles Scott Sherrington (University of Oxford)
who was a post-doc for

|

Michael Foster (University of Cambridge)
who was a grad student for

|

Thomas Henry Huxley
who was a collaborator, friend and colleague of

|

Charles Robert Darwin (Independent)

Darwin created the foundation for evolutionary biology; Huxley created the biological curriculum for universities of his day; Michael Foster was a pioneer in physiology; Sherrington stood at the precipice between general physiology and neurobiology; Eccles, then Katz, strode into neurobiology; Hoyle stepped into the realm of invertebrate neuroethology using insects; Macmillan, while still a neuroethologist, preferred crustaceans as subjects; and I try to follow as best I can.

Descent with modification, indeed.

Research paper title of the moment

How could you not click a link to read a paper with this title?

Martinez-Solano I, Lawson R. 2009. Escape to Alcatraz: evolutionary history of slender salamanders (Batrachoseps) on the islands of San Francisco Bay. BMC Evolutionary Biology 9: 38. doi:10.1186/1471-2148-9-38

Love the title, but the ideas in the paper seem pretty interesting, too. The idea is that the salamanders were on the islands before they were islands! They were inhabiting hilltops when the water level was lower, then got stuck as rising water levels turned hilltops into islands.

Putting food on the table, science style

Stephen Quake, subbing in for Olivia Judson, has a superb column in the New York Times detailing how science currently runs: tax money and the very occasional private foundation.

For instance...

It strikes me as one of the ironies of modern life that professorial faculty... accept such a brutal free-market approach to their livelihood. If they can’t raise grants to support their research every year, they won’t get paid. So not only do they have to worry about publish or perish, it’s also funding or famine, in the very real sense that without a grant there might not be food on the family dinner table!

Fortunately, I am in a position where my base is not dependent on my getting grants. But let me add that there's a spillover effect. I have a grant for undergraduate researchers. I have the potential to have a big impact on the pay going to a set of students. And being responsible to bring in money for other people is also pretty stressful.

Google takes on journals?

The reaction to this will be interesting... At first glance, it looks like Google is firing a shot across the bow at, oh... pretty much every scientific research journal.

As long as big journals provide a useful service, this tool will only enhance their effectiveness. But the more they take months to review our publications, and the more they give unqualified reviews, and the more they force us to clear irrelevant hurdles prior to publication, and the more they lock up our works behind fees and copyright transfers, the more this tool will provide an alternative to their services.

Update, 14 August 2014:After years of silence, Wired has an article that picks up this thread as a rumour.

Google is allegedly working on a free, open access platform for the research, collaboration and publishing of peer-reviewed scientific journals.

Blog swarm!

I have never heard of the concept of a blog swarm before, but I'm in! The Blog For Darwin project caught my attention, and I'm planning on participating... come back Thursday!

Quotes that scientists hate: Part 1

Mark Twain blamed Benjamin Disraeli, but, as far as I can find, nobody has found when Disraeli said:

"There are three kinds of lies: lies, damned lies and statistics."

I hate that quote. Or, to be more accurate, I love its humour, but I hate how it gets brandished around like a club.

I was reading about possible lottery fraud, and this comment popped out at me:

Statistics can be shown to mean whatever they want.

Whenever someone wants to dispute a finding that relies on numbers, Twain's quote is never far from the surface. People bring it out as though it were some logical proof or eternal verité, instead of being a punch line.

For the non-scientist, numbers are slippery, unpredictable and untrustworthy things. You can't look them in the eye. You can't question their motives.

For scientists, numbers are the real deal. You dispute the interpretation, the analysis, the experimental design, what have you... but it is highly unusual to dispute the numbers. One saying goes, "Interpretations may change, but the data should be valid forever."

Fortuitously, this article in New Scientist makes a similar point. When climate scientists say "Very likely," they are expressing a confidence that the probability is more than 90%. In comparison, nearly half of non-scientists thought the probability was less than 66%.

Such things tap into of important differences between how non-scientists and scientists approach problems.

Vestigial icons

Quick! What's the icon circled in red mean?

"Save," right?

Now, what does that icon depict?

It's a 3½" floppy disk.

When was the last time you used a 3½" floppy disk?

I'm guessing it's been about 5 years since most people have touched one.

So why is that still showing up as an icon for "save"?


I wonder how long it'll be before that 3½" floppy fades as a symbol for "save." What will replace it? Will it be a flash drive icon, or perhaps something less computer centered, like a bank vault?. I wonder if there are computer users now how recognize that it means "save," but not why it means save.

The textbook conundrum

I don’t know what to do about textbooks.

On the one hand, textbooks are obsolete. They had a very clear and useful purpose: to summarize relevant technical research, originally published in disparate technical papers piecemeal across hundreds of journals, in one place in a reasonably authoritative manner. If a student wanted to learn about the basics of a subject by reading the original papers, it would have been a phenomenally daunting task. It would take days scouring through compilations like the Zoological Record and Psychological Abstracts to find the key papers. Even then, many papers would be may have published in journals that not even all university libraries had.

Internet resources should have killed textbooks dead about five years ago.* More and more and more research papers, even quite obscure ones, can be found online. And there are specific databases and search engines devoted to scouring only those scientific sources, like Google Scholar. And the researchers themselves are making their knowledge more available online. Now, I can usually get up to speed on a topic in a couple of days – a task that used to take me weeks.

On the other hand, I hear things like this all the time:

The #1 habit successful people share with me is this: They read books to learn. They do it often and with joy. It’s cheap (or free, at the library or online) and portable and specific.

That particular riff is from Seth Godin.

Below, Chris Anderson talks about the importance of starting to read again after the .com bubble burst in 2000. (It’s about 4:50 in, but it will have more impact if you listen to the those preceding 4 minutes.) It comes up again at about 11 minutes, where Anderson says, “Books kind of saved me in the last couple of years.”



Over and over and over again: There is something valuable and important about reading. It leads to deeper, more reflective thinking. Particularly books.

So I’m completely conflicted. Students are notoriously recalcitrant to buy textbooks. They don’t see value in them (by which I don't just mean the often extreme cost). But I think they need the sort of deep thinking skills that they get from reading.

* Maybe textbooks are dead, and they’re just twitching.