cognitive science and more
cognitive science and more
Git for non-hackers pt. 1: Organizing your research one commit at a time

Version control is all the rage in academia. And when people talk about version control, they generally mean Git, which is by far the most popular version-control system. But what exactly is Git? We all want to control our versions. Especially when you have experienced versions-run-amock situations like these:


But how?!

In very simple terms, Git is a program that allows you to take snapshots of your files at a particular moment. A snapshot is called a ‘commit’. A ‘repository’ is a collection of files that are monitored by Git. If you are familiar with DropBox, there is an obvious parallel: Your DropBox folder is your repository, and DropBox automatically ‘commits’ each and every change. But Git is far more flexible and controlled.

Git has been developed by Linus Torvalds to manage the development of the Linux kernel. Managing a project as large as the Linux kernel is very complicated, and Git has lots of advanced functionality that allows people to work in parallel on the same project, without things drifting hopelessly apart. Therefore, git can be a tool for hardcore nerds. But it doesn’t need to be. Git is equally suitable for managing a simple, one-man project. And in this case, Git is very simple to use.

Can you brain-train your way to perfect eyesight?

Over the past month I’ve seen a huge increase in the number of visitors to the Gabor-patch generator on this site. A Gabor patch is a type of stimulus that psychologists like to use for experiments. It’s a pretty weird stimulus, as you can see in the example below, not really useful for anything except experimentation. So why the sudden interest? Why are thousands of people suddenly generating Gabor patches?

A Gabor patch

The rush on Gabors appears to have been triggered by a paper that appeared last month in Current Biology. In this paper, Deveau and colleagues claim that you can dramatically improve vision through repeated training on a simple visual task that uses–you guessed it!–Gabor patches. Even more remarkably, the participants in the study, who were university baseball players, even showed a marked improvement in on-field baseball performance!

Whoah! Improving your eyesight simply by looking at some weird images! If you can’t wait to get started, you can buy the training program in the form of an iPad app called ULTIMEYES Pro ®. The app, priced at a mere $5.99, is developed by Carrot Neurotechnology, a company founded by the senior author of the paper.

But wait, what’s that smell? Oh yes … It’s something fishy.


Reading with Spritz: Twice as fast, half as good?

Boston-based start-up Spritz aims for the sky with its recently announced mobile application, which, according to the developers, will drastically change the way we read. Forget about sentences, paragraphs, and layout. Spritz fires text directly at your eyes, one word at the time, at a break-neck speed. The motivation behind this presentation mode is straightforward: The eye movements that we make during reading are just a waste of time and energy. Remove these eye movements from the equation, and our reading pace easily doubles–or even quadruples–without much extra effort. With hardly any practice, anyone should be able to “spritz” at an astonishing rate of a 1000 words per minute. The prospect of devouring The Hobbit in merely one-and-a-half hour made Spritz go viral on the Internet. Even though the application is yet to be released, the world seems ready to welcome it with open arms.

But is the hype justified? Here, we take a critical look at the science behind this reading of the future.

Taking The High Road to publication: my experience with pre-prints and data sharing

Scientists should do lots of things. Just search for #openscience on Twitter. It’s buzzing with reform!

Scientists should make their papers freely available, and no longer hide them behind the paywalls that are put up by commercial publishers. They should make their datasets available, so that analyses can be independently verified. They should post their ongoing work to pre-print servers (as many from the exact sciences already do), where it can be discussed, shared, and debated without unnecessary publication delays. They should spend more time replicating each others findings. They shouldn’t care about journal impact factors, but judge quality on a per-manuscript basis, using altmetrics. And the list goes on!

Sharing can be a little scary at first. But a young generation of scientists is doing it more and more. (Source)

But despite all the buzz, actual scientific practice has hardly changed. And I’m at fault here as much as anyone. I’ve written a few blogs on the subject, but I haven’t really conducted much #openscience at all. So, with our new-years resolutions fresh in mind, my colleagues and myself decided to put our money where our mouth is, and take the ‘high road’ to what will hopefully become our next publication.

The colorful world of the Mantis shrimp

Mantis shrimp are are colorful little critters. Especially in their own eyes.

Animals are able to perceive color because the eyes contain different types of light-sensitive cells, or photoreceptors, each of which is most sensitive to a different part of the visible-light spectrum. Human eyes have three such photoreceptors, with a peak sensitivity to greenish, blueish, and reddish light. (There is also a fourth type of photoreceptor, which is used mostly for peripheral vision, and vision in darkness.) In other words, humans are trichromatic. The tri in trichromatic doesn’t mean that we perceive only three colors, but that all colors that we perceive can be reduced to a mixture of three colors (see also my post on color vision).

Most other mammals, as well as colorblind humans, have only two types of photoreceptors for color vision, and are therefore bichromatic. Most birds, on the other hand, are tetrachromatic (i.e. four photoreceptors for color vision), and therefore have a slightly more colorful visual palette than we do. But the variation between species is relatively small: Most animals have two to four types of photoreceptors for color vision. And there is good reason for this evolutionary agreement: Two to four photoreceptors are all that is needed to capture the colors that are actually present in the environment. Adding a fifth photoreceptor does relatively little to improve color vision.

Source: National Geographic

But the Mantis shrimp is a remarkable exception. This coral-reef-dwelling crustacean is endowed with 12 to 21 different types of photoreceptors! And the structure of their eyes is very peculiar as well. The upper and lower parts of the eye are typical compound-eye structures, quite similar to the eyes of most insects and other crustaceans. The remarkable part is the eye’s midband: Color vision is mediated by a horizontal band of photoreceptors in the middle of the eye. You can see this midband very clearly in the photo above.