Wednesday, February 29, 2012

The scope of your brain and your connectome

One cubic millimiter of brain tissue contains a hundred thousand (100.000) neurons. Between these 100.000 neurons there is 1 billion ( connections. In one cubic millimeter that is!!! Your brain contains millions of miles of wiring, tens of times longer than the circumference of our planet.

Sebastian Seung recently published a book called "connectome" where he lays out the hypothesis that "you are your connectome". What is connectome you ask. Your connectome is all your neurons and the connections between all of your neuron. This statement is more attractive than the statement "you are your genes" because unlike genes, your connectome changes in response to everything that happens to you. I have not looked up the numbers, but I am in no doubt that every second of your life is associated with the formation of new synapses, destruction of other synapses and change in strength of yet other synapses.

The only way this hypothesis can really be tested is by mapping the human connectome, which, according to Seung (and I agree), won't happen for a few decades at least...

In the TED lecture professor Seung presents his ideas.

By the way, the brain actually does not contain 100 billion neurons but more like 86 billion neurons. And we do not just use 10% of our brain - we use 100%!

See also: The Human Connectome Project

Tuesday, February 28, 2012

Use Google Reader to get most recent publications from specific author or journal

As a PhD student you are often overwhelmed by the huge number of science articles that are published all the time. It is simply impossible to keep up with everything that is going on even in a rather small field. According to this article in science, as many as 27.000 articles are published weekly!

In this information overload, one of the best tools you can have is google reader (or your RSS reader of choice). Pubmed (best place to search for scientific publications) allows you to generate RSS feeds based on any search that you do.

For example, one prominent researcher in my field is Christopher Yeo, at UCL in London. Whenever he publishes a new article, independent of whether it is in Science, Nature, or J.Neuroscience, I want to know it immediately. The times when you would simply browse each individual journal are gone, so how do you do it? This is how I do it. (All you need is a google account).

1. First, go to pubmed:

2. Second, search for whatever it is that you are interested in. In my case it is an author "Yeo CH", but it could also be a number of search terms, e.g. "Classical conditioning" and "Cerebellum".

3. When you get your search results, push the red button saying "RSS" just below the search bar. Choose how many items you want to be able to see (usually I just take the maximum which is 100).

4. Right click on the xml symbol and choose copy link adress. 

5. Next go to google reader:, and log in with you google username and password.

6. Press the red subscribe button in the top left corner of your reader window, paste the link adress from Pubmed and press subscribe. 

7. Now you have a list of the 100 most recent articles that match the search terms that you used - and better yet, whenever there is a new item on Pubmed that matches your search terms, this list will get automatically updated. 

Personally I have created an RSS feed for around 20 individual authors that are of particular interest to me. I have also created a feed for about 20 scientific journals that I pay extra attention to.

Below you will find pictures describing the same process.

Monday, February 27, 2012

Dead salmon sensing human emotions...(?)

As anyone who know me will testify, I am a strong proponent of the scientific method. It is quite simply the best available method we have to gain knowledge about the universe, and it has a fantastic track-record.

Theoretically, science is I think, flawless. However, science is done (mostly) by scientists, i.e. people, and we all know that people are, in general, not quite perfect. This is why scientists are so obsessed with writing out the method. Doing so means that other scientists can replicate the experiment and see if they get the same results.

One excellent replication of a scientific method was done by Bennet et. al. Bennet and his colleagues were concerned that a popular statistic method used for fMRI data actually produced statistically significant results that did not represent any real activity. fMRI, in short, is a method that that measures blood flow in the brain, which in turn, is a measure of neural activity (because brain regions with active neurons will consume more oxygen which is delivered by the blood). A statistically significant result is a result that is very unlikely to happen by chance alone.

As mentioned Bennet et al were concerned that a popular method for analyzing fMRI lead to unwarranted conclusions. To prove this he took a trip to the local market were he bought a Salmon, a dead, frozen salmon. He took this fish back to the laboratory and put it in the fMRI machine. The salmon was then shown pictures of situations depicting different emotions (e.g. anger). Bennet then used the fMRI data to see if there were differences in the dead and frozen salmon brain, depending on what type of situation it had just seen, and guess what, there was! Does this prove that dead and frozen salmon have the ability to see what type of emotion a particular situation depicts? No, of course not. Rather, the experiment is an elegant way of showing that the statistical method used lead to invalid conclusions.

See the poster, which is actually quite funny, here.

In a second example appeared in the excellent journal "Psychological Science". This article was perhaps more worrying since the the author Simmons and co-workers reached absurd conclusions using perfectly valid mathematical/statistical methods. Specifically the authors showed that when you listen to music about old age, you become younger - you don't feel younger, you actually get younger. They reached this conclusion simply by varying some decisions about the analysis, after the experiment was done, which is something I believe many scientists do. Ideally you should decide which exact tests you will use before the experiment and then stick with that analysis - if you find unexpected results these have to be checked in another experiment.

The good news is that science is self-correcting i.e. science, unlike say religion, eventually detects its own error, and it is also worth noting that in both examples above, scientists, following the scientific method, found the problems and reported them.

Thursday, February 23, 2012

The rise of antibiotic resistance and the meat industry

This post was inspired by an interview with Maryn McKenna, published by Scientific America

I think that most parent are aware of the importance of being strict with the use of antibiotics. When you have started taking it or (more likely) giving it to your child then you have to continue giving the antibiotic for the period prescribed by your doctor, even if you or your child get well before that. Why? Because you want to make sure that you kill all the bacteria. You want to do this because otherwise a few hardy bacteria that survived the antibiotics will hang around and procreate until there is a whole army of bacteria that know how to survive this type of antibiotic. In other words, if you are unlucky you will end up with a whole army of the bacterial equivalent of "William Wallace" in Braveheart.

Lesson: Finish your prescription.

However, it turns out that people's misuse of antibiotics pales in comparison to the misuse within the meat industry. An astonishing 80% of the antibiotics sold in the US are used in animals. To make things even worse, these antibiotics are not primarily used (as you would think), for sick animals but rather they are given to healthy animals in small doses at regular intervals. Now if you are really really eager to get antibiotic resistant bacteria, this is the way to do it. Why, you may ask, is antibiotics given to healthy animals. The reason is that the animal reach its goal-weight a little bit faster. That is it!

What happens then? Well, as mentioned the bacteria in these animals learn to deal with the antibiotics and become resistant. When the animal is slaughtered these bacteria frequently end up all over the meat. Commonly resistant bacteria thrives in the meat storage facilities as well. What about the meat bought in the stores? About 25% of it has antibiotic resistant bacteria on it. Usually they die when you cook it but sometimes they survive and they are becoming a major health problem, throughout the world.

Other examples of this dangerous misuse of antibiotics include over the counter, non-prescription sales of antibiotics, and non-prescription sales of antibiotics online...

For another great blog post on this, with more details, visit: