Can Tamiflu prevent the Flu?

Just watched a supposedly competent pharmacists mocking the people trying to prevent swine flu by taking Tamiflu. Apparently many are buying Tamiflu from spammers and dubious online pharmacies for sometimes exorbitant prices. These unwashed masses, however, are right and many of the so-called “experts” on TV are wrong. Tamiflu (Oseltamivir) and Zanamivir, another antiviral, can be used for prophylaxis, see for example here or here.

Being right doesn’t mean that those people aren’t idiots. Unless you’re in Mexico or treating infected people, you’re still very unlikely to be exposed to the new virus. And if you’re in a developed country it’s probably better to get infected now than later, when the virus could have mutated and become more harmful, medical supplies have been exhausted and hospitals are overwhelmed. Get swine flu right now and you’ll see a Nobel Prize reunion happening at your bedside plus immunity for the rest of your life.

The Heilbronn DNA Mixup

I wish I’d written earlier about this to appear really smart. Anyway, here’s the backstory: DNA traces of an unknown eastern-European woman had been found at almost

The Culprit

17 crime scenes, including two murders (including a 22 year old police officer) but also car jackings, unprofessional break-ins and on a bullet fired in a marital dispute. The crimes where spread around a large area including south-west Germany, France and Switzerland.

It now turns out that the several-hundred-men task force might have really been chasing a phantom. Alarmed by the apparent randomness of the crimes, involving both highly professional work and seemingly amateur break-ins, they started checking for contaminations in the labwork. The likeliest suspect now are the cotton swabs used to collect evidence at the crime scene. All the swabs used in the forensics works were sourced from the same supplier, a company in northern Germany that employs several eastern-European women that would fit the profile. Even more inciminating, the state of Bavaria lies right in the center of the crimes’ locations, without ever finding matching DNA in crimes on its territory. Guess what: they get their cotton swabs from a different supplier.

While the suspicion had already been growing in the last few months, the smoking gun apparently was a case where they tried to match a burned (male) corpse to DNA collected from fingerprint samples an asylum-seeker had given a few months earlier. The first test showed a match between those fingerprints and the Phantom’s DNA while a second test did not.

By the way: contaminated cotton swabs aren”t as trivial to avoid as one might think. It’s relatively easy to sterilize cotton to prevent infections. Forensics however require a complete destruction or removal of any DNA contamination, which is apparently a lot harder.

Shooting mosquitos with lasers

Ever since I read a job posting regarding tracking bees with a radar I have dreamt about combining a system like that with a laser to automatically (or manually for extra fun) shoot mosquitos. It seems I’ve not been the first nor the last person to have that idea. While I quickly learnt that the bees in that project were equipped with radar-reflecting material, I found an old post at some brainstorming website that discussed a system using three microphones to triangulate a mosquito’s position. Now a similar idea has made the Wall Street Journal’s frontpage. Wood and Kare are testing system that currently uses image recognition to locate the bugs. Using radar is also discussed in that article, so it seems that radar actually has at least the theoretical ability to track a single mosquito. Must be fun to get paid to work on a project like that.

More on pyMOL

The people from pyMOL responded to my last post, where I made a comment that DeLano is “heavily trying to commercialize” pyMOL. I felt I should write a little more on that.

Firstly, I wasn’t really passing judgement. There’s nothing wrong with commercial software, I’ve written enough of that myself. Nor is there anything wrong with soliciting contributions to open source software projects, especially when they’re as good as pyMOL. However, looking at the pyMOL website and download page, it seems that DeLano Sc. is trying to create the impression that a subscription is necessary. There’s a list of commercially available builds and bunch of ways to get inferior or education-only versions. The source download is right there at the bottom, but I somehow missed that when I first went to the site and I know of at least two other people who where also confused. All the options are obvious now, but it is a bit misleading for a first-time user.

I guess it’s the old problem of how to get people to contribute to open source project, and the approach is much like MySQL’s. I’m not sure how useful it is, though. A student using pyMOL once or twice for assignments is not going to pay for it anyway. Any researcher or institution, OTOH, will learn quickly that there’s a OSS version available. They’re used to open source, so there shouldn’t be much corporate red tape that can be avoided with buying commercially, nor will they afraid of compiling it themselves or require much support. The actual value of a subscription is therefore quite low, and many will just choose to pay to support the project.

There is, then, not much use in misleading people into thinking the OSS version is inferior, or hiding it below a long list of commercial options. There’s nothing wrong with asking people for a little goodwill, and many will happily do so especially when it’s not their own budget. I just wished DeLano where a bit more open about it.

Update: the response by pyMOL below is worth reading.

Measuring Angles in PyMOL

PyMOL is probably one the coolest molecular visualization tools there are, but the interface is sometimes a little awkward. This is how to measure a bond angle in PyMOL:

1. Select Wizard -> Measurement from the main menu
2. (This is the non-obviousness) The headline “Distance” in the toolbox in the lower right-hand corner is actually a dropdown. Click on it and select “angle” or “dihedral”.
3. Click on any three (four for dihedrals) atoms that define the bond you want to measure.

Additional tip: the people behind PyMOL are heavily trying to commercialize it, but free versions are available here. They call those versions “outdated”, but there’s nothing wrong with them.

Neurogenesis Basics

As I wrote Sunday, neurogenesis is the process by which neurons are created. So let’s start with those.

Neurons and Glia

Rat Neurons (Image: Dmitry Sarkisov@flickr)

A neuron is basically a cell that can conduct an electric signal, and therefore information. There are about 10¹¹ (100 billion) neurons in the average human brain¹, each of which can have thousands of connections to other neurons. While a single neuron’s activity is simple (it either fires its action potential or not), the connections are not. It might require activation by two or more different incoming neurons with a certain timing for a neuron to fire. Neurons can also depress each others activity, so if neuron A fires, neuron B will remain silent, even if it is excited. These connections are though to be the critical factor in allowing the complexity we see in human and even animal behavior to emerge from a rather simple basic building block, the neuron.

There is another type of cell in your brain that deserves mention, called glia. Outnumbering neurons 10 to 1², glia cells have traditionally been thought of as the brain’s maintenance brigade, providing structural support, nutrition and immune defenses. In recent years, there is growing support for assigning glia a more important role in the CNS, as interactions between glia and neurons have been found³

Now to neurogenesis. Obviously a large amount of neurons (a complete brain) are created even before birth. I might revisit pre-natal neurogenesis at a later point⁴, but for now, when I use the term neurogenesis, I’m talking about adult neurogenesis.

Adult Neurogenesis

Adult Neurogenesis in humans is, like continental drift and epigenetics, a relatively new concept. Consensus until 1998 was a fixed amount of neurons that could only be lost, never gained. Though it is a relatively new proposition, adult neurogenesis is now widely accepted and the evidence is strong. When my previous article hit Hacker News⁵ a user called a-priori was skeptical:

Let me be the first to say, “sources please”. Adult neurogenesis in humans is largely speculative, which leads me to think you’re confusing it with neuroplasticity.[..]⁶

It is important to continually challenge scientific theories, and it’s even more important not to take “but the majority believes it” as definite proof. So let’s take a look at the evidence. The standard method to detect and measure neurogenesis uses a substance called Bromodeoxyuridine

BrdU-Labeled Cells in the Human Brain (Image: Peter S. Eriksson)

or BrdU. It’s a molecule that closely resembles Thymidine, the T in the ACGT alphabet DNA is written in. When cells divide, they copy their DNA. If there’s BrdU around (i. e. if an evil scientist has injected it), it will be incorporated into the newly synthesized DNA. When the animal dies, new cells contain BrdU that can be colored so they show up clearly under a microscope. The image shows a slice of human brain tissue with three BrdU-labeled cells. These cells must have been created after the BrdU injections.

While the decades-old dogma that adult neurogenesis does not exist in humans was overturned should caution us not to blindly accept the new, reversed dogma, this evidence is much stronger than before (“I cannot find my wallet” does not proof that my wallet does not exist, while “I have my wallet in my hand” is pretty good evidence that the wallet does exist).

Adult neurogenesis was first shown in canaries by Goldman and Nottebohm⁷ It took until 1998 before it was shown in humans⁸ . So adult neurogenesis in humans exists. The next questions will be where in the brain it is located, what goes on in those regions and what effects neurogenesis actually has.

1. Wikipedia: Brain [↩]
2. Society for Neuroscience [↩]
3. Haydon P: Glia: listening and taking to the synapse, Nature Reviews Neuroscience 2001 [↩]
4. at least some of the ideas I’ll be talking about should also be applicable in pre-natal neurogenesis, such as anything regarding substance abuse [↩]
5. http://news.ycombinator.com/item?id=397537 [↩]
6. http://news.ycombinator.com/item?id=397628 [↩]
7. Goldman et al. … Production, Migration, and Differentiation in a Vocal Control Nucleus of the Adult Female Canary …. Proceedings of the National Academy of Sciences (1983) [↩]
8. Eriksson et al. Neurogenesis in the adult human hippocampus. Nature Medicine (1998) [↩]

15 square inches of fame?

It’s interesting how doing something just mildly good and putting it on the internet can take on its own life. When Obama made his famous appearance in Berlin last summer, I took a bunch of photos. Not only has the one below been used in Wikipedia and other publications around the net, now Time Magazine actually sent an email asking for permission to print it.

Barack Obama in Berlin