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Biology

A Romantic, Maybe too Romantic, Scientist

In the Hatena story about symbiosis, I posted the following picture drawn by Ernst Haeckel: Beautiful!  In this day and age of imaging, high resolution photography, and molecular graphics, we forget that scientific drawing was a skill as necessary to life scientists  as microscopic imaging, or molecular graphics is today.  Indeed, biology was very much […]

From predator to plant in one gulp

The story of a predator that, upon eating a certain food, suddenly becomes a peaceful plant. Sort of. Free-living versus symbiotic A working definition for symbiosis is two or more species that live and interact. Mutualism means that each derives a certain benefit from the other, or at most causing no harm to each other. […]

The Incredible Shrinking Genome

Mass Extinctions and Genomics The geological signs for mass extinctions are very distinct: the photo shows the boundary of the Cretaceous-Tertiary KT extinction that happened ~65 million years ago (Mya), and killed some 70% of the species on Earth, most famously the dinosaurs. This was the last mass extinction, and its effects on Earth’s life […]

(Not Only) Microblogging ISMB 2009

Intelligent Systems in Molecular Biology (ISMB) is a large international gathering of  computational biologists, mostly from the bioinformatics side: genomics, structural bioinformatics, computational genomics, etc. This year there is a friendfeed room for microblogging ISMB 2009. So if you are not in Stockholm, or also if you are, look it up. Most of the microbloggers […]

Yeah, yeah, the flu virus

Since the Swine Influenza Media and Blogging Pandemic has died for now, I think I can finally write about ‘flu myself.  A quick aside: until I was about 15, I thought that the word Influenza came from the Arabic “Inf-Il-enza” meaning “goat’s nose”, which it is a bit runny, like a dog’s, or like someone […]

Hamburgers are pathological

From Annals of Diagnostic Pathology. This is what happens when you bring a pathologist to a fast food joint. Hat tip to Laura for pointing this out. Here were my initial thoughts about these findings. “Bleaaachhhh!” (I’m very verbal when reading scientific papers). Well, it looks bad.. but. But. Cooked ground beef can have up […]

Da Vinci, F0-F1 ATPase: a copyright-driven Update

Harvard University has removed from YouTube the video I embedded  in my Leonardo Da Vinci and the F0-F1 ATPase post, due to copyright concerns. It is a pity. I believe the main sufferer from this step is the lab that actually created this video, and now has one outlet less to publicize its work. One […]

Blood, sweat and spit

A short follow up to the previous post on latherin. A quick reminder: latherin is a protein that exists in the horse’s sweat and saliva. In the sweat, latherin acts like a detergent, wetting the horse’s coat to allow for better water evaporation and hence better cooling. In the saliva, it helps wet the horse’s […]

Glowing like a horse

Dennis Mitchell: “Margaret, you are all sweaty” Margaret Wade: “Dennis, girls don’t sweat. Horses sweat, boys perspire and girls glow” Dennis Mitchell: “Margaret, you are glowing like a horse”.                               — Dennis the Menace / Hank Ketcham Horses and humans sweat but most other mammals do not. Sweating lowers the body’s surface temperature by evaporating […]

Skin Flick 2: Statistic Boogaloo

Reports on the first metagenomic survey of skin bacteria (see my previous post) did not go unnoticed by the popular media. Reports appear in US News & world Report, LA Times, Times of India, National Geographic, and Scientific American. All these articles have one thing in common: they are wrong. Yes, even Scientific American. All […]

Short bioinformatics hacks, ch. 2: chunk it.

First, a non-bioinformatic one liner, which is very relevant to most of us working on 3 different machines simultaneously, not including the 80 in our cluster. ssh-ing and giving your password each time is painful, and makes it almost impossible to do scripted file transfers, like backups. A good solution is shared key ssh in […]

Skin flick

Interesting report in Science today about the human skin metagenome. The skin is a fairly large organ, and it is home to an estimated 1012 bacteria. It is the first barrier our body poses against pathogens, toxins, and sarcastic comments.  An adult’s skin area is about 2m2, virtually all of it exposed to the outside […]

Leonardo Da Vinci and the F0-F1 ATPase

Offspring #2 (O2) and I  spent last weekend visiting the Da Vinci Experience exhibit at San Diego’s Air & Space Museum. The exhibit is engineer’s heaven: large wood models based on and inspired by LDV’s drawings. Gears, crankshafts, pulleys. O2 was interested in the military stuff:  catapults, the tank , a mobile bridge. I did […]

Short Bioinformatics Hacks, ch. 1

In any programming gig, and that includes bioinformatics, a lot of repeat scriptology comes cropping up. I decided to share some of that, pro publico bono, and also because I hope to start some sort of ongoing cookbook  for short bioinformatics hacks. If you have any cool short scripts you like to share, please email […]

Light for Cellular Communication?

Don’t you know We’re all light Yeah, I read that someplace –XTC This is interesting: an article in PLoS ONE that claims that Paramecia can communicate using light. The author, Daniel Fels from the Swiss Tropical Institute in Basel, separated two Paramecia populations using quartz or glass vials, grew them in the dark, and checked […]