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Filling in the evolutionary blanks, genome by genome

After hearing Jonathan Eisen and Nikos Kyripdes talk about GEBA in various meetings, it is great to see the paper finally come out, and under a CC license too. Good move for everyone. GEBA is the Genomic Encyclopedia of Bacteria and Archaea. The idea is simple: we have >1000 prokaryotic genomes in GenBank as of […]

The Genomic Ark: 10,000 vertebrate genomes

The first bioinformatics meeting I went to was in 1996 at the  Nachsholim resort,  north of Tel Aviv. I received a fellowship for the duration, and shared a room with the brilliant Golan Yona, then a grad student at the Hebrew University. I was doing biochemistry at the time and knew next to nothing about […]

Weekly poll: Replicators First vs. Metabolism First

I am preparing a class on the origins of life for next week. The textbook I am using does not  go into the Replicators First vs. Metabolism First argument, but I probably will, if I have time. Below, a quick refresher for those who know of the competing theories, and an unsatisfying introduction for those […]

Richard Dawkins and Francis Collins on Colbert Nation

Stephen Colbert had an interesting lineup for the past two nights: Richard Dawkins on Sep 30, and Francis Collins last night. Enjoy the vids: The Colbert Report Mon – Thurs 11:30pm / 10:30c

It ain’t necessarily so

First, a short glossary. Homologous genes are descended from a common ancestral gene. There are two types of homology: Orthology is homology due to a speciation event. So if there is a gene A’ in humans and A” in mice, and they are obviously similar in sequence, we infer that they homologous. We usually also […]

An Ontology for Biological Similarities

I griped here twice about the abuse of the term homology in biology. And to quote the Bellman in The Hunting of the Snark:  “What I tell you three times is  true”. But while I gripe, someone is actually doing something about the whole terminology muddle. Specifically, Marc Robinson-Rechavi and his group in The University […]

A Flurry of Red and Green

UPDATE: I submitted this post to the National Evolutionary Synthesis Center’s sponsored contest for a travel award to ScienceOnline2010. Let’s see how it goes… #scio10 In a previous post about Hatena we saw what might very well be the beginning of a (beautiful?) [:ttip=”symbiosis where one partner lives inside the cell of the other” id=”10″]endosymbiotic[:/ttip] […]

Distant homology and being a little pregnant

(Thanks to F.B.  for the inspiration). Sigh… people don’t seem to learn. It’s been almost 22 years (yikes!) since a distinguished group of scientists published a letter in Cell calling for a responsible use of the word “homology”. If you were born when that letter was published, then in the US you can already drink […]

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 […]

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 […]

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 […]

Blog for Darwin: on Mass Extinctions

Happy Darwin Day! If you are reading this then you probably do not need an introduction to Charles Darwin, the importance of his work, how his theory of evolution by natural selection shaped modern Biology. Or if you do, I bet there are plenty of posts in today’s blogswarm that will address this. There is […]

Blog for Darwin

I just went to Shirley Wu’s blog and found this. Apparently February 12-15, 2009 there will be a Blog for Darwin blogswarm, in honor of his 200th birthday and 150th anniversary of the publication of On the Origin of Species (First time I hear this term, blogswarm; not sure if I like it). I wrote […]

Just “teach”

The celebrations of Darwin’s 200th birthday and 150 years for the publication of The Origin of the Species are in full swing. We are apes equipped with 10 digits on our forelimbs, which we use in just about everything we do. We like numbers that are multiples of 10; even better if they are 10 […]