Category: Misc.

Open genetics: genome rearrangement videos and more

A little late I know, but I was going through my draft postings and I rediscovered this one from July. There is an interesting paper in PLoS Genetics by Aaron Darling et al (full disclosure — Aaron is now working in my lab as a Post Doc … though I started writing this before I realized the paper was his). The paper is about genome rearrangement in bacterial populations (see Dynamics of Genome Rearrangement in Bacterial Populations). Though the science in the paper is quite interesting, the part I want to promote here are the fun genome rearrangment videos in the supplemental material.
//www.youtube.com/get_player

The figure and video are from Darling AE, Miklós I, Ragan MA (2008) Dynamics of Genome Rearrangement in Bacterial Populations. PLoS Genet 4(7): e1000128. doi:10.1371/journal.pgen.1000128.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Who do Nobel Laureates Endorse (guess …)

Not much more to say – just thought I would post a link to this posting from “A Vote for Science” by Michael Stebbins (A Vote For Science : 61 Nobel Laureates in Science Endorse Obama)

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Strange Helicopter Sighting over Davis




Strange military style helicopter came very close to houses in Wildhorse this PM.  Not sure what they were doing but they seemed to be searching for something and it came just after hearing some very loud car-like motors revving by.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Twisted Tree of Life Award #2: Science Friday on the Five Kingdoms

Well, I love Science Friday. I listen to podcasts of it now almost every day when I bike to work. It is a brilliant show, covering a wide range of science and science related topics in depth. Plus it is freely downloadable in a variety of formats. And they have a great website too. But every once in a while they get something a bit wrong. Yesterday, on my way home from a new introductory biology class we are teaching at Davis on “The Tree of Life” (which I will write more about later), I was listening to a Science Friday about Fungi (Science Friday Archives: The Fabulous Fungi). And unfortunately, in the introduction, Joe Palca started off with a pretty outdated discussion of the tree of life.

When you ask people to name the kingdoms, most people get the big ones, animals, plants, bacteria. Some people may even come up with the protists. But there is one more. Here’s a hint. Yeast are part of it. So are shitakes. Are you getting it? Well the answer is fungi.

Yes, they are in fact referring to the Whittaker “Five Kingdoms” tree of life, which is no longer in use. (I am placing an image here from my Evolution Textbook) where we talk in Chapter 5 about the history of various trees of life that have been used. The figures from our book are available for free at the book site)

Today we talk about the Three Domains (Bacteria, Archaea and Eukaryotes) and within each of those domains, they are many lineages (which are sometimes referred to as kingdoms). But the five kingdom concept is done and gone. The modern tree looks more like the following (which is an adaptation for our book of a tree by Baldauf).

Mind you, the show on Fungi is worth listening to (although they did miss the opportunity to use the tree of life to answer a question that came up on “Are fungi from outer space?” – the answer should have been – “No, fungi are deeply embedded within the tree of life on this planet, so if life came from elsewhere, it was at the beginning of the origin of life”).

Unfortunately, I could not call in to the show (as I have done before) to try and comment on these issues (since I was not listening live). So instead, I am giving Science Friday my Second “Twisted Tree of Life” Award for ignoring the new concepts of the tree of life that have been in play since Woese, Fox and others first laid the groundwork for the existence of the Archaea.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Congrats to Gary Andersen, Developer of the Phylochip, for Getting a WSJ Technology Award

The Phylochip, developed by Gary Andersen, of Lawrence Berkeley National Lab, and colleagues, has won a Wall Street Journal, Technology Innovation Award. For more see the Wall Street Journal here. Their phylochip is a microarray which can be used to rapidly survey rRNAs from different organisms and get a measure of the types and abundances of organisms present in a sample. It is similar in concept although different in design from a rRNA chip that was used by David Relman, Pat Brown, Chana Palmer and others. Not sure why the chip from Brown et al did not also win the award (it probably was not nominated, or something like that), but still, always good to see cool things in microbiology win awards like this.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Wanted – Evolutionary Genomicist at UCSB

Todd Oakley, of UCSB and more importantly, the Evolutionary Novelty Blog, forwarded this to me.  UCSB is looking for an Asst. Prof. in Evolutionary Genomics.  If only they had said “Phylogneomics” then I would have written a longer posting …

See here for more detail. Also see the ad on Oakley’s blog.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Davis wetlands pictures





——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Davis Outdoor Art



I am planning to keep posting pics of Davis outdoor art whenever I can. Here are some pictures from the UC Davis Vet Hospital in an art display in honor of companion animals

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Drew Endy talking at Davis tomorrow ….

For those from UC Davis or the area who read the blog and have an interest in genetic engineering or synthetic biology or open science, you should come to this talk.

Genome Center Colloquium
Storer Life Sciences Endowment Presents

Drew Endy, PhD
Stanford University

“Post-Synthesis Genetics & Engineering Biological Simplicity”

Friday, September 26, 2008

10:00 a.m., 1005 GBSF Auditorium

For more on Drew Endy, well, use google of course or go here:

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Funny Davis Signs #1

Going to start a new section here … posting pictures of funny Davis
signs. This is one of my favorites.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–