Saturday, October 4, 2008

The DNA Network

The DNA Network

Single issue voting [Mary Meets Dolly]

Posted: 04 Oct 2008 01:33 PM CDT

I am not ashamed to say I am a one issue voter. If a candidate is not right-thinking on the sanctity of life from conception to natural death, then I believe that they will be wrong-thinking on all of the other social justice issues that matter. How can a candidate allow for the killing of the smallest and weakest of the human species, and then try to make life better for humanity? I do not believe they can. Bishop Joseph Martino of Scranton wrote this pastoral letter where he states my opinion in a more meaningful way:

Being "right" on taxes, education, health care, immigration, and the economy fails to make up for the error of disregarding the value of a human life. Consider this: The finest health and education systems, the fairest immigration laws, and the soundest economy do nothing for the child who never sees the light of day. It is a tragic irony that "pro-choice" candidates have come to support homicide -- the gravest injustice a society can tolerate -- in the name of "social justice."


Furthermore, National Right to Life reports that 48.5 million abortions have been performed since 1973. One would be too many. No war, no natural disaster, no illness or disability has claimed so great a price.

I think this video pretty much sums it up for me.

An Open Letter to Baroness Warnock on Assisted Suicide [Mary Meets Dolly]

Posted: 04 Oct 2008 01:17 PM CDT

As a follow up to Embryos and Elderly: duty to die, here is an An Open Letter to Baroness Warnock on Assisted Suicide by Rita Marker, a remarkable woman who has been fighting for the rights of the sick and elderly for decades.

Open genetics: genome rearrangement videos and more [The Tree of Life]

Posted: 04 Oct 2008 09:57 AM CDT

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.

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 posting includes an audio/video/photo media file: Download Now

Notes from the road: Bio-1, WIRED, NJBEC, and biotechnology in New Jersey [Discovering Biology in a Digital World]

Posted: 04 Oct 2008 08:00 AM CDT

Long Branch, NJ, is a lovely town on the Atlantic Ocean, with long beaches and brand new shops and condos. It is also part of an area in, central New Jersey, where biotechnology education is entering an exciting time thanks to efforts of NJBEC, Bio-1, and a WIRED grant from the U.S. Department of Labor.

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White blood cell chasing bacteria [Think Gene]

Posted: 04 Oct 2008 12:18 AM CDT

It’s amazing how the cells look like conscious organisms chasing one another. Organisms on any level that are effectively predator and prey behave the same, be they single cells, insects, or animals.

Long overdue, Gene Sherpas quoted twice in journal! [The Gene Sherpa: Personalized Medicine and You]

Posted: 03 Oct 2008 07:38 PM CDT

After a week from hell I am back. I am sad that I missed a week's worth of cancer genetics patients, but they wouldn't have found me very useful at the time! As I recover, I wanted to point you in...

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Who do Nobel Laureates Endorse (guess ...) [The Tree of Life]

Posted: 03 Oct 2008 12:17 PM CDT

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)

Open Access Pioneer Award #4: Carl Malamud and Public.Resource.Org [The Tree of Life]

Posted: 03 Oct 2008 12:17 PM CDT

This is not about science but I think this guy deserves an award.  I just read an interesting and funny story in the S.F. Chronicle (Sebastopol man puts code manuals online) by Matthew Stannard about Carl Malamud who has been putting building codes, plumbing codes and other codes online at Public.Resource.Org.

Basically, he is doing this because many of the codes are only available for a fee.  He says
"Not everybody is going to read the building code, but everybody who wants to should be able to without putting 100 bucks in the slot," Malamud said. "Primary legal materials are America's operating system."
And though his work has been questioned by some (who would like to make money off of the codes) he appears to be on solid legal ground. 
"It's very clear in American law that you can't get intellectual property protection for law," said Pamela Samuelson, co-director of the UC Berkeley Center for Law and Technology. "Law belongs to everybody."
So for this work, I am giving Malamud by Open Access Pioneer Award (#4).  Keep up the good work.

For more see (among many):

Newick C++ parser in Boost.Spirit [Mailund on the Internet]

Posted: 03 Oct 2008 02:37 AM CDT

Here’s the Newick parser for C++ I mentioned in a previous post.  It is written in Boost.Spirit, so it is a recursive decend parser.  This might give you problems with the stack if you are parsing really deep trees, but for moderately sized trees (a few thousands of taxa) it shouldn’t be a problem.

It is code I pulled out of a tool for coalescence trees, so it only handles rooted binary trees.  To make it a little more useful I’ll add code for re-rooting the tree.  I have that code already, but in a different tool that only works on the tree topology, so I need to handle the branch lengths before I can add it here.

Let me know what you think.

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

Posted: 02 Oct 2008 09:56 AM CDT

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.

code_swarm [Mailund on the Internet]

Posted: 02 Oct 2008 03:16 AM CDT

I just learned about code_swarm today.  A cool visualisation of software evolution that shows how files are created and modified over time.

The evolution of Python:

code_swarm - Python from Michael Ogawa on Vimeo.

ABI Announces SOLiD v3.0. Weekend warriors rejoice. []

Posted: 02 Oct 2008 01:35 AM CDT

Just finished up day 1 at the SOLiD users group meeting. Was a good meeting with both a look at AB R&D, and quite a few good customer presentations. The highlight for me (aside from the customer presentations) was hearing about the next version of SOLiD. Minor changes to the instruments liquid handling setup end up meaning major changes in hands-on time and overall run time. In addition longer frag and mate reads dramatically increase throughput. On the hardware side they are moving...

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1 comment:

das said...

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