Tag Archives: evolution

Visit the Galapagos Islands, for free

Ok, that got your attention didn’t it? It got mine. It’s not really a genomics post, it’s not really a database post, but like almost every evolutionary biologist I know (and most biologists and a lot of others), a visit to the Galapagos has been something I’ve always wanted to do. Only thing is, it’s expensive to get and stay there, and eco-tourism is having it’s not-so-great side effects. Well, the University of Cincinnati, in order to commemorate the 150th anniversary of Darwin’s “Origin of Species” has set up a “Second Lifetour of the Galapagos.

I’ve resisted roaming Second Life, even though Nature has a presence there as “Second Nature.” But for the Galapagos? I’ll go :). Now, I wonder if they could do a tour of the Genome in Second Life?

HT: Discovering Biology in a Digital World

Extinct Genomes in PLOS One

ResearchBlogging.orgtasmanian tigerA paper published today in PLoS One reports on research that shows the feasibility of taking a gene or genomic region from an extinct species and inserting it into the genome of an extant species and resurrect the extinct species DNA function in the transgenic mice. The extinct species was the Tasmanian tiger or Thylacine (that links to the wikipedia page, anyone want to become the curator for the EOL page which is pretty minimal at this point?) and the ‘surrogate’ species was Mus musculus.

And, as the abstract says,

While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity.

It is an fascinating piece of research.

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a sleep database

sleepheartdiseases.jpgI love my job, databases intersect with my personal interests often. “A blog around the clock” reports on a new open access Sleep Journal and a “Sleep Database.” As someone with sleep apnea (and whose CPAP machine changed his life), I am fascinated by the entire subject. So I’ll be keeping tabs on the journal, and the database (Phylogeny of Sleep) is fascinating. The database’s purpose, as the homepage states:

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Laying Eggs

platypusThat is what Platypus do, even as mammals :). Two days ago the Platypus genome was published in Nature. So if you haven’t already read it, might be worth a skim at least. So, they aren’t model organisms and not a medically or agriculturally important animals (unless someone starts figuring out how to cook platypus omelets), but platypus (platypi?) do hold a fascinating place in evolutionary history having mammalian (milk, fur) and reptilian (eggs, venom) characteristics. Their genome obviously holds clues to some of this unique history.

For example, the eggs and fertilization genes can tell us a bit of how that evolved…

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Open Access Evolution

Dr. Eisen at UC Davis has started a new blog theme on his “Tree of Life” blog called “Open Evolution” (open access publications, open source programs, etc) and has started with open access journals. He has listed a few open access journals (and there’s a good discussion in the comments about the difference between ‘open access’ and ‘free online access’ journals) and is asking if anyone knows of any others. He hasn’t asked for it yet, but I’ve got some ideas for open source/access phylogeny analysis programs and/or databases. I’ll post a few of those in the coming week or so, but for now here is a link to a list of such programs (some on this list I’m not sure are open source, I’ll cull these later too).

Encyclopedic Tree of Life

Tree of Life image In 1993 I remember discovering the web. It wasn’t much longer after that I discovered the “Tree of Life (ToL).” I was studying for my Ph.D. in evolutionary biology and heard about it by word of mouth. Sometime in 1996 I found it on the web and was intrigued. It has grown since then, though still has a way to go. It’s goal? “… to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct.

Today saw the unveiling of the “Encyclopedia of Life (EOL),” which is “an ambitious… project to organize and make available via Encylopedia tree of lifethe Internet virtually all information about life present on Earth.” Carl Zimmer reports on the EOL on his blog and in a NYTimes article.

Those goals overlap a lot it would seem. So I did some checking of the ToL and the EOL for two things that are most interesting to me: genomic information and evolutionary information. A short critique below (with the caveat that EOL is VERY slow today because of the launch):

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Tip of the Week: Viewing data across databases

Vista tip Today’s tip looks at one example of how to view the same genomic data across several databases simply by browsing. You can download the data from analysis tools and databases in several formats and use that in others, and someday we’ll do a tip on that. But today’s tips shows you that many databases link out between them allowing you to view data in one context and then another simply by clicking a link. We are going to start by looking at comparative genomic data in VISTA , there’s much more in depth tutorial on VISTA here (free), then link out to the UCSC Genome Browser (free tutorial) to view the data there and then off to Ensembl (tutorial, subscription).

Non-coding, non-functional or junk ncRNA

ResearchBlogging.orgI just finished reading this paper out this month in PNAS, “Specific expression of long noncoding RNAS.” From the looks of it, the paper has conjured up an interesting discussion in the science blogosphere surrounding the paper and the term “Junk DNA.” Before I get to that discussion, let me give a brief synopsis of and thoughts on the paper (and a link to a ncRNA database at the end). Continue reading

Acceleration of human adaptive evolution

I’ve been following a fascinating conversation about this paper: Recent acceleration of human adaptive evolution by John Hawks et al. In this paper the authors found that:

Genomic surveys in humans identify a large amount of recent positive selection. Using the 3.9-million HapMap SNP dataset, we found that selection has accelerated greatly during the last 40,000 years.

There is an interesting discussion going on in the blogosphere. Continue reading

Basic Biology Concepts

You have some non-biologist colleagues (attorney? manager? programmer?) you need to get up to speed, or you need to brush up on some concepts yourself? A good place to start is this list from John Wilkins (Evolving Thoughts). It is a list of links to blog post across the blogosphere that explain and expound on various basic concepts in science. The list for the life sciences ranges from basic evolution to clade to biomes to linkage disequilibrium to a lot else. It includes a list of lectures from Bora Zivkovic at Blog Around the Clock in basic biology. Additionally, make sure to read the comments to the first link, commenter contributed a lot of their own. A wealth of information out there in the blogosphere.