January 16, 2009
Category: Admin
This is the final post ever at evolgen. It was a fun 4+ years, the last three spent at ScienceBlogs, but it has come time for me to close up shop.
When I first got into blogging, I did it as a way to share what was on my mind to the few people who would read what I had to say (usually in topics related to evolution and genetics, but not always). It was a fun hobby, and my blog gave me a public venue to talk about articles I was reading, concepts that I found interesting, and summarize important areas of research.
However, the blog has begun to feel more like a burden. I no longer post because I feel like I have something I want to say, but rather out of obligation (to my contract with Seed, to the five readers who read this site regularly, to my own need to keep generating new content because the blog needs new content). It wasn't fun anymore. This is reflected in the sporadic posting over the past year -- small bursts of inspiration surrounded by frequent periods of ennui (what you now call meh).
I had a really good time blogging at the ScienceBorg, but the time has come for me to move on. I'm not sure whether I'll ever start blogging again, but, if I do, it will be at a new venue. I'll make sure to let y'all know what's up via obnoxious emails and requests for more highly-trafficked folks to link to my new internet cave.
Posted by RPM at 1:30 PM • 38 Comments
January 2, 2009
Category: Blog Carnivals • Genetics
Mendel's Garden is the original genetics blog carnival. The next edition will be hosted by Jeremy at Another Blasted Weblog. If you would like to submit a blog post to be included in the carnival, send an email to Jeremy (jcherfas at mac dot com). The carnival should be posted within the next few days, so get your submissions in ASAP.
Also, hosts are needed for future editions of Mendel's Garden. If you would like to host, please send me an email (evolgen at yahoo dot com). A new edition is usually posted around the first Sunday of each month.
Posted by RPM at 9:15 AM •
December 20, 2008
Category: Science Policy
John Hawks points out that Eric Lander has been appointed to co-chair Obama's Council of Advisers on Science and Technology along with science adviser John Holdren and Nobel Laureate Harold Varmus. Here's how the AP article describes Lander:
Lander, who teaches at both MIT and Harvard, founded the Whitehead Institute-MIT Center for Genome Research in 1990, which became part of the Broad Institute in 2003. A leading researcher in the Human Genome Project, he and his colleagues are using the findings to explore the molecular mechanisms behind human disease.
Read on »
Posted by RPM at 12:30 PM • 6 Comments
December 18, 2008
Category: Genomics • Molecular Evolution • Science Education
A couple of years ago, there was talk in the bioblogosphere about getting the general public interested in bioinformatics and molecular evolution:
The idea was inspired by the findings of armchair astronomers -- people who have no professional training, but make contributions to astronomy via their stargazing hobbies. With so much data available in publicly accessible databases, there's no reason we can't motivate armchair biologists to start mining for interesting results.
But how do we train these new comp-bio code-monkeys? The field of bioinformatics requires both some computational skills, as well as an understanding of biology. Finding people with both skill sets (and interests) can be tricky. Well, a framework has been laid out in a recent paper in PLoS Biology for teaching the skills (doi:10.1371/journal.pbio.0060296). The authors present a web-based interface through which students implement standard online tools for DNA sequence analysis (Annotathon).
Read on »
Posted by RPM at 11:30 AM • 2 Comments
December 17, 2008
Category: Genomics • Molecular Biology
Larry Moran points to a couple of posts critical of microarrays (The Problem with Microarrays):
Microarrays are small chips that are covered with short stretches of single stranded DNA. People hybridize DNA from some source to the microarray, which lights up if the DNA hybridizes to the probes on the array.
Most biologists are familiar with microarrays being used to measure gene expression. In this case, transcribed DNA is hybridized to the array, and the intensity of the signal is used as a proxy for the transcriptional level of a large sample of genes. Other uses include identifying copy number polymorphism, genotyping single nucleotide polymorphisms (SNPs), and capturing sequences of interest for downstream analysis.
Read on »
Posted by RPM at 9:00 AM • 9 Comments
December 16, 2008
Category: Population Genetics • Speciation
Over at Wilkins' cabana, there's a post (Some new work on speciation and species) on a paper by Nitin Phadnis and Allen Orr (doi:10.1126/science.1163934). Phadnis and Orr isolated a gene responsible for both reproductive isolation and sex-ratio distortion between two populations of Drosophila pseudoobscura. Wilkins doesn't like speciation genes, and he's rails on the concept in his post.
Read on »
Posted by RPM at 11:00 AM • 7 Comments
November 24, 2008
Category: Blog Carnivals • Genetics
The 26th edition of Mendel's Garden will be hosted by A Free Man on December 7. If you have written a blog post about any topics in Genetics in the past month or so, send a link to Chris (chris[at]afreeman[dot]org) to be included in the carnival.
We're also looking for hosts for upcoming editions. If you would like to host the original genetics blog carnival, send me an email (evolgen-at-yahoo-dot-com). Every month from February onward is available.
Posted by RPM at 9:00 AM •
November 19, 2008
Category: Genomics • Science News
Back in the day, you could sequence a genome and get a Nature paper out of it. Pretty soon, the sexiness of genome sequencing wore off, and it took a bit more to get into a vanity journal. You had to sequence something cute and cuddly, something extinct, or a lot of genomes at once. Any other genome sequencing projects were relegated to lower tier journals.
Now, it appears that even sequencing the genome of charismatic megafauna only gets you a press release. As TR Gregory points out, the sequencing of the Kangaroo genome was announced in such a manner (Science by press release). But check out the title on the press release:
Australian First: Kangaroo Genome Mapped
They report that the genome was "mapped". Not sequenced. This is the incorrect terminology. One the positive side, at least they didn't say the genome was decoded.
Posted by RPM at 8:30 AM • 5 Comments
November 16, 2008
Category: Population Genetics
Population biologists often want to infer the demographic history of the species they study. This includes identifying population subdivision, expansion, and bottlenecks. Genetic data sampled from multiple individuals can often be applied to study population structure. When phylogenetic methods are used to link evolutionary relationships to geography, the approaches fall under the guise of phylogeography.
The past decade has seen the rise in popularity of a particular phylogeographical approach for intra-specific data: nested clade analysis (Templeton et al. 1995; Templeton 2004). Many of the methods used in intra-specific phylogeography have been called into question because of their lack of statistical rigor, as I have described previously (How do you really feel, Dr. Wakely?). Nested clade phylogeographical analysis (NCPA) is no exception. Lacey Knowles summarizes the criticisms of NCPA in the most recent issue of Evolution (Why does a method that fails continue to be used?).
Read on »
Posted by RPM at 12:30 PM • 6 Comments
November 12, 2008
Category: Genetics
You would think that geneticists would have a good definition of "gene". After all, genes are what we study. In introductory biology courses, you may have been introduced to the concept of the gene as the unit of heredity. That's all well and good, but when you begin to study genes at a molecular level (i.e., looking at DNA sequences), that definition ceases to be practical. The advent of DNA sequencing led to the concept of the gene as an open reading frame, and the post-genomic era has challenged the very idea of the gene.
I've previously discussed the definition of gene (What is a gene?, What is a gene? -- yes, two different posts with the same title), but I didn't get into very many details. Alas, I don't feel like spending much time laying out my opinion, suffice it to say I think "gene" is an obsolete, overly generic term that should be replaced by a more specific term whenever possible. Luckily, the New York Times has published an article by Carl Zimmer sketching out some of the possible interpretations (Now: The Rest of the Genome ). This lets me pick and chose my favorite meaning from a variety of opinions represented in Carl's piece.
Read on »
Posted by RPM at 11:00 AM • 7 Comments
We talk about molecular population and evolutionary GENETICS and GENOMICS. You know, the caliper measurement of a gene's evolvability in moles.
