evolgen

This is a Good-bye Post

Fri, 16 Jan 2009 13:30:00 -0500

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.

Read the comments on this post...

Mendel's Garden #27 - Call for Submissions

Fri, 02 Jan 2009 09:15:00 -0500

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.

Eric Lander Teaches?

Sat, 20 Dec 2008 12:30:00 -0500

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 the rest of this post... | Read the comments on this post...

The Implementation of Molecular Evolution for the Masses

Thu, 18 Dec 2008 11:30:00 -0500

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 the rest of this post... | Read the comments on this post...

Do people still use microarrays?

Wed, 17 Dec 2008 09:00:00 -0500

Larry Moran points to a couple of posts critical of microarrays (The Problem with Microarrays):

Why microarray study conclusions are so often wrong

Three reasons to distrust microarray results

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 the rest of this post... | Read the comments on this post...

All those types of speciation

Tue, 16 Dec 2008 11:00:00 -0500

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 the rest of this post... | Read the comments on this post...

Call for Mendel's Garden #26 Submissions

Mon, 24 Nov 2008 09:00:00 -0500

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.

Genome Sequenced, Published via Press Release

Wed, 19 Nov 2008 08:30:00 -0500

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.

Read the comments on this post...

Is Nested Clade Analysis Worthwhile?

Sun, 16 Nov 2008 12:30:00 -0500

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 the rest of this post... | Read the comments on this post...

Genes in the Post-Genomic Era

Wed, 12 Nov 2008 11:00:00 -0500

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 the rest of this post... | Read the comments on this post...

I Voted . . . Blindly

Tue, 04 Nov 2008 20:45:00 -0500

If you hold on until the end of the post, you'll see that it's got science content. But you'll have to wait until the end.

First, here's how it starts. I had an optometrist appointment at 8am this morning. I could have voted prior to the appointment, but the polling place is in between the optometrist's office and work, so I figured I'd vote after getting my eyes checked. Big mistake. The eye doctor dilated my pupils, which, much to my surprise, made me far-sighted (I'd never had both pupils dilated simultaneously before). I did not realize this until, when checking out of the office, I could not read the credit card receipt I signed. I thought, "Fuck, how the hell am I gonna vote if I can't read the ballot?"

An aside: the doctor had a picture of his daughter posing next to Dick Cheney with her violin. Doc said something about her being a musician, so I imagine she won some competition that earned her a trip to the White House.

So, I ride my bike to the polling place (don't worry, the pupil dilation didn't affect my distance vision). Thankfully, there was a short line. When I checked in, I asked the retired people how small the writing on the ballot is. They pointed me to a sample ballot across the room. I could not read it. Ever resourceful, I asked if anyone had reading glasses. I figured one of the five retirees staffing the place would be able to lend me a pair. They did not. Luckily, a nice lady waiting in line to vote let me borrow her specs, which, while not perfect, allowed me figure out which line on the ballot corresponded to each party.

Read the rest of this post... | Read the comments on this post...

Mendel's Garden #25

Sun, 02 Nov 2008 20:00:00 -0500

After a few months off, here's the return of Mendel's Garden.

Blast from the past: rENNISance woman gives us a post on viral genetics.

Figuring out DNA looping with unbelievably advanced technology: Greg Laden reviews a paper on the structure of nucleic acids.

In the fly, delayed reproduction also delays aging: Ouroboros describes research on senescence in Drosophila.

Balancer Chromosomes: Larry Moran describes this marked chromosomal inversions (see also Hermann Muller Invented the Balancer Chromosome).

The Genetics of Voting: From Bayblab, a post on the heritability of filling the ballot box.

Science Tuesday: Back into the hornets' nest: A free man tries to understand the causes of autism.

Freedom of the Genetic Press? Can newly created letters of life's alphabet be patented?: Tom Payne's Ghost considers the patenting of novel amino-acids.

Slightly Deleterious in Trans: I wrote about a new chapter in the cis vs. trans debate.

That's it for this month's edition of Mendel's Garden. If you'd like to host in December, or a subsequent month, shoot me an email (evolgen-at-yahoo-dot-com).

Read the comments on this post...

Another Call for Submissions to Mendel's Garden #25

Tue, 28 Oct 2008 10:00:00 -0500

I will be hosting the next edition of Mendel's Garden on Sunday, November 2. If you have written any blog posts about genetics in the past few months, send me a link (evolgen[at]yahoo[dot]com). Also, if you've seen any good genetics posts on other people's blogs, let me know.

For those not in the know, Mendel's Garden is the original genetics blog carnival. On the first Sunday of every month, the carnival plays host to the best genetics blogging of the past month. After a hiatus of a few months, the carnival is back.

They are NOT fruit flies

Mon, 27 Oct 2008 09:00:00 -0500

In the recent kerfuffle over Sarah Palin's disparaging remarks about "fruit fly" research, an important point was missed by the general public, scientists, and even Drosophila geneticists: she wasn't talking about Drosophila. Now, this point has been clarified by a few people (notably Mike the Mad Biologist), and I think people are starting to get it. But it was remarkable how people automatically assumed she was talking about Drosophila.

Okay, maybe it wasn't so remarkable, given that even Drosophila researchers refer to these little insects as "fruit flies". The problem with that nomenclature is that Drosophila are not fruit flies. The olive fruit flies to which Palin was referring are true fruit flies (Tephritids), and these guys are major agricultural pests. She was actually criticizing applied research (as opposed to basic), which makes her comments even more absurd.

But everyone out there assumes that she's ragging on Drosophila research (which, for the most part, tends to be quite basic in nature -- note that basic does not imply worthless), even Drosophila geneticists. I've been notified of "Sarah Palin's attack on Drosophila" by multiple Drosophilists, only to point out to them that she wasn't going after us. Funny thing is, there is at least one Drosophila geneticist who also works on Bactrocera (the genus to which Palin's olive fly belongs): Michael Eisen. He's also fed about by the Drosophila/fruit-fly mix-up. And you should be too. The least we can hope for is that people who actually study Drosophila will know that they're not fruit flies.

Read the comments on this post...

Get Your Masatoshi Nei Trading Card

Thu, 09 Oct 2008 12:30:00 -0500

The Penn State Alumni Association has produced trading cards featuring the best and the brightest of the university's faculty (Pa. trading cards highlight brains, not brawn). The cards are only available at University President Graham Spanier's tailgate parties on home football weekends. The biologists featured include entomologist Jim Tumlinson and molecular evolution pioneer Masatoshi Nei.

I haven't been able to find a complete list of all ten faculty members featured, and I don't think that individual images of the ten cards are available online. If anyone can track them down, post a link in the comments.

Update: Nina Fedoroff has a card as well.

Read the comments on this post...