genomics
mikethemadbiologist | June 19, 2007NIH, in about six months, will release a huge sum of money to fund the study of the human 'microbiome': those microorganisms that live on or in us. One of the things that will be done with this money is meta-genomics which is "the study of genomes recovered from environmental samples as opposed to from clonal cultures." (In this case, the samples would be fecal, vaginal, your mouth, etc.). In other words, we can sample the 'community' of genomes (or perhaps we should call it the community ecology of genomes). So I have a question: what do we learn from meta-genomics of the human…
evolgen | June 3, 2007Let's go through the basics again. Cracking the genetic code refers to figuring out how DNA encodes the information to make proteins -- that was done decades ago. Sequencing a genome does not mean that you have decoded the genome; presumably, decoding a genome would mean you've figured out the function of every part of a sequenced genome, but there really isn't a proper definition. In genetics, mapping refers to determining the location of genetic elements, which is different than sequencing. And deciphering has no real meaning.
With that said, check out the newest New York Times article on…
evolgen | June 1, 2007Last year, New York Times science writer Nicholas Wade wrote a few articles in which he referred to genome sequencing as "decoding". I chastised him for his poor use of terminology, was pleasantly surprised when he began to correct himself, and then realized that he would never overcome his inability to communicate science clearly.
It appears that Wade has found a new, yet still incorrect, term for genome sequencing. In an article published today, Wade reports on the 454 sequencing of Jim Watson's genome. Only he reports the Dr. Watson's genome was "deciphered". At least he isn't writing…
sporte | May 31, 2007I want my genome sequenced, too!
Apparently, it's become a popular thing to get your genome sequenced. Craig Venter was the first. Jim Watson's genome (of Project Jim) was ceremonially released this morning (courtesy of 454), and now George Chuch, Larry King, cosmologist Stephen Hawking, Google co-founder Larry Page, Microsoft co-founder Paul Allen and former junk-bond trader Michael Milken want theirs done, too (1).
Two articles from different GenomeWeb releases made a strange combination this morning when I turned on my computer. In one release, GW mentioned that NHGRI (the National…
sporte | May 28, 2007Is the case for open access truly "open and shut"?
Will open access impede science by limiting genetic studies with families?
tags: genetics, genetic privacy, bioethics, open access
Microsoft's brave new world
The April ALPSP conference began with songs for the open access choir. Microsoft's Lee Dirks painted visions of a utopian future where everything will be open, labs shall be judged by the worthiness of their databases, and even scientists will learn to share.
According to Dirks, "Open access to scientific content, specifically data, will become the norm."
Since I've had a few data…
evolgen | May 28, 2007A couple of weeks ago I suggested that the National Human Genome Research Institute (NHGRI) would no longer be funding de novo genome sequencing projects via white papers. They appear to be shifting their focus to resequencing projects to study variation (ie, this) and take a closer look at well studied organisms (ie, ENCODE, which now has Drosophila and Caenorhabditis versions). But the distribution of genomic resources is extremely biased towards a few species. What should those researchers who work on organisms without genome sequences do if they can't solicit funds from the NHGRI?
As…
evolgen | May 14, 2007Paul Erdos was an extremely prolific and mobile mathematician who has left a legacy in academia in the form of the Erdos Number -- a count of your "academic distance" from Erdos. Anyone who published a paper with Erdos has an Erdos number of one (Erdos, himself, had a number of zero), people who published with anyone with an Erdos number of one have an Erdos number of two, and so on. It's a point of pride for a mathematician or other researcher to have a small Erdos number.
There is no widely recognized equivalent of the Erdos number for the life sciences. Given the diversity in the field, it…
evolgen | May 9, 2007For the past decade, when a research community wanted to sequence the genome of their favorite species, they submitted a white paper to the National Human Genome Research Institute (NHGRI). Despite its name, the NHGRI funds genome sequencing projects of not only non-human mammals, but also non-mammalian animals and even non-animals (see here for a list). If a bunch of researchers want their species' genome sequenced, they would get together and explain why the genome should be sequenced. These should not be confused with typical research grant proposals that a principal investigator will…
evolgen | May 3, 2007Here's some interesting science:
A commonly used medicinal leach may have been misidentified as the wrong species.
Here is a description of the Human Variome Project, which seems more focused on mapping disease genes than doing cool population genetics. That's too bad.
Science has an article on the benefits of undergraduate research. The most important one: to get into grad school.
You can use molecular markers to determine that a lonesome tortoise has no reason to feel alone.
The central nervous system is homologous across all animals.
What is the greatest innovation? I've tackled this…
evolgen | April 26, 2007
The recent Scientific American article on junk DNA (discussed here) has instigated a quite a furor in the bioblogosphere. Here is a collection of links:
ERV linked with a tone of disgust.
I restated my frustration with the term junk DNA.
JR Minkel, the author of the Scientific American article, responded to my criticisms.
Ryan Gregory replied to Minkel's SciAm blog post, introducing the term "junctional DNA" to replace junk DNA describe sequences with unknown function. Gregory also tells us how a genome is like an onion (let me count the ways), or something of the sort wonders why onions…
evolgen | April 24, 2007Would I write about junk DNA? No. Never. Not me. Not even when Scientific American publishes sub par articles on junk DNA. Well, they're at it again.
The most recent junk DNA article describes a study by Gill Bejerano of Stanford University which I can't find published anywhere (neither can ERV). Is Scientific American describing unpublished research on their website? Either way, they're doing it poorly. The study described in the article identified non-coding sequences that were conserved across all sequenced mammalian genomes but missing from the chicken genome. Five percent of the…
evolgen | April 23, 2007Because my browser consists of a growing forest of tabs containing stuff waiting to be blogged, and there is no way I can write a complete entry on each one, and I want to at least link to the relevant sites so that I can close those tabs, I give you a link dump with maximal run-on sentences:
Remember my post on the evolution of zombie populations? If so, you've got a good memory. If not, who cares? Anyway, there's an article in arXiv about ghosts, vampires and zombies. (Via Ortholog).
The evolution of snake venom genes. They make up part of the venome.
Jonathan Eisen on the Human…
evolgen | April 20, 2007It seems like everything is coming in twos the past couple of days. Yesterday we mentioned two books on the evolution of genomes and two stories involving either Wolbachia or sex determination. Today, we have two stories involving criticisms of scientific papers. One deals with the evolution of the bacterial flagellum, and the other addresses natural selection on the brain expressed gene ASPM in humans.
The first story involves everyone's favorite irreducibly complex cellular apparatus: the bacterial flagellum. During the Kitzmiller v. Dover trial, Nick Matzke worked with the plaintiffs (the…
evolgen | April 19, 2007Oxford University Press will be releasing a new book in June entitled Darwinian Detectives: Revealing the Natural History of Genes and Genomes. From the OUP description of the book:
Molecular scientists exploring newly sequenced genomes have stumbled upon quite a few surprises, including that only one to ten percent of the genetic material of animals actually codes for genes. What does the remaining 90-99% of the genome do? Why do some organisms have a much lower genome size than their close relatives? What were the genetic changes that were associated with us becoming human?
Ignoring the…
evolgen | April 17, 2007A lot of interesting evolutionary genetics research gets published, and I don't have time to write an insightful commentary on all of it (some may argue that I have never written an insightful commentary on anything). Here's a brief overview of the stuff I have missed in the past few weeks:
A population of sheep was started with the introduction of two individuals on a remote island in the southern region of the Indian Ocean. Surprisingly, genetic diversity has increased over time in this population (reported here). This increase in heterozygosity (measured by the amount of microsatellite…
evolgen | April 17, 2007Two recent papers have been published that both deal with chromosomal aberrations and autism. One paper reports de novo copy number mutations associated with some cases of autism. These are copy number polymorphisms not present in either parent; the mutation arises in the parental germ line, although, I believe it is also possible the mutation happens after fertilization. The other paper presents data using SNPs and copy number variants to map regions of the genome associated with autism risk. I'm not all that interested in the autism component of this research, but the prevalence of…
evolgen | April 14, 2007
As you've probably already heard, George Allen's favorite primate has had its genome sequenced. I promised to blog on the article, but this is not the post. Instead, this post is to kvetch about the coverage of this story in the popular press. It's another adventure in bad science reporting!
Here are two examples of people misreporting the sequencing of a macaque genome:
The Los Angeles Times reports that the "Macaque genome is decoded". They also report, "A team of researchers has deciphered the genome of the rhesus macaque". Decoded and deciphered, but not sequenced. Thomas H. Maugh II,…
evolgen | April 11, 2007Those of us who work on non-human systems often grumble about the total disregard human geneticists (that's geneticists who study humans, not humans who are geneticists) have toward non-human research (that's research on non-humans, not non-humans doing research). I get the feeling that plant biologists have the same attitude toward non-plant researchers, and I imagine there is some unwritten chain of superiority wherein you must pay respect to the researchers working on a system "above" you and ignore the research done on a system "beneath" yours -- and, yes, I realize the higher and lower…
evolgen | April 6, 2007Jonathan Eisen reveals the real motivations behind Craig Venter's ocean metagenomics project.
It was just a few years ago that Dr. Venter announced that the human genome sequenced by Celera Genomics was in fact, mostly his own. And now, Venter has revealed a second twist in his genomic self-examination. Venter was discussing his Global Ocean Voyage, in which he used his personal yacht to collect ocean water samples from around the world. He then used large filtration units to collect microbes from the water samples which were then brought back to his high tech lab in Rockville, MD where he…
evolgen | March 27, 2007We've told you about the manatees making their move from the southeastern United States to the northeast. We warned you that the sea cows ain't as dumb as you thought they were. We took you inside their training camps. We showed you the future of the manatees.
But now, thanks to a patriotic group of researchers, we have information on the organization of the manatee genome -- an important first step in preventing the manatee invasion. The researchers, from the University of Florida and the National Cancer Institute, conclude that the closest living relatives of the manatees, dugongs, and…