genetics
pharyngula | June 13, 2013I'm shocked. Just totally surprised. And it was unanimous — the Supreme Court determined that human genes cannot be patented. This is excellent news.
Why is it a good decision? Because medical DNA analysis was turning into a patchwork of competing landgrabs. Sequencing technology is coming along so nicely that more and more diagnostic tools are available, that can analyze big chunks of the genome for, for instance, known dangerous mutations. But at the same time, many stretches of DNA were 'owned', or patented by various companies. A company called Myriad had the patents on the genes BRCA1…
pharyngula | April 27, 2013Casey Luskin is such a great gift to the scientific community. The public spokesman for the Discovery Institute has a law degree and a Masters degree (in Science! Earth Science, that is) and thinks he is qualified to analyze papers in genetics and molecular biology, fields in which he hasn't the slightest smattering of background, and he keeps falling flat on his face. It's hilarious! The Discovery Institute is so hard up for competent talent, though, that they keep letting him make a spectacle of his ignorance.
I really, really hope Luskin lives a long time and keeps his job as a frontman…
oracknows | April 24, 2013I had a long day in the operating room yesterday; so I was tired last night. As a consequence, I thought that today might end up being one of those rare weekdays free of new Insolence. Then, in the morning as I was doing my usual brief perusal of e-mail and blogs before heading to work, I noticed a post on that wretched hive of antivaccine scum and quackery, Age of Autism, that was such a perfect distillation of the reason why antivaccinationists refuse to accept all the evidence that autism has its roots largely in genetics that I couldn't help but whip off a quickie post. The post revealed…
pharyngula | March 17, 2013After that debate between Tzortzis and Lawrence Krauss that was overshadowed by the disgraceful anti-egalitarian exhibition of Muslim misogyny, iERA is now trying a new tactic: they're releasing tiny snippets of the debate that they believe they can spin into anti-Krauss sentiment. Here's a perfect example, Krauss's reply to a question about the morality of incest.
The audience gasped when Krauss said it's not clear to him that incest is wrong, and then he went on to argue that there are biological and societal reasons why incest is not a good idea, but that he'd be willing to listen to…
pharyngula | February 6, 2013It's a harsh world for us men. Oh, sure, we've got all the political and economic power, and we've got most of the guns, but step into a senior citizens' center and you'll notice the preponderance of elderly women. Men die younger, on average. I'm also acutely aware of the growing disparity as we get older: my wife seems to be aging at about half the rate I do. If you've been watching House of Cards on Netflix, you may have noticed that the character played by Kevin Spacey, face a bit puffy and deeply lined, is married to a character played by Robin Wright (Princess Buttercup!) who is looking…
pharyngula | February 5, 2013I have a bit of a peeve with a common analogy for the human genome: that it is the blueprint of the body, and that we can find a mapping of genes to details of our morphological organization. It's annoying because even respectable institutions, like the National Human Genome Research Institute, use it as a shortcut in public relations material. And it is so wrong.
There is no blueprint, no map. That's not how the system works. What you actually find in the genome are coding genes that produce proteins, coupled to regulatory elements that switch the coding genes off and on using a kind of…
pharyngula | December 27, 2012I've constricted my anus 100 times, and it isn't helping! I'm still feeling extremely cranky about this story from the NY Times.
Scientists intend to sequence Adam Lanza's DNA. They're looking for genetic markers for mass murder. Why? Because some scientists are stupid.
Some researchers, like Dr. Arthur Beaudet, a professor at the Baylor College of Medicine and the chairman of its department of molecular and human genetics, applaud the effort. He believes that the acts committed by men like Mr. Lanza and the gunmen in other rampages in recent years — at Columbine High School and in Aurora,…
gregladen | December 3, 2012I might be exaggerating slightly about the ready availability of the materials...
Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves by George Church and Ed Regis looks like a futurist tome on what could happen when technology finally catches up with human imagination and everything changes. Except it isn't. Most futurists are people with some knowledge of technology, a fertile imagination, and a publicist. Regenesis is by a scientist (working with a writer) who is busy making a different future and who has been involved in every stage of development of the technology under…
pharyngula | October 29, 2012I approve this plan. A number of researchers have gotten together and worked out a grand strategy for sequencing the genomes of a collection of cephalopods. This involves surveying the phylogeny of cephalopods and trying to pick species to sample that adequately cover the diversity of the group, while also selecting model species that have found utility in a number of research areas — two criteria that are often in conflict with one another. Fortunately, the authors seemed to have found a set that satisfies both (although it would have been nice to see the Spirulida and Vampyromorpha make…
pharyngula | September 23, 2012I can take it no more. I wanted to dig deeper into the good stuff done by the ENCODE consortium, and have been working my way through some of the papers (not an easy thing, either: I have a very high workload this term), but then I saw this declaration from the Electronic Frontier Foundation.
On September 19, the Ninth Circuit is set to hear new arguments in Haskell v. Harris, a case challenging California’s warrantless DNA collection program. Today EFF asked the court to consider ground-breaking new research that confirms for the first time that over 80% of our DNA that was once thought to…
gregladen | September 12, 2012A number of lines of evidence have converged on the apparent fact that how you feel about Cilantro is a relatively simple genetic system. That Cilantro hatred is inherited genetically and not culturally has long been suspected, but now it is becoming clear enough that this could be a new module in the Science Classroom where kids are forced to taste it and record their level of disgust. It's all written up here, in Nature.
In hopes of identifying the genetic basis for these traits, researchers led by Nicholas Eriksson at the consumer genetics firm 23andMe, based in Mountain View, California…
pharyngula | July 23, 2012The NY Times is touting a computer simulation of Mycoplasma genitalium, the proud possesor of the simplest known genome. It's a rather weird article because of the combination of hype, peculiar emphases, and cluelessness about what a simulation entails, and it bugged me.
It is not a complete simulation — I don't even know what that means. What it is is a sufficiently complex model of a real cell that it can uncover unexpected interactions between components of the genome, and that is a fine and useful thing. But as always, the first thing you should discuss in a model is the caveats and…
pharyngula | July 21, 2012If you're looking for a meaty weekend read, look no further than Paul McBride's thorough dismantling of Science and Human Origins, the new bad book from the Discovery Institute, by Gauger, Axe, and Luskin. It's in 6 parts, taking on each chapter one by one: Part 1, Part 2, Part 3, a prediction about what will be in chapter 4 before reading it, Part 4 (prediction confirmed!), and Part 5.
The creationists are howling. McBride's evisceration, with Carl Zimmer's detailed description of the evidence for chromosome fusion, all discrediting what they thought would be a hot new text on the scientific…
pharyngula | July 20, 2012I always have unwarrantedly high expectations of creationists. I know that there are some flamingly ignorant nutjobs out there, all your Hams and Hovindses and Luskins, but lurking in my mind is always this suspicion that somewhere there has to be one or two biologically competent ideologues on their side of the fence. And I am always disappointed.
For example, there's this one fellow, Douglas Axe, who has a legitimate and well-earned doctoral degree in chemical engineering, and several published papers in real science journals (not the fake journals creationists create). The Discovery…
jhalper | May 31, 2012Would you learn a language by taking a written text and changing letters here and there, or moving a few words around, and asking whether the meaning has changed? That may not be the most efficient way to learn French, but a Weizmann Institute scientist is betting that it will be a very useful way to improve our grasp of what is written in our DNA. Prof. Eran Segal, a computer scientist cum biologist, and his team developed a quick method for rewriting DNA that enables thousands of changes to be created at once, each in its own little, living cell, and measuring the effects of each such…
milhayser | May 24, 2012
On the Weizmann Wave, researchers have made a discovery surrounding exons—"bits of genetic code that are snipped out of the sequence and spliced together to make the protein instruction list." When a cell needs to make a protein, it pulls exons out of pre-messenger RNA and stitches them together to form messenger RNA. Alternating sequences called introns are left out. By tracking the unused introns, researchers observed that "in some cases, pre-mRNA production shot straight up - to ten times or more than that of the mRNA that followed." They call this "production overshoot," for when "the…
pharyngula | May 7, 2012Vertebrates are modified segmented worms; that is, their body plan is made up of sequentially repeated units, most apparent in skeletal structures like the vertebrae.
Arthropods are also modified segmented worms. Look at a larval fly, for instance, and you can see they are made up of rings stacked together.
So here's a simple and obvious question: can we infer that the last common ancestor of vertebrates and arthropods was also a segmented worm? That is, is segmentation a common ancestral trait, or did arthropods and vertebrates invent it independently? At first thought, you might assume they…
pharyngula | April 25, 2012A while back, I told you all about this small piece of the biochemistry of the fly eye — the pathways that make the brown and red pigments that color the eye.
I left it with a question: if even my abbreviated summary revealed considerable complexity, how could this pathway evolve? Changing anything produces a failure or change in the result. Before I answer, let's make the problem even harder, because I love a challenge (although actually, I'm cheating — it's going to turn out that complexity is not a barrier, but an opportunity).
The pigment pathways above are far downstream: they operate…
gregladen | April 24, 2012This is a proof of concept blog post. Please give it a try and let me know if it works for you!
Double Helix from the Wolfram Demonstrations Project by Sándor Kabai
milhayser | March 19, 2012
We've all heard of bird and swine flu, but bats, which comprise "about a fifth of all known mammalian species," also carry a diverse host of viruses. By swabbing the rectums of little yellow-shouldered bats, researchers in Guatemala discovered a new influenza virus that defies easy classification. Flu viruses are described by two key genes—hence the name 'H1N1.' Tara C. Smith writes "The novel bat virus was a completely new H type—type 17 (provisional, they note, pending further analyses). The NA gene was also highly divergent." Smith continues "the authors did do some molecular work…