Molecular Biology
pharyngula | September 25, 2013
I'm trying to raise money for the The Leukemia & Lymphoma Society, and I promised to do a few things if we reached certain goals. I said I'd write a post explaining what tumor suppressor genes are, while wearing a pirate hat and nothing else, if we raised $5000. Shiver me timbers, I did! And it's cold!
If you want more, go to my Light the Night fundraising page and throw money at it. I'll write about microRNAs and cancer when we hit $7500. Note that we're also getting matching funds from the Todd Stiefel Foundation, so join in, it's a good deal.
There's a basic principle in…
pharyngula | September 21, 2013
I'm trying to raise money for the The Leukemia & Lymphoma Society, and I promised to do a few things if we reached certain goals. I said I'd write a post explaining what oncogenes are, while wearing a pirate hat, if we raised $2500. So here you go, arrr.
If you want more, go to my Light the Night fundraising page and throw money at it. I'll write the next part when we hit $5000. Note that we're also getting matching funds from the Todd Stiefel Foundation, so join in, it's a good deal.
Cancer is not a creative, original disease; it has not been honed by ages of evolution to craft…
pharyngula | August 7, 2013You know I was really pissed off at the crap ENCODE was promoting, that the genome was at least 80% functional and that there was no such thing as junk DNA. And there have been a number of better qualified scientists (like W. Ford Doolittle and Dan Graur and many others) who have stood up and registered their vehement disagreement with that nonsense. But there are some who agree that the genome must be largely functional, like John Mattick. Larry Moran reminds me that Mattick is the author of this infamous chart, however, which is best known as the original Dog's Ass Plot.
That is so…
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 | March 23, 2013There's another paper out debunking the ENCODE consortium's absurd interpretation of their data. ENCODE, you may recall, published a rather controversial paper in which they claimed to have found that 80% of the human genome was 'functional' — for an extraordinarily loose definition of function — and further revealed that several of the project leaders were working with the peculiar assumption that 100% must be functional. It was a godawful mess, and compromised the value of a huge investment in big science.
Now W. Ford Doolittle has joined the ranks of many scientists who immediately leapt…
pharyngula | February 22, 2013I rarely laugh out loud when reading science papers, but sometimes one comes along that triggers the response automatically. Although, in this case, it wasn't so much a belly laugh as an evil chortle, and an occasional grim snicker. Dan Graur and his colleagues have written a rebuttal to the claims of the ENCODE research consortium — the group that claimed to have identified function in 80% of the genome, but actually discovered that a formula of 80% hype gets you the attention of the world press. It was a sad event: a huge amount of work on analyzing the genome by hundreds of labs got…
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 | November 20, 2012A while back, two physicists, Paul Davies and Charles Lineweaver, announced their explanation for cancer with a novel theory, which is theirs, that cancers are atavisms recapitulating in a Haeckelian reverse double backflip their premetazoan ancestry. They seemed very proud of their idea.
I was aghast, as you might guess. They even claimed that human embryos go through a fish/amphibian stage with gills, webbed feet, and tails in a pattern of Haeckelian development. They do not understand evolution, development, or cancer, facts that were apparent even in the absence of their admission that…
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…
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 | 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…
pharyngula | December 19, 2011I've been guilty of teaching bean-bag genetics this semester. Bean-bag genetics treats individuals as a bag of irrelevant shape containing a collection of alleles (the "beans") that are sorted and disseminated by the rules of Mendel, and at its worst, assigns one trait to one allele; it's highly unrealistic. In my defense, it was necessary — first-year students struggle enough with the basic logic of elementary transmission genetics without adding great complications — and of course, in some contexts, such as population genetics, it is a useful simplification. It's just anathema to anyone…
pharyngula | December 5, 2011So you read that cool summary of how to build a molecular biology lab for $500. But wait, you don't know what you'd do with the mobio toys! Here's how to correct that: go to a workshop.
THE MICHAEL SMITH LABS AND ADVANCED MOLECULAR BIOLOGY LAB PRESENTS OUR MOLECULAR BIOLOGY WORKSHOPS 2012 WINTER/SPRING Session.
ONE WEEK VERSION (5 DAYS) - MOLECULAR TECHNIQUES WORKSHOPS
FEB 13 - 17, 2012 (CAN$1400)
DESCRIPTION: Recently updated: This intense 5 day workshop will focus on a myriad of different techniques used in the molecular manipulation of DNA, RNA and protein, as well as inclusion of…
pharyngula | December 4, 2011The future is arriving fast. Here are the instructions for assembling a $500 home molecular biology laboratory — you can do it! And it's getting cheaper all the time!
The widespread and increasing availability of second-hand professional laboratory equipment or inexpensive new commercial surrogates means that it is now unchallenging to set up a fully functional molecular laboratory for less than $500 in equipment costs. Coupled with the presence of sources for all reagents and supplies needed in formats that are safe for general use, the work presented here demonstrates that capacity to set…
pharyngula | December 2, 2011Yeah, I gave a talk at Skepticon like several other rascals here at Freethoughtblogs. Now, even if you didn't make the pilgrimage to Springfield, Missouri, you can watch it too.
It's a straight science talk with several swipes at creationism, so unfortunately, I don't think it will make any ice cream salesmen cry.
(Also on FtB)
pharyngula | October 26, 2011This is an article about cephalopods and eye evolution, but I have to confess at the beginning that the paper it describes isn't all that interesting. I don't want you to have excessive expectations! I wanted to say a few words about it, though, because it addresses a basic question I get all the time, and while I was at it, I thought I'd mention a few results that set the stage for future studies.
I'm often asked to resolve some confusion: the scientific literature claims that eyes evolved multiple times, but I keep saying that eyes show evidence of common origin. Who is right? Why are you…
pharyngula | October 20, 2011In my previous post, I described the misguided approach Gauger and Axe have taken to criticizing evolution, and one of the peculiarities of their criticism is that they cited another paper by a paper by Carroll, Ortlund, and Thornton which traced (successfully) the evolutionary history of a class of proteins. Big mistake. As I pointed out, one of the failings of the Gauger/Axe approach is that they're asking how one protein evolved into a cousin protein, without considering the ancestral history …they make the error of trying to argue that an extant protein couldn't have directly evolved into…
pharyngula | August 21, 2011Jerry Coyne is mildly incensed — once again, there's a lot of
recent hype about epigenetics, and he doesn't believe it's at all revolutionary. Well, I've written about epigenetics before, I think it's an extremely important subject central to our understanding of development, and…I agree with him completely. It's important, we ought to spend more time discussing it in our classes, but it's all about the process of gene expression, not about radically changing our concepts of evolution. I like to argue that what multigenerational epigenetic effects do is blur out or modulate the effects of…