Molecular Biology
pharyngula | July 12, 2011That's not hyperbole. I really mean it. How else could I react when I open up the latest issue of Bioessays, and see this: Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules. Just from the title alone, I'm immediately launched into my happy place: sitting on a rocky beach on the Pacific Northwest coast, enjoying the sea breeze while the my wife serves me a big platter of bacon, and the cannula in my hypothalamus slowly drips a potent cocktail of cocain and ecstasy direct into my pleasure centers…and there's pie for dessert. It's like the…
pharyngula | July 7, 2011I found a recent paper in Nature fascinating, but why is hard to describe — you need to understand a fair amount of general molecular biology and development to see what's interesting about it. So those of you who already do may be a little bored with this explanation, because I've got to build it up slowly and hope I don't lose everyone else along the way. Patience! If you're a real smartie-pants, just jump ahead and read the original paper in Nature.
A little general background.
Let's begin with an abstract map of a small piece of a strand of DNA. This is a region of fly DNA that encodes a…
pharyngula | May 4, 2011So you're tantalized by this strange obsession creationists have with junk DNA. It offends them mightily, I think because they find comfort in the idea that everything in the universe must have a purpose, because if it doesn't, maybe that means they are nothing more than spots of dandruff on a dead rock hurtling blindly through space, and we can't have that then.
It's true that the odious Jonathan Wells has written a whole book declaring that everything in the genome has a glorious function implicitly designed by his god, the Rev. Sun Myung Moon. Larry Moran has begun the process of…
pharyngula | April 27, 2011
I've been giving talks at scientific meetings on educational outreach — I've been telling the attendees that they ought to start blogs or in other ways make more of an effort to educate the public. I mentioned one successful result the other day, but we need more.
I give multiple reasons for scientists to do this. One is just general goodness: we need to educate a scientifically illiterate public. Of course, like all altruism, this isn't really recommended out of simple kindness, but because the public ultimately holds the pursestrings, and science needs their understanding and support.…
pharyngula | December 28, 2010
My direct experience with prokaryotes is sadly limited — while our entire lives and environment are profoundly shaped by the activity of bacteria, we rarely actually see the little guys. The closest I've come was some years ago, when I was doing work on grasshopper embryos, and sterile technique was a pressing concern. The work was done under a hood that we regularly hosed down with 95% alcohol, we'd extract embryos from their eggs, and we'd keep them alive for hours to days in tissue culture medium — a rich soup of nutrients that was also a ripe environment for bacterial growth. I was…
pharyngula | December 27, 2010
When last we left this subject, I had pointed out that the phenomenon of embryonic similarity within a phylum was real, and that the creationists were in a state of dishonest denial, arguing with archaic interpretations while trying to pretend the observations were false. I also explained that constraints on morphology during development were complex, and that it was going to take something like a thorough comparative analysis of large sets of gene expression data in order to drill down into the mechanisms behind the phylotypic stage.
Guess what? The comparative analysis of large sets of…
pharyngula | August 12, 2010One of the subjects developmental biologists are interested in is the development of pattern. There are the obvious externally visible patterns — the stripes of a zebra, leopard spots, the ordered ranks of your teeth, etc., etc., etc. — and in fact, just about everything about most multicellular organisms is about pattern. Without it, you'd be an amorphous blob.
But there are also invisible patterns that you don't normally see that are aspects of the process of assembly, the little seams and welds where disparate pieces of the organism are stitched together during development. The best known…
pharyngula | July 30, 2010Spiegel has a wonderful interview with Venter. The more I hear from Venter, the more I like him; he's very much a no-BS sort of fellow. He's the guy who really drove the human genome project to completion, and he's entirely open about explaining that its medical significance was grossly overstated.
SPIEGEL: So the significance of the genome isn't so great after all?
Venter: Not at all. I can tell you from my own experience. I put my own genome on the Internet. People had the notion this was the scariest thing out there. But what happened? Nothing.
There really was a lot of hysteria in the…
pharyngula | July 24, 2010
Most of you don't understand evolution. I mean this in the most charitable way; there's a common conceptual model of how evolution occurs that I find everywhere, and that I particularly find common among bright young students who are just getting enthusiastic about biology. Let me give you the Standard Story, the one that I get all the time from supporters of biology.
Evolution proceeds by mutation and selection. A novel mutation occurs in a gene that gives the individual inheriting it an advantage, and that person passes it on to their children who also gets the advantage and do better than…
pharyngula | July 15, 2010
Sometimes, I really hate fossils. I hate them with the passion of a spurned lover, one who is consumed with desire but knows that he will never, ever be satisfied. They drive me mad.
Right now we're at a point in our technology where we can take a small sample from a living organism and break it down into amazing detail — we can extract every gene, throw them into a computer, and compare them with every other gene that has been similarly sampled. We can look for the scars of evolution, we can analyze and figure out where on the tree of life this cell resides, we can even figure out what…
pharyngula | July 14, 2010Bleh. MSNBC is running a terrible article that claims they have "proof" that chickens came before eggs. It's just an awful mess, and one of the scientists is at least partly responsible.
The scientists found that a protein found only in a chicken's ovaries is necessary for the formation of the egg, according to the paper Wednesday. The egg can therefore only exist if it has been created inside a chicken.
…
"It had long been suspected that the egg came first but now we have the scientific proof that shows that in fact the chicken came first," said Dr. Colin Freeman, from Sheffield University…
grrlscientist | June 28, 2010tags: Evolution in Action by AMNH, Congo River, fishes, AMNH, American Museum of Natural History, evolution, variation, biodiversity, Melanie Stiassny, streaming video
This video tells the story of speciation in Central Africa's roiling, rapid Lower Congo River. This river is home to an extraordinary assortment of fish -- many truly bizarre. This new video by Science Bulletins, the American Museum of Natural History's current-science video program, features Museum scientists on a quest to understand why so many species have evolved here. Follow Curator of Ichthyology Melanie Stiassny and her…
pharyngula | June 13, 2010Nicholas Wade of the NY Times has written one of those stories that make biologists cringe — it just gets so much wrong. It's a look back at the human genome project, and I was turned off at the first paragraph. The HGP was badly marketed from the very beginning in the sense that there was a misrepresentation of the scientific goals; it was well-marketed if your goal was wringing money out of congress. Unfortunately, now we've got to deal with science writers complaining that nobody has generated any miracle cures from all that work. Pay attention to what Harold Varmus said:
"Genomics is a…
pharyngula | June 10, 2010
I've gotten some email asking for a simplified executive summary of this paper, so here it is.
A large study of almost a thousand autistic individuals for genetic variations that make them different from control individuals has found that Autism Spectrum Disorder has many different genetic causes: there isn't one single gene responsible for ASD, but a constellation of hundreds, each with the potential to affect the development of the brain and cause the symptoms of autism. They don't know exactly how each of these genes contributes to the disorder, but they have found that many of them are…
pharyngula | June 7, 2010I keep telling people there's junk in them thar genomes, and lots of it. ERV has a nice summary of some recent work in which a detailed comparison of the distribution of LINE retrotransposons (selfish DNA that does nothing but insert copies of itself into your DNA; they make up about 20% of your genome) was made — and what they found was that variations were common, new insertions were relatively frequent, and that they can be used to map out human relatedness (although we've known that one for a while).
LINEs are super useful for determining/tracing human ancestry. As Im sure you all have…
neurophilosophy | June 7, 2010TRICHOTILLOMANIA (or hair pulling) is a condition characterised by excessive grooming and strong, repeated urges pull out one's own hair. It is classified as an obsessive-compulsive disorder (OCD), and is relatively common, affecting about 2 in 100 people. Sufferers normally feel an increasing sense of tension before pulling out their scalp hair, facial hair, and even pubic hair, eyelashes or eyebrows. This provides gratification, but only briefly.
Hair pulling is usually thought of as being psychological in origin, but an intruiging new study now suggests that it occurs as a result of…
pharyngula | May 24, 2010They're discussing Venter's nifty new toy on Edge, and I've tossed my own contribution into the mix. It's a response to the doomsday fears I keep seeing expressed in response to the success of this project.
I have to address one narrow point that is being discussed in the popular press and here on Edge: is Venter's technological tour de force a threat to humanity, another atom bomb in the hands of children?
No.
There is a threat, but this isn't it. If you want to worry, think about the teeming swarms of viruses, bacteria, fungi, and parasites that all want to eat you, that are aided (as we…
pharyngula | May 24, 2010Randy Stimpson is someone a few may recall here: he was a particularly repetitious and dishonest creationist who earned himself a spot in the dungeon. One of the hallmarks of his obtuse way of 'thinking' is that he is a computer programmer, and so he was constantly making the category error of assuming the genome was a computer program, and therefore the product of intelligent design (never noticing that he himself is an example of how programming a computer requires relatively little intelligence). He objects to the notion of junk DNA on the Panda's Thumb, and I just have to tear apart his…
pharyngula | May 22, 2010I've been following the reaction to the synthesis of a new life form by the Venter lab with some interest and amusement. There have been a couple of common directions taken, and they're generally all wrong. This is not to say that there couldn't be valid concerns, but that the loudest complaining voices right now are the most ignorant.
Hysteria and fear-mongering
Pearl-clutching and fretting over the consequences is fairly common, with a representative example from The Daily Mail (Stridently stupid 'journalistic' outlet).
But there are fears that the research, detailed in the journal Science…
pharyngula | May 20, 2010Get in the mood for this bit of news, the synthesis of an artificial organism by Craig Venter's research team.
Here's the equivalent of that twitching hand of Frankenstein's monster:
Those are two colonies of Mycoplasma mycoides, their nucleoids containing entirely synthesized DNA. You can tell because the synthesized DNA contained a lacZ gene for beta-galactosidase, making the pretty blue product. That's one of the indicators that the artificial chromosome is functioning inside the cell; the DNA was also encoded with recognizable watermarks, and they also used a cell of a different…