evolution
sa smith | August 28, 2012Ive always wanted a ferret. When I was little, because of this (1m59s):
Now, because of stuff like this:
Ferrets arent just super cool pets, they also have a very rare 'gift'-- While all organisms genomes are littered with pirate DNA and endogenous retroviruses, endogenous lentiviruses have only been found in three creatures: Bunnies, lemurs, and now, ferrets!
Endogenous Lentiviral Elements in the Weasel Family (Mustelidae)
Lentiviruses are 'complex', in that they have the basics retroviruses need to survive, LTRs, gag, pol, and env, plus some bonus genes. In this case, vif, tat, and rev…
sa smith | August 27, 2012Paleovirology seems to work the opposite of the way the Creationist want. The more information we have, the further back the timeline shifts, not vice versa.
For example, we used to think HIV-1 started in humans ~1930, but after we found more 'old' HIV sequences, the clock got pushed back to 1902-1921.
We used to think Simian Immunodeficiency Virus emerged 1266-1685, but after we found more 'old' SIV sequences, the clock got pushed back 76,794 years.
After a recent finding in fish, the evolutionary history of retroviruses got pushed back... 400 million years.
An Endogenous Foamy-like Viral…
jrosenhouse | August 20, 2012A while back I did a post criticizing the idea that theistic evolution is a form of intelligent design. My argument was that theistic evolutionists accept modern evolutionary science as essentially correct, but also believe that it is not the whole story. This is relevantly different from those who say that modern science is rotten to the core. In the political arena theistic evolutionists are on the right side of issues in science education, whereas the ID folks are on the wrong side. For those reasons, it is simply unfair to equate the two. Or so I argued, at any rate.
I stand by that…
sa smith | August 17, 2012ARR!
I mean, ERV!
I mean, NIRV!
Phylogeny, integration and expression of sigma virus-like genes in Drosophila
As my blag tagline goes, 'If we are made in Gods image, God is made of gag, pol, and env', the components of retroviruses. Our, and other organisms, genome is inhabited by lots of bits of selfish DNA, including retroviruses.
But retroviruses are not the only group of viruses who have made themselves right at home in our DNA-- once we started looking, it turns out that there are allllll kinds of viruses just hangin out!
Its not hard to imagine how endogenous retroviruses came to be--…
sa smith | August 1, 2012The Evolutionary Consequences of Blood-Stage Vaccination on the Rodent Malaria Plasmodium chabaudi
The concept of vaccination is, superficially, simple-- Safely mimic 'infection' so your immune system learns how to fight a pathogen, without needing to get sick from the genuine pathogen. Then if you are ever exposed to the real, scary pathogen, your immune system already knows how to deal with it.
But things dont always go according to plan...
In 1966, a novel vaccine against Respiratory Syncytial Virus was a tragic failure. The lucky kids didnt respond at all. The unlucky kids made a…
jrosenhouse | July 30, 2012With all of my recent travels, I feel like most of the last few weeks have been spent either on the road or preparing to go on the road. I will be making another pilgrimage to New York next week, mostly business this time, but some pleasure as well. As a result, a lot of good blog fodder has been falling through the cracks.
So, let's try to get caught up on a few things. The first orders of business are two recent posts from Michael Ruse. In the first, he once more offers his thoughts on the question of human inevitability in evolution. He writes:
The problem is this. If Christianity…
sa smith | July 30, 2012I know I give physicians crap sometimes on my blag, but I really do appreciate what they--along with nurses, physical and respiratory therapists, and other health professionals-- do.
They interact with people when they are at their 'worst'-- a normally cheerful, charming person is sick, scared, in pain, frustrated, worried, hurt, angry, drugged up when they are at the hospital. They are not themselves. And when patients are in this 'altered' state, they are helpless, relying on these professionals for help. I dont just mean 'helpless' in the sense most of us have no idea how to remove a…
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…
pharyngula | July 19, 2012Somedays, it's just awful to have the mind of a 12 year old boy. So I'm reading this serious and interesting paper on Neandertals, and learn something new.
Two particular characteristics have received considerable attention; pronounced humeral diaphysis strength asymmetry and anteroposteriorly strengthened humeral diaphyseal shape. In particular, humeral bilateral asymmetry for cross-sectional area, and torsional and average bending rigidity, appear exceptionally high in Neandertals (averaging 24–57%) compared to skeletal samples of modern Holocene H. sapiens (averaging 5–14%).
That's…
pharyngula | July 12, 2012I'm always telling people you need to understand development to understand the evolution of form, because development is what evolution modifies to create change. For example, there are two processes most people have heard of. One is paedomorphosis, the retention of juvenile traits into adulthood — a small face and large cranium are features of young apes, for instance, and the adult human skull can be seen as a child-like feature. A complementary process is peramorphosis, where adult characters appear earlier in development, and then development continues along the morphogenetic trajectory…
pharyngula | July 11, 2012If you ever get a chance, spend some time looking at fish muscles in a microscope. Larval zebrafish are perfect; they're transparent and you can trace all the fibers, so you can see everything. The body musculature of fish is most elegantly organized into repeating blocks of muscle along the length of the animal, each segment having a chevron ("V") or "W" shape. Here's a pretty stained photo of a 30 hour old zebrafish to show what I mean; it's a little weird because this one is from an animal with experimentally messed up gene expression, all that red and green stuff, but look at the lovely…
oracknows | July 9, 2012Something came up that made me think it would be a good idea to mention a couple of features of the new WordPress template, just in case anyone missed them when I mentioned them before. I apologize to any who might find this repetitive, but there do appear to be some newbies here; so I think it's worth a quick repeat.
A commenter who borders on trollish wrote:
One thing I forgot. I wanted to congratulate you and the team for closing ‘Evolution and Medicine’ just when you did, leaving the impression that I am EXTREMELY dangerous. Well, I’m not in the least little bit dangerous, but it’s…
sa smith | July 5, 2012The questions I get asked most often are:
How many ERVs are there?
How many do we have in common with chimpanzees/gorillas/orangutans/etc?
Its hard to answer this. Depends on what your definition of 'ERV' is. Because sometimes scientists mean a complete/nearly complete ERV (LTR-gag, pol, env-LTR), and sometimes they mean either LTR, Gag, Pol, or Env, or any combination. There are very few of the former, and a lot of the latter.
But how many are there total? Well, its hard to say. Sure, we sequenced the human (and chimpanzee, etc) genome, but we skipped a lot of the parts that are just…
oracknows | June 27, 2012And now for something completely different.
Except that it isn't really. I say that it isn't really different because, although this post will seem to be about politics, in reality it will be about a common topic on this blog: Anti-science. And where is this anti-science? Sadly, it's in the platform of a major party of one of the largest states in the country. It also meshes with the anti-science inherent in a lot of so-called "complementary and alternative medicine" (CAM) and all comes together in one place: The proposed 2012 Platform of the Republican Party of Texas. It's all there, as you…
pharyngula | June 24, 2012Red hair. Freckles. Pale skin. Soulless. What good are they?
Seriously — I have a red-haired son and brother and cousins, and you've got to wonder why evolution has spawned all these strange color variants — there's no known advantage to ginger-ness, and plenty of disadvantages.
The biochemical cause of these differences are known. Pigmentation is produced by the deposition of a complex light absorptive polymer called melanin in cells. We vertebrates produce primarily two forms of melanin, eumelanin and pheomelanin.
Eumelanin is a dark pigment; cells loaded up with it look black or dark…
pharyngula | June 20, 2012I've been working up a science talk for the fall — I am going to do a basic review of many the mechanisms other than selection that contribute to evolution for lay audiences. And then I discover that T. Ryan Gregory has already done some of the work for me.
Maybe I should just plagiarize it?
(No, not really: my talk is less genomics, more development, and gets more basic than this one. But Gregory's talk is very, very good.)
(via Sandwalk.)
gregladen | June 20, 2012The Rocks Don't Lie: A Geologist Investigates Noah's Flood by David Montgomery is new book on the Noachian flood. It is by a real life geologist and is not a creationist book. Might be a good gift for your annoying creationist relative.
Here is a write-up from the publisher:
In Tibet, geologist David R. Montgomery heard a local story about a great flood that bore a striking similarity to Noah’s Flood. Intrigued, Montgomery began investigating the world’s flood stories and—drawing from historic works by theologians, natural philosophers, and scientists—discovered the counterintuitive role…
pharyngula | June 18, 2012I found this very satisfying: Steven Pinker summarizes all the problems with group selection. It's a substantial essay, but if you just want the gist of it, here's the conclusion.
The idea of Group Selection has a superficial appeal because humans are indisputably adapted to group living and because some groups are indisputably larger, longer-lived, and more influential than others. This makes it easy to conclude that properties of human groups, or properties of the human mind, have been shaped by a process that is akin to natural selection acting on genes. Despite this allure, I have argued…