evolution
pharyngula | January 4, 2015Oh, look. The creationists have been routed, and the problem of the origin of life has been solved. Would you like to learn about the brilliant new science that has creationists and the Christian right terrified?
The Christian right’s obsessive hatred of Darwin is a wonder to behold, but it could someday be rivaled by the hatred of someone you’ve probably never even heard of. Darwin earned their hatred because he explained the evolution of life in a way that doesn’t require the hand of God. Darwin didn’t exclude God, of course, though many creationists seem incapable of grasping this point.…
pharyngula | December 30, 2014Since we still have someone arguing poorly for the virtues of the ENCODE project, I thought it might be worthwhile to go straight to the source and and cite an ENCODE project paper, Defining functional DNA elements in the human genome. It is a bizarre thing that actually makes the case for rejecting the idea of high degrees of functionality, which is a good approach, since it demonstrates that they've at least seen the arguments against them. But then it sails blithely past those objections to basically declare that we should just ignore the evolutionary evidence.
Here's the paragraph where…
sporte | December 27, 2014Sometimes when you go digging through the databases, you find unexpected things.
When I was researching the previous posts on insulin structure and insulin evolution, I found something curious indeed.
Human insulin, colored by rainbow. Image from the Molecule World iPad app by Digital World Biology.
I wanted to find out how many different organisms made insulin, so I used a database at the NCBI called Blink. Blink is a database of protein blast search results. Using Blink can save you lots of time because it organizes blast results from all the organisms in the non-…
pharyngula | December 7, 2014Also, master of molluscan anatomy, and clever tool user. This paper, Homo erectus at Trinil on Java used shells for tool production and engraving, by Joordens et al. tells an interesting story from some mundane artifacts made half a million years ago.
What the investigators have is a jumble of clam shells, found in the strata where Homo erectus bones have been found elsewhere. These shells have been modified -- the inference is that H. erectus was living along the shore, gathering clams, and popping them open to eat.
First, evidence of tool use. Many of them have small holes, precisely gouged…
sa smith | December 5, 2014For some reason, pop news became enamored with this paper last month (unfortunately while I was away at a conference):
HIV infection en route to endogenization: two cases
Inexplicable media frenzy--
Scientists find mechanism for spontaneous HIV cure
French scientists find genetic mechanism by which two men were spontaneously cured of HIV.
HIV discovery offers new lead in finding cure
I have a lot of problems with this paper. Starting with the first sentence.
The long-term spontaneous evolution between humans and the human immunodeficiency virus (HIV) is not well characterized.
"Spontaneous…
sa smith | December 4, 2014I write about lots of things on ERV, but I didnt anticipate ever getting to the point where I can write new blog posts on new publications by cutting and pasting from old blog posts on old papers...
Lots of news outlets have been talking about this new paper:
Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence
Ive covered the themes of this paper several times in the past.
1-- Some people progress to AIDS after HIV infection, some dont, or do so slowly. One of the reasons why one person might not progress to AIDS would be their particular MHC Class I…
pharyngula | November 30, 2014Everyone I know is raving about this short, speculative video about the future of space exploration.
Wanderers - a short film by Erik Wernquist from Erik Wernquist on Vimeo.
I'm not so enthused; I even find the words of Carl Sagan troubling. It's lovely and all, but…
There's nothing in those exotic landscapes as lovely and rich as mossy and majestic cedars of the Olympic Peninsula, or the rocky sea stacks of the nearby coast. The northern tundra is more alive than an icy plain on a distant moon; having Saturn's rings as a backdrop is not as glorious as an earthly sunset. If you want desert…
oracknows | November 24, 2014(Orac note: I was away at Skepticon over the weekend, where I gave a talk entitled The Central Dogma of Alternative Medicine. (When the talk’s up on YouTube, I’ll provide a link, of course.) Because of all the fun and travel delays I didn’t get a chance to turn my slides and notes into a blog post yet. Also, I’m on vacation this week. However, this gives me the opportunity to resurrect a blog post from 2007, because I think the concept is interesting. I even use it in a slide that shows up in many of my talks (above). I’ve updated dead links and added some text to include relevant links to…
pharyngula | November 16, 2014Just consult the chart.
Dated phylogenetic tree of insect relationships. The tree was inferred through a maximum-likelihood analysis of 413,459 amino acid sites divided into 479 metapartitions. Branch lengths were optimized and node ages estimated from 1,050,000 trees sampled from trees separately generated for 105 partitions that included all taxa. All nodes up to orders are labeled with numbers (gray circles). Colored circles indicate bootstrap support (left key). The time line at the bottom of the tree relates the geological origin of insect clades to major geological and biological…
sa smith | November 6, 2014Attention those of you in the Atlanta area!
The students in Kennesaw State University Atheists United have invited Richard Dawkins to speak on campus, and they are opening up their event to the public!
Tickets are available for purchase HERE!
Im gonna get him to sign our Nightwish poster!!! :-D
sa smith | October 23, 2014The title of this article by Answers In Genesis is a good question:
Where Did Ebola Come From?
*shrug* Look, I love making fun of Creationists, but this is a great question!
Ebola is not 'supposed' to be a human pathogen. Like many emerging infectious diseases, the natural reservoir for ebola is bats. Specifically, fruit bats.
By studying the genomes of many small mammals, we have determined that ebola-like viruses have existed on Earth, infecting small mammals, for 12 to 24 million years.
YAY! Straight forward answer to an interesting, valid question.
...... But with Creationists, things are…
sa smith | October 20, 2014October 2012, I got to see Nightwish at a small venue in OKC.
1-- This was one of the first nights Floor Jansen was officially the New Singer for Nightwish. She blew me away.
2-- This was a *tiny* venue. Nightwish fills huge stadiums and auditoriums all over the world, but OKC? Teeny venue. And that band played for us the same way they would have played for an audience of thousands. They *WAILED*.
3-- It was my partners birthday, and while the security guys couldnt let us backstage, he did get us an autographed poster:
They are an extremely talented group of musicians and singers, and just…
gregladen | September 30, 2014This discussion has been going on for some time, and a handful of recent events have prompted me to jump into it (beyond a simple comment or two). First, I saw a bunch of yammering among various biology teachers about this topic. Then Michael Osterholm wrote a well intentioned but seemingly deeply flawed opinion at the New York Times, then Dina Fine Maron wrote an excellent piece at Scientific American deconstructing Osterholm's piece, then the latter two (and more) were summarized and expanded on in a post by Ann Reid at the NCSE.
Here, I will expand on this by applying first principles…
pharyngula | September 27, 2014
Creationists are much vested in the idea of "suddenly" -- they love the idea of inserting the fingersnap of God into every abrupt transition. This is why they are infatuated with the Big Bang and the Cambrian Explosion, and why they flirted with the idea of renaming "Intelligent Design" to "Sudden Origins" theory. If something had no antecedents, no gradual build up, well then, we have to explain it with "God did it!".
Unfortunately, the media plays along with it. I found a bit of scientific misinformation on the Raw Story -- such obvious stupidity that anyone with any basic training in…
pharyngula | September 23, 2014Vestigial organs are relics, reduced in function or even completely losing a function. Finding a novel function, or an expanded secondary function, does not make such organs non-vestigial.
The appendix in humans, for instance, is a vestigial organ, despite all the insistence by creationists and less-informed scientists that finding expanded local elements of the immune system means it isn't. An organ is vestigial if it is reduced in size or utility compared to homologous organs in other animals, and another piece of evidence is if it exhibits a wide range of variation that suggests that those…
pharyngula | September 4, 2014JBS Haldane is said to have responded to a question about how evolution could be disproved by saying, "A Precambrian rabbit". What was meant by this, of course, is any substantial discovery that greatly disrupted the evidence for the chronological pattern of descent observed in Earth's life. That pattern of descent is one of the central lines of evidence for evolution, so creationists would dearly love to find something that wrecked it -- this is why they send expeditions to Africa to find a living dinosaur, Mok'ele-mbembe, or more conveniently, to Canada in search of a plesiosaur, Manipogo.…
pharyngula | August 31, 2014I made the mistake of reading some of the comments on those last youtube videos. There were some good ones, but they were also laced with the usual grunting assholes complaining about gays and "trannies" and quoting the Bible and making racist remarks about Africans. Let us pass over those contemptible arguments; there's no dealing with them rationally. Spit and move on.
But there's another flavor of argument that annoys me to no end: people who cite science and evolution to support their ignorant misconceptions about human nature. I want to address two, one anti-gay and the other pro-gay,…
dr. dolittle | August 30, 2014 Image of seals from www.fanpop.com/clubs/the-animal-kingdom/images/14060694/title/seal-wall…
Paleogeneticist Dr. Johannes Krause (University of Tübingen, Germany) and colleagues were interested in the origin of tuberculosis (TB) in the Americas. Since strains of TB found in the Americas are related to strains found in Europe, prior theories held that Spaniards may have introduced it to the Americas while colonizing South America. The problem with those theories is that pre-Columbian skeletal remains showed signs of TB much earlier.
Dr. Krause was quoted in Scientific American, “Pathogens…
pharyngula | August 28, 2014Sometimes, people email me with good questions. Here's one.
When I was a kid, my own visualization of evolution was Lamarckism.
But I didn't know it. In reading Dawkins and others, I know it doesn't exist. But it seems this article is claiming it does to some extent. Can you comment? I'm curious as to the current consensus as I've been reading a lot about genes that can be turned on and passed to offspring. Can you take a look?
This is a fairly common question. Looked at naively, developmental plasticity seems to be Lamarckian -- we're talking about organisms responding with…
pharyngula | August 20, 2014Susan Blackmore always lectures entertainingly -- really, if you get a chance to hear her, you should -- so I can guess how surprised she was when students claimed offense and walked out on her talk. They were religiously indoctrinated, and simply shut down their brains when the word "evolution" came up, and when she started presenting rational and secular explanations for the existence of religion, just forget it -- there were a lot of students who thought you could only quote the Bible and Koran with unstinting reverence, accepting their divine claims at face value.
It is sad to see young…