evolution
sa smith | December 9, 2013Bone marrow transplants and HIV. I have been writing about this topic for a long time. Quick recap.
1. Some people with HIV-1 infection subsequently get blood cancers.
2. Sometimes those blood cancers need to be treated with bone marrow transplants.
2a. If the patient gets a transplant from a CCR5 negative donor, its great! HIV prefers to use CCR5 for a co-receptor, so if its not there, HIV has a bad time. Example: Berlin patient.
2b. If the patient gets a transplant from a regular immunological match, they are taken off of antiretrovirals during treatment. Treating the cancer is a priority,…
gregladen | December 7, 2013The Accidental Species by my friend and colleague Henry Gee is a new, and excellent, book on Human Evolution. I recommend it. I'll even review it soon. But in the meantime, you can get a free chapter of it by clicking this link to download a PDF supplied by the NCSE.
pharyngula | December 7, 2013Razib Khan poked me on twitter yesterday on the topic of David Dobbs' controversial article, which I've already discussed (I liked it). I'm in the minority here; Jerry Coyne has two rebuttals, and Richard Dawkins himself has replied. There has also been a lot of pushback in the comments here. I think they all miss the mark, and represent an attempt to shoehorn everything into an established, successful research program, without acknowledging any of the inadequacies of genetic reductionism.
Before I continue, let's get one thing clear: I am saying that understanding genes is fundamental,…
pharyngula | December 3, 2013The one thing you must read today is David Dobbs' Die, Selfish Gene, Die. It's good to see genetic accommodation getting more attention, but I'm already seeing pushback from people who don't quite get the concept, and think it's some kind of Lamarckian heresy.
It's maybe a bit much to ask that the gene-centric view of evolution die; it's still useful. By comparison, for instance, it's a bit like Mendel and modern genetics (I'll avoid the overworked comparison of Newton and Einstein.) You need to understand simple Mendelian genetics — it gives you a foundation in the logic of inheritance, and…
gregladen | November 24, 2013Catching Fire is apparently a very popular book and/or movie that everyone is very excited about. But Catching Fire: How Cooking Made Us Human is a different a book about some interesting research I was involved in about the origin of our genus, Homo.
You can pick up a copy of our paper on this page. We call it "The Cooking Hypothesis." The basic idea can be summarized with these points:
1) Cooking food transformed human ecology. Many potential foods in the environment can't be consumed by humans (or apes in general) without cooking. But adding cooking to our species-specific technology,…
sa smith | November 21, 2013Well, some of you! And maybe me!
Last year, scientists combed through Neanderthal and Denisovian DNA sequences (yeah, those exist!) and found fourteen ERVs that were in Neanderthals and/or Denisovians, but NOT humans.
Neandertal and Denisovan retroviruses
SUMMARY:
Modern humans (Homo sapiens) last shared a common ancestor with two types of archaic hominins, Neandertals and Denisovans, roughly 800,000 years ago, and the population leading to modern H. sapiens separated from that leading to Neandertals and Denisovans roughly 400,000 years ago [1,2,3,4]. Genome sequences for these two types of…
sa smith | November 14, 2013I love viruses, and I love ERVs, but I am not the only one :-D
Here are some links to pieces people have written about these lovely pirates, from three different perspectives.
1-- Nicholas Covington at Humes Apprentice (formerly AIG Busted!) is more a philosopher than a scientist, but even as a 'layman', he gets what ERVs are, and their place in evolutionary biology:
Proving Darwin: Fun with Endogenous Retroviruses!
2-- Carl Zimmer is no stranger to viruses. While he is still a 'layman', he has turned a personal fascination into a professional interest in viruses and ERVs. I love his…
sa smith | November 11, 2013I have no idea how the leopard got its spots, but scientists have figured out how horses got their leopard spots!
Evidence for a Retroviral Insertion in TRPM1 as the Cause of Congenital Stationary Night Blindness and Leopard Complex Spotting in the Horse
Get this!
Scientists have known for a few years that it is mutations within 'transient receptor potential cation channel subfamily M member 1' (TRPM1), that cause leopard spots and sometimes night blindness in horses. It turns out the bugger causing both of these phenotypes is a retrovirus that decided to plop into TRPM1.
The retrovirus did…
pharyngula | November 9, 2013I am not a fan of the convergent evolution argument for humanoid aliens. I can well believe that it's likely that intelligent aliens exist out there in the universe, but I'm not even going to try to predict what they look like: there are too many alternative paths that are possible. But for some reason, many people like to insist that it's reasonably likely that they'd resemble us in general, if not in detail, and they'll then go on to extrapolate that behaviorally and culturally they'll share many properties with us. Usually, as with Simon Conway Morris and now George Dvorsky, this argument…
oracknows | November 4, 2013It occurs to me that things have been perhaps overly serious here at the ol' blog for the last couple of weeks. Don't get me wrong. I think I done good lately, if I do say so myself. However, the constant drumbeat of quackery and depressing stories takes its toll after a while. I need a break.
And our old buddy, Deepak Chopra, was kind enough to give it to me.
So what is it this time? Chopra's been a frequent topic of this blog for a long time, albeit nos so much lately. Indeed, longtime readers know that I was the one who coined a term—Choprawoo—for the pseudoprofound metaphysical mystical…
pharyngula | November 3, 2013I've had, off and on, a minor obsession with a particular number. That number is 210. Look for it in any review of evolutionary complexity; some number in the 200+ range will get trotted out as the estimated number of cell types in a chordate/vertebrate/mammal/human, and it will typically be touted as the peak number of cell types in any organism. We have the most cellular diversity! Yay for us! We are sooo complicated!
It's an aspect of the Deflated Ego problem, in which scientists exercise a little confirmation bias to find some metric that puts humans at the top of the complexity heap.…
pharyngula | November 2, 2013I prepared for the Carnival of Evolution late at night over the last several days, bracketing the Halloween holiday, and coupled them with my traditional custom of watching horror movies. It wasn't a good match. The evolutionary stories were far more frightening!
Terrifying complexity!
psynetresearch
Let us consider the mind-blasting madness of dealing with tens of thousands of genes interacting epistatically with one another.
The second problem is that while it may in theory be possible to assign fitnesses to individual alleles at individual loci, there are some 25,000 loci in humans,…
oracknows | October 23, 2013One of the things that I've noticed over the last (nearly) nine years blogging about pseudocience, quackery, and conspiracy theories is that a person who believes in one form of woo has a tendency to believe in other forms of woo. You've probably noticed it too. I've lost count of the examples that I've seen of antivaccinationists who are into other forms of quackery, of quacks who are 9/11 Truthers, of HIV/AIDS denialists who are anthropogenic global warming denialists, and nearly every combination of these and many other forms of pseudoscience, pseudohistory, and denialism. Several years…
pharyngula | October 8, 2013James May, one of the presenters on Top Gear, is trying his hand at providing a little science education. I want to say…please stop. Here he is trying to answer the question, "Are humans still evolving?" In the end he says the right answer — yes they are! — but the path he takes to get there is terrible.
It's little things that make me wonder if anyone is actually editing his copy. For instance, he helpfully explains that you, the viewer, were produced by your parents having sex. Then he says:
That's how evolution is driven: by reproduction. But is that still true?
Uh, yes? We haven't…
pharyngula | October 4, 2013This cat is going to be insufferable
You may have heard we've got this satanic feline padding about the house now, getting into mischief -- she has discovered my collection of cephalopodiana, and her favorite toy is one of my stuffed octopuses that she wrestles and bats around the floor. It's like she's rubbing it in.
Anyway, a new paper in Nature Communications describes a comparative analysis of the genomes of tigers, lions, snow leopards, and…housecats. I'm not letting her read it, lest she acquire delusions of grandeur (oh, wait, she's a cat — she already has that.)
There's nothing too…
gregladen | September 29, 2013I've been a guest or interviewer on Minnesota Atheist Talk radio a number of times. I never talk about atheism because I'm nothing close to an expert on that or related issues (though I do have a chapter in a book about it, here!). And, of course, I'm very involved, professionally, in certain church-state separation issues (like this and this). But on Atheist Talk Radio I mainly engage in either science (lately climate change science but also evolution) or the afore mentioned church-state separation issues vis-a-vis the evolution-creationism "debate."
Anyway, I've been meaning to finally…
pharyngula | September 20, 2013I've mentioned the Earthviewer app from HHMI before: think of it as a bit like Google Earth, only you can dial it back to any period in the planet's history. There have been a couple of developments: it's also available for Android, and it's added some new features, including tracking for major fossils. So now you can see the long strange journey of Tiktaalik's bones on the screen.
They're also making available a lovely big poster of earth's history. This year, we here at UMM are putting together a teacher training program to be implemented in the summer of 2015, and it's going to be a lot of…
sa smith | September 11, 2013After I cleared up everyones confusion on why chicken gonads are lopsided, and why we have white chickens, I thought I would tackle another one of lifes great mysteries.
Admit it. Youve wondered where the hell blue chicken eggs come from.
Source: http://www.lespetitesgourmettes.com/recipes/gorgeous/
I 'get' brown eggs. I 'get' white, kinda. BUT WHERE THE HELL DID BLUE COME FROM?
'Well, you see when a chicken lays an egg mid-flight on a bright, sunny day, predators on the ground have a harder time seeing the blue egg...'
WAT?
No, seriously, whats up with blue chicken eggs?
Turns out it is a…
pharyngula | August 15, 2013OK, that's not saying much. Lots smarter. Here she takes apart his stupid video.
gregladen | August 12, 2013Whitey Bulger has finally been convicted of a small percentage of all the bad things he is said to have done. The Boston Globe has the details.
James J. “Whitey” Bulger, the notorious Boston gangster who rampaged through the city’s underworld for decades before slipping away from authorities and eluding a worldwide manhunt for more than 16 years, was convicted today in federal court of charges that will likely keep him in prison for the rest of his life.
Don't count on that. Whitey has slipped from the clutches of justice several times before. He'll probably make a break for it between…