Actually, it’s from the I Fucking Love Science website:
Okay, paleobiology buffs—is that number accurate?
I keep a safe lab
June 3, 2013 • 7:19 am
The discovery of the molecule of heredity: Matthew’s new Guardian piece
June 3, 2013 • 5:56 am
This is another anniversary in the history of genetics: it’s been seventy years since three investigators at Rockefeller Institute in New York City (now Rockefeller University, where I began grad school)—Oswald Avery, Colin MacLeod, and Maclyn McCarty (“AMM”)—discovered that DNA was the genetic material. Although their paper on this work was published in 1944 (reference and link below, full pdf here), May 26, 1943 was the day that Oswald Avery wrote to his brother announcing the discovery. (You can see Avery’s scrawled letter here.)
This finding truly was the beginning of the frenzy in molecular genetics that led directly to the discovery of the structure of DNA by Watson and Crick, and then to elucidating how DNA produced proteins. For it wasn’t until we knew what the genetic material actually was that we could determine its structure. And before the AMM paper, nobody knew for sure.
I’ve read the paper several times, and it’s a masterpiece of meticulous work and scientific exposition. What it showed was that one could change the hereditary nature of pneumonia-causing bacteria (that is, whether they could be virulent) by “transforming” nonvirulent strains with DNA. These strains had been killed, but could be revitalized (and made virulent) by replacing their DNA with that from nonvirulent cells. The virulence persisted (i.e., was inherited) after transformation. This transformation was not effected by protein, so that ruled out proteins as the genetic material. The way that AMM did this in those early days of molecular biology was masterful.
But I’ll let Matthew tell you about it in his new article in the Guardian, “Oswald T. Avery, the unsung hero of genetic science.” Avery had two collaborators on this, Colin MacCleod and Maclyn McCarty, but Avery was the driving force behind the research.
Their discovery, which was soon replicated, certainly deserved a Nobel Prize, but none of the three men ever got it. I suppose that’s why Matthew calls Avery an “unsung hero.” If you’re not a biologist you probably won’t have heard of the three men and their paper. But those of us working in genetics all know the work simply as “Avery, MacCleod andMcCarty”, and it’s a good time for all of us to remember their contribution. Go read Matthew’s article now: it’s very good and clearly explains what they did and why it was important.
This is what scientific history looks like: the title and summary of their paper. Note the “conclusion”. You can read “hereditary material” for “fundamental unit of the transforming principle.
One side note: the authors cite my academic grandfather, Theodosius Dobzhansky, for recognizing that the phenomenon of transformation itself gives a clue that the genetic material might be involved. I’m chuffed that support for DNA as the hereditary molecule came from an evolutionary geneticist:
Here’s the part of Avery’s 14-page letter where he says that, after “many heartaches and heartbreaks,” they figured out that the transforming principle seemed to be DNA. “Who could have guessed it?”, he adds. 
And here are the three unsung heroes:
You can read more about this experiment at Wikipedia, which has a more detailed description, or in Horace Freeland Judson’s masterful account of the history of molecular genetics, The Eighth Day of Creation.
And isn’t it amazing that a primate could figure this out?
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Avery, Oswald T.; Colin M. MacLeod, Maclyn McCarty (1944). “Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III”. Journal of Experimental Medicine 79 (2): 137–158. doi:10.1084/jem.79.2.137
I saw Santa!
June 2, 2013 • 12:33 pm
And it was in the Detroit airport. Taking a well-deserved summer break from the Arctic, Santa was clearly heading for warmer weather. Practically everything he was wearing was red, and he was even reading a red book and toting a red suitcase. Don’t tell me he’s not playing up the image.
He was also wearing a “USMC” (U.S. Marine Corps) tee shirt, so Santa is clearly one of the few and the proud.
I restrained myself from sitting in his proffered lap, though I wanted to ask him to let me pet a baby tiger for Christmas.
Turtle origins
June 2, 2013 • 12:30 pm
by Greg Mayer
In a paper soon to be published in Current Biology (abstract), Tyler Lyson and colleagues propose a model for the origin of turtles, using the Permian (ca. 260 mya) fossil Eunotosuarus as a transitional form.
The origin of turtles is a fascinating and important area of study, although one that is perhaps generally underappreciated (Burke 2009). The reason for its importance is that the turtle shell is probably the most novel and highly derived of all skeletal structures in the vertebrates. Nothing in human evolution, for example, compares. What do we have that’s distinctive? A really short tail? It’s been done to death, and just involves some reduction in size and number of bones. Bipedality? Also done many times. A large cranium? Just a few bones getting bigger.
What have turtles done? They’ve moved their shoulder and pelvic girdles inside their rib cages! If you want to appreciate what this means, reach behind your back and touch your shoulder blades, then reach down and touch your hip bones. Now feel your ribcage, front and back. And now imagine getting your shoulder blades and hips inside your rib cage– that’s what turtles have done.
Understanding of the origin of turtles has been hampered by the lack of a good fossil record. For many years the earliest known turtle was Proganochelys from the Late Triassic (ca. 210 mya), which, while primitive in various respects, had a full shell, both top (carapace) and bottom (plastron). The first fossil breakthrough came in 2008, when Li and colleagues described Odontochelys, a Late Triassic turtle a bit older than Proganochelys, but in which the plastron was well formed, but the carapace (top) consisted of only neural bones above the vertebrae, and enlarged ribs.
Lyson and colleagues extend the model of shell origins, incorporating further data on shell ontogeny in modern turtles, and, most significantly adding Eunotosaurus as an early ancestral turtle, which has a proto-carapace of expanded ribs. They also point to Milleretta, another Permian reptile, as a possible very first step in the direction of turtles. (At this point, we pause for Snappy to say hello, so readers don’t forget what the object of our discussion is.)
There are two phylogenetic controversies that are involved in this scenario of turtle origin. First, although Eunotosaurus has long been bandied about as a turtle precursor, the consensus has long been that it is not, although Lyson and colleagues (2010) have argued it is. Second, there is great debate about where turtles fit in amongst reptiles in general. Because of the generally primitive nature of their skulls (lacking any openings or fenestrations), turtles have often been linked with one or another of various early reptile groups, and Lyson and colleagues favor this view. There is an almost equally old hypothesis, however, that turtles, despite lacking any skull openings, are nonetheless members of the Diapsida, the great group of two-fenestra reptiles (and their modern feathery descendants) that includes Archosaurs (crocodiles and birds among living taxa, dinosaurs and pterosaurs among the extinct) and Lepidosaurs (tuatara, lizards and snakes among living taxa, mosasaurs among the extinct).
Recent molecular data, including two new genome studies (Wang et al. 2013, Shaffer et al. 2013; see Gilbert and Corfe 2013), have supported earlier molecular studies (including one of my own) in placing turtles among the Diapsida, and indeed, well within the Diapsida, as the sister group of the extant archosaurs. Although the resolution of these latter debates will have bearing on the full turtle origin story, one thing that I think is now clear is the stepwise origin of the turtle shell, with the various components having been assembled sequentially.
h/t P
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Burke, A.C. 2009. Turtles… …again. Evolution & Development 11:622-624.
Gilbert, S.F. and I. Corfe. 2013. Turtle origins: picking up speed. Developmental Cell 25:326-328.
Kirsch, J.A.W. and G.C. Mayer. 1998. The platypus is not a rodent: DNA hybridization, amniote phylogeny and the palimpsest theory. Philosophical Transactions of the Royal Society B 353:1221-1237. pdf
Li, C, X.-C. Wu, O. Rieppel, L.-T. Wang and L.-J. Zhao. 2008. An ancestral turtle from the Late Triassic of southwestern China. Nature 456:497-501. abstract
Lyson, T.R., G.S. Bever, B.S. Bhullar, W.G. Joyce, and J.A. Gauthier. 2010. Transitional fossils and the origin of turtles. Biology Letters 6:830-833. pdf
Lyson, T.R., G.S. Bever, T. M. Scheyer, A.Y. Hsiang, and J.A. Gauthier. 2013. Evolutionary origin of the turtle shell. Current Biology in press. abstract
Shaffer, H.B. et al. 2013. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology in press. pdf
Wang, Z., et al. 2013. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nature Genetics 45 701-706. pdf
A few comments that didn’t get through
June 2, 2013 • 9:54 am
I get tons of comments like the three below, and usually bin them, but occasionally post a few just to show how the faithful react to this website. Here are a couple of good ones for your Sunday delectation:
From “Mike”:
Surely the existence of multiverses would prove that God does exist.
Think about it.
If there is an infinite number of universes, then everything that can happen, does happen.
Therefore anything is possible including the existence of God.
I think Mike is conflating “logically possible” with “physically possible.”
Reader “Jeff Phelps” comments on my post, “Would it help if this person read my book?” a response to another antievolution rant:
So the intelligentsia fascists are at it again with their circular logic that defines the work of GOD as outside the realm of science so therefore it is not science. Nice little word game you play but you don’t fool me. I’ve been on your side and your side is full of holes. Of course you wouldn’t listen if I listed them so why bother? I just wanted to stop by and remind you to keep up your Fascist Local 666 dues. How dare anyone question the almighty “professor” (who professes to know what he’s talking about since we’re playing word games – he doesn’t fool most people). I do have to give you kudos for an astounding arrogance that boggles the imagination. How could any ego ever be more obsessed than to swear they know the secret to the creation of life itself. But we all know you don’t. You’re guessing and professing. That’s it.
I can run circles around you when it comes to logic but you’re so high on your own fumes that you wouldn’t listen if God Himself walked up and smacked you on the forehead and declared you to be a dummy.
But whatever I say will be pearls before swine. You can discredit the idea that your religion is just a religion all you want. You aren’t fooling anyone but the minions who have to parrot what you say to get a grade.
Come back when you’ve seen reality. You clearly haven’t or you wouldn’t be sticking to your dogmatic rendering of reality. When you see a miracle face to face you’ll know it. And wow have you ever missed the boat on that. All those fumes won’t change that fact and it is a FACT despite your childish game of “I’m rubber and you’re glue”. How much do you get paid to recite that 100 times a day anyway? Too much. I already knew the answer to that.
Miracles hot shot. When you see one your entire perspective will change. I can hear your disdain from 1000 miles away and two weeks into the future. You’re just so predictable it’s ridiculous. And you will be until you’ve seen your first miracle.
I know you don’t want to know mine but here goes anyway. I’m still alive 24 years after having stage 3 cancer after a “professor” professed that I would be dead in 6 months. In fact the entire professing union professed the chances of me surviving beyond a short time didn’t exist. Guess what? They don’t make those decisions.
But that’s just the tip of the iceberg. Go back and read your Kierkegaard as if it would do you any good. You can’t see it from the outside. Through a glass darkly but one day face to face honcho. More than just prose or history. It’s called prophecy and I’ve seen that work too. But you wouldn’t even understand how signficant that is. Those fumes have pickled your brain.
And they call atheists arrogant??? Is every recovery from stage 3 cancer a miracle that proves God’s existence? I guess the larger number of people who succumb, including children, prove God’s maliciousness. But don’t worry, there aren’t any dues in “Fascist Local 666”.
And I just love the argument of reader “Alex”. It’s the best reader comment yet trying to make virtues from necessities.
Hello all!
Many of you apparently feel very comfortable being atheists. I sometimes wish I were one. Why? Mainly because I am like most of us not always willing to be responsible to a higher authority for my sinful actions.
The heavy opposition to the existence of God suggest that God exists.
The very existence of so much evil in the world points me to the necessary existence of a just God, who will ultimately bring to justice all those evil doers. Someone has to be held accountable for the 6 million jews during holocost, or 20 million during Stalins [sic] reign, or 40-50 million abortions (child murders) in the USA and the list goes on…
Our innate sense of justice and inner moral compass is to me one of the strongest evidences for God. Who doesn’t believe that raping children is very evil? or Slaughtering innocent people? Why do feel so outraged when such attrocities take place?
The very fact that many in the prosperous west are falling away from Christ demonstrates the truth of Jesus’ words. At the same time, the fastest growing number of christians can be found in China, Iran etc. These are countries who heavily persecute followers of Christ. Why would someone follow an imaginary person and subject oneself to such brutality from the authorities? True christians always thrive under extreme pressure.
I believe that Jesus is the very best role model for all humans, especially to men. [JAC: why “especially to men”?] If we only truly and daily practiced the command of Jesus to love one another as He loved us and gave His life for us, we would not have any of the above mentioned tragedies and indeed would have heaven on earth life. But who is willing to humble himself or herself to live such a lifestyle: denying their own selfish ambitions and serving their fellow man?I hope readers of these thoughts may find reasons to reconsider their position on life.
for those who are scientifically oriented I would suggest visiting AnswersInGenesis.org for a good challenge to the modern religion of evolution responsible for communism, fascism, eugenics, rascism [sic] etc.
The heavy opposition to the efficacy of homeopathic medicine also proves that it works, as does the opposition to the existence of UFOs, which prove that they exist.
The monster tiger beetle: a “voracious killing machine”
June 2, 2013 • 6:50 am
Nature photographer Piotr Naskrecki, whom we’ve met before, is in Mozambique and, at his website The Smaller Majority, is documenting his adventures. Several days ago he wrote about the larva of the Monster Tiger Beetle (Manticora redux), which led me to his post last month on the adult of the same species. I don’t want to reprise most of what he said about this nasty but amazing piece of work, so go over and read about it yourself.
(Note to pedantic readers and creationists: by “piece of work” I am speaking metaphorically and not implying that there was a creator who designed this beetle! And do I really have to say stuff like this?)
Anyway, here’s the adult nomming a grasshopper: Piotr notes (his words are indented):
It is the world’s largest tiger beetle (Cicindelinae), with a robust, heavily sclerotized body that easily reaches 65 mm in length. Its head, especially that of the male, is equipped with a pair of mandibles that would not look out of place on a stag beetle but, unlike the mostly ritualistic function of large mandibles in stag beetles, those of Maticora are very much functional.
Despite its size Manticorabehaves in a way quite similar to smaller tiger beetle species. Its movements are agile, and it can run like hell and change direction in a split of a second; they cannot fly, however. These beetles hunt anything that moves, although prefer orthopterans, but unlike other tiger beetles it appears that the sense of smell rather than vision is their main tool for locating their victims. Once prey is located the beetle clasps it with its enormous mandibles and literally chops it to pieces. I watched it find and kill a large wolf spider – at first I thought that the spider would put up a fight, but about two seconds later what was left of the spider was a nicely masticated ball of tissue and a small pile of legs. After the main body was consumed the beetle picked the legs, one by one, off the ground and ate them, too.
Apparently the mandibles do double duty (see Piotr’s caption):
The larvae of Manticora are similarly carnivorous, but rather than actively pursuing their prey the way their parents do, they are sit-and-wait predators. At that time I had not been able to see or collect Manticora larvae, but tonight I finally managed to snag one.
Like other tiger beetles, the larvae of Manticora hunt from the safety of their narrow, nearly vertical burrows in the sand. Their soft body is safely tucked inside the tunnel, and the only thing that is visible on the surface is a large, heavily sclerotized head and pronotum, both of which form a shield that blocks the access to the burrow. The mandibles of a Manticora larva are pointing upwards so that any insect unlucky enough to step on the head is instantly grabbed by its leg and pulled underground. Imagine walking down the street and stepping on one of those round metal plates that cover sewer manholes, only the plate turns out to be the head of monster, and you are instantly sucked underground – this is what it must feel to a cricket or an antlion as it is being dragged by Manticora.
When Piotr tried to extract one of these from its burrow, he had a tough time, and thereby discovered a cool adaptation:
Eventually, I used the insect’s own voracity to catch it – I gently touched the head with the forceps, and when the mandibles snapped around it I grabbed the head and pulled the larva out. It was not easy as the 5th abdominal tergite of the larva is modified into a large, spiny structure that effectively anchors the animal in its burrow. The larva’s morphology reminded me of marine polychaete worms that use a similar tactic for catching prey from the confines of their burrows.
An unlucky cricket is seized by its leg and dragged underground to its doom:
h/t: Matthew Cobb
Is religion a mental illness?
June 2, 2013 • 5:00 am
Several readers have sent me this link, but I have to say I’m not that convinced that the views expressed in this news item have any substantive content, or will catch on in society.
The piece, “Leading neuroscientist: Religious fundamentalism may be a ‘mental illness’ that can be ‘cured’” (note the scare quotes), is from The Raw Story, and refers to a talk at the Hay Literary festival by Kathleen Taylor a neurobiologist at Oxford University who studies the psychology and neuroscience of belief. This is the part that got all the attention (my emphasis):
During a talk at the Hay Literary Festival in Wales on Wednesday, Kathleen Taylor was asked what positive developments she anticipated in neuroscience in the next 60 years.
“One of the surprises may be to see people with certain beliefs as people who can be treated,” she explained, according to The Times of London. “Somebody who has for example become radicalised to a cult ideology – we might stop seeing that as a personal choice that they have chosen as a result of pure free will and may start treating it as some kind of mental disturbance.”
“I am not just talking about the obvious candidates like radical Islam or some of the more extreme cults,” she explained. “I am talking about things like the belief that it is OK to beat your children. These beliefs are very harmful but are not normally categorized as mental illness.”
“In many ways that could be a very positive thing because there are no doubt beliefs in our society that do a heck of a lot of damage, that really do a lot of harm.”
Well, in what respect is religion is a “mental disturbance” as opposed to a “personal choice”? Even the free-will compatibilists among us don’t think that one can “choose” to be religious any more than one can “choose” one’s political affiliation, taste in foods, or friends. It’s all a matter of your genes and your environments, and environments include what you’re exposed to—including childhood indoctrination. There is no such thing as the “pure free will” that Taylor is discussing here. (Granted, I was not at her talk, and am going on the news report.)
And yes, religion might be a “brain disorder,” in the sense that it resides in the configuration of your neurons, but so is being a Republican. But I doubt that it’s anything like a genetically-based neurological disease. It’s based largely on wish-thinking and the credulity of children: two things endemic in almost everyone. Yes, religious belief delusional, but so is being a Republican. And yes, we know that in some cases religious belief can be cured—many of us were once believers. But that cure may well involve getting rid of childhood indoctrination, as well as exposure to the arguments of atheists.
Going by the brief news report, I think Taylor sees religion as a ‘mental illness’ on two grounds: the fact that it isn’t based on real evidence, and that it has, as she implies, harmful effects on society. But so are many ‘beliefs’ that aren’t seen as mental illness—for example, the Republican view that increasing taxes on the wealthy will destroy the economy or that legalizing assault weapons is good for society. I’m not convinced, either, that being an “Islamic fundamentalist” has radically different causes from being an observant Catholic. It’s all what you’re exposed to in your culture, and how that exposure interacts with your neurology.
If religion is to be extirpated, it’s useless to begin that endeavor by identifying it as a “mental illness”. Such illness, however unfairly, is seen as a stigma in many societies, and telling believers that they’re mentally ill is not going to make them suddenly flock to psychiatrists. (The alternative, forcible treatment, is simply not in the cards.) It’s better to identify faith, as New Atheists do, as a delusion, and try to “cure” it simply by convincing people that they need good reasons for what they believe.
Finally, as I’ve said many times, the best way to “cure” religious belief is to eliminate the conditions that promote it, and that’s best done by building a more secure, just, and egalitarian society.
Amazing photo of chemical bonds
June 1, 2013 • 1:21 pm
I don’t have a lot of time to post today, but alert reader Ginger brought this cool item to my attention. It’s a press release of a finding to appear in the “early edition” of Science, and shows the formation of benzene-ringlike structures from a complex chemical reaction. The details are given here. An excerpt:
When Felix Fischer of the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) set out to develop nanostructures made of graphene using a new, controlled approach to chemical reactions, the first result was a surprise: spectacular images of individual carbon atoms and the bonds between them.
“We weren’t thinking about making beautiful images; the reactions themselves were the goal,” says Fischer, a staff scientist in Berkeley Lab’s Materials Sciences Division (MSD) and a professor of chemistry at the University of California, Berkeley. “But to really see what was happening at the single-atom level we had to use a uniquely sensitive atomic force microscope in Michael Crommie’s laboratory.” Crommie is an MSD scientist and a professor of physics at UC Berkeley.
What the microscope showed the researchers, says Fischer, “was amazing.” The specific outcomes of the reaction were themselves unexpected, but the visual evidence was even more so. “Nobody has ever taken direct, single-bond-resolved images of individual molecules, right before and immediately after a complex organic reaction,” Fischer says.
Here you go; these are unbelievable photos:
The technique used to get these images, called noncontact atomic force microscopy, which in effect uses a single atom as a camera lens, is equally amazing. We should all be proud that our species can do something like this:
The collaborators then turned to a technique called noncontact atomic force microscopy (nc-AFM), which probes the surface with a sharp tip. The tip is mechanically deflected by electronic forces very close to the sample, moving like a phonograph needle in a groove.
“A carbon monoxide molecule adsorbed onto the tip of the AFM ‘needle’ leaves a single oxygen atom as the probe,” Fischer explains. “Moving this ‘atomic finger’ back and forth over the silver surface is like reading Braille, as if we were feeling the small atomic-scale bumps made by the atoms.” Fischer notes that high-resolution AFM imaging was first performed by Gerhard Meyer’s group at IBM Zurich, “but here we are using it to understand the results of a fundamental chemical reaction.”
The single-atom moving finger of the nc-AFM could feel not only the individual atoms but the forces representing the bonds formed by the electrons shared between them. The resulting images bore a startling resemblance to diagrams from a textbook or on the blackboard, used to teach chemistry, except here no imagination is required.
The atomic “theory” is verified once again. When I was younger I never thought we’d be able to see individual atoms, but now that’s almost routine. It’s stunning that we can even see the bonds between them, looking like the Tinkertoys I played with as a child.
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Reference: “Direct Imaging of Covalent Bond Structure in Single-Molecule Chemical Reactions,” by Dimas G. de Oteyza, Patrick Gorman, Yen-Chia Chen, Sebastian Wickenburg, Alexander Riss, Duncan J. Mowbray, Grisha Etkin, Zahra Pedramrazi, Hsin-Zon Tsai, Angel Rubio, Michael F. Crommie, and Felix R. Fischer, will appear in Science and is now available on Science Express,http://www.sciencemag.org/content/early/2013/05/29/science.1238187.abstract