March 2011 Archives

Ediacaran_lizard.jpgIt’s hard to believe, but a reptile has been found in Precambrian strata (specifically Ediacaran) – with preserved skin. This sometimes happens in more recent deposits, but there has never been a case this old. Plus, this fossil is the first one I’ve ever seen that could meet Haldane’s criteria for falsifying evolution: a Precambrian rabbit. I mean, I guess now that push comes to shove I have to say that I wouldn’t give up evolution because of one out of place fossil, but I’ve always prided myself on sticking to the evidence, so I figured I should post it as soon as I heard about it.

I wouldn’t normally trust a find like this before it’s been published, but it was discovered by long-time, reliable talk.origins veteran Chris Nedin. It was only the creationists who said “Nedin cannot be trusted”, us evolutionists knew he was as good as gold.

By Paul S. Braterman
British Centre for Science Education

Michael Gove, UK Education Secretary, has said in as many words that “teaching creationism is at odds with scientific fact.” This is progress. The existing curriculum guidelines stated only that creationism and ID should not be taught as science, leaving room for them to be advanced as philosophical or religious doctrines (in the UK, there is no separation of Church and State). In any case, the publicly funded “Free Schools” now being set up are not constrained by the language of the curriculum. Some half-dozen Evangelical church schools with pro-creationism policies have applied for Free School status. We hope, in the light of the Secretary’s words, that these applications will now be rejected.

More below the fold…

Extinctions weirdness

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When a paper gets press, the authors get some weird reactions. With the extinctions paper, one guy emailed us to say that he agreed that species extinctions were a big problem, and that humans were the cause. However, he said, we had the details of the cause was wrong. The real cause was contrails.

That, though, was not nearly as weird as this: “Congrats Nick Matzke for Publishing ID Sympathetic Paper in Nature!” by Sal Cordova.

Can anyone explain the psychology here? I’m normally pretty good at psyching out creationists, but this one leaves me mystified.

vertuvian_colour_small.jpgFellow Oregonians – this looks like a great series! I’ve seen Bustamante talk before, he does amazing research. So it should be great, if you can stand hanging out with the Ducks, that is…

(And, by the way, evolutionary theory is literally the warp and woof of genomics. If you took genomics and somehow deleted all of the methods and analyses derived from evolutionary theory, the whole field and industry would crumple into a quivering pile of meaningless digital goo. There are areas where ID people are wrong and can at least state arguments of some sort – but then there are vast areas like population genomics where ID people don’t even know enough to realize that there is a vast, hugely successful enterprise that is entirely built upon principles they would disagree with.)

OK, end of rant.

Subject: Upcoming Seminar Series at University of Oregon Date: Wed, 30 Mar 2011 19:10:30 -0700 From: Roo Vandegrift

Hello,

I’m a graduate student at the Center for Ecology and Evolutionary Biology (CEEB) at the University of Oregon. Our graduate student group within CEEB has put together a public seminar series for the spring that you and some of your readers might find interesting. It’s titled The Individual in the Genomics Era. Here’s some information on the dates and topics:

*What genomics means for our past, present, and future * April 5 Dr William Cresko University of Oregon

*The Personal Genome Revolution * May 3 Dr Lee Silver Princeton University Supported by the Oregon Humanities Center Endowment for Public Outreach in the Arts, Sciences and Humanities

*Reconstructing the great human diasporas from genome variation data* May 23 Dr Carlos Bustamante Stanford University

Further information can be found on the website, including the exact location on the University of Oregon campus the talks will be held, the press release, etc. http://www.uoregon.edu/~grebes/seminar Additionally, I’ve attached a copy of the flier for the series.

I hope some of you in the Pacific Northwest might consider attending! And if not, if you know of anyone who might benefit from this series, please let them know.

Peace, Roo

Roo Vandegrift CEEB - University of Oregon

Freshwater: ODE Punts with Letter of Admonishment

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The Ohio Department of Education (ODE) has issued a Letter of Admonishment to John Freshwater. In the March 22, 2011, letter that I obtained via a Public Records Request, ODE’s Office of Professional Conduct said “[T]he Department determined that you used poor judgment when you permitted students to volunteer to touch a live Tesla coil which resulted in an injury to a student. In mitigation, you ceased the use of the Tesla coil and removed it from your classroom.” It further said that “[Y]ou are admonished that if you engage in any further conduct unbecoming to the teaching profession, including further violations of Revised Code 3319.31, the State Board may initiate disciplinary proceedings to revoke, limit or suspend your teaching credential(s).” A copy of the Letter of Admonishment goes in Freshwater’s ODE file.

It appears that no other state sanction will occur. Freshwater’s teaching certificate expired in 2010 and according to the Letter of Admonishment he has applied to the ODE Office of Educator Licensure for a five-year professional high school teaching license. The letter says that the application will be granted: “Your pending application will be forwarded to the Office of Educator Licensure for issuance of your teaching credential.”

ODE’s letter does not mention the administrative hearing findings that led to Freshwater’s termination–his violation of the Establishment Clause and insubordination–and refers only tangentially to his teaching creationism, saying “The allegations that you did not follow the curriculum are employment related and are addressed at that level.” In other words, ODE doesn’t consider insubordination and teaching creationism to be “immoral, incompetent, negligent” or “conduct unbecoming to the teaching profession,” the statutory standards it supposedly enforces via its disciplinary and licensing procedures.

ODE punted. It had access to all the evidence and testimony of the administrative hearing along with the referee’s recommendation for termination and it punted on third and short.

AFAIK (I’ve been out of service for some weeks) Freshwater’s appeal of his termination by the Mt. Vernon Board of Education is still pending in federal court, it having been transferred there from the Knox County Court of Common Pleas. The federal judge has asked for briefs concerning the appropriate venue for the appeal.

Brian O’Meara (University of Tennessee, NIMBioS) speaks Wednesday, March 16th at 2pm EST on “Making comparative methods as easy as ABC.” The seminar will take place online and anyone can participate. Instructions on how to join can be found at a http://phyloseminar.org/.

Abstract:

For decades, biologists have addressed evolutionary and ecological questions using measurements of species traits, phylogenies, and an assortment of comparative methods. Unfortunately, while there is a large assortment of these methods, they are still fairly limited and development of new methods is slow. It took seven years between the introduction of using a simple Brownian motion model for looking at trait evolution (Felsenstein, 1985) and the use of this same model for looking at rates of trait evolution (Garland, 1992), and an additional 14 years to more powerful tests using a small modification of the basic model (O’Meara et al., 2006). Still other promising methods are described and even tested but remain unavailable to empiricists because they are not put into software. As a result, the questions empiricists can ask about the world are limited by the research productivity of the few dozen scientists who develop and implement new methods in phylogenetics. We describe a new approach based on Approximate Bayesian Computation and implemented in R that will allow researchers to easily develop their own models for trait evolution without requiring them to have specialized mathematical or computational knowledge.


Japan 03:00 (03:00 AM) on Thursday, March 17
New Zealand 07:00 (07:00 AM) on Thursday, March 17
West Coast USA 11:00 (11:00 AM) on Wednesday, March 16
East Coast USA 14:00 (02:00 PM) on Wednesday, March 16
England 18:00 (06:00 PM) on Wednesday, March 16
France 19:00 (07:00 PM) on Wednesday, March 16

For more information on how to attend this and other seminars, visit http://phyloseminar.org/.

Intelligent design news from the 23rd of March to the 29th of March, 2011.

This week marked the highly notable, first ever mention of yours truly in an official Discovery Institute blog post, which is rather exciting. It’s a pity then that, as I already said today, the mention was a horribly confused jumble of misinterpretation and laziness that made me come off like an undefinable supporter of ID-dualism, or something like that.

But whatever, that doesn’t really matter in the scheme of things. What else happened this week in the online world of intelligent design?

Fratercula arctica

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Photograph by Sarah Boosey.

P8090069_Puffin_600.JPG

Fratercula arctica – Atlantic puffin, off the coast of Iceland, 2010.

Uncommon Dissent

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by Joe Felsenstein
http://evolution.gs.washington.edu/felsenstein.html

Over at Uncommon Descent an unusual discussion has erupted. A commenter named “MathGrrl” who has been occasionally active there as a critic of ID has actually been allowed to make a guest posting. She gave several examples of situations where one could make a specification of what were the best genotypes, and asked how in these cases Complex Specified Information could be defined. She has handled the discussion with great restraint. Several hundred comments later no consensus has emerged. Commenters at anti-ID blogs ( here, here, here, here, and here), have concluded from this that the concept of CSI is vacuous.

I’d like to give a perspective that may be unpopular here. I don’t think Complex Specified Information is a vacuous concept, though we usually do not have enough information to actually calculate numbers for it.

sudo laugh again

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xkcd: Beauty

Creo Catfight in Kentucky!

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CatHam.jpg I had the displeasure of personally experiencing Kan Ham’s vitriol, applied to scientists at the time, way back in 1995, when he brought his creation seminar to Albuquerque. Time has passed, but Ham is still dispensing the vitriol. What’s changed is that now, he’s railing against his fellow Creationists!

The Lexington (Ky.) Herald-Leader reported on March 24th that

Ken Ham, the man behind the Creation Museum and the future Ark Encounter amusement park, has been disinvited from a homeschool convention in Cincinnati next week because he made “ungodly, and mean-spirited” comments about another speaker, according to the convention’s organizers.

Ham also will be excluded from future conventions, according to a statement by Brennan Dean of Great Homeschool Conventions.

“The board believes that Ken’s public criticism of the convention itself and other speakers at our convention require him to surrender the spiritual privilege of addressing our homeschool audience,” Dean said in the statement.

At issue are criticisms by Ham of Peter Enns of the Biologos Foundation, who has said the fall of Adam and Eve can be construed as a symbolic story of Israel’s beginnings, rather than a literal description of human beginnings.

On his blog and in other statements, Ham takes issue with this view and Enns’ homeschool curriculum.

“In fact,” Ham wrote in a recent blog post, “what he teaches about Genesis is not just compromising Genesis with evolution, it is outright liberal theology that totally undermines the authority of the Word of God.” …

On the Web: Answers in Genesis Explains the Rift

Discuss.

PrimordialSoupPPR.jpg

It’s been a while since I wrote about Primordial Soup - and it’s Back in the News!

Science Daily reports on March 21st that

Stanley Miller gained fame with his 1953 experiment showing the synthesis of organic compounds thought to be important in setting the origin of life in motion. Five years later, he produced samples from a similar experiment, shelved them and, as far as friends and colleagues know, never returned to them in his lifetime.

More 50 years later, Jeffrey Bada, Miller’s former student and a current Scripps Institution of Oceanography, UC San Diego professor of marine chemistry, discovered the samples in Miller’s laboratory material and made a discovery that represents a potential breakthrough in the search for the processes that created Earth’s first life forms.

Former Scripps undergraduate student Eric Parker, Bada and colleagues report on their reanalysis of the samples in the March 21 issue of Proceedings of the National Academy of Sciences. Miller’s 1958 experiment in which the gas hydrogen sulfide was added to a mix of gases believed to be present in the atmosphere of early Earth resulted in the synthesis of sulfur amino acids as well as other amino acids. The analysis by Bada’s lab using techniques not available to Miller suggests that a diversity of organic compounds existed on early planet Earth to an extent scientists had not previously realized.

“Much to our surprise the yield of amino acids is a lot richer than any experiment (Miller) had ever conducted,” said Bada.

continued…

Discuss.

Intelligent design news from the 16th of March to the 22nd of March, 2011.

So, another week of intelligent design! The Discovery Institute was fairly quiet this week, with only five posts published on Evolution News & Views, a below average result, but quite a bit of it was pure gold. Well, for me, anyway. The fact that I do this every week means that I must be getting some entertainment out of it, right? I hope so - I don’t see myself as the masochistic type…

But anyway, this week’s three posts are on ID research (and rhetoric), revisiting the concept of biological “mistakes” as evidence against ID, and ID proponents in academia and the “Dissent from Darwin” list. Let’s get into it!

Meles meles

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Photograph by Sarah Boosey.

P6270008_Badger_doctored_600.JPG

Meles meles – European badger, England, 2010.

According to an article in the Guardian, the European Court of Human Rights has reversed its own earlier decision and now says that it is lawful to display a crucifix in a state schoolroom. The earlier decision caused “uproar,” so the full court reconsidered its earlier decision and concluded that the crucifix was “an essentially passive symbol.” As the philosopher Sidney Morgenbesser might have said, Yeah, yeah, and a Christmas tree is just a secular symbol.

France, meanwhile, has banned religious symbols worn by students in state schools. So here is a philosophy question: Can you both permit and prohibit religious symbols at the same time?

While reading Signature in the Cell by Stephen C. Meyer, I realised something important that I had previously overlooked in the debate between pro- and anti-ID camps. It’s always perplexed me why ID proponents, especially those at the Discovery Institute, constantly talk about “materialistic evolution”. If their contention is that ID is secular, why muddy that position by bringing in what seems like a theistic idea - non-materialism?

According to a couple of articles by Stephen Glain, one in The Nation and one in Foreign Policy, right-wing fundamentalists have been allowed to proselytize in the United States military and in particular in the Air Force Academy. As far as I know, the only organization actively opposing these fundamentalists is the Military Religious Freedom Foundation, headed by Mikey Weinstein.

Intelligent design news from the 9th of March to the 15th of March, 2011.

Another week, another lot of posts by the ID community to sort through. As you may have noticed by now, I’ve given up on devoting much time to anything posted on Uncommon Descent (except for quick links), due to their insular nature (they seem to be read only by their preexisting, fervent community), their complete lack of substantial and interesting discussion, and their overwhelmingly religious tone, which I’m fairly sure robbed them of any pretence of being an objective, scientific and secular place for formal and informal discourse on all matters ID and evolution.

Evolution News & Views, however, remains far more tightly regulated by the Discovery Institute’s PR machine, straying into religious territory fairly rarely, and only really when Michael Egnor decides to swing by, which is, I’m afraid to say, not as often as it used to be. Perhaps he tired of defending dualism from Steven Novella’s neurological assaults, or attacking abortion from a completely secular and scientific perspective. I know I would. Anyway, EN&V remains a good target because people who might be removed from the ID debate have the greatest chance of taking it seriously over any of the other pro-ID blogs out there. It looks snazzy and professional, what can I say?

Also, hello if you’re reading this on The Panda’s Thumb (to which this lede is cross-posted)! This is just my weekly series where I look at at least three posts from the major intelligent design blogs - focusing on Evolution News & Views in particular, for the reasons stated above - and examine their arguments and rhetoric. What I really look for is anything novel: there are plenty of posts out there that simply retread copiously-trodden ground. Then again, sometimes old topics can be given a reboot through a nice rhetorical twist…

Enough of that, let’s get into it!

Continue reading “This Week in Intelligent Design - 15/03/11” at Homologous Legs.

Phyloseminar rescheduled

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Brian O’Meara’s phyloseminar has been rescheduled for 3/30.

Charadrius vociferus

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Photograph by Paul Burnett.

BurnettKilldeer_600.jpg

Charadrius vociferus – killdeer, Alameda, California, 2008.

Walter Fitch Passes Away

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Note: Passing along a letter I received.

Dear Colleagues,

I am sorry to report that a beloved member of our campus community, Dr. Walter Fitch, passed away in his sleep this morning [2011/03/11] at his home in University Hills. We will miss him dearly as a friend, as a colleague, and as a towering intellectual presence.

Walter was born in San Diego in 1929, and earned his Ph.D. in Comparative Biochemistry from the University of California, Berkeley in 1958. He was a post-doctoral scholar at both Stanford and University College (London) and held full professorships at the University of Wisconsin and the University of Southern California. He came to UC Irvine in 1989 as a Distinguished Professor and later became the Chair of the Department of Ecology and Evolutionary Biology.

Walter was a founding father of the field of molecular evolution, and established methods for constructing phylogenetic trees from amino acid and nucleic acid sequences. He also made contributions to virology, the origin of life, taxonomy, genetics and molecular biology. For his work he was elected to the National Academy of Sciences, the American Academy of Arts and Sciences and the Linnean Society (England). He founded the Society for Molecular Biology and Evolution and was the editor-in-chief of its journal, Molecular Biology and Evolution for its first 10 years. He contributed mightily not only to the intellectual process but as a mentor to young scientists.

Walter is survived by his beloved wife, his four children and several grandchildren. Funeral arrangements are pending.

Sincerely,

Brandon Gaut
Professor & Chair
Department of Ecology and Evolutionary Biology

Quakes and fakes

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By Donald Prothero, Occidental College

As many of us watch the horrors of the nonstop news coverage from Japan, a lot of misinformation seems to be sweeping through the media and the blogosphere. Since I’m a geologist trained in seismology, and also the author of the new book Catastrophes: Earthquakes, Tsunamis, Tornadoes, and other Earth-Shattering Disasters (Johns Hopkins University Press), I’ve been asked to write up a brief summary of the fact and myths about the earthquake.

Over at Science in Pen and Ink Lelia Battison has an in-depth discussion of Richard Hoovers’ paper on alleged “fossil” bacteria in CI1 Carbonaceous Meteorites in the Journal of Cosmology. It is an excellent article that covers a lot of issues not previously covered, and brings together some other information that has been scattered around. I’m referenced as well. Go have a read of Microbes on a Moonbeam, disentangling the Meteorite Microbe claims.

(for reference my posts on the subject are here and here)

Science: Human males not horny

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Most mammals (the males, anyway) have a baculum, or penis bone. Human males, however, do not. Inasmuch as men and women have the same number of ribs, some people have suggested that the human baculum had to be sacrificed in order to make Eve (see here for a survey). For my part, I think it is just as well to have an upright posture and no baculum.

Now comes a report in Science to the effect that the penises of most male mammals are covered with spines of keratin, the substance of which horns are composed. Owing to a gene deletion, however, male humans lack these spines and therefore are not horny.

Additionally, we see that the human penis not only has no backbone, but also no spine.

The Journal of Cosmology has now posted 21 commentaries on the “Fossils of Cyanobacteria in CI1 Carbonaceous Meteorites” paper by Richard Hoover that I have critiqued in my “Life from Beyond Earth on a Meteorite, or Pareidolia?” post.

The majority are uncritical (some don’t even seem to have read the actual paper), and zoom off on tangents assuming the Hoover’s paper is valid. Two posts are critical (commentary 5 and commentary 9), and bring up the same issue I do (but with more references), that abiotic minerals can imitate the shapes of bacteria, and that without further tests, there is no way to say these filaments are fossils of any sort.

As for the majority, well, largely I think they are sad. The near complete absence of any critical engagement with the paper is very telling, and there is much leaping to unsupported conclusions. I would dearly love for extra-terrestrial life to be found, but I’m not going to grasp at epsonite straws to pretend it’s been found. Hoover’s flawed paper is not evidence of extra-terrestrial life.

Oh, and the journal has added a long rant to before the main article:

Have the Terrorist(sic) Won? Only a few crackpots and charlatans have denounced the Hoover study. NASA’s chief scientist was charged with unprofessional conduct for lying publicly about the Journal of Cosmology and the Hoover paper. The same crackpots, self-promoters, liars, and failures, are quoted repeatedly in the media. However, where is the evidence the Hoover study is not accurate?

Few legitimate scientists have come forward to contest Hoover’s findings. Why is that? Because the evidence is solid. But why have so few scientist come forward to attest to the validity? The answer is: They are afraid. They are terrified. And for good reason.

Apparently I am a crackpot and charlatan (sighs expressively), at least I’m in good company with Phil Plait, PZ Myers and Rosie Redfield (and really, read commentary #9 carefully).

Brian O’Meara (University of Tennessee, NIMBioS) speaks Wednesday, March 16th at 2pm EST on “Making comparative methods as easy as ABC.” The seminar will take place online and anyone can participate. Instructions on how to join can be found at a http://phyloseminar.org/.

Abstract:

For decades, biologists have addressed evolutionary and ecological questions using measurements of species traits, phylogenies, and an assortment of comparative methods. Unfortunately, while there is a large assortment of these methods, they are still fairly limited and development of new methods is slow. It took seven years between the introduction of using a simple Brownian motion model for looking at trait evolution (Felsenstein, 1985) and the use of this same model for looking at rates of trait evolution (Garland, 1992), and an additional 14 years to more powerful tests using a small modification of the basic model (O’Meara et al., 2006). Still other promising methods are described and even tested but remain unavailable to empiricists because they are not put into software. As a result, the questions empiricists can ask about the world are limited by the research productivity of the few dozen scientists who develop and implement new methods in phylogenetics. We describe a new approach based on Approximate Bayesian Computation and implemented in R that will allow researchers to easily develop their own models for trait evolution without requiring them to have specialized mathematical or computational knowledge.


Japan 03:00 (03:00 AM) on Thursday, March 17
New Zealand 07:00 (07:00 AM) on Thursday, March 17
West Coast USA 11:00 (11:00 AM) on Wednesday, March 16
East Coast USA 14:00 (02:00 PM) on Wednesday, March 16
England 18:00 (06:00 PM) on Wednesday, March 16
France 19:00 (07:00 PM) on Wednesday, March 16

For more information on how to attend this and other seminars, visit http://phyloseminar.org/.

As predicted by Joe Meert, Florida’s legislature is once again considering antievolution legislation. This particular attempt is done as a change to a law rather than as a standalone effort.

And the strategy in this one is to label it “critical analysis”, like Ohio did in 2002.

See the Florida Citizens for Science blog for further coverage and advice on activism.

(More at the Austringer.)

Geysir

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GeysirMontage_600.jpg

Geysir, Haukadalur Valley, Iceland, 2010. Actually, Geysir (from which derives the English word geyser) is not so active these days; the pictures show the nearby Strokkur geyser, which erupts every 20 minutes or so. The eruption is preceded by a short-lived blue dome. The four pictures shown here are not all the same eruption. The blue dome in particular was somewhat hard to photograph.

Fossils of life or inorganic fibers? Image of alleged “microfossils” from “Fossils of Cyanobacteria in CI1 Carbonaceous Meteorites: Implications to Life on Comets, Europa, and Enceladus Richard B. Hoover Journal of Cosmology, 2011, Vol 13, xxx.

A recent paper published in the Journal of Cosmology has claimed to have discovered evidence of fossil bacteria in a rare subclass of carbonaceous meteorite. The implications of this paper, should it be correct, are enormous and the blogosphere has gone into overdrive discussing it. There are interesting analyses by the Bad Astronomer, PZ Myers and Rosie Redfield.

Rosie Redmond’s analysis is more detailed (and Rosie being the microbiologist who burst the “Arsenic Bacteria” bubble, knows she her stuff), but all posts quickly get to the heart of the matter; the “evidence” is a bunch of squiggly stuff that bears little resemblance to actual bacterial fossils unless you obscure the details by rescaling the images.

(scroll down for an update)

Barnosky_etal_2011_Nature_Fig1.jpgThis isn’t exactly about creationism/evolution, but it’s still pretty cool. And I will find a way to tie it in, since I haven’t blogged on PT in, I think, months.

Contrary to what creationists believe, evolutionary biologists don’t sit around in biology departments plotting to overthrow God and morality. We spend our time doing things like statistics and programming and specimen preparation and experimental manipulation and DNA sequencing and field observation, and then give and hear talks and discussions about this research. The main thing we are interested in is not “proving evolution”, it is discovering cool facts and devising hypotheses to explain them, and then devising tests of those hypotheses (typically, statistical tests, something which creationists almost always ignore). In short, it’s like any other science.

This paper is a case in point:

NATURE | REVIEW

Barnosky, Anthony D.; Matzke, Nicholas; Tomiya, Susumu; Wogan, Guinevere O. U.; Swartz, Brian; Quental, Tiago B.; Marshall, Charles; McGuire, Jenny L.; Lindsey, Emily L.; Maguire, Kaitlin C.; Mersey, Ben; Ferrer, Elizabeth A. (2011). “Has the Earth’s sixth mass extinction already arrived?” Nature 471(7336), 51-57. (DOI - Link)

sudo laugh

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xkcd: Herpetology

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