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29 Jul 21:33

#497 Java Code

by treelobsters
29 Jul 19:44

Textual Criticism is not Creationism!

by Joachim D.
Over at Nothing in Biology Makes Sense, Sarah Hird mistook a piece of textual criticism as creationism judging: "this argument is an odd mix of science and creationism."

Textual criticism is concerned with the identification and removal of transcription errors in the texts of manuscripts including scripture. It is part of language sciences. Insofar as creationists regard scripture as sacred and never even suspect that scribes may have screwed up their translations, textual critics are diametrically opposed to the creationist frame of mind. They treat scripture like any other human manuscript and analyze it that way. By the way, the comparative approach of textual criticism (stemmatology) has a lot in common with phylogenetics and even predated it in some respects.

The paper in question is textual criticism informed by medical and anatomical knowledge being published in an odd place (a medical journal). The following sentences, however seem to make it clear that they have no creationist agenda:
One of the creation stories in Genesis may be an explanatory myth wherein the Bible attempts to find a cause for why human males lack this particular bone. [...]
This translation, enshrined in the Septuagint, the Greek Bible of the early church, fixed the meaning for most of western civilization, even though the Hebrew was not so specific. Gilbert and Zevit (2001. Congenital human baculum deficiency: The generative bone of Genesis 2:21-23. American Journal of Medical Genetics, 101(3):284-285)
It is admittedly odd to find a piece of textual criticism of the bible in a medical journal, but even Richards Dawkins, the poster child of new atheism, relished engaging in a piece of textual criticism in The Selfish Gene. In my edition of 1989 (reissued with new cover in 1999 by Oxford University Press) it starts at page 16 (chapter 2) and then descends into an endnote:

We tend to regard erratic copying as a bad thing, and in the case of human documents it is hard to think of examples where errors can be described as improvements. I suppose the scholars of the Septuagint could at least be said to have started something big when they mistranslated the Hebrew word for 'young woman' into the Greek word for 'virgin', coming up with the prophecy: 'Behold a virgin shall conceive and bear a son ...'* Dawkins (1989, p. 16)
* p. 16 'Behold a virgin shall conceive ...'
Several distressed correspondents have queried the mistranslation of 'young woman' into 'virgin' in the biblical prophecy, and have demanded a reply from me. Hurting religious sensibilities is a perilous business these days, so I had better oblige. Actually it is a pleasure, for scientists can't often get satisfyingly dusty in the library indulging in a real academic footnote. The point is in fact well known to biblical scholars, and not disputed by them. The Hebrew word in Isaiah is עלמה (almah), which undisputedly means 'young woman', with no implication of virginity. If 'virgin' had been intended, בְּתוּלָה (bethulah) could have been used instead (the ambiguous English word 'maiden' illustrates how easy it can be to slide between the two meanings). The 'mutation' occurred when the pre-Christian Greek translation known as Septuagint rendered almah into παρθένος (parthenos), which really does usually mean virgin. Matthew (not, of course, the Apostle and contemporary of Jesus, but the gospel-maker writing long afterwards), quoted Isaiah in what seems to be a derivative of the Septuagint version (all but two of the fifteen Greek words are identical) when he said, 'Now all this was done, that it might be fulfilled which was spoken of the Lord by the prophet, saying, Behold, a virgin shall be with a child, and shall bring forth a son, and they shall call his name Emmanuel' (Authorized English translation). It is widely accepted among Christian scholars that the story of the virgin birth of Jesus was a late interpolation, put in presumably by Greek-speaking disciples in order that the (mistranslated) preophecy should be seen to be fulfilled. Modern versions such as the New English Bible correctly give 'young woman' in Isaiah. They equally correctly leave 'virgin' in Matthew, since there they are translating from Greek. Dawkins (1989, p. 270)

29 Jul 19:40

Life’s Definition — Discoveroids In a Dither

by The Curmudgeon

There’s a very interesting interview of Gerald Joyce, a professor and investigator in the Skaggs Institute for Chemical Biology at the Scripps Research Institute, that appears in Astrobiology Magazine: Forming a Definition for Life. It says:

A working definition [of life] lately used by NASA is that “life is a self-sustaining system capable of Darwinian evolution.”

This definition is often credited to Gerald Joyce … [who] discusses the history and thinking behind it. He also reveals why it’s been so hard to come up with a definition that encompasses all the aspects and dimensions of life as we know it.

It’s good reading, but the fun part is the reaction of the Discoveroids. At their creationist blog they just posted this: Gerald Joyce Defines Life as Darwinian Evolution. It’s a classic example of not only science denial, but logic denial as well. Here are some excerpts, with bold font added by us:

Joyce seems enamored with the “Darwinian” aspect of the definition. He used the term “Darwinian evolution” 31 times in the short interview, 6 times in this paragraph alone: ….

Yes, and each time Joyce uses that term the Discoveroids become increasingly furious. But the most infuriating thing for them is what Joyce does with that term. Here’s some of the paragraph the Discoveroids quoted:

The coolest thing in the discussion, which wasn’t in the plan document, was appreciating how Darwinian evolution achieves the key attribute of life, which is to allow complex systems to persist despite an often unpredictable and changing environment. And it does so through molecular memory in the form of genetic information that arises and is maintained by Darwinian evolution. Is there an entirely different way to do that? Not our life, not anything that we’ve ever seen, but perhaps there is another way to skin that cat? That would be a huge breakthrough, if there was some paradigm other than Darwinian evolution that gets you what Darwinian evolution gets you. [Emphasis supplied.]

That drives the Discoveroids into a sputtering rage. They say:

By dismissing intelligent causes at the outset, Joyce and his peers were left with non-intelligent, natural causes. Thus, the only “credible” proposal that “gets you” life is Darwinian evolution. Simple!

The conclusion may be simple, but the important thing is how that conclusion was achieved. Note that Joyce said:

Is there an entirely different way to do that? Not our life, not anything that we’ve ever seen …

In other words, there’s no evidence of any other way. Now you understand the Discoveroids’ anger. They sputter:

[T]he “Darwinian” aspect of Joyce’s definition entails much more: the common ancestry of all organisms, from chemicals to man, by means of unguided, impersonal, non-intelligent processes. Logically, everything in between, from flagellum to Flight to Flamenco guitar playing had to “arise” as “innovations” by unguided natural processes. Somehow that view is “credible.”

Did you notice the Discoveroids’ phrase “from chemicals to man”? That sounds like Ken Ham’s formula: “molecules to man.” Deep down, all creationists are quite similar. The Discoveroids sputter on:

We know from uniform experience, however, that it is not credible to expect specified complexity (e.g., functional machines of multiple interacting parts, like those in locomotion and photosynthesis) to arise apart from intelligence.

Yeah, they “know” that. Then they quote some more from Joyce:

My own lab has developed a self-sustained chemical system capable of undergoing Darwinian evolution. All of the bits that are necessary for it to evolve are within the evolving system. So why isn’t that life? Well, there’s a little more to it, I think, which has to do with the “capable” part. We really need to expand that part of the working definition. Our laboratory system is capable of evolving, but thus far it has not evolved any new functions.

You can guess the Discoveroids’ response to that, can’t you? Sure you can. It’s based on one of our Ten Laws of Creationism. It’s our Third Law:

Anything found in nature was Designed, unless it can be reproduced in the lab. Corollary: Anything intentionally done in a lab is not natural; it’s a purposeful result. Therefore, all lab results are evidence of Intelligent Design.

Predictably true to their dogma, the Discoveroids say:

He seems to have missed the logic point that if he set up a system to undergo Darwinian evolution, he added bits to the system, employing intelligence to do it.

BWAHAHAHAHAHA! We’ll jump to the final paragraph, where the Discoveroids say:

Joyce is a deep thinker, but is not thinking deeply enough here. He has provided no example of Darwinian evolution coming up with innovation; he only assumes it did. He has spoken of information, but denied the only known cause of information, intelligence. He has ruled out intelligent causes in all of life, but employed them in his lab. He has denied a puppeteer, but played the part of one. He thought, but has undermined the validity of thinking.

So there you are. We suggest that you read all of the Joyce interview. Then you’ll be able to appreciate the Discoveroids’ reaction even more.

Copyright © 2013. The Sensuous Curmudgeon. All rights reserved.

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29 Jul 19:39

Second fiddle, better fiddle

by naylorsa
Fiddlin Bill Henseley, Mountain Fiddler, Asheville, North Carolina by Ben Shahn, 1937

Fiddlin Bill Henseley, Mountain Fiddler, Asheville, North Carolina by Ben Shahn, 1937

Sometimes you spend years working on a project and then, right as you are about to share your progress with the world, someone else beats you to it. I’d imagine Meng-Tsen Ke, Satoshi Fujimoto, and Takeshi Imai were feeling pretty disgruntled in June when the Deisseroth lab published their technique for making brain tissue optically clear.  The press coverage of CLARITY was immense, I even wrote a post about it. But it turns out while we were all drooling over clear brains, another group was coming up with a cheaper and easier way to make brain tissue see-through.

The Imai group at RIKEN in Japan developed a new technique called SeeDB (See Deep Brain) that makes brain tissue optically clear. This technique relied on finding an aqueous (water-based) solution with a refractive index close to that of fixed tissue. In the past, solutions with high concentrations of sucrose have been used to reduce light scattering in brain tissue. To optimize this process they changed the sugar to fructose and found even more success. The high fructose solution provided optimal tissue clearance and caused very little tissue shrinkage.

However, in order to get the fructose solution to soak into very large tissues, some heat must be applied. An unfortunate side effect of this heat is the activation of the Maillard reaction (browning) which we happen to love on our steaks, but is not so great in tissue we are trying to make as clear as possible. To stop this from happening, a reducing agent is added to the high fructose solution.

Soaking the tissue in increasing amounts of fructose, and finally in a fructose/reducing agent solution until the tissue is clear takes approximately three days. Other passive tissue clearing methods can take weeks. This technique is far more simple and much cheaper than the CLARITY method. While the results are not quite as perfect, they are certainly sufficient to image to great depths in larger pieces of brain tissue. This technique will enable labs with less money and equipment to continue to explore neural structures deep within the brain. So even if all the fanfare over clear brains has passed, I think this second fiddle technique will be important to the field of neuroscience and widely adopted very soon.

29 Jul 09:33

Reader Mail

by David

Reader Mail

29 Jul 05:00

Since when is cancer not caused by mutation?

by Mike White

I feel a major rant about epigenetics coming on… must hold it back until a more convenient time. But I can’t refrain from commenting on just how wrong this is:

“We used to think that cancer was caused mainly by mutations of genes, but we now believe that epigenetic aberrations are responsible for more than half of cancer cases,” says Trygve Tollefsbol, who is a senior scientist at the University of Alabama at Birmingham’s Comprehensive Cancer Center.

“That’s an important change because genetic mutations are very difficult, if not impossible, to correct, while epigenetic marks are potentially reversible,” he explains.

- Nutrition Action HealthLetter, July/Aug 2013, p. 10

I’ve heard a lot of BS claims made in the name of epigenetics, but this one takes the cake. Can anyone point me to an instance of any cancer that does not involve mutations? And where is the evidence that “more than half of cancer cases” are not caused by mutations? Anyone?

(And if you haven’t read this, you should: Mark Ptashne, “Epigenetics: core misconcept” Proc Natl Acad Sci U S A. 2013 Apr 30;110(18):7101-3.)

NOTE: The article is not online yet, but comes from a big story on epigenetics in the July/Aug issue of the Nutrition Action Health Letter.

29 Jul 02:01

Every friggin’ dead thing is “CHUPACABRA”!

by idoubtit
Who decided that a chupacabra is anything you want to gain attention for and think is hideous? This photo uploaded to a local news site was called a chupa and is getting lots of attention. I have no idea why. Viewer uploads ‘chupacabra’ photo. A viewer named Ramona uploaded a photo she headlined “Chupacabras do…
29 Jul 01:55

Creationists Abandon Loch Ness Monster?

by The Curmudgeon

A year ago we wrote In Scotland They’re Laughing at Louisiana, in which we learned that the customarily dour Scots were howling over the fact that schoolchildren in Louisiana were being taught: (1) the Loch Ness monster is real; and (2) Nessie’s existence disproves Darwin’s theory of evolution.

The Sunday Herald of Glasgow informed us that besides laughing at Louisiana, the Scots were quick to see the silver lining in the situation. They also reported:

Of course, the Scottish tourist industry might well reap a dividend from the craziness of the American education system. Nessie expert Tony Drummond, who leads tours as part of Cruise Loch Ness, has a few words of advice to the US schools in question: come to the loch and try to find the monster.

That was last year. Today the same newspaper has this story: Nessie cut from creationism. That is a shocking headline! The story says, with bold font added by us for emphasis:

New editions of Accelerated Christian Education (ACE) biology textbooks do not contain the controversial idea that Scotland’s most famous mythological beast may have been a real living creature. The updated book is only available to creationist-taught pupils in Europe, but campaigners say America is likely to follow suit.

What is motivating the creationist publisher to offer the new edition only in Europe? How can there be two versions of The Truth™? Perhaps this will be explained as we continue with the news story:

The previous edition of one ACE textbook said: “Are dinosaurs alive today? Scientists are becoming more convinced of their existence. Have you heard of the ‘Loch Ness Monster’ in Scotland? “‘Nessie’ for short has been recorded on sonar from a small submarine, described by eyewitnesses, and photographed by others. Nessie appears to be a plesiosaur.”

There was also a claim that a Japanese whaling boat once caught a dinosaur. In the new editions, both claims have been removed. However, it still suggests that dinosaurs co-existed with humans.

Aside from the problem of selling two wildly different versions of the book, there’s something else here that we find disturbing. We’ve never seen the facts in a creation science text changed — not ever. New facts may be added, but old ones don’t get dumped. How can they throw away facts that prove scripture? Something is definitely wrong here.

While we’re mulling that over, let’s read on:

Jonny Scaramanga, from Bath, went through the ACE programme as a child but now campaigns against Christian fundamentalism. He said: “In the new editions they’ve replaced Nessie with talk of folk tales from China and Ireland – They still want to prove that dinosaurs and humans existed at the same time.”

Jonny sometimes visits our humble blog. Perhaps he’ll enlighten us about the new data. We’re especially interested in that Irish dinosaur.

But we’re more interested in the fact that a creation science book is actually being changed. One of the virtues of creationism is that it’s reliable and unchanging, whereas science is constantly being revised. Aha — at the end of the story that issue is addressed:

Arthur Roderick, founding director of Christian Education Europe, part of ACE, said: “As with any text books – curriculum is subject to revision and change.”

This is an outrage! If they can dump Nessie, then why not dump Adam & Eve? Without Nessie there is no truth, no morality, no hope for eternity. We may as well all be Darwinists, fornicating like animals.

Something must be done, and because everyone else is too cowardly to speak up, your Curmudgeon shall boldly step forward and take command of the situation before all is lost. We exhort the creationist schools in Louisiana and elsewhere:

Don’t adopt the new textbook from ACE. The old creation science is always the best.

Copyright © 2013. The Sensuous Curmudgeon. All rights reserved.

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28 Jul 22:28

Something sassy

by Grant Jacobs

Aww, ain’t she purty.


Very sleek, yes.

Enough to knock your caps off.

She’s got 5 megabytes, Chuck.

5 million alphanumeric characters.

’pparently IBM reckons they got no way to sell one with more.

Chuck clicks in appreciation.

6 bits for each character. With a parity bit!

Right, right.

Takes only point-six seconds to locate a record.

Imagine what you could do with that!


In 1956 IBM launched the 305 RAMAC, the first computer with a hard disk drive. The hard drive unit weighed over a ton and stored 5 MB of data. It was moved about with a forklift and large cargo aircraft.

Think of this next time you look at your 8Gb USB stick.

All factoids for the dialogue are lifted from the wikipedia entry. (Hey! – it’s a lazy Sunday piece written while watching a movie.)

My first computer with a hard disk was a IBM PC clone. Before that I owned an Apple ][e clone that used a consumer tape player as it’s external storage.

My original source for the photograph was a re-tweet by @dgmacarthur of  a tweet by Rich Powell (@cultmojo).

Other articles on Code for life:

Sinclair ZX envy

Consumer brain-computer interface

What use now is handwriting?

Teaching bioinformatics at high school

Retrospective–The mythology of bioinformatics

28 Jul 22:27

Carnival of Evolution 62: The Whig History

by Joachim D.

Whig history is abridged retro-spective. Double Refraction has a discerning post on different shades. A whiggish image of the evolution of man is the marching band of hominids.

ADAM BENTON explains why this picture is not only abridged but also false at EvoAnthditto ZEN FAULKES at Neurodojo. It is also sexist. I am not sure, however, whether the female version at the left would be received as non-sexist. It surely is as triumphant, and hopefully as funny, as its male version above.

When it comes to the history of evolutionary theory, a whiggish image could look something like this:
I leave it to the readers to come up with a female version (including, for example, Maria Sibylla Merian, Rosalind Franklin, Barbara McClintock, Christiane Nüsslein-Volhard).

Arranging July's posts that I found interesting or entertaining as well as the few submitted by others according to a Whig history of evolutionary theory in the following is purely ornamental and does, of course, not imply any whiggishness on the side of the contributors.

Evolution vs Creation
Jean-Baptiste de Lamarck
KEN WEISS poses a Question of the Campagna? The poignant side of 'Intelligent Design' at The Mermaid's Tale.

JOHN S. WILKINS is Evolving Thoughts about the animal nature of humans here and here.

Ball State Univerity hires intelligent design leader to teach astronomy, says SETH SLABAUGH at The Star Press.

PETER keeps an Eye on the ICR and on Creationism at University.

EVIN BARIŞ ALTINTAŞ guest posts at SciLogos: Turkey’s science agency says evolution is ‘too controversial’ (see also here).

MASSIMO PIGLIUCCI deals with Plantiga's Evolutionary Argument Against Naturalism at Rationally Speaking. Platinga managed to create a paradox that pits evolution against naturalism, but the conclusions do not necessarily follow from the premises.

The equivalent of Batesian and agressive mimicry in academic publishing is described by CHRIS SMITH at Nothing in biology makes sense.

Variation & Selection 
Charles Darwin 
JOSH JONES shares the vintage documentary The Blind Watchmaker at Open Culture.

At Aeon, LEWIS SPURGIN sets his research into a broad context about the role of chance in evolutionary change.

CHARLES GOODNIGHT introduces The multivariate breeder’s equation and explains the founder effect with drift and epistasis at Evolution in Structured Populations.

XAVIER reveals the trick behind 'magic' traits at eco-evolutionary dynamics.

See a newly discovered, historic photo of Darwin and Wallace together at BUG GIRL's Blog.

CARL ZIMMER describes how Archaeopteryx becomes a minor find among a crowd as new finds of feathered dinosaurs and primitive birds Loom large.

Particulate Inheritance 
Gregor Mendel
Mathbionerd M. WILSON SAYRES explains evolutionary changes in the Young sex chromosomes of Silene latifolia.

NATHANIEL COMFORT asks whether the discovery of The Arsehole Gene will change the perspective on a socially stigmatized group at Genotopia.

Researcher at work, SIMON URIBE-CONVERS, describes his research on parasitic plants (Bartsia) at Beacon.

ANNE BUCHANAN updates you on progress in gene therapy at The Mermaid's Tale.

Soma & Germ-Line 
August Weismann
The Conversation of JUSTIN ST. JOHN invites you to Meet Mama, Papa and Mama: how three parent IVF works.

Feeling older than you are? DAVID MORRISON from The Genealogical World of Phylogenetic Networks can help you understand.

CARL ZIMMER asks What good is half a sucker? at The Loom and finds hints in the development and fossils of Remora fishes.

Arizona State University fused cancer research with physics geekdom in the Center for the Convergence of Physical Science and Cancer Biology. Surprise! The new theory is sophisticated and evo-devo, but the physicists PAUL DAVIES and CHARLES LINEWEAVER came up with it.

Mutation vs Selection
Thomas Hunt Morgan

Researcher at work, SUDARSHAN CHARI, explains his research about compensatory mutations or 'context dependence' in evolution at Beacon.

Every non-lethal genome position is variable in the human population says M. WILSON SAYRES (AKA mathbionerd) quoting Tuuli Lappalainen citing Daniel Wegmann at Panda's Thumb.

RAZIB KHAN sets new finding on genetic hitchhiking into context at Gene Expression.

ANNE BUCHANAN thinks that The extent of what we can't know about gene function is infinite at The Mermaid's Tale.

The Synthesis
Ronald A. Fisher
ZEN FAULKES relates how Everything is connected and a snail in a lake helps a crab in the sea at NeuroDojo.

While Teaching Biology, MARC SROUR starts to change his mind about non-genetic inheritance in evolution.

DAVID MORRISON highlights the achievements of a largely forgotten historical source of The Genealogical World of Phylogenetic Networks.

The NCSE shares a preview of "Darwin's Lost World" by MARTIN BRASIER, a tale of scientists taking a gap in the record as a challenge for further research rather than an excuse for dismissing Darwin's theory.

BRADLY ALICEA argues from non-optimlity at Tumbld Thoughts and Synthetic Daisies (see also here).

The Double Helix
Watson & Crick
On the occasion of several anniversaries, RICKI LEWIS reviews the history of DNA forensic profiling at the DNA Science Blog of PLoS.

MIKE WHITE is Finding function in the genome with a null hypothesis (see also part 2) at the Finch + Pea.

MARC SROUR shares a recipe for extracting DNA at home that is suitable for children at Teaching Biology.

W.D. Hamilton
MATT ZWOLINSKI defends William Graham Sumner against Richard Hofstadter's social Darwinism slur at Libertarianism (see also here).

Has the brain center been discovered that is involved in ideas getting viral? PsyPost reports on How the brain creates the ‘buzz’ that helps ideas spread.

RANDAL S. OLSON models swarming behavior in a digital selfish herd and realized that Evolution isn't over until you click stop.

The Darwin Wars 2.0 feature evopsych vs freethought. One frontier delineates an anti-Whig history -- a Torie Story as it were -- seeing human evolution frozen in the Flintstones' stage instead of progressing triumphant. I abstain from taking sides by adding any link. Just follow the smoke.

Individuals vs Groups 
George C. Williams
Not a blog, but free and very lucid, STUART WEST & ANDY GARDNER defend inclusive fitness as the maximand of adaptation in the latest issue of Current Biology. JOHN MAYNARD SMITH once called inclusive fitness "an absolute swine to calculate," in an interview deposited at Web of Stories.

In Evolving Economics JASON COLLINS comments on a piece that David Sloan Wilson published at Aeon.

BRIAN McGILL wonders whether deans are committing the same error as hen breeders at Dynamic Ecology.

Females & Males 
John Maynard Smith
Why Evolution is True, a blog (sic:-) by JERRY COYNE, shows the Emei mustache toad - another freak of nature.

SARAH HIRD revives a debate about the lost penis bone of human males at Nothing in biology makes sense (see also here).

I doubt that the data On earwig parthenogenesis warrant the conclusions of a recent paper and show the waxing and waning of interest in the evolutionary significance of sexual reproduction via Ngrams.

Gilf el Kebir: Cave of Swimmers, Neolithic art
ADAM MARCUS of Retraction Watch informs us that a Journal pulls insect-global warming paper after questions arise over results.

Elaine Morgan died aged 92. Her acclaim swings between great feminist and bad evolutionist.

For those - like me - who love wacky hypotheses, the Aquatic Ape has yet another successor: The Porcine Ape. As the entertainment value dwindles of the hypothesis that the Neanderthals preyed on and raped Homo sapiens (see CoE 49), PZ MYERS pharyngulates another revolutionary revelation: Humans are hybrids of chimpanzees and pigs. I predict the merger of the Aquatic and Porcine Ape in a future revelation. Until then, have fun with ZEFRANK's True Facts About the Sea Pig.

On equal footing, DONALD PROTHERO deals with the discovery of Bigfoot DNA at Skepticblog. This footage of Bigfoot spotted in Canada comes as a side dish.

The Onion has American voices on Jane Auten's replacing Charles Darwin on the ten pound note.

[Excepting the tinkered "Whig images" at the top.]
  • LAMARCK: Galerie des naturalistes de J. Pizzetta, Ed. Hennuyer, 1893, via Wikimedia Commons.
  • DARWIN: portrait by George Richmond, 1840, © D. Bayes / Lebrecht Music&Arts.
  • MENDEL: US National Library of Medicine (public domain), via Wikimedia Commons.
  • WEISMANN: Edwin G. Conklin, "August Weismann" Proceedings of the American Philosophical Society, Vol. 54, No. 220. (Oct. - Dec., 1915), pp. iii-xii.
  • MORGAN: created for the 1891 Johns Hopkins yearbook of 1891, see Shine and Hobel (1976). Thomas Hunt Morgan. The University Press of Kentucky.
  • FISHER: Original uploader was Bletchley at en.wikipedia, Released under the GNU Free Documentation License; PD-OLD-70.
  • WATSON & CRICK: Structure of DNA, 30 April 2009, The Pauling Blog (go there for excerpts of a biography on Ava Helen Pauling and much more information related to Linus Pauling).
  • HAMILTON: University of New England, Human Nature Project, Hamilton Memorial Lecture (
  • WILLIAMS: A Conversation With George C. Williams by Frans Roes (
  • MAYNARD SMITH: Back cover of "The Theory of Evolution." A Pelican Book by Penguin, 1958, my scan.
  •  GILF EL KEBIR: Cave of Swimmers, rock art, © Angelika Mair, 2008.* 

Also visit Carnival of Evolution on Facebook, Twitter and the Blog.

CoE needs volunteers for the next issues. If you trawl the web for posts related to evolutionary biology anyway, it will not be hard - though the ratio of external submissions to host submissions seems to be a shrinking.
28 Jul 20:29

Bruce Chapman—"The Pseudo-Science Guy"

by Matt Young

by Steven Mahone

Bruce Chapman, the Big Cheese over at the Discovery Institute, is apparently feeling a bit threatened by an interview that Bill Nye (“The Science Guy”) recently did for the Seattle Times. Chapman wrote an article expressing concern that Bill’s straight talk about science literacy might somehow implicate his cherished “Intelligent Design” theory by lumping it in with young earth creationism, thereby leading some to conclude that ID is nothing more than the pseudo-scientific equivalent of those get-rich-working-from-home schemes so ubiquitous on the radio and Internet.

Nye is a respected, reasonable voice who is imploring our educators and politicians to cut to the chase and dispense with the myths and misunderstandings that cloud our public policy and educational system. Otherwise, the challenges set out before us will only be made more difficult to remedy. Nye knows that we have an obligation and a responsibility to leave our descendants with the intellectual insight and courage to take on the universe for what it is; there are no shortcuts, nor are there any get-rich-quick alternatives. How does Chapman react to Nye’s honorable efforts? He accuses him of being the “Red Herring Guy” and essentially calls him a liar. Geez.

The irony of the “Red Herring” claim is that Chapman has burdened Nye with naming a congressional district that has mandated equal time for young earth creationism; yet Nye has never made such a claim and Chapman knows it! The misdirection here is all Chapman’s, who evidently intends that you pay no attention to the Gallup Poll showing that nearly 50% of Americans believe that man was created less than 10,000 years ago. He’s also hoping that you separate his organization from those other creationist Ponzi schemes; all Chapman wants is the academic freedom to present alternatives to well-established scientific principles that have attained expert consensus. That’s not too much to ask, is it? Only if you ignore that pesky Dover trial, which settled this issue years ago. Unfortunately for Chapman, Nye has a pretty good memory.

While we’re at it, here are some of the other typical talking points that Chapman’s organization offers, along with a translation into the vernacular:

“Random mutation and natural selection can’t account for the complexity of the cell!” is equivalent to, “A single mother in Miami is now enjoying a Darwin free life after purchasing the DI’s new best seller on Cambrian explosion!”

The ever popular, “Highly qualified professors are being persecuted by the Darwinian establishment for simply suggesting alternative reading materials for their courses!” is actually, “The Designer still loves you, even if you’re taking a rigorous upper division physics course at a prestigious university run by heartless, amoral liberals.”

And finally, “Intelligent Design makes no claims about who the designer is, nor is it a religious idea!” can be summed up as, “Even though our Fellows at the DI appear on the same Christian programs as Ray Comfort and Kirk Cameron, our claims are different and you need not be concerned that we didn’t make the Nobel Prize shortlist!”

Sorry, Mr. Chapman. The jig is up. You know it, Bill Nye knows it, and sooner rather than later, everyday people like me and that single mom in Miami are going to figure out that there’s no substitute for diligence and hard work, especially where the payoff will be long term success for our progeny. My concern now is how you’re going to handle the upcoming remake of Cosmos: A Space-time Odyssey which will be hosted by Neil deGrasse Tyson and underwritten by Fox (yes, the same Fox that employs Bill O’Reilly!) My suggestion is that you choose your insults carefully on this one. Remember in the movie “Casablanca” when the character of Rick (Humphrey Bogart) is asked, “You despise me, don’t you, Rick?” Bogart then utters the greatest back-handed slight of all time: “If I gave you any thought I probably would.” I recommend that you not put Dr. Tyson on the spot with a similar question.

Steven Mahone is an Engineer and a founding member of Colorado Citizens for Science.

27 Jul 22:52

07/26/13 PHD comic: 'How's the data?'

Piled Higher & Deeper by Jorge Cham
Click on the title below to read the comic
title: "How's the data?" - originally published 7/26/2013

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27 Jul 22:28

OTP Part 5

by Maki

Drawing this series has taught me much about early triassic life, and the writing has proved to be a bigger challenge than I thought. As I try to research the details of the time period, I’m realizing there isn’t much to go on.

Dinosaurs only first appeared during this era, and wouldn’t rise to the dominance that we know and love them for until the Jurrassic period. Suffice to say, you won’t have our Broomistega running into any velociraptors, but that doesn’t mean there weren’t any equally fightening animals around. Likewise, some of the earliest wasps and flies began to make their appearance after the Great Dying, but not in the form we know of today. Granted, there wasn’t a whole lot left on Earth at the time. (Also, fossil evidence shows that grass didn’t crop up until as early as 65 million years ago… oops)

While looking for more information, I not only noticed that images from this comic series and accompanying memorabilia have begun to creep into google searches, but Wits University and the folks who had the now-famous burrow cast scanned, have 3D printed the skeletons. Check out the photo at Wired.

This is huge.

The act of recovering a fossil from the surrounding stone is delicate and dangerous work (for the fossil). What they’ve shown is that we now have the capability to image and recreate entire skeletons without ever removing them from the safety of their native stone. I’m already having fantasies of scanners imaging large chunks of earth and printing out fossils without ever having to excavate. We live in a fascinating age.


There is not much time left to support my Kickstarter, which not only helps me produce Sufficiently Remarkable, but also a Donald of Mars miniseries, a Crowlmes and Flockson miniseries, and a full-on Pineapple Maki websisode. If that’s not enough, think of the awesome rewards you can get, including limited edition* pins, plushes, and even your very own erotic scarf.


Take a look at this rundown of what you can get.


*I’m serious, none of this stuff will be available after the campaign. I’m dedicated to providing backers with exclusive items to show their status as early adopters.




27 Jul 22:13

Ellis Washington: Darwin Destroyed Detroit

by The Curmudgeon

Buffoon Award

The Retard-o-tron™ has been getting quite a workout lately. Its blaring sirens and flashing lights caused us to dash to the computer, which was locked onto an article in WorldNetDaily (WND). It’s in their honor that our jolly buffoon logo is displayed above this post.

The Retard-o-tron™ had found another intellectual masterpiece by one of our WND favorites — Ellis Washington. In this earlier post we described Ellis and his intellectual style, so we won’t repeat all that again. But we should point out that Ellis has an entry in the Encyclopedia of American Loons: #404: Ellis Washington.

Today’s essay from Ellis is titled Detroit (1701-2013) … R.I.P. WND says it’s an “Exclusive.” Of course it is — where else except WND can you find material like this? It’s a rant about the downfall of Detroit. By now you surely know that the city of Detroit has declared bankruptcy. But do you know the cause — the real cause? Ellis does. And soon you will too.

Most of what Ellis says doesn’t interest us, so this is going to be an uncharacteristically brief post, but you can click over to WND to read read all of his essay if you like that sort of thing. We’ll show you only what got our attention. But first we need to set the stage. He starts out saying:

I was born and raised in Detroit. … Detroit, like most big cities in America, is the result of unbridled political policies of the Democratic Socialist Party running wild for decades. Detroit is a city that is rampant with crackhouse neighborhoods, crime, gangs, despair, Democratic Machine corruption, legalized thievery ubiquitously referred to as “welfare,” food stamp fraud, 73 percent illegitimate birthrates, Marxist bloodsucking unionism, 47 percent of Detroiters functionally illiterate, compromised Christians, phony preachers and the leftists purposeful deconstruction of the black family. All of these factors in part contributed to the deconstruction of Detroit.

The essay continues like that for several paragraphs. Much of what Ellis says about Detroit and its problems is correct, but we’re skipping almost all of it. What triggered the Retard-o-tron™ was this, with bold font added by us:

Utopians, Darwinists, evolution atheists, humanists, environmentalists and leftists in general always concoct social welfare programs for one purpose and one purpose only: democide, the murder of any person or people by the government usually based on race, ethnicity or national origin. FDR’s “New Deal” killed the Constitution and the American spirit. LBJ’s “Great Society” killed the black family. Obamacare will kill America.

That’s it. Really, it’s the only thing in Ellis’ rant we wanted to show you. Most of you already know about Detroit’s woeful history of problems, but what we didn’t know (until now) is that Darwin and evolution were the root cause. It’s quire a revelation, one that is only available at WND, thanks to their top intellectual — Ellis Washington. He concludes by telling us:

Detroit has demonstrated to the world that liberal fascism will always fail because it will always collapse upon the weight of its own immorality.

Yes, and now we know it’s Darwin’s fault. We feel rather foolish that we weren’t able to figure it out for ourselves. Thanks, Ellis!

Copyright © 2013. The Sensuous Curmudgeon. All rights reserved.

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27 Jul 22:12

Darwin’s Doubt in review; Meyer, Matzke, and some of their critics

by Paul Braterman

paul_book_-1Yesterday I wrote about Casey Luskin’s critique of Nick Matzke’s review of Meyer’s Darwin’s Doubt, but not everyone knows (why should they?) who Luskin is, or who said what in which way about whom. So I’ve written this brief survey of the dramatis personae, and review of reviews of reviews.

Luskin is Program Officer of the DI’s Center for Science and Culture, of which Meyer is director, Berlinksi a Senior Fellow, and Kenyon a Fellow. According to his bio on the CSC website, he ‘is co-founder of the Intelligent Design and Evolution Awareness (IDEA) Center, a non-profit helping students to investigate evolution by starting “IDEA Clubs” on college and high school campuses across the country.’ His 5 year stint with Scripps Institute of Oceanography produced one publication; he was one of several junior authors on a study of paleaomagnetic dating of sediments, which has attracted 17 citations. So, moderately useful routine work. No life science qualifications or experience.

David Berlinski is a Senior Fellow of the CSC, mathematician and philosopher, and has written serious works in his own area, including a 1972 article on the philosophy of molecular biology. As the review I cited shows, he writes powerfully and amusingly, even when (as here) he is attacking a fictional straw man.

Dean Kenyon is a CSC Fellow. He was at one time a respected biologist, but in the 1970s was converted by Morris’s Genesis Flood to Young Earth Creationism. He was co-author of Of Pandas and People.

Nick Matzke is just finishing the formalities of his PhD at Berkeley,and will be moving to a postdoc at NIMBioS at U. Tennessee Knoxville in September. Web of Knowledge lists him as author of 19 publications, with a total of 330 literature citations to date.

The only other serious reviews of Darwin’s Doubt are this in the New Yorker, “a masterwork of pseudoscience”, and Don Prothero’s shredding on Amazon (this review has attracted three times as many comments on Amazon as the book itself). Donald is the author of over 100 technical publications since 1989, the masterly Evolution; What the Fossils Say and Why it Matters (a much thumbed copy on my bookshelf as I write), half a dozen other popular/semipopular books (including  Abominable Science, due for release in August, on Nessie, Yeti, and other phantasms; but alas no chapter on the Intelligent Designer), and five textbooks, and has received numerous awards for his publications and teaching.

Stephen Meyer, Director of the CSC and Senior Fellow of the Discovery Institute, holds a joint degree in physics and earth science from Whitworth, a private Christian liberal arts university, and a PhD in the philosophy of science from Cambridge, and has taught at  Palm Beach Atlantic, a faith-based liberal arts college. He is now director of the Discovery Institute’s Center for Science and Culture, and author or co-author of a number of works of fiction, including Explore Evolution, a pseudotextbook that shows that the creationists have discovered Batesian mimicry, other works of fiction including Signature in the Cell, and, of course, Darwin’s Doubt. Which is where we came in.

Filed under: Creationism, Evolution in general Tagged: Casey Luskin, Center for Science and Culture, Darwin's Doubt, Discovery Institute, Don Prothero, Intelligent designer, Meyer, Nick Matzke, Stephen Meyer, Young Earth creationism
27 Jul 08:08

NRA: The imminent Rapture is not imminent

by Fred Clark

Nicolae: The Rise of Antichrist; pp. 167-174

During a long, rambling conversation over dessert with Rayford Steele, Hattie Durham reminds her former non-boyfriend that he was always too old for her anyway. “[Buck] and I are closer in age,” she says.

She underscores the point on the following page, saying of Nicolae Carpathia: “He was only about as much older than Buck as Buck was older than I.” At that point I felt like I was reading a word problem from the PSATs (“Rayford is twice as old as Hattie. Nicolae is as much older than Buck as Buck is older than Hattie. If Hattie is 22 years old, what color is the Norwegian’s house?”).

This discussion of the characters’ relative ages got me to thinking about my own age relative to theirs — and that’s a disastrous line of thinking when it comes to the central claim of these books. Buck Williams was 29 years old in the first book of this series, which was published in 1995. In 1995, I was 27 years old, so Buck is two years older than me.

Bladerunner (1982).

That would mean that today, in 2013, Buck is 47 years old. But Buck Williams doesn’t get to live to see 47 because seven years after these books begin, Turbo Jesus comes back and destroys life, the universe and everything. So the world was supposed to end in 2002.

Spoiler alert: The world did not end in 2002.

Heck, in 2002, Tim LaHaye and Jerry Jenkins hadn’t even finished writing this series of books.

But wait, that’s not entirely fair. That first book wasn’t set in 1995. It was set in an undefined not-so-distant future. The problem is that the not-so-distance between 1995 and this future is asked to serve two contradictory functions.

On the one hand, this distance must be very, very short because the story begins with the Rapture. LaHaye, like everyone who believes in the idea of the Rapture, believes that it is imminent. Type “Imminent Rapture” into Google and you’ll find hundreds of thousands of results, even though the phrase is redundant. To believe in the Rapture is to believe that it could occur at any second — maybe this very day, maybe this very hour, maybe before you finish reading this post or even this sentence! (Phew — looks like we’re all still here.)

A Rapture-believer like Tim LaHaye cannot provide one of those sci-fi introductions when telling a Rapture story. It cannot be specific, like the first lines of John Carpenter’s 1981 film Escape from New York: “In 1988, the crime rate in the United States rises four hundred percent. …” No one knows the day or the hour of when the Rapture will come. But it is undoubtedly imminent. No one knows the day or the hour, but it must always be possible that it is this day and this hour.

The imminence of the Rapture means that this book, published in 1995, also had to, at least in a sense, be set in the world of 1995. The story couldn’t include any elements that would have seemed “futuristic” in 1995 — flying cars, rocket packs, domed cities, cell phones, wi-fi, a black president, etc. All of those would have signaled that the Rapture is not imminent, but some future event still years or even generations away. They would serve to increase the not-so-distance of the book’s future setting, contradicting the imminent-Rapture requirement that this not-so-distance be as short as possible.

The imminent Rapture requires that this story be set in a present that’s just about to happen. That presented Jerry Jenkins with a bit of a dilemma as it took the authors 12 years to finish publishing their narrative of how they believe the final seven years of history will unfold. Jenkins needed to preserve the Rapture’s imminence by avoiding futuristic technological details and only including the technology of the present day, but the present-day technology of 2007 was quite different from the present-day technology of 1995. Jenkins’ cleverly pragmatic response to this problem was simply to incorporate new technologies as they arose while pretending this doesn’t create any anachronistic conflicts between his earlier books and his later ones. So in the first book we have airport pay-phones (ask your parents) and by the third book we have cell phones. That can sometimes be jarring, but I give Jenkins a pass on this because telling a story set in the imminent future is a difficult business.

The one bit of futuristic technology the authors do include in their story is Dr. Chaim Rosenzweig’s Miracle Formula. The chemistry and biology of this seems so unlike anything possible today that the presence of such a formula in our story seems to push its setting decades further into the future, destroying the whole sense that the Rapture it describes might be “imminent.”

I suppose the authors might counter that Rosenzweig’s formula wasn’t so much a scientific breakthrough as it was an actual miracle. Like the Rapture itself, it was an act of divine intervention in the natural world and thus, like the Rapture itself, something that might be regarded as imminent. That’s a bit unsatisfying, though. To paraphrase Arthur C. Clarke, any act of miraculous intervention is indistinguishable from sufficiently advanced technology.

The larger problem for the authors and for their insistence on the imminence of this story is that their focus on avoiding futuristic technology didn’t extend to an avoidance of futuristic politics. The political world in which Left Behind (1995) is set has as much relation to present-day politics as the technological world of Star Trek has to present-day technology. Peace in the Middle East, for example, is presented as a fait accompli. Israel is said to be at peace with all of its immediate neighbors — a state of affairs the authors describe as somehow involving Israel absorbing all of its immediate neighbors, annexing much of Syria, Jordan, Lebanon, Iraq and Egypt without disrupting or disturbing the residents of those countries while also not altering in any way the distinctive identity of Israel as a Jewish nation.

Such a development doesn’t seem particularly imminent. It seems utterly unlikely, if not impossible. For the authors, though, this is something that will and must happen — a fulfillment of what they believe is divine prophecy. They also believe this to be a necessary precondition for the “imminent” Rapture. Let’s play along with that idea as best we can. Forget about 1995, start with today, July 26, 2013. How long do you imagine it would take to get us from where we are today to this prophesied future world of a Greater Israel beloved and unthreatened by those neighbors it hasn’t yet absorbed? Can you imagine this happening in a single decade? A single generation? A single century?

I can’t. And if this development is a prerequisite for the Rapture — if this must be accomplished before the Rapture can occur — then it seems to me that this Rapture cannot be in any way described as imminent. If this is a necessary precursor to the Rapture, then — based on Tim LaHaye’s own rules of “Bible prophecy” — the odds are that we’ll see a colony on Mars long before this “imminent” Rapture could ever occur.

And keep in mind that these books are about prophecy, not playful prediction. If the future they foretell does not come to pass as they foretell it, then these books utterly fail. That is their central claim.

That makes for a very different sort of problem than the fun-but-mistaken discussion of the supposedly failed predictions of science fiction stories. George Orwell wrote 1984 in 1949. I quoted from Escape From New York above, which described a future world of 1988 in which Manhattan had been transformed into a penal colony. The image above is from the 1982 movie Blade Runner, which portrayed the Los Angeles of 2019 (getting close!) as a cramped city wracked by climate disruption and police drones (getting close!). But Blade Runner also predicted “off-world colonies” and androids indistinguishable from their human creators — developments that seem more than six years distant from our present. Or consider one of my favorite books, Infinite Jest, which depicted the Year of the Depends Adult Undergarment as a 2009 that wasn’t even called “2009.” David Foster Wallace nearly predicted Netflix, but northern New England hasn’t been transformed into a concavity overrun with mutant feral hamsters, so he loses points for “accuracy” there.

But this game of spot-the-failed predictions misrepresents what those stories are about. They’re not about the future, but about the present. The point wasn’t an attempt to make an accurate prediction about where we are inevitably headed, but a way of using such predictions as a mirror to reflect and examine where we are now. The words on the screen in that still from Blade Runner really mean just the same thing as the words at the beginning of Terry Gilliam’s Brazil: “Somewhere in the 20th Century.” Those stories aren’t predictions about the future, but rather commentaries on the present (and on the perennial).

That’s also true for the alleged source material for the Left Behind series — the apocalyptic literature of the Bible. Apocalyptic literature is not making predictions about the future, but rather it attempts to unveil (“Revelation”) the true reality of the present or perennial human condition. It is prophetic in the sense that, like the prophets, it passes judgment on the world and renders a verdict. But it is not meant to be “prophetic” in the carnival-huckster sense of foretelling future events.

Unfortunately for LaHaye and Jenkins, their books are meant to be predictive “prophecies” in that latter sense. These books are fictional, but they’re meant to provide a fictionalized description of future events that will occur just as described — a kind of historical fiction about the future. That means the standard for accuracy that it would be unfair to apply to 1984 or to Blade Runner must be applied to these books. By fudging on the precise year in which their story is set they don’t allow us to state conclusively that their predictions have failed and that their prophecies have gone unfulfilled. But we can state conclusively that the imminent “Rapture” they continue to prophesy was not and is not and cannot be “imminent.”

This may seem like an overlong response to just a couple of sentences from Hattie in this section of Nicolae, but her whole conversation with Rayford is infused with her nostalgic musing about her past. That past, even as sketchily and carelessly described by Jenkins, is situated in time. Combined, then, with Hattie’s discussion of all the characters’ ages one gets a clearer sense of when the imminent present of this scene is set — and that actually seems to be earlier than 1995.

“Think about it, Rayford. All I ever wanted to be was a flight attendant. The entire cheerleading squad at Maine East High School wanted to be flight attendants. We all applied, but I was the only one who made it. I was so proud. …”

Hattie is supposed to be a member of Generation X, but Jenkins describes her childhood dreams and teenage fantasies using his own Baby Boomer imagination. This seems like something out of the world of Bye Bye Birdie or Mad Men. If Hattie grew up reading Vicki Barr Flight Stewardess books as a child and she’s in her early 20s, then this story can’t be set much later than the Reagan years — 1985 rather than 1995.

Back in 1985, of course, Tim LaHaye was preaching about the same “Bible prophecies” he later fictionalized in 1995 and that he’s still preaching today in 2013. He was preaching that the central focus of every Christians’ life ought to be the Rapture. And the Rapture, he said in 1985, is imminent.

27 Jul 04:30

This strip was Not Invented Here on Wednesday, July 24, 2013

Help Kickstart Upgrade Path: the new Not Invented Here collection

Not Invented Here strip for 7/24/2013

That's not what they teach you in Paparazzi school.

Our Upgrade Path Kickstarter reached the baseline funding goal in just two and a half days! Now let's see how much bigger and better we can make this book. We'd like to add many more pages, with guest strips from some of our favorite cartoonists. Please pledge today!

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27 Jul 04:18

Wanted: young creation “scientists”

by whyevolutionistrue

Sevreal readers pointed me to an essay/ad by the Institute for Creation Research asking Christian youth to go into science. For your delectation: “Wanted: Young creation scientists” by Jake Hebert, Ph.D. (doctorate in physics from the University of Texas at Dallas). Pay special attention to the last two paragraphs.

Picture 1

If you need a sign that creationists are getting desperate, here’s a good one, for this “ad” literally begs Christian youth to go into science solely to become “stealth creationists” like Jon Wells.

The first paragraph, about the advances of creation science and its superiority over “real” science (i.e., evolutionary biology) is of course a complete lie. But the real motivation for co-opting Christian youth into science is in the last two paragraphs, advising these students “to not draw attention to your creationists beliefs while you are a student.”

But if those beliefs have, as the ICR asserts, trumped modern evolutionary biology, why hide them? Well, it’s because of the “anti-Christian sentiment” in society and the “academic persecution in the secular universities.” What this means is simply that people with creationist beliefs have those beliefs questioned in a good secular university. That’s what a university is for, and it’s not “persecution.” But it’s better to keep your mouth shut until you get that Ph.D., whereupon you can come out as a full-throttle creationist like John Wells and Michael Behe.

This is a form of child abuse in three ways. It take a child’s natural interest in science and perverts it by forcing it into the Procrustean bed of creationism, turning the child into a liar for Jesus. Second, it tries to distort scientific understanding before the “candidate” even gets to the classroom, by urging the the student to hold onto his/her views in the face of counterevidence. Finally, it is unbearably cynical, for it makes the child a tool of the creationsts/fundamentalists—a minion who can fulfill their desire to overthrow real science by subverting it from within. They are producing the equivalent of those little Iraqi children who were urged to run through minefields to detonate unexploded mines.  Suborning a child’s curiosity about the world by enlisting it in the cause of superstition is true child abuse.

h/t: Tom

27 Jul 04:17

Discovery Institute says Matzke can’t read, misuses cladistics

by Paul Braterman

paul_book_-1Yes, that is a deliberately ambiguous heading. Discovery Institute really does say that Matzke misuses cladistics. But the most prominent example that I can find of that particular misuse comes from a fellow of the DI itself.

Nick Matzke’s “hopeless monster” review of Darwin’s Doubt must have really got to the Discovery Institute. Evolution News and Views, one of their many glossy web publications dedicated to denying evolution, has singled it out for extensive criticism twice in three days.

On July 16, we had that well-known expert on the palaeontological literature, Casey Luskin (MS Earth Sciences), telling us that Matzke actually used to be paid money by the National Center for Science Education to present the arguments in favour of evolution, so obviously his opinion in its favour is biased. An interesting argument. I seem to remember being paid money myself, by four separate universities over the course of my career, to present the arguments in favour of the reality of atoms. Roll over Darwin, roll over Dalton. Worse, Nick is only a graduate student, so how dare he criticise a full-fledged PhD like Stephen Meyer (BS Physics/Earth Science, PhD Philosophy)?

By the way, congratulations, Nick, on your paper making the front cover of Proceedings of the National Academy of Sciences. An elegant use of duplicated genes to reduce the error bars on the dating of nodes in phylogenetic trees.

DB 3.png

Two days later, David Berlinski (PhD Philosophy) criticises Nick for saying Meyer should have used cladistics. Berlinski thinks these are worthless. Why? Because (true enough) we can twiddle a clade about its root node and this changes the order in which we list the termini. Which Berlinski thinks means that we are changing the meaning of the cladogram (utter bollocks). Check out his actual posting which includes the above diagram, meant to expose the stupidity of any one using cladistics.

One small irony is that I have only once seen cladistic reasoning misused in the way that Berlinski suggests. I refer to Of Pandas and People, which claims ( on p. 37) that molecular biology “contradicts the Darwinian expectation”, because it places all vertebrates at the same distance from arthropods, whereas (present-day) fish ought to be closer to them than reptiles are. Joint author of this piece of garbage, Dean Kenyon, fellow of the Discovery Institute.

To conclude, DI’s criticism of Matzke and his credentials reminds me of an old definition of Chutzpah; an ant climbing an elephants leg with intent to rape.

Filed under: Creationism, Evolution in general, Philosophy, Uncategorized Tagged: Darwin's Doubt, Doubt (2008 film), Nick
27 Jul 04:04

God did it – who needs scientists? Still, the ICR wants some

by idoubtit
I’m going to link to the Fark version of this because it seems more appropriate. Try not to laugh too hard. This is like Bizarro World news. | Wanted: scientists to ignore science for Jesus. ICR [Institute for Creation Research], together with the rest of the creation science movement, has made great strides in…
27 Jul 03:56

Working in the Quote Mines

by John Pieret

The Sensuous Curmudgeon has uncovered a quote mine new to me.
Nearly 40 years later Ernst Mayr, Ph.D. of Harvard, an outstanding evolutionist, declared: "The fact that the evolutionary theory is now so universally accepted is no proof of its correctness … the basic theory is in many instances hardly more than a postulate."
In my (mostly self-appointed) role as keeper of the quote mines, here is some more information on this:

It comes from Mayr's Populations, Species and Evolution: An Abridgement of Animal Species and Evolution," p. 6, which can be found in Google Books.

As background, Mayr was discussing the time when, in the 1930s, "many dissenting theories were fused into a broad unified theory, the 'modern synthesis.'" He opines that the previous theories suffered from an attempt to explain evolution by "a single-factor theory," giving as examples Lamarck (internal self-improvement), Geoffroy (environmental induction of genetic change), Wagner (evolution by isolation), and De Vries (mutationalism). In addition to Darwinian natural selection, the synthesis included "concepts of mutation. variation, population, inheritance, isolation and species ..." According to Mayr (who not all scientists agree with) the main change was brought about by "[t]he replacement of typological thinking by population thinking."

Mayr goes on to write:
Recalling this history should make us cautious about the validity of our current beliefs. The fact that the synthetic theory is now nearly universally accepted is not itself proof of its correctness. It will serve as a warning to read with what scorn the mutationists (saltationists) in the first decade of this century attacked the contemporary naturalists for their belief in gradual changes and in the immense importance of the environment. ... [Emphasis added]
It is not until the following paragraph, that Mayr says:
The essentials of the modern theory [that is, the modern synthesis] are to such an extent consistent with the facts of genetics, systematics, and paleontology that one can hardly question their correctness. The basic framework of the theory is that evolution is a two-stage phenomenon: the production of variation and the sorting of the variants by natural selection. Yet agreement on this basic thesis does not mean that the work of the evolutionist is completed. The basic theory is in many instances hardly more than a postulate and its application raises numerous questions in almost every concrete case. [Emphasis added]
The quote miners are committing several sins here. First and foremost they are confusing the "modern synthesis," a theory about the mechanisms that cause evolution, with the fact of evolution (common descent). They even substituted [without any indication] "evolutionary theory" for "the synthetic theory" in the original. Mayr is in no way questioning the overwhelming evidence for common descent; he is only cautioning that our understanding of its mechanisms may change, as it has changed in the past.

Another sin is, as the Curmudgeon noted, that the ellipsis is hiding the stitching together of disparate thoughts ... a caution about falling too much in love with a theory about the mechanisms of evolution with another thought about the difficulty in applying any theory to particular, concrete, facts.

And then there is my particular bête noire: the nonexistent period. The quote miners put a period after "hardly more than a postulate" when, in fact, Mayr went on to say "and its application raises numerous questions in almost every concrete case." Not that the implication that the quote mine was a complete thought would have made any difference to their fellow creationists (thoughts, complete or otherwise, have nothing to do with them) but innocent passersby might, if they had been given the entire sentence or even an ellipsis, have had a glimmer of the quote miners' dishonesty.

The insertion of that period, when they are so otherwise free with ellipses, is what we lawyers call "evidence of the knowledge of guilt."
27 Jul 03:54

My equipment doesn’t work…

by Marcus Wilson
We're three weeks into our 'B' semester here. One of the papers I'm teaching (just on the fringes of) is our main first year physics paper. When I say 'on the fringes of', it means I'm supervising one laboratory session a week. It's good to keep in contact with what's going on at first year - all my other teaching is 2nd or 3rd year or graduate level. One thing that seems to be happening is that, every year, the incoming cohort of students is less confident in their use of equipment in their physics lab classes. Is this because they are doing less and less practical work at school? One thing...

[Click on the headline above for the full story]
27 Jul 03:53

Worst ID Argument Ever?

by John Pieret

Someone named Jerry Newcombe has an "Exclusive" article at WingNutDaily (which, as Ed Brayton often points out, means it is too crazy to find the light of day anywhere else), entitled "Explaining 'Darwin's Doubt."

Here's how he starts:
Every time I log into a computer and have to enter my password, I'm reminded of how impossible evolution is.

One little mistake on the keypad and I can't log in. There's even a website where I seem to be in permanent "log-in purgatory." I can't log in ever. Granted, it's operator error. But still …

How does this tie to evolution? Because if evolution were true, then we are to believe a whole series of complex sequences managed to get everything right – repeatedly.
Of course, to begin with, to buy this argument you have to assume that there is one and only one solution to your problem. And, yes, if you assume that there is only one way to have an eye or an immune system, it looks harder to get "from here to there." But we have evidence that there are multiple routes to such things. And if the "differential reproductive success" of many species depends on "finding" such disparate routes, then if some, by chance, do, then they will be the likely survivors. The ones that don't are likelier to become extinct, which some 98% of all species have done.

It is like Newcombe's ancestors achieving the highly improbable task of managing to "get everything right," in terms of having sex that resulted in children who lived long enough to, in turn, have children and so forth, for thousands (at least) years, ultimately resulting in an unbroken line of "improbable" events in order to unleash his ignorance upon an unsuspecting world.

But, once again, the ID unwashed just can't help letting the cat out of the bag:
Meyer adds, "It's just like in computer science. If you want to have a new function on your computer, you've got to have lots of code, lots of instruction. If you want to build these complex animal forms, we now know, you need information, you need instructions. And that's the crucial question that is really creating an impasse in evolutionary theory. Where does that information come from?"

Oh, I get it – "In the beginning was the Word …"
Yep, it's all about the Bible and creationism. Newcombe recognizes it. Science supporters recognize it. Heck, even the Discovery Institute recognizes it. The only thing is that the DI is dishonest enough to lie about it.
26 Jul 23:15

The NUKEMAPs are here

by Alex Wellerstein

I’m super excited to announce that last Thursday, at an event hosted by the Center for Nonproliferation Studies at the Monterey Institute for International Study, I officially launched NUKEMAP2 and NUKEMAP3D. I gave a little talk, which I managed to record, but I haven’t had the time (more details below on why!) to get that up on YouTube yet. Soon, though.

A Soviet weapon from the Cuban Missile Crisis, centered on Washington, DC, with fallout and casualties shown.

A Soviet weapon from the Cuban Missile Crisis, centered on Washington, DC, with fallout and casualties shown.

NUKEMAP2 is an upgraded version of the original NUKEMAP, with completely re-written effects simulations codes that allow one a huge amount of flexibility in the nuclear detonation one is trying to model. It also allows fallout mapping and casualty counts, among other things. I wanted to make it so that the NUKEMAP went well beyond any other nuclear mapping tools on the web — I wanted it to be a tool that both the layman and the wonk could use, a tool that rewarded exploration, and a tool that, despite the limitations of a 2D visualization, could work to deeply impress people with the power of a nuclear explosion.

The codes that underly the model are all taken from Cold War effects models. At some point, once it has been better documented than it is now, I’ll probably release the effects library I’ve written under an open license. I don’t think there’s anything quite like it out there at the moment available for the general public. For the curious, there are more details about the models and their sources here.

The mushroom cloud from a 20 kiloton detonation, centered on downtown DC, as viewed from one of my common stomping grounds, the Library of Congress.

The mushroom cloud from a 20 kiloton detonation, centered on downtown DC, as viewed from one of my common stomping grounds, the Library of Congress.

NUKEMAP3D uses Google Earth to allow “3D” renderings of mushroom clouds and the nuclear fireball. Now, for the first time, you can visualize what a mushroom cloud from a given yield might look like on any city in the world, viewed from any vantage-point you can imagine. I feel like it is safe to say that there has never been a nuclear visualization tool of quite this nature before.

I got the idea for NUKEMAP3D while looking into a story for the Atlantic on a rare photo of the Hiroshima mushroom cloud. One of the issues I was asked about was how long after the detonation the photograph was taken — the label on the back of the photograph said 30 minutes, but there was some doubt. In the process of looking into this, I started to dig around the literature on mushroom cloud formation and the height of the Hiroshima cloud at various time intervals. I realized that I had no sense for what “20,000 feet” meant in terms of a cloud, so I used Google Earth to model a simple 20,000 foot column above the modern-day city of Hiroshima.

I was stunned at the size of it, when viewed from that perspective — it was so much larger than it even looked in photographs, because the distance that such photographs were taken from makes it very hard to get a sense of scale. I realized that modeling these clouds in a 3D environment might really do something that a 2D model could not. It seems to switch on the part of the brain that judges sizes and areas in a way that a completely flat, top-down overlay does not. The fact that I was surprised and shocked by this, despite the fact that I look at pictures of mushroom clouds probably every day (hey, it’s my job!), indicated to me that this could be a really potent educational tool.

That same 20 kiloton cloud, as viewed from airplane height.

That same 20 kiloton cloud, as viewed from airplane height.

I’m also especially proud of the animated mode, which, if I’m allowed to say, was a huge pain in the neck to program. Even getting a somewhat “realistic”-looking cloud model was a nontrivial thing in Google Earth, because its modeling capabilities are somewhat limited, and because it isn’t really designed to let you manipulate models in a detailed way. It lets you scale model sizes along the three axes, it allows you to rotate them, and it allows you to change their position in 3D space. So I had to come up with ways of manipulating these models in realtime so that they would approximate a semi-realistic view of a nuclear explosion, given these limitations.

It’s obviously not quite as impressive as an actual nuclear explosion (but what is?), and my inability to use light as a real property (as you could in a “real” 3D modeling program) diminishes things a bit (that is, I can’t make it blinding, and I can’t make it cast shadows), but as a first go-around I think it is still a pretty good Google Earth hack.1 And presumably Google Earth, or similar tools, will only get better and more powerful in the future.

Screen captures of the animation for a 20 kt detonation over DC. These screenshots were taken in 10 second intervals, but are accelerated 100X here. The full animation takes about five minutes to run, which is roughly how the cloud would grow in real life.

Screen captures of the animation for a 20 kt detonation over DC. These screenshots were taken in 10 second intervals, but are accelerated 100X here. The full animation takes about five minutes to run, which is roughly how the cloud would grow in real life.

If you’ve been following my Twitter feed, you also probably have picked up that this has been a little bit of a saga. I tried to launch it on last Thursday night, but the population database wasn’t really working very well. The reason is that it is very, very large — underneath it is a population density map of the entire planet, in a 1km by 1km grid, and that means it is about 75 million records (thank goodness for the oceans!). Optimizing the queries helped a bit, and splitting the database up helped a bit. I then moved the whole database to another server altogether, just to make sure it wasn’t dragging down the rest of the server. But on Monday, just when the stories about NUKEMAP started to go up, my hosting company decided it was too much traffic and that I had, despite “unlimited bandwidth” promises, violated the Terms of Service by having a popular website (at that point it was doing nothing but serving up vanilla HTML, Javascript, and CSS files, so it wasn’t really a processing or database problem). Sigh. So I frantically worked to move everything to a different server, learned a lot about systems administration in the process, and then had the domain name issue a redirect from the old hosting company. And all of that ended up taking a few days to finalize (the domain name bit was frustratingly slow, due to settings chosen by the old hosting company).

But anyway. All’s well that ends well, right? Despite the technical problems, since moving the site to the new server, there have been over 1.2 million new “detonations” with the new NUKEMAPs, which is pretty high for one week of sporadic operation! 62% of them are with NUKEMAP3D, which is higher than I’d expected, given the computer requirements required to run the Google Earth plugin. The new server works well most of the time, so that’s a good thing, though there are probably some tweaks that still need to be done for it to happily run the blog and the NUKEMAPs. There is, though I don’t want to make it too intrusive or seem too irritating, a link now on the NUKEMAP for anyone who wanted to chip in to the server fund. Completely optional, and not expected, but if you did want to chip in, I can promise you a very friendly thank-you note at the very least.

Now that this is up and “done” for now, I’m hoping to get back to a regular blogging schedule. Until then, try out the new NUKEMAPs!

  1. The difficulty in dealing with light is one of the reasons I have the clouds rendered so darkly — it’s the only way that keeps them from looking “plasticky” because lighter models in GE are very reflective. So I went with more of a “Joe-1” look to compensate for that.
26 Jul 05:01

07/24/13 PHD comic: 'Academically'

Piled Higher & Deeper by Jorge Cham
Click on the title below to read the comic
title: "Academically" - originally published 7/24/2013

For the latest news in PHD Comics, CLICK HERE!

26 Jul 04:59

"The Last Pancake Breakfast," intended to be a limited edition...

"The Last Pancake Breakfast," intended to be a limited edition print reward for the Carol Kickstarter (beginning in a couple weeks).  The art is basically done, and WHEW, it was one of the most intensive pieces of art I’ve ever rendered.  I love it, but I’m glad it’s done.

It’s interesting, in that it represents the cast of the comic near its theoretical end, even though when the comic premieres it’ll largely be about Carol’s childhood.  It’s like I’m releasing promo art for season six of a TV show before even shooting the pilot.

Anyway, from left to right, we have Saint Alfonzo, Judas, Jesus, Mary M, Carol, Miriam, Thomas, and Leonardo di Vinci.  Under the table is Simon Peter and Carol’s pet dragon, Captain Fantastic.


26 Jul 04:51

YES of COURSE i added all these new words invented here to my spell check dictionary on account of how i'm not a FOOL

archive - contact - sexy exciting merchandise - cute - search - about
recovering from san diego! dinosaur comics runs mon/wed/fri this week :0

← previous July 24th, 2013 next

July 24th, 2013: San Diego Comics Convention was a lot of fun: I won an award and got rescued by a hunky lifeguard! These two events were unrelated. OR WERE THEY? Anyway thank you to everyone who came out to meet me and say hi - it was great to see you all!

One year ago today: real answer: this has happened several times in the past, but in each instance the International Olympic Committee sued the new "Brain Olympics" so hard that they literally got erased from the timeline

– Ryan

26 Jul 04:41

PhD Unknown - Preface - Page 10

by (Erin Burt)
New comic!
Today's News:

And thus we come to the end of the preface!  Now we start to get into the real meat of PU.  (PhU?  PhUnk? We need to figure out this abbreviation thing at some point.  Suggestions welcome.)

We hope you've enjoyed the comic so far, and can't wait to start digging into more of Ben's, Dr. Mann's, and Vonnie's story with you!


26 Jul 04:03

Get a Job: Dallas, Texas (USA)

by (Laurence A. Moran)
The Chair of my department1 asked me to post this job advertisement in case any biochemists might be interested. It's a challenging position in Dallas, Texas. You'll have plenty of opportunity to investigate some of the weirdest subjects in all of biology. All you really need is an inquisitive mind—with a few minor restrictions [Wanted: Young Creation Scientists].
ICR, together with the rest of the creation science movement, has made great strides in the last 40 years. In many areas, the superiority of the creation worldview has been clearly demonstrated. Even now, ICR is making exciting discoveries in the fields of biology and geology, and we have started new research initiatives in the field of astronomy. However, there is much work that still needs to be done, and this work is hindered by a lack of trained scientists.

Therefore, we appeal to any Bible-believing young person with an interest in science—have you considered cultivating that science interest for the glory of God?

Many young people choose careers for all the wrong reasons (e.g., maybe a college major is “easy” or they can earn a lot of money). Yet some choices in this area can have negative consequences later in life.What good is it to earn a large salary if your job is unfulfilling? Is it worth it to major in an easy field if you ultimately get a job that you dislike? Little wonder that so many adults are eager to retire from the workforce—they hate their jobs!

How much better to choose a career path that will bring ultimate fulfillment, a decision inspired by a God-given desire to work in a field that will bring glory to the Creator. Young Christian, if God has given you a desire to serve Him in a particular area, then consider His promptings. Maybe He is leading you to serve Him in the field of science. It may involve short-term sacrifice, but God’s best often requires hard work.

If you have an interest in science, then pursue it. An aptitude and a genuine love for science is a rare gift—maybe you can be the one to make a startling discovery or a life-changing advancement in the field. Maybe history will be different because of you. Perhaps you can be the one to finally break the evolutionary monopoly on our institutions of higher learning.

Of course, not everyone has an interest in science. God has given us all different gifts (1 Corinthians 12:4-7) and called us to different areas of service. But Christian young people might consider the challenge to seek God’s wisdom about their future, to consider His direction when they are making their career choices.

For those who do have an interest in science, we wish to offer a few words of advice. Work hard to get the best possible grades and push yourself to truly understand the material. When choosing a school, choose one with a rigorous academic program and a research program that truly interests you. Although you should not be dishonest about what you believe, it’s probably prudent to not draw attention to your creationist beliefs while you are a student, particularly if you are in a field that directly touches upon the origins controversy (such as paleontology, biology, or geology).

Given the increasing anti-Christian sentiment in society and the academic persecution in the secular universities, there may very well come a day when it will no longer be possible for a Bible-believing Christian to get an advanced degree in the natural sciences. Academically gifted young Christians should therefore “redeem the time” (Ephesians 5:16) before that door of opportunity closes.
They don't say how many letters of reference they need. They also don't mention salary. Something in the range of $100,000 - $120,000 would be typical for real scientists at a good school in Texas. ICR probably has to pay more in order to get the very best candidates.

Start-up funds are negotiable but you should probably ask for one million dollars to set up a decent lab. That's about the minimum you're going to need since your chances of getting NIH or NSF funding are pretty slim.

1. He has a great sense of humor. I'm not sure if he wants to be identified by name on this blog but you can find him on our website under Justin Nodwell, Chair.
26 Jul 04:02

Every non-lethal genome position is variable in the human population

by (Laurence A. Moran)
Melissa Wilson Sayres blogs at mathbionerd and Panda's Thumb. A recent post on Panda's Thumb address a tweet from Daniel Wegmann where he said "Every non-lethal genome position is variable in the human population."

She asks "Is this true?" and proceeds to show that it is [How many mutations?]. She assumes that the human mutation rate is 1.2 × 10-8 per sit per generation. Multiply this by 7.16 billion people on the planet and you get an average of 86 mutations at every single base pair in the human genome.1

Many of these mutations will be deleterious and they will be quickly eliminated from the population if they are lethal or cause severe problems. Some moderately and slightly deleterious mutations will be present in the population because they haven't yet been eliminated by negative selection. (Some will have no effect if they are present in only one copy of your diploid genome.)

To a first approximation, the statement is pretty accurate. If it's true that most of our genome is junk then the nucleotide sequence is not important.2 As we sequence more and more genomes we should see heterogeneity at 90% of the base pairs in the genome. We haven't reached this sort of coverage but all available evidence is consistent with the idea that most positions can be variable.

1 I prefer a larger mutation rate of 100 new mutations per generation for a total of 112 mutations at every site.

2. This doesn't rule out functions that are not sequence-specific. Such functions are known to exist but there are no reasonable hypotheses that justify such functions for most of the genome.