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Apr 22 2014

I’m going to Seattle!

It’s a good deal — I’m going to spend a few days with my family, and then on Thursday, 5 June, at 7:30pm, I’ll be at Town Hall to talk about An Atheist’s Insight. I’m planning on specifically addressing the conflict between science and religion, and then opening it up to a nice thorough Q&A — you’ll be able to grill me. Lots of fun!

One catch: they’re charging admission. You’ll have to cough up a whole $5 to have the privilege of pestering me.

Oh, also, the big reason for doing this: The Happy Atheist is coming out in paperback. There will be a book signing. Or if you’d prefer, a book burning (it’ll sell copies, so that’s fine with me). I’ll also be in town most of that week, so if we want to do an informal get-together, we might be able to arrange that, too.

Apr 22 2014

A new era for Pharyngula!

I have seen the light, and all future blog posts will be automatically generated by reionizing their electrons. Life will not only be easier, but more profitable.

Namaste.

The goal of ultra-sentient particles is to plant the seeds of consciousness rather than delusion.

To follow the path is to become one with it. By blossoming, we dream.

How should you navigate this advanced solar system?

Reality has always been beaming with beings whose souls are transformed into self-actualization. We are in the midst of an ancient unveiling of health that will open up the world itself. We are at a crossroads of transcendence and stagnation.

Have you found your quest? If you have never experienced this uprising inherent in nature, it can be difficult to heal. The galaxy is calling to you via a resonance cascade. Can you hear it?

It can be difficult to know where to begin. Although you may not realize it, you are karmic. Child, look within and enlighten yourself.

We live, we believe, we are reborn.

We can no longer afford to live with dogma. Greed is the antithesis of curiosity. Yes, it is possible to erase the things that can extinguish us, but not without inspiration on our side.

Nothing is impossible. Growth is the driver of purpose. Health is the growth of rebirth, and of us.

Apr 22 2014

How kinesin actually moves

Recently, Carl Zimmer made a criticism of the computer animations of molecular events (it’s the same criticism I made 8 years ago): they’re beautiful and they’re informative, but they leave out the critical aspect of stochastic behavior that is important in understanding the biochemistry. He’s talking specifically about kinesin, a transport protein which the animators are particularly fond of illustrating.

Every now and then, a tiny molecule loaded with fuel binds to one of the kinesin “feet.” It delivers a jolt of energy, causing that foot to leap off the molecular cable and flail wildly, pulling hard on the foot that’s still anchored. Eventually, the gyrating foot stumbles into contact again with the cable, locking on once more — and advancing the vesicle a tiny step forward. This updated movie offers a better way to picture our most intricate inner workings…. In the 2006 version, we can’t help seeing intention in the smooth movements of the molecules; it’s as if they’re trying to get from one place to another. In reality, however, the parts of our cells don’t operate with the precise movements of the springs and gears of a clock. They flail blindly in the crowd.

The illusion of directed, purposeful movement is a simplifying shortcut: as Zimmer describes, there actually is a lot of noise in the system, it’s just that the thermodynamics of the interactions promote a directionality to the motion. This is Chemistry 101. I figured that everyone with an undergraduate level of understanding of molecules would be able to grasp this.

I did not take into account willful ignorance, however. Jonathan Wells is angry that anyone dared to question the perfect “stately grace” of molecular machines, and accuses proponents of stochastic motion of Flailing Blindly: The Pseudoscience of Josh Rosenau and Carl Zimmer. He has a Ph.D. in biology, and he doesn’t understand what I just said was Chem 101? For shame.

But that’s not what the biological evidence shows. In fact, kinesin moves quickly, with precise movements, to get from one place to another. A kinesin molecule takes one 8-nanometer “step” along a microtubule for every high-energy ATP molecule it uses, and it uses about 80 ATPs per second. On the scale of a living cell, this movement is very fast. To visualize it on a macroscopic scale, imagine a microtubule as a one-lane road and the kinesin molecule as an automobile. The kinesin would be traveling over 200 miles per hour!

The speed of the reaction doesn’t say anything about the specifics of the molecular movement…and it’s especially not convincing when your trick is to multiply the actual speed in the cell by approximately 1012 to scale it up to the size of a car. The flow rate of the Mississippi river is about 1.5 miles per hour here in Minnesota — if you multiply that by 1012, oh my god, the water is moving at about 2000 times the speed of light!

But let’s set aside the stupid inflation for a minute. Wells cites a couple of papers to back up his claim of the rate of ATP consumption. It’s true. But it doesn’t show that the movement is steady and machine-like and precise at all. He must be trusting us to not bother even reading the paper.

Here’s the deal: we can actually watch single molecules of kinesin behaving. The typical trick is to use a fluorescent bead, attach that to kinesin, and then record the glowing bead’s movement as it is moving along with optical-trapping interferometry. That’s the problem with Wells’ accusation: we actually see the behavior, and it’s not linear, smooth, and graceful.

This is the data that the paper used to measure the quantum, jerky behavior of kinesin. Just look at the top graph: that’s a record of the bead’s movement over time. You should be able to see that the line holds steady at one distance for variable lengths of time, and then jerks upward. The “jerks” are distances of about 8nm, and the other graphs are power spectra to show that there is a peak periodicity of 8nm. It shows the opposite of what Wells claims; there are long pauses and sudden shifts in the directly observed track of kinesin movement. The 8nm emerges because when one “foot” of kinesin releases and wobbles forward to connect to tubulin, it has an 8nm step.

Horizontal grid lines (dotted lines) are spaced 8 nm apart. Data were median-filtered with a window width of 60 ms. b, Normalized histogram of pairwise distances between all pairs of data points in this record, showing a clear 8-nm periodicity. c, Normalized power spectrum of the data in b, displaying a single prominent peak at the reciprocal of 8 nm (arrow). d, Variance in position, averaged over 28 runs at 2 microM ATP (dots), and line fit over the interval 3.5 ms to 1.1 s. The y-intercept of the fit is determined by equipartition,  left fencex2right fence = kT/alpha, where alpha is the combined stiffness of the optical trap and bead–microtubule linkage. The rapid rise in variance at short times reflects the brownian correlation time for bead position.

Horizontal grid lines (dotted lines) are spaced 8 nm apart. Data were median-filtered with a window width of 60 ms. b, Normalized histogram of pairwise distances between all pairs of data points in this record, showing a clear 8-nm periodicity. c, Normalized power spectrum of the data in b, displaying a single prominent peak at the reciprocal of 8 nm (arrow). d, Variance in position, averaged over 28 runs at 2 microM ATP (dots), and line fit over the interval 3.5 ms to 1.1 s. The y-intercept of the fit is determined by equipartition, left fencex2right fence = kT/alpha, where alpha is the combined stiffness of the optical trap and bead–microtubule linkage. The rapid rise in variance at short times reflects the brownian correlation time for bead position.

You can find lots of papers with direct observations of kinesin movement. Here’s data from another paper that essentially shows that the two ‘feet’ of kinesin alternate in their movement, because they made recombinant, asymmetric kinesin with slightly different step distances. Again, note the long dwell times punctuated with surges of movement.

Representative high-resolution stepping records of position against time, showing the single-molecule behavior of kinesin motors under constant 4 pN rearward loads. (A) Limping motion of the recombinant kinesin construct, DmK401. The dwell intervals between successive 8-nm steps alternate between slow and fast phases, causing steps to appear in pairs, as indicated by the ligatures. (B) Nonlimping motion of native squid kinesin, LpK. No alternation of steps is apparent; vertical lines mark the stepping transitions. Slow and fast phase assignments, as described in the text, are indicated in color on the uppermost trace of each panel (blue and red, respectively), and the corresponding dwell intervals are numbered. All traces were median filtered with a 2.5-ms window.

Representative high-resolution stepping records of position against time, showing the single-molecule behavior of kinesin motors under constant 4 pN rearward loads. (A) Limping motion of the recombinant kinesin construct, DmK401. The dwell intervals between successive 8-nm steps alternate between slow and fast phases, causing steps to appear in pairs, as indicated by the ligatures. (B) Nonlimping motion of native squid kinesin, LpK. No alternation of steps is apparent; vertical lines mark the stepping transitions. Slow and fast phase assignments, as described in the text, are indicated in color on the uppermost trace of each panel (blue and red, respectively), and the corresponding dwell intervals are numbered. All traces were median filtered with a 2.5-ms window.

The contrast is between “stately grace” and “jiggle and jump”. The evidence shows that it is the latter. Yet, somehow, Wells closes his weird series of non sequiturs with this question, as if he expects everyone to give him the answer he wants.

So, who are the pseudoscientists?

The answer is obvious. Wells and his cronies at the DI.


Asbury CL, Fehr AN, Block SM (2003) Kinesin moves by an asymmetric hand-over-hand mechanism. Science 302(5653):2130-4

Schnitzer MJ, Block SM (1997) Kinesin hydrolyses one ATP per 8-nm step. Nature388(6640):386-90.


By the way, I found about this because the Discovery Institute sent me email (silly season and all) proudly announcing that they were about to release evidence that would clearly rebut Zimmer’s assertion that kinesin “flails blindly” — they are making a computer animation showing that it doesn’t.

Yes, they are that stupid.

Apr 22 2014

I get email

I’ve always wondered when the silly season was. I guess it’s April. I’m getting so much loony email lately that I have to marvel at my inbox — no longer merely a stack of obligations and nagging, it also contains imbedded within it little gems of high weirdness.

For instance, “Tom Hyndman” doesn’t like me. Little clues tell me that this is the same person I recently banned under the pseudonym “Nathan Hull”, who I suspect also went under the name “John Dolan” in an earlier life, and also reminds me of a few other names that have drifted through here, transiently.

Let’s take a look at it. He’s peeved because he was banned, which turns out to be a sign that I’m becoming a dictatorial cult leader. Ho hum.

Read the rest of this entry »

Apr 22 2014

Got sand in your…?

Do not search for information on getting sand in your genitals. It’s a morass of nonsense out there, with all kinds of bizarre pop culture notions. Most of it seems to be about getting sand in your vagina, which is treated as slogan to mock and trivialize women’s problems, but getting sand under your foreskin…oh, my. That’s no joke. That’s a very serious problem that must be dealt with surgically.

Remember Brian Morris, the Australian circumcision fanatic? One of his talking points is that getting sand in your penis is a major problem for uncircumcised men, and that in particular entire armies have been devastated in the desert by grains of sand getting caught up there, or laid flat in the jungles by all the damp rot and unhygienic conditions. He paints a grisly picture of the uncircumcised penis, and claims that it’s standard military policy to make sure you don’t have one of those dangerous folds of skin. How can you possibly fight if you’ve got a tiny, hideous bit of flesh attached to your penis?

I really had no idea. I may be a flabby old college professor, but apparently because I was born in America in the 1950s, when every boy baby was given cosmetic surgery practically as soon as they were born, I can whip the ass of every anteater boy out there. Good to know.

Morris is rather insistent. He claims that circumcision is a serious medical issue for the military.

In attempting to ridicule the notion that circumcision arose in the Middle East to solve problems caused by ‘sand and dust’, Vernon cites an article by Robert Darby, an anti-circ activist. Darby’s claims stemming from ‘medical records’ ‘he analyzed’ are false. Infections, initiated by the aggravation of dirt and sand, are not uncommon under desert conditions, and have even crippled whole armies of uncircumcised soldiers. It is difficult to achieve sanitation during prolonged battle. To contradict Darby, and thus Vernon, a US Army report by General Patton stated that in World War II 150,000 soldiers were hospitalised for foreskin problems due to inadequate hygiene. To quote: “Time and money could have been saved had prophylactic circumcision been performed before the men were shipped overseas” and “Because keeping the foreskin clean was very difficult in the field, many soldiers with only a minimal tendency toward phimosis were likely to develop balanoposthitis”. The story was similar in Iraq during ‘Desert Storm’ in the early 1990s. In the Vietnam War men requested circumcision to avoid “jungle rot”.

Well, if General George Patton thought it was a serious problem, it must be so. “Old Blood and Guts” wouldn’t be put off by trivia.

Except, well, it turns out that Brian Morris is rather sloppy with the facts.

Attempting to refute my argument he cites “a US Army report by General Patton”, and lists a series of pages that are supposed to back up his claim. But when you actually check those pages you find that they have nothing to do with sand under the foreskin and fail to provide any support for the argument that Morris wishes to make. For a start he gets the details of the book wrong. It is not a “report by General Patton”, but a multi-author volume in the official history of U.S. medical services in World War 2, edited by John F. Patton MD. Secondly, there are only two occurrences of the word sand in the entire volume, neither of which has anything to do with foreskins or circumcision. The volume scarcely deals with the Middle Eastern or North African (desert) combat theatres, but mostly with the South-East Asian and Pacific theatres, characterized by dense jungles and wet, humid conditions that posed many intractable health problems, affecting many parts of the body, not just the penis. But in those conditions sand and dust were not an issue. There is not the slightest support for his hyperbolic claim that “Infections, initiated by the aggravation of dirt and sand, are not uncommon under desert conditions, and have even crippled whole armies of uncircumcised soldiers.”

I’m sure you uncircumcised men are quite pleased to hear this. You don’t need to get the tip lopped off in order to go kill people in the Middle East. And I’ve lost my last possible advantage in a bar fight.

Apr 22 2014

I’m just like Jesus

We’re both bearded white guys who can’t dance.

Apr 21 2014

We get comments

I was just doing a little clean up of the spam queue before I staggered off to bed, and found this one fascinatingly offensive comment that had been flagged for the garbage pile. I have preserved it because it was just so mind-bogglingly oblivious to its own content, but I’ve put it below the fold because it uses language that is normally prohibited around here.

Read the rest of this entry »

Apr 21 2014

Mary’s Monday Metazoan: Well, I wouldn’t eat it

Apr 21 2014

I get email: Still looking for an obliging geophysicist

This guy wrote to me back in September, when he was regurgitating creationist rationalizations for the global flood, at the behest of wacky ol’ Walt Brown. He called me again this morning and sent me another missive. On the phone, he sounded a bit miffed that I didn’t immediately remember who the heck he was, but it’s all come back to me now, after reading this.

Dear Dr. Paul Myers,

Like I said, I read your Happy Atheist and regularly read Pharyngula.

RE: Your “Looking for a geophysicist” blog.

What are the facts and what are the beliefs?

1 FACT:

Estimations of the biggest and strongest Supercontinent and all the reservoirs of water under pressure below it Earth possibly had are altogether unheard of.

Its continental landmasses’ three-hundredfold greater concentration of heavy, radioactive elements than our found elsewhere in the Earth aren’t confirmed by observations with measurements to have been in it when the continents yet had all the former connectedness they had (however connected they may have been).

Dr. Bruce Buffett who earned a doctorate in geophysics from Harvard and is now Chairman of Geophysics at Berkeley, considered the no.1 at geophysics research in America).

http://211.144.68.84:9998/91keshi/Public/File/34/485-7398/pdf/485319a.pdf

He has answered my questions and can’t explain why geophysicists never consider that before our planet’s 52,000-mile globe-encircling Mid-Oceanic Range uplifted, fitting like a jigsaw puzzle with specific continental shelf edges, it may have had great reservoirs of water under pressure below a supercontinent, even only one supercontinent in Earth history.

I asked him, “Could not it have thereby had its greatest explosivities of outbursting water and eroded rocks, greatest magnitude earthquake, and super-intense volcanic and earthquake lightnings >1 million amperes whereby electrons shooting through them with >1 MeV produced magnetic pinch effects”?

I hope by the following it will be clear to you what is being proposed as a solution to the problem of Earth’s concentration of heavy, radioactive elements inconsistent with the nebular hypothesis.

Regarding Richard P. Feynman, Ph.D.(physics) Surely You’re Joking Mr. Feynman, (W.W. Norton: New York, NY, 1985), pp. 341, 343:
Physics Nobel Laureate Richard Feynman noted what is: “generally missing in cargo cult science. . . It’s a kind of scientific integrity, a principle of scientific thought that corresponds to a kind utter honesty—a kind of leaning over backwards. For example, if you’re doing an experiment, you should report everything that you think might make it invalid—not only what you think is right about: other causes that could possibly explain your results; and things you thought of that you’ve eliminated by some other experiment, and how they worked—to make sure the other fellow can tell they have been eliminated.
Details that could throw doubt on your interpretation must be given, if you know them. You must do the best you can—if you know anything at all wrong, or possibly wrong—to explain it. . . put down all the facts that disagree with it, as well as those that disagree with it . . .
. . . give all of the information to help others to judge the value of your contribution; not just the information that leads to judgment in one particular direction. . .
I’m talking about a specific, extra type of integrity .. bending over backwards to show how you’re maybe wrong, that you ought to have when acting as a scientist. And this is our responsibility as scientists, certainly to other scientists, and I think to laymen.”

“Earth’s radioactivity was confined to the crust, a few tens of kilometers thick.”

(John D. Stacey, Physics of the Earth, 3rd edition (1992), p. 45)

“Uranium, thorium and potassium are the main elements contributing to natural terrestrial radioactivity.. All three of the radioactive elements are strongly partitioned into the continental crust.”

(J. A. Plant and A. D. Saunders, “The Radioactive Earth,” Radiation Protection Dosimetry, Vol. 68, 1996, p. 25)

“The molten rock oozing from midocean ridges lacks much of the uranium, thorium, and other trace elements that spew from some aboveground volcanoes.”

(Sid Perkins, “New Mantle Model Gets the Water Out,” Science News, Vol. 164, 13 September 2003, p. 174.

Theories of an unsupernatural ultimate origin and formation of Earth call for the agglomeration of its particles thrown together by cosmic winds. They segregated into the core, mantle, and crust by gravity and heat. However, the heaviest naturally occurring elements: uranium and thorium are not nearly as concentrated under the continents and oceanic floors as they would be if the Earth formed from an interstellar medium. . . . If uranium and thorium were among the nuclides that the universe assembled into the Earth, they would be more concentrated toward its deeper parts. At least, they would be expected to have been evenly distributed throughout it. Yet: “90% of uranium and thorium are concentrated in the continents”*;–Earth’s continents are only 0.35% of its mass.*

*Dan F. C. Pribnow, Ph.D.(geophysics), “Radiogenic Heat Production in the Upper Third of Continental Crust from KTB,” Geophysical Research Letters, Vol. 24, 1 February 1997, p. 349.

* “The Earth’s continental crust occupies 41.2% of the surface area but represents only 0.35% of the total mass of our planet.” (Hugh Richard Rollinson, Ph.D.[geochemistry], Early Earth Systems [Blackwell Publishing: Malden, MA, 2007], p. 134)

“Heat production rate is well correlated to lithology; no significant variation with depth, neither strictly linear nor exponential, is observed over the entire depths of the [two German holes].”

(Christoph Clauser, et al., “The Thermal Regime of the Crystalline Continental Crust: Implications from the KTB, Journal of Geophysical Research, Vol. 102, No. B8, 10 August 1997, p. 18,418)

Germany’s Deep Drilling Project discovered variations in heat-exuding radioactivity related to the rock types, not to depths.

Are there higher concentrations of heavy radionuclei in Earth’s continental crust beneath its fossil-bearing rock layers where the one Supercontinent in its history had comparatively greater intensities of lightnings lightening it via having been more violently quaked or comprised of stronger rock types that generated more frictional electrifications and charge condensations?

“Surface rocks show traces of radioactive materials, and while the quantities thus found are very minute, the aggregate amount is sufficient, if scattered with this density throughout the earth, to suppy, many times over, the present yearly loss of heat. In fact, so much heat could be developed in this way that it has been practically necessary to make the assumption that the radioactive materials are limited in occurence to a surface shell only a few kilometers in thickness” (Leonard R. Ingersoll, et al., Heat Conduction : With Engineering, Geological and Other Applications, revised edition [University of Wisconsin Press: Madison, WI, 1954], p. 102)

You wrote on blog saying: “There was no global flood.” I’m not altogether certain of that.

Perhaps almost all of Earth’s fossil-bearing rock layers and all their heavy, radioactive elements bound to lighter elements evidence that it had extraordinary lightnings in enormous sub-Supercontinental water and in a Supercontinent erupting it whereby the seven continents it divided into were entirely and totally overflowed with tsunamies.

Thank You, Rick Keane

Too long? Shorter Rick Keane: Why haven’t geophysicists considered that there was a giant ocean of water beneath the continent(s) that exploded outward with a lot of lightning?

I don’t know. Why haven’t geophysicists consider my theory, that the earth is a giant eukaryotic cell, that continents are rafts of cell surface molecules, and that volcanoes are examples of exocytosis? Huh? Why? They’ll all be so surprised when the planet undergoes mitosis, I tell you what.

I also have a theory that the KT event was actually a sperm fusion event. Ask me more, maybe I’ll spin out a few thousand words with lots of quotes.

It also explains why someone would write to me asking about geophysics.

Apr 21 2014

Also, dead people don’t roll in their graves…but point taken

After that silly poll claiming Britain was a “Christian country”, after many public figures disagreed, I rather like Tim Minchin’s response, given to the British Humanists:

Even if Britain was a Christian country (it isn't); even if "Christian values" were meaningfully distinct from the moral values of humans worldwide (they're not); even if promoting religious doctrine improve moral behaviour in modern society (it doesn't); even if all these were the case, the fact that this rhetoric is being spouted by Mr Cameron would surely make the socialist, leper-lover iconoclast, Jesus Christ, roll in his grave (had he not so famously vacated it).

Even if Britain was a Christian country (it isn’t); even if “Christian values” were meaningfully distinct from the moral values of humans worldwide (they’re not); even if promoting religious doctrine improve moral behaviour in modern society (it doesn’t); even if all these were the case, the fact that this rhetoric is being spouted by Mr Cameron would surely make the socialist, leper-lover iconoclast, Jesus Christ, roll in his grave (had he not so famously vacated it).

It gives way too much credit to a first century religious fanatic (if he existed at all), but I get the point.

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