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Apr 23 2014

The "you’re freakin’ kidding me" poll

Trying to do theology by internet poll sounds … unwise.

Is Jesus Christ the son of God?

Yes 56.9%

No 43.1%

Apr 23 2014

Right-wing lies flourish on their propaganda organs

Wheee! I’m featured on OneNewsNow, the Far Right Christian online ‘news’ organization. It’s the same old thing.

University of Minnesota-Morris Professor Paul Z. Myers has encouraged students to gather up and trash all copies of an independent student newspaper [Not true. I said the university ought to prohibit their racist rag in the same way we would refuse the Ku Klux Klan the right to insult our non-white students on campus] with which he disagrees [Not true. I said we do have conservatives on campus; the basis of my disagreement wasn't their politics, but the racism of this particular small group of extremists. And also their incompetence.]. The politically radical [Sorry, no. I'm pretty much a rock solid liberal/progressive. Not very radical at all.] professor blogged that the Morris NorthStar student newspaper was a disgrace and has "worn out its welcome and must go."[Correct! When your approach is to hide behind Trayvon Martin's corpse and accuse university administrators of racism because they aren't nice enough to white people…you're not really bright enough or responsible enough to appreciate an education, let alone benefit from it.]

"We ask UMM to publicly condemn these instances of theft and destruction [They did!], investigate what happened [They did! Although I haven't seen any evidence that this 'theft' even occurred; it was a free paper, widely distributed across campus, and all of a sudden, we have known far-right media clowns claiming some were "stolen". Really? How could you tell?], and prosecute those responsible, [Yes, even if it is a stunt by the students who put out the North Star. So why are you harassing me? I had nothing to do with it.]" Theriot says. "The university must take steps to protect the NorthStar [Not necessarily. They could also banish it from campus as a disruptive, dishonest, and scurrilous pile of shit.] and all other student publications from such viewpoint-based [Is that what Republicans are calling their racism now?] censorship [There is no evidence of censorship! Saying it over and over again doesn't make it true.] in the future."

While copies of the newspaper were being stolen, trashed, and defaced, ADF attorney David Hacker says the university quietly stood by.[Again: no evidence of theft, except the claim by the North Star. It's a free paper that students were encouraged to take. What was the university supposed to do, put guards around the distribution racks and yell at anyone who takes a copy?]

It is simply bizarre. The university throughout has repudiated any attempt to destroy the paper; the chancellor sent out a campus-wide email saying so way back in December. They’ve got no case against the university. I used my free speech rights to say that the paper is garbage and that we ought to have some standards and reject the distribution of the libelous, poorly written crap, and yet they’re claiming that there must be an absolute right to free speech everywhere and at all times. They are going to have a hard time making a case that a free paper could be or even was stolen, and they’ve made this patently bogus case against me based on the idiot editor’s claim that there was a sciencey smell around one of the racks. That’s it. A contrived and implausible claim by a dope with an agenda, and that’s what these right-wingers are leaping upon.

It’s the same dishonest O’Keefeian tactics again. We’re just waiting for someone to ask if these people have any decency at all.

Apr 23 2014

The Deepening Rift

When I visited Iceland a while back, one of the sights I got to see was the dividing line between Europe and North America — one spot on the actual, physical dividing line between the tectonic plates. It was a literal rift.

rift

Another fascinating thing about it is that it’s growing. These plates are slowly drifting apart, and we expect the Atlantic Ocean to grow larger in the coming millions of years. This is not a bad thing or a good thing, it’s just what is.

You can see a growing rift right now: just look at the atheist movement. In particular, one really good marker right now is to look at Melody Hensley. Melody has been a vigorous activist for CFI, organizing many meetings in the Washington DC area, and in particular acting as the driving force behind the impressive Women in Secularism meetings. If there are real Brave Heroes in this movement, she’s one of them. I’m on Melody’s side of the rift.

On the other side…well, a mob of shrill nobodies, who don’t seem to do anything for the movement at all, but are really good at non-stop whining and lying. They are entitled shits who get furious if you block them on twitter or ban them from your personal blogs, but mainly seem to be involved in pursuing vicious vendettas against feminism, social justice, or anyone who dares to suggest that atheists ought to be doing more than just chanting that god is dead.

I am not on their side. I’m actually wishing we had a nearby subduction zone so they’d get sucked down into a more appropriate region.

Their latest cause célèbre is to howl in rage because Melody has been diagnosed (by a professional, not some ignoramus on Twitter) with post-traumatic stress disorder, PTSD, as a consequence of years of harassment and bullying. This is a legitimate diagnosis: years of watching crime dramas on TV may have given you the impression that PTSD only affects soldiers in war zones, but real psychologists and real doctors will tell you otherwise: all kinds of prolonged stressors can produce PTSD symptoms. So if you’re one of the idiots ranting that you can’t get PTSD from bullying/stalking/harassment, you’re on the other side of the rift from me, and you’re also factually wrong. Which is amazing, considering that atheists should be putting a very high premium on following the evidence.

Then the other response is that if Melody can get PTSD from ‘mere’ online bullying, then she is demeaning the experience of soldiers who get PTSD from bombs going off near them— you know, ‘legitimate’ PTSD. This is absurd. They’re trying to rank degrees of trauma? That doesn’t discredit the fact that they’re all trauma. Someone saying they’ve got PTSD from source X is not an attack on someone getting PTSD from source Y. It’s painful to watch: it’s as if someone said they had prostate cancer, and instead of sympathy and help, they got accused of belittling breast cancer patients, because that’s a real cancer…and then someone starts tearing into those people because saying that breast cancer is a serious disease is equivalent to shitting all over pancreatic cancer patients. No, it’s not. They’re all bad. It’s a group of outsiders trying to establish a hierarchy of suffering solely so they can disparage one group. It’s dishonest and despicable.

I’m on the side of the people citing the scientific and medical evidence. I’m not on the side of people abusing the facts to further bully others.

And now, of course, their real agenda is becoming apparent: the Melody-haters who also reject the medical facts are finding common cause with misogynists and the usual incoherent ranters of the inappropriately named Men’s Rights Movement are are upset that mere rape and death threats against a woman might be wrong. It’s clear that the reason for all the bullying isn’t that Melody is weak, or lying, or oppressing people, because she isn’t — it’s because she’s a prominent, strong activist fighting for better representation of women in atheism and skepticism. That is her crime. And so those people on the other side of the rift will hound her to oppress and silence her.

Here I stand, on my side. Not only will I take pride in my choice, but if you try to tell me that I somehow have to heal this rift, I’ll ask you…”WHY?”

Apr 23 2014

What is it about the word "choice" that you don’t understand?

I don’t follow the British popular press very closely, but Josie Cunningham must have done something truly evil.

To read Cunningham’s mentions on Twitter is to explore a world of medieval morality I didn’t think still existed in the UK. The "murdering cow" needs "locking up", you see. "It’s a mental institute you need," explains one man. One woman tells her to throw herself off a cliff, while a man named Warren patiently explains that, "someone needs to throw acid on you." "I sincerely hope this woman is flattened by a lorry," prays another. Women who’ve never met her call her an "ugly no good cunt," a "rank slut," who "doesn’t deserve the ability to conceive" and needs "a good hard kick in your piss flaps." Many talk erroneously about murdering babies or children, one woman asking if she can feel the 18-week-old foetus kicking inside her.

What did she do? She chose to state on television that she was pregnant and was going to get an abortion. She had a mix of good reasons — not wanting to be tied to the father, wanting to focus on her career — and bad reasons — her chosen career is to be a TV celebrity — but that doesn’t matter. The whole point of being pro-choice is that women get to make their own decisions about their own bodies. You can also have bad reasons for wanting to have a baby, but we shouldn’t also vilify women for making that choice (it’s a double-whammy: a single career woman who chooses to have a baby can also be vilified for selfishness and not fitting the maternal stereotype sufficiently well).

I don’t know much of anything about this woman, but if she wants to have an abortion, that’s her decision, not mine. And it doesn’t really matter why she wants it.

Apr 23 2014

Ben Affleck’s new Batman costume…revealed!

There were groans of dismay throughout Nerd-dom when it was announced that Ben Affleck would be playing Batman in the next movie in the franchise. But then the always over-the-top Kevin Smith saw the costume.

“I saw the Batman costume. More than that, I saw a picture of [Ben Affleck] in the costume…I don’t want to give anything away ’cause that is up to them and stuff, but I am going to say this…I instantly bear hugged [Snyder]. You have not seen this costume on film before. For a comic book fan, it was mind-bending… Because every other movie does this Matrix-y black armor thing…There wasn’t a single nipple on this suit. I think everyone is just gonna be like ‘Holy S**t!’ It’s its own thing. We haven’t been down this path before. Even the hardest core [most skeptical] person will be like ‘Alright, I’m ready.’…It seemed like it was very [Redacted] influenced.”

And as we all know, the most important thing in a superhero movie isn’t the plot or the acting — it’s the special effects and the fancy costumes.

But I have to agree with Smith. I have seen the costume, and it is awesome. It’s going to make the movie for sure. And here it is.

Read the rest of this entry »

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.

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