Pink Spandex, the Human Epigenome and Apostasy

Workout notes
Yoga with Ms. Vickie:

No, we didn’t do this, and no, there was no awesome pink spandex in the class. What we have is not so much a true yoga class as an exercise class in which the moves are inspired by yoga poses. The goal is to get stronger and more flexible rather than better at yoga.

Then I ran 6 miles:

(click the small photo for the full sized one)

No, I didn’t see this….this time. 😉
It was a cool, dry day. I jogged 1 mile to the gooseloop. Then I did 9 laps (3.24 miles) in 29:59 (9:55, 10:13, 9:51) where I ran .5 miles reasonably hard, then .22 miles (to make 2 loops) easy and repeated this; the only exception is that the last “hard” part was one full loop (.36 miles). Then I walked and then tried to jog two miles; that was hard. In fact, I had to walk twice during my super slow cooldown jog.

I did better two and three weeks ago (in terms of total time), but this time, I ran the interval bits harder and really slowly shuffled my recovery.

This workout reminds me of some in the book Running Tough by Michael Sandrock. One of my favorites is one that Robert de Castella used to do: he would warm up and do 8 x 400 m at 5K race pace. But he would recover 200 meters at something like a 6 minute per mile pace (which was about 20 percent slower than his marathon race pace!). You’d end up with 5K and he’d time the whole thing. The temptation is to take a bit off of the 400 meter interval part; that is a mistake. One way a mortal could do this: 400 meters at 5K pace, with a marathon pace recovery (since we tend to race marathons at a proportionally slower pace than the pros do); perhaps we could add 1 minute to the marathon pace. That workout is a killer.

Find the Kitten in the photo; you’ll see that house cats have amazing camouflage characteristics!

You can see just a short clip of a film and, from the colors, determine if the film is from yesteryear or from the present day. Why is that? Mano Singham talks about this and links to a couple of interesting sources.

Example: watch the first two minutes of this; notice the colors:

Yes, you can tell it was late 1960’s-early 1970’s era (even if you didn’t recognize a still-young Roger Moore; yes this was the last film he made prior to assuming the James Bond role).

In a nutshell: producers in those days didn’t have the option of changing color by computer; hence they paid more attention to color quality while filming. Now-a-days, producers digitally alter the color to give a flatter, somewhat bluish effect.

this is a two part interview with Richard Dawkins. If you like evolution and science, you’ll like this interview. He discusses things like punctuated equilibrium. He doesn’t come across as strident at all, at least not to me.

More science: Europe will attempt to map the human epigenome (roughly speaking: the chemicals that allow for gene expression):

DNA-modification studies get a multi-million euro boost.

The health-research division of the European Commission launches its largest-ever project next week with a €30-million (US$41-million) investment in understanding the human epigenome, the constellation of DNA modifications that shape how genes are expressed.

With the project, called BLUEPRINT, Europe intends to become a major player in the International Human Epigenome Consortium (IHEC), set up last year to help biologists understand how the epigenome influences health and disease.

All the cells that make up an individual originate from the same fertilized egg and share the same genome. But during development, cells acquire epigenetic changes — such as chemical modifications to DNA, and changes in the shape of its tightly coiled three-dimensional structure — that affect which genes will be active in which cells at a given time and which will be silent.

The epigenome then remains largely stable, so that a liver, for example, remains a liver throughout life. But small parts of the epigenome change constantly as the cell responds to environmental changes. The epigenome also changes in diseases, including cancer.

The importance of the epigenome in health and disease is becoming increasingly clear. But researchers studying it have faced a big hurdle: the lack of a reliable library of high-quality, quantitative reference epigenomes against which new data can be compared. Little is known, even, about how much the epigenome normally varies between individuals, or between the different cells in an individual.

Enter BLUEPRINT, which unites 41 institutions and more than 50 principal investigators across Europe who will contribute a further €10 million to the project. BLUEPRINT will provide at least 100 reference epigenomes toward the IHEC’s goal of amassing 1,000 reference epigenomes by 2020.

BLUEPRINT has chosen to focus on the blood system. This should help move discoveries quickly into the clinic, as many diagnostic tests rely on blood samples. “Blood is also what gets stored in biobanks and used for genome analysis,” says BLUEPRINT coordinator Henk Stunnenberg at the Nijmegen Center for Molecular Life Sciences in the Netherlands.[…]

This is an attempt to respond to a “defense of naturalism”. Meh. If there are other ways of “discovering” or “knowing” truth (other than by naturalism), then please present such a result. That is all. 🙂

Why I have no automatic respect for religion or religious belief
Ok, let me be clear about what I am saying: many religious are genuinely nice, intelligent people. And yes, many beliefs and practices ARE commendable. For example, there is one organization that I have given money to and they are religious; they get out there and feed and house the hungry and homeless.

But the beliefs that I respect get my respect because the beliefs and commendable and because they lead to good actions; I do NOT automatically respect a belief because it is “religious”. If I encounter a belief or an idea that catches my interest, I critique the same way I critique any other idea (science, social, political, etc.)

So, here is an action that is being taken in the name of religion that I find horrific:

The Foreign Secretary and the Archbishop of Canterbury intervened last night to try to save a Christian pastor in Iran who has refused to renounce his faith to escape a death sentence.

An Iranian court gave Youcef Nadarkhani, 34, a third and final chance to avoid hanging, but he replied: “I am resolute in my faith and Christianity and have no wish to recant.”

The panel of five judges will decide within a week whether to confirm his execution for apostasy, Mohammed Ali Dadkhah, his lawyer, told The Times.

William Hague said he “deplored” Pastor Nadarkhani’s plight, and a senior Foreign and Commonwealth Office diplomat telephoned the Iranian chargé d’affaires in London to protest.

“This demonstrates the Iranian regime’s continued unwillingness to abide by its constitutional and international obligations to respect religious freedom,” Mr Hague said. “I pay tribute to the courage shown by Pastor Nadarkhani, who has no case to answer, and call on the Iranian authorities to overturn his sentence.”

The Archbishop of Canterbury, Dr Rowan Williams, broke his silence to express “deep concern” at the sentence faced by Pastor Nadarkhani, and at the persecution of religious minorities in Iran generally.

Sources said that Christian clerics and advisers had been working hard behind the scenes to save the pastor’s life, but had sought to avoid “megaphone diplomacy” in case it did more harm than good.

The US Department of State has also condemned the Iranian judiciary for demanding that Pastor Nadarkhani renounce his faith or face execution.

Yes, a few hundred years ago, Christian authorities did exactly the same thing, and the Jewish Bible describes the same thing being done to others.

This is a case of a nonsensical, downright evil religious belief. Yes, “the State” would do the execution, but this would be required by their form of clergy.

I challenge anyone to claim that they respect this religious belief, idea or practice.

And no, the irony is NOT lost on me (that one is being killed by one follower of an imaginary entity because the soon-to-be victim believes in some other imaginary entity…or professes a different way of worshiping the said fictional character.)

And I’ll say this: anyone who finds this sort of religious conduct to be acceptable or even tolerable does not belong in the United States.

September 30, 2011 Posted by | blogs, books, civil liberties, evolution, movies, nature, politics/social, running, science, social/political, spandex, superstition, time trial/ race, training, world events, yoga | Leave a comment

This is just wrong….wrong I tell you.

September 29, 2011 Posted by | humor | 1 Comment

28 September 2011 issues

Workout notes
First, walking on the university indoor track: I had a 13:46 first mile and then did: 2-1-2-1-4-1-2-1-10 where the 1’s represent recovery 200 meter laps. My miles: 13:36, 11:44, 11:29, 10:25 for 47:25 for 4.

I then swam 2200 yards; the guard didn’t open the pool until 7:15 so I had only 45 minutes. So I did 2000 yards straight in 38:00 (very slow for me) then 200 front/back pull.

College Football
So the Aggies (Texas A&M) is headed to the SEC. Good riddance. They’ll fit right in; at halftime they can start with a prayer-revival service and end with a public execution, no doubt to a loudly cheering crowd. But there are past games that I remember fondly and this is one:

Well, they held the Longhorns to only 49 points, so what the heck. 🙂

As for what Rice University thinks of the Aggies:

Non-football posts

Remember when Rush Limbaugh did this?

Well, I wondered what English speakers sound like to non-English speakers.
This outstanding web page has a collection of videos of non-English speakers imitating English. What I noticed: how they imitate English depends on, surprise, their own native language.

Here is one of the better ones (short)

and here is the best one (much longer)

Science and Health

3-quarks daily pointed us toward this post which reminds us that sometimes the solution to health problems are, well, simple.

Take what must be the greatest cheap medical fix in all of history: the bar of soap. Soap never stops proving itself. As recently as 2005, a study from the slums of Karachi, Pakistan, showed that free bars of soap (and lessons in how to use them) cut rates of childhood killers like diarrhea and pneumonia by half.

But you don’t find soap in American hospitals anymore, at least not in its classic solid rectangular form. A variety of expensive improvements have replaced it, all created in response to the various ways in which modern doctors and patients reflexively undermine good, inexpensive tools.

First, we automatically capture these things for our own personal use: Bars of soap left in any public place are likely to disappear in short order. (That is why toilet paper rolls are generally locked into their little metal houses.)

Second, we find fault with them. People will actually use the observation that bar soap is “dirty” as an excuse not to wash their hands. (Studies have shown that you will not pick up somebody else’s germs from a piece of soap, however dingy it may look.)

Finally, we ignore them. Who notices a bar of soap? It does nothing for you unless you notice it — but it is so humble and boring; and sudsing, rinsing and wiping are so pedestrian. Also, if you are in a hurry, they seem prohibitively time-consuming. Studies continually show low hand-washing rates among rushed hospital personnel. Hence the large-scale adoption of more convenient liquid products, and the slow segue into alcohol-based hand sanitizers, which obviate the rinsing and wiping.

There is more there.

I remember reading in Jared Diamond’s book Guns, Germs and Steel that, right now, humans have a much lower probability of dying a violent death than at any time in human history. Now there is a book which explores (and proves) this claim, and more.


Will Governor Christie run and if he does, will it matter? Frankly, I think that Nate Silver greatly overstates Mr. Christie’s talent. Sure, he sometimes says good stuff (here and here) but on the whole, he is too thin skinned and high tempered; the national media would have field day with him. Yes, he is obese and that would have been a negative a long time ago, but not in today’s America and certainly not with today’s Republicans. 🙂

Besides, if *I* find stuff to like about him, he probably won’t play well with the Republican base.

September 29, 2011 Posted by | 2012 election, college football, football, political/social, politics, politics/social, Republican, republican party, republicans, republicans political/social, republicans politics, rick perry, Rush Limbaugh, science, swimming, training, walking | Leave a comment

Ok, what do you see here?

I know what I saw.

Can you guess what I missed? 🙂

September 28, 2011 Posted by | big butts, spandex | Leave a comment

Shilling, Zombie Ideas and other Republican nonsense…

Mathematics and Statistics
I am going to have to look at some of these fun-sounding pop-science statistics books. But I was really struck at one statistician’s comment:

What do you mean by “risk literacy” and why do you think it is so important for people to have it?

I am a statistician and I know that people find probability and statistics quite difficult to understand, and not intuitive. And after years and years of careful research I have finally concluded that it is because probability and statistics really are difficult to understand and unintuitive. I think knowing something about how chance works in the world is a basic skill that people should have, along with reading, writing and basic numeracy. Otherwise you can be subject to all sorts of manipulations, and that will come out in some of my book choices.

Paul Krugman seems distressed. First he notes that conservatives are cherry picking from past data to bolster what they already want to believe. Check out the graphs: the conservatives are ignoring the large trends and instead are pointing out the “wiggle” (aka “noise”). In fact, he is distressed to the point of claiming that economics, as a discipline, is actually REGRESSING instead of getting better:

I’ve never liked the notion of talking about economic “science” — it’s much too raw and imperfect a discipline to be paired casually with things like chemistry or biology, and in general when someone talks about economics as a science I immediately suspect that I’m hearing someone who doesn’t know that models are only models. Still, when I was younger I firmly believed that economics was a field that progressed over time, that every generation knew more than the generation before.

The question now is whether that’s still true. In 1971 it was clear that economists knew a lot that they hadn’t known in 1931. Is that clear when we compare 2011 with 1971? I think you can actually make the case that in important ways the profession knew more in 1971 than it does now.

I’ve written a lot about the Dark Age of macroeconomics, of the way economists are recapitulating 80-year-old fallacies in the belief that they’re profound insights, because they’re ignorant of the hard-won insights of the past.

What I’d add to that is that at this point it seems to me that many economists aren’t even trying to get at the truth. When I look at a lot of what prominent economists have been writing in response to the ongoing economic crisis, I see no sign of intellectual discomfort, no sense that a disaster their models made no allowance for is troubling them; I see only blithe invention of stories to rationalize the disaster in a way that supports their side of the partisan divide. And no, it’s not symmetric: liberal economists by and large do seem to be genuinely wrestling with what has happened, but conservative economists don’t.

Remember: being a conservative means that one doesn’t need evidence for one’s beliefs and positions.

It doesn’t help that people forget who correctly predicted what: liberal economists said AT THE TIME that the stimulus was too small and bound to fizzle. It did have some effect but not a large enough effect; hence conservative “intellectuals” (those who can write in complete sentences and use existing vocabulary) are crowing about the stimulus being a massive Keynesian failure. Why Dr. Krauthammer is considered an authority on anything remains a mystery.

Republican Shilling
I keep up with Dick Morris; part of the reason is that I want to know what is being fed to the rank-and-file NewsMax Republican (mostly the undereducated “Obama is a Muslim and evolution is a hoax” crowd). Part of the reason: it is good comedy.

Back in April, Mr. Morris was all but writing off Mitt Romney.

Now he is touting Mr. Romney. 🙂

So what is he saying this time? Well, he is saying that President Obama might not run for reelection:

He stays on this theme by talking about how Bill Clinton is attacking Obama’s jobs plan.

Then Mr. Morris cherry picks from polls and even declares that Blacks are leaving President Obama!


I am not saying that President Obama’s path to reelection is sure; it isn’t. In fact, he has dipped below 50 percent on Intrade (and at times rose above it).

But…it still appears that the Republicans are not happy with their field either.
Upshot: this coming election appears as if it will be a hard, close, nasty contest; I’d rate it as a “toss up”. But to hear Mr. Morris talk, well, President Obama doesn’t stand a chance.

I hope that the Republicans keep believing that.

September 28, 2011 Posted by | 2012 election, Barack Obama, economics, economy, mathematics, political/social, politics, politics/social, Republican, republican party, republicans, republicans political/social, republicans politics, statistics | Leave a comment

Indecision 2012 – The Great Right Hope – The Ideal Candidate – The Daily Show with Jon Stewart – 09/26/11 – Video Clip | Comedy Central

The Republican base is at war with its own talking points. Airdate – 09/26/11

Vodpod videos no longer available.

Indecision 2012 – The Great Right Hope – The Id…, posted with vodpod

September 27, 2011 Posted by | 2012 election, political humor, politics, republicans | Leave a comment

Global Warming – The Colbert Report – 2011-26-09 – Video Clip | Comedy Central

In the face of all the mounting evidence for climate change, America has stood with one voice and boldly proclaimed, “Eh.”

Vodpod videos no longer available.

Global Warming – The Colbert Report – 2011-26-0…, posted with vodpod

September 27, 2011 Posted by | environment, humor, political humor | Leave a comment

Christine O’Donnell in her youth?

Seriously, this makes an important point. The government isn’t allowed to promote a particular religion. So if you allow one type of organized prayer in a public school….be prepared for HAIL SATAN! Or “PRAISE BE TO THE FLYING SPAGHETTI MONSTER!!”

Actually, the MIGHTY CALVIN remains one of my favorite deities:

Now THIS reminds me a bit of the traditional Jewish sky-god (the Christian “Old Testament deity”). 🙂

September 27, 2011 Posted by | civil liberties, humor, political humor, politics/social, religion | 1 Comment

27 September 2011: Centrist Obama and the falling slinky

Workout notes
Monday: weights then a swim.
Swim: 500 of 25 fist, 25 3g, 25 fist, 25 swim
250 of 25 kick, 25 free (fins)
250 of 50 free (5 second pause)
250 of 25 kick, 25 free (fins)
250 of 25 fist/25 free (5 second pause)
500 of 50’s (5 second pause)
200 free/back (fins)

Weights: rotator cuff, 1 set of lunges
Hammer Row: 3 sets of 10 x 200
Pull down: 3 sets of 10 x 145
dumbbell curls: 3 sets of 12 x 25 lb.
Bench: 10 x 135, 8 x 155, 6 x 155
Incline: 2 sets of 10 x 125
dumbbell military press: 2 sets of 15 x 40 (seated), 5 x 45 standing
adduction: 3 sets of 10 x 180
abduction: 3 sets of 10 x 180
push back: 2 sets of 10 x 110
sit ups: 100 (2 sets of 50)

Tuesday: yoga followed by a sloooow 6 mile (+) run; It was my basic 5.1 mile course plus 3 more goose loop laps. Time was 1:10, but that included a 3 minute walk at 27 minutes when my “behind the knee” area got achy. I was ready to bail but after a bit of relaxing walking, I was able to start up with no difficulty. It was one of those “cramps that needed to be stretched” things.

The falling slinky
(hat tip: Jerry Coyne)

Note: even a seemingly solid rod will have this effect; remember that there is no such thing as a purely rigid object.


No, politics these days is NOT “both sides” being unreasonable:

Greg Sargent touches on a point I’ve been meaning to make; he does it in the context of third-party fantasies, but it’s true more broadly of calls for “centrism”. Namely, the hypothetical position self-proclaimed centrists want somebody to take — Michael Bloomberg, a chastened Obama, whatever — is almost always the position actually held by the Democratic party. But to seem “balanced”, the pundits involved have to ignore that inconvenient fact.

Greg puts it this way:

One of the two parties already occupies the approximate ideological space that these commentators themselves are describing as the dream middle ground that allegedly can only be staked out by a third party.

That party is known as the “Democratic Party,” and it alreadly holds many of the positions these commentators want a third party to espouse.

Well, it’s not just the third party thing. I was struck by this passage in Tom Friedman’s last column:

We know what to do — a Grand Bargain: short-term stimulus to ease us through this deleveraging process, debt restructuring in the housing market and long-term budget-cutting to put our fiscal house in order. None of this is easy and the economy will not be fixed overnight; it will take years. But there is every chance it will get healed if our two parties construct the Grand Bargain we need.

Who is the “we” who knows this? Well, me; Christy Romer; President Obama. The GOP, on the other hand, is fiercely opposed to any form of stimulus — it insists that we need to slash spending right now, that anti-stimulus is the way to create jobs. And anger over the prospect of helping delinquent debtors was, you might recall, where the Tea Party got started.

September 27, 2011 Posted by | physics, political/social, politics, politics/social, Republican, republicans, republicans political/social, republicans politics, science, swimming, training, weight training | Leave a comment

Someone is drowning…a Democrat and a Republican go to help

(note: I’ve taken a joke that I saw on facebook and changed it just a bit).

There is someone who is 100 feet away from shore and they are drowning; they cry out for help….

The Democrat shows up and throws the victim 300 feet of rope. The excess rope weighs the victim down and the victim drowns.

The Republican shows up and throws out 50 feet of rope and demands that the victim take some responsibility for himself and swim to the rope. He can’t and drowns.

A libertarian shows up and shrugs “it isn’t my problem” and just goes away; the victim drowns.

A bunch of Tea Party types show up. One throws the victim a heavy rock; the victim drowns and all of the tea party types cheer.

A Green Party type shows up. He yells at the victim for polluting the water. The victim drowns.

September 26, 2011 Posted by | political humor | 1 Comment