(click for the full size poster)
I’ve read some of it and I’ll have to read more.

Virus Evolution
Some viruses can mutate to become more contagious very quickly. Carl Zimmer in the New York Times explains:

Viruses regularly evolve new ways of making people sick, but scientists usually do not become aware of these new strategies until years or centuries after they have evolved. In a new study published on Thursday in the journal Science, however, a team of scientists at Michigan State University describes how viruses evolved a new way of infecting cells in little more than two weeks.

The report is being published in the midst of a controversy over a deadly bird flu virus that researchers manipulated to spread from mammal to mammal. Some critics have questioned whether such a change could have happened on its own. The new research suggests that new traits based on multiple mutations can indeed occur with frightening speed.

The Michigan researchers studied a virus known as lambda. It is harmless to humans, infecting only the gut bacterium Escherichia coli. Justin Meyer, a graduate student in the biology laboratory of Richard Lenski, wondered whether lambda might be able to evolve an entirely new way of getting into its host.

The standard way for lambda to get into a cell is to latch onto its outer membrane, attaching to a particular kind of molecule on the surface of E. coli. It can then inject its genes and proteins into the microbe.

Mr. Meyer set up an experiment in which E. coli made almost none of the molecules that the virus grabs onto. Now few of the viruses could get into the bacteria. Any mutations that allowed a virus to use a different surface molecule to get in would make it much more successful than its fellow viruses. “It would have a feast of E. coli,” Dr. Lenski said.

The scientists found that in just 15 days, there were viruses using a new molecule — a channel in E. coli known as OmpF. Lambda viruses had never been reported to use OmpF before.

Surf to read the rest; nature can be very efficient….and it is indifferent to the comfort of humans. True, nature cares about our being able to reproduce so we do evolve some defenses against diseases that kill prior to our child bearing years.

Politics
Republicans are fed a mess of lies and distortions from the right wing media. Here is one whopper (surf to the Salon article by Michael Lind to read more)

Here is misleading argument No. 1:

Spending on Social Security, Medicare, Medicaid and Obamacare alone currently account for 46 percent — or nearly half of — federal spending, excluding interest payments. Over the next 25 years, that percentage will explode to 66 percent, or close to two-thirds, according to the Congressional Budget Office.

This claim, while true, is misleading. This statistic, without any measure of how the projected federal spending grows (relative to GDP) is meaningless. Here is why: suppose next year, we completely cut military spending and we keep the above programs exactly the same. Guess what: the spending on those programs, as a percentage of the federal budget, would go way up and we wouldn’t be spending any more money! Of course that is an extreme example. A more honest statistic would be how much spending on these programs would grow AS A PERCENTAGE OF GDP.

I am not saying that we shouldn’t try to reform Medicare because, well, more of us are living longer and most medical expense comes at the end of life. But we should be honest about the numbers.

Other lies you might hear: “Obama is taxing you more” (no, he isn’t; he is taxing you LESS), “Obama Raised Taxes 19 times”; here is what Mr. Romney really meant by that:

We’ll list the 19 provisions in four groupings that reflect how much consensus there seems to be from our reporting.

Items that are clearly taxes, and that are already in effect

• Increasing the federal excise tax on tobacco. Obama signed legislation raising taxes on cigarettes and other tobacco products soon after taking office; that money goes to pay for children’s health insurance programs. The law went into effect in 2009.

• A 10 percent excise tax on indoor tanning services. This tax is narrowly targeted at tanning bed users, but it is still a tax. This took effect July 1, 2010.

• Increasing corporate taxes by making it more difficult for businesses to engage in activities that reduce their tax liability. This appears to refer to the closing of a half-dozen existing exemptions and credits relevant only to large international corporations. (We wrote about this recently.) While this is a provision targeted narrowly at big conglomerates — and while it’s popular as a way to keep deep-pocketed countries from sheltering excessive amounts of income — our experts said it does count as a tax increase. Obama signed the bill into law on Aug. 10, 2010.

• Imposing an annual fee on manufacturers and importers of branded drugs, based on each company’s share of the total market. While some industry-specific levies are intended to help foot the bill for regulatory processes, this one is more of a revenue raiser for the more general goals of the health care overhaul. It took effect on Jan. 1, 2011.

Follow the link to see the rest; it is in dispute whether some of the changes really are “taxes”.

You might also hear about how “Obama grew government”. Actually we have fewer non-military employees than when President Reagan was in office (automation?). If you are talking about spending (Paul Krugman):

One of the things everyone knows right now is that Obama has presided over a huge increase in government spending. But like so many of the things everyone knows, it isn’t true.

A few considerations to bear in mind:

1. You don’t want dollar amounts, especially when comparing over time; you really want to scale spending by the size of the US economy.

2. But even dividing by GDP isn’t quite enough, because we’re still a deeply depressed economy, so government spending as a share of GDP will look high even if actual spending hasn’t risen at all, simply because it’s divided by a smaller number. So a better guide is spending as a share of potential GDP, for which I use the CBO measure.

3. You really want to consolidate federal spending with state and local — especially because a significant part of the stimulus was aid to state and local governments designed to help them limit spending cuts.

It just isn’t true: President Obama isn’t a big government president.
NOTE: this graph is “spending vs. POTENTIAL GDP which is currently below the actual GDP due to the recession, so many being out of work, etc.”

Obama Derangement Syndrome
The bottom line, many conservatives hate Obama for, well, doing stuff that he didn’t actually do:

The right’s core case is that Obama has governed as a radical leftist attempting a “fundamental transformation” of the American way of life. Mitt Romney accuses the president of making the recession worse, of wanting to turn America into a European welfare state, of not believing in opportunity or free enterprise, of having no understanding of the real economy, and of apologizing for America and appeasing our enemies. According to Romney, Obama is a mortal threat to “the soul” of America and an empty suit who couldn’t run a business, let alone a country.

Leave aside the internal incoherence—how could such an incompetent be a threat to anyone? None of this is even faintly connected to reality—and the record proves it. On the economy, the facts are these. When Obama took office, the United States was losing around 750,000 jobs a month. The last quarter of 2008 saw an annualized drop in growth approaching 9 percent. This was the most serious downturn since the 1930s, there was a real chance of a systemic collapse of the entire global financial system, and unemployment and debt—lagging indicators—were about to soar even further. No fair person can blame Obama for the wreckage of the next 12 months, as the financial crisis cut a swath through employment. Economies take time to shift course.

Obamacare? That was really the Heritage Foundation’s plan that was offered by Bob Dole to President Bill Clinton (with some modifications, of course).

So, liberals hated President George W. Bush too, so what is the difference? Well, as Bill Maher points out: we hated President Bush for what he REALLY DID DO: run up a ton of debt, attack a country that didn’t attack us and do so under false premises and give big tax cuts that mostly benefited the wealthy. He really did do these things.

There is nothing wrong with disliking President Obama (though I like him very much); there is a lot wrong with pretending that he did things that he didn’t do.

Today: the course had scattered, isolated patches of snow/ice; none was longer than 20-30 meters or so. It took me 2:25:43 to do the course (10.5 miles; this was 13:52 minutes per mile) and I was walking at a very relaxed effort. I noted some soreness in my RIGHT hip (the one without the piriformis issue). Whether I like it or not, I’ll have to do regular PT for it. My butt muscles are weak.

I am ashamed that I even thought about walking inside today; it was sunny (9 am), slightly breezy and right around freezing.

I wore my trail shoes (Brooks Cascadias) and tried to focus on posture and on staying upright. The knees were fine though I made no effort to “stay legal” on the ice/snow patches nor on the very steep uphill near mile 10. This course featured 360 feet of climbing.

On the way back I saw one of my differential equations students; he runs for the cross country team and makes fast running look so easy.

Spring 2012: goal setting
I am mostly over my infection; I’ll give myself one more “general week” to recover prior to thinking about training. But then I’ll have to focus on something…or make the decision to not focus on anything and just do what I can, when I can and perhaps push my goals back to fall.

Who says that one needs a goal? I am enjoying my current round of “doing a little bit of everything” though I won’t like the race results I’ll get from doing this.

So the possibilities are:

1. No goal at all. The upside: I get to vary my training. The bad: my results will not be good.
2. Running: run a sub 24 5K. The upside: easy to train for in that I have an indoor track and a hilly course; I’ll have plenty of time to put in base, run hills, run a few tempo runs and then start racing hard in May. Also, this type of training is easy on my piriformis. The downside: I’ll have to keep my long walk “moderate” (e. g., like today’s).
3. Running: finish the Steamboat 15K “respectably” or perhaps a half marathon. The upsides and down sides are similar to 2, though I might combine this with 2.
4. Walking: walk a marathon (5:20) or a 50K (6:30). Upside: there is a “Walkers only” marathon/50K in Minnesota this May and I can make it this year. If you get DQ’ed for knees in the racewalk division, they’ll let you finish as a “general walker”. Downside: I’ll need to really up my long walk (I have the time) and add a medium long “tempoish” walk midweek; this means reducing the number of runs I can do per week. But mostly: I don’t know if my piriformis can handle the training. I’ll really have to take time to stretch it and PT it.

Where I am: 2:34 half marathon walk and about 56:50 for the 10K run; these are training like baselines.

I suppose I can just ramp up my general program (gradually) and make a decision by the end of February.

Chris Christie should know better
Christie is upset that a gay marriage law might end up on his desk; he threatened to veto it. He thinks that gay rights ought to be decided by popular referendum? (uh, we have a liberal democracy, not a “majority rule” but never mind). But he said something that was incredibly stupid:

The fact of the matter is, I think people would have been happy to have a referendum on civil rights rather than fighting and dying in the streets in the South.”

Uh, he really thinks that southern whites of that time period would have “granted” rights to the blacks? What planet is this clueless idiot person living on? Ok, Mr. Christie isn’t an idiot but he sure screwed up when he said that and he isn’t known for admitting to making mistakes.

As far as those who aren’t in politics
Our newspaper decided to publish this letter to the editor as “in the spotlight”; they said that this woman (Gina Zindt) is an “administrator in higher education”; in fact she is a human resource director for Knox College (NOT an academic).

She doesn’t like President Obama (nothing wrong with that) but she goes on to blame HIM for gridlock in Congress???

The absence of effective leadership from Obama has directly caused the immeasurable dysfunction of Congress. First, Obama doesn’t know his sport. He has no meaningful leadership knowledge or experience. He refuses to visualize outcomes from both Democratic and Republican perspectives. Rather, he continually fuels the division between them by blaming Republicans. Congress has never been more polarized: They are deadlocked on almost every issue because of his inability to inspire or motivate. It’s no wonder that Congress has its lowest approval rating ever.

Like Congress, we the people are more polarized than ever before. From the Tea Party to the Occupy movement – and all the passions in between – voters are beyond disappointed. We are disgusted and angry. But we can’t get lost in the seemingly endless infighting that will go on during all the campaigning this year. We simply must stay focused on the goal: removing Obama from our White House.

Uh, well, thought I don’t like John Boehner, even HE can’t keep his own caucus in line. From David Frum

At some point, Speaker John Boehner was going to have to show the most conservative members of his caucus that he would get work done in the House without them.

Yesterday revealed that day has not yet come. The ramifications of the failure to pass the Continuing Resolution (CR) for FY12 in the House will be far-reaching. It’s true that Democrats took advantage of the Tea Party defections from the GOP leadership and aided in killing the CR. But this was the second embarrassment on a critical vote for the House Republican leadership this year.

Rep. Eric Cantor had predicted that the votes were there to pass the CR. “All is well.” It wasn’t.

In blunt terms, the Speaker asked his caucus to endorse a deal that the House of Representatives had made with the Administration. The CR conformed to the Budget Control Act that was passed to increase the debt ceiling. The House and its Speaker had made a deal. The CR was the natural legislative result of that deal.

This was not perfidy on the part of the President, or some RINO conspiracy. This was the word of the House of Representatives, given and vouched for by the Speaker to the President. For members of his own caucus to publicly fail to help the Speaker keep his commitment shows that Republicans in the House (and in the country) are divided. They are in danger of becoming the equivalent of Serbia, Croatia, Bosnia, Albania, Macedonia, and Kosovo after the Third Balkan War.

If the United States had a parliamentary system, the Speaker would have to step down. His leadership of his own party has been repudiated by the right of the right.

My goodness; to think that people like this live among us.
In this woman’s “mind” (or what passes for a mind), President Obama is some uncompromising liberal. WRONG.

Lifting
I did my usual routine at a slightly slower pace.
Circuit one
rotator cuff (pulley), rows (Hammer Machine), curls (pulley), pull downs (lat machine)
row: 10 x 180, 10 x 230, 10 x 230
curl: 10 x 42, 10 x 47, 10 x 50
pull down: 10 x 140, 10 x 160, 10 x 160

Circuit two
Bench press plus sets of 20 sit ups (one after each bench press set)
10 x 135, 3 x 175, 5 x 170

Circuit three
Pull ups followed by sit ups (20 at the highest incline)
7, 7, 6, 6. The 7′s were done with knuckles facing me, the 6′s were done in a shoulder friendly position (knuckles facing sideways)

Circuit four
Incline bench press with one more set of sit ups:
7 x 135, 6 x 135

Circuit five

I finished with dumbbell rotator cuff exercises and two sets of 15 x 40 lb. dumbbell military presses.

Then I stretched and ran 10K on the track: my time was 56:50 for 50 laps (about 6.25 miles, slightly longer than 10K)

9:38, 9:21 (18:59), 9:12 (28:11), 8:57 (37:09), 8:47 (45:57), 8:40 (54:38), 2:12 (56:50)

Note that I was mostly by myself for the first 4-4.5 miles and then I paced off of one young woman for about .5 miles (4.5 to 5) and then took it in on my own.

Evidently I am almost over my illness; this 56:50 was only 30 seconds slower than what I did at a 10K race this September, and I had a warm up prior to that and I didn’t lift weights first. Then again, this was a springy track with no wind, hills, pot holes, etc. But it wasn’t a bad workout.

One funny note: near the track there is a mat where people can stretch or work with an exercise ball. As I completed one of the middle laps I saw a woman with a larger butt doing this (facing away from the track, almost perpendicular to it:

(click on the thumbnail to see the full size photo).

I got distracted for just a moment and regretted not having a camera. Well, not really.

Then again, had I seen this, I might have gotten a heart attack:

(click on the thumbnail for the full size photo)

Posts

Note: Presidents of both parties have been complaining about his “hold” policy for years. Yes, I thought it was dumb even when President Bush was in office. There might be some breakthrough in reaching an agreement to at least amend some of these procedures.

I don’t have the data on Senate holds but I do know that the Republicans have used the filibuster at an unprecedented rate.

Newt Gingrich and his Super Pac “Winning our Future”
Here is a Gingrich ad:

(note: Mr. Huckabee said that he was taken out of context and did NOT endorse the ad)

Winning Our Future’s ad

Notice how slick this ad is and how is very quickly slips in the appropriate disclaimers; Mitt Romney is never exactly accused of any direct wrongdoing. In fact, this ad presents what is old news in Massachusetts. But the tone is designed to scare the voters rather than to inform them. Very devious…:)

So how well are the candidates themselves doing on truthfulness? Here Nate Silver makes an analysis; one should read Mr. Silver’s cautions though.

Mormon Practice: Baptizing the Dead
I was a bit surprised to see atheists being upset over this:

Gawker’s substantial Mormon readership has come through for us: Two readers have sent us confirmation that Edward Davies, Mitt Romney’s militantly atheist father-in-law, was indeed posthumously converted to Mormonism by his family, despite the fact that when he was alive he regarded all religions as “hogwash.”

Just to set the record straight: this is NOT lying about a “death bed conversion”; no one is claiming that this man DID anything. And no, this isn’t desecrating a burial place as nothing physical was done. (I said these two things right off of the bat because I got remarks such as these).

My question: why does any atheist care who does what ceremony in whose name? Sure, right now, I’d be a bit concerned if some religious leader condemned me to death in some spiritual sense but ONLY because some whack job might attack me. But aside from direct physical acts, who cares? Really…those nut jobs who baptized the dead are DOING NOTHING AT ALL. It is the same as some kid pretending to cast a spell or something. Really….

They didn’t say that
Though I sometimes talk politics, I don’t like it when people repeat stuff that isn’t true. One of the favorite memes of the polyester pants set is that Al Gore said that he “invented the internet”. He never said that. He was clearly talking about policy and legislation and while you might argue that he took too much credit, he clearly was not talking about “inventing it”.

But this is not a left-right issue.
Dan Quayle never intimated that people in Latin America speak Latin; this meme came from a comedian’s joke.

And no, Spandex Sarah (Sarah Palin) never said that “she could see Russia from her house” though she did (correctly) say that you can see a part of Russia from a part of Alaska. The “seeing Russia from her house” was a Tina Fey joke.
This is what she really did say (which was bad enough):

Living in a Bubble
Joe Paterno died recently. My view: he was a good coach who did a lot right (gave back to community, got his players to graduate, etc.) but what he did wrong (NOT calling the police) was inexcusable; he should have been fired IMHO. It appeared to me that he was more concerned with his job and legacy than stopping a horrendous wrong.

Nevertheless, at the funeral, you are seeing much sentiment at how Paterno was giving a raw deal (example, example)

The pro-Paterno people are living in some bubble, I think. My guess is that this will hurt them in the long run; note that this year the got the Big Ten 7′th pick (8′th if you count the Michigan Sugar Bowl team) despite their fine on the field record. Some of that was the scandal, but this type of blind loyalty to Paterno isn’t helping.

But here was a funny part:

I had to laugh; right now I am “debating” who would win that ride. Surely Mr. Romney could afford the best bike.
But though I don’t like her politically, Ms. Palin would beat all of them easily and not even break a sweat.

Topics
This is just a FAIL on so many levels:

Mitt Romney’s problem with evangelical Christian voters has been well documented.

But as the Republican presidential nomination fight heats up in Florida, a Mormon rite that leaves many Jews seething could prove awkward for the candidate in a state that’s home to more Jewish people than any other besides New York and California.

The religious rite is proxy baptism for the dead. According to the Church of Jesus Christ of Latter-day Saints, or Mormon Church, these posthumous “blessings” are intended to “save” ancestors and others who weren’t baptized in life or were baptized “without proper authority.”

Any Mormon may baptize any person posthumously. [...]

Let’s see: some members of one religion are upset with what some other people are doing in a ritual for “dead people”…in private. Ahem: no one is is really doing anything other than magic and hocus-pocus.

Tell you what: I said a prayer that would automatically baptize you in the name of the Great Frog God if you have read this far.

Politics

Social
This article is a bit interesting; it contrasts the French way of raising a kid with the English/US model:

Every so often a new parenting book triggers the sort of conflicting passions most recently associated with the Arab Spring. Pamela Druckerman’s French Children Don’t Throw Food, is just such an incendiary work. We mothers are a notoriously touchy lot at the best of times, so when another woman dares to suggest there might be a better way of rearing our offspring than muddling through, bribery, intemperate amounts of wine, empty threats and inconsistency, forgive us for digging in our heels. [...]

“In France, children are presented with a fait accompli and the phrase “C’est moi, qui decide” – I make the decisions – is used a lot,” says Druckerman, who has a daughter aged five and twin boys of three. It’s this discipline that sets us monarchist slackers apart from the rigorous republicans. French parents believe that saying “Non” is a responsibility and “rescues children from the tyranny of their own desires”.

Also, their authority derives from a consensus about how children should be brought up. While we pick and mix our attitudes, in France boundaries are reinforced by society. Couples are in charge, the children are not. C’est tout. It may be old-fashioned, but it appears to work.

“Children are an important part of the family, but family life doesn’t revolve round them,” points out Druckerman. “In America and Britain, there’s a belief that having children must entail self- sacrifice and that we must push them to succeed. The French are more patient and allow their children far more freedom. You never see French mothers hovering anxiously round their children in a park.”

French women don’t dedicate themselves selflessly to motherhood. French fathers aren’t enslaved at weekends, driving children to activities. And babies are seldom breast-fed for long – the emphasis instead being on the mother’s sex life returning to normal as soon as possible.

Of course this article ends with a paragraph about how this mom has…wait for it…wonderful kids (surprised?) and how she likes them just as they are.

Social/Political
Paul Krugman shares a snippet about our current lack of economic class mobility (he is quoting John Quiggin):

For years, opinion leaders have told us that it’s all about family values. And it is — but it will take a while before most people realize that they meant the value of coming from the right family.

Politicfact
Paul Krugman takes politifact to task for saying “half true” (upgraded to “mostly true”) by politifact and then makes a larger point:

Unfortunately, Politifact has lost sight of what it was supposed to be doing. Instead of simply saying whether a claim is true, it’s trying to act as some kind of referee of what it imagines to be fair play: even if a politician says something completely true, it gets ruled only partly true if Politifact feels that the fact is being used to gain an unfair political advantage. In the case of Obama’s job statement, Politifact first called it only half true, then upgraded that to mostly true, not because Obama said anything factually incorrect, but because Politifact perceived Obama as trying to imply that he was responsible for the gains.

This is deeply wrong on two levels. First, fact-checking should be about checking facts — not about trying to impose some sort of Marquess of Queensbury rules on how you’re allowed to use facts. Aside from undermining the mission, this makes the whole thing subjective — notice that Politifact wasn’t even analyzing what Obama said, they were analyzing their impression about what he might have been trying to imply. Leave that for the talking heads!

Second, in practice this turns into a partisan affair. The simple fact is that in today’s US political scene, Republicans make a lot more factual howlers than Democrats. Sorry, but that’s just the way it is. Yet Politifact wants to be seen as nonpartisan.

I take a slightly different view; this is how and why:

Ok, here is a dissenting opinion (sort of): yes, a fact checker should check to see if the statement is factual or not, but there is some duty, IMHO, to see if the fact is being used responsibly.

Remember the statements about the “lucky duckies” that pay no federal income taxes, as in “in year 200x, 4x percent of Americans paid no Federal Income taxes.” That statement is literally true. However it is deceptive because it cherry picks both a particular year (atypical) and it leaves off things like payroll tax, local taxes, etc.

Climate change deniers do this all the time; they say things like “hey, the average temperature of the planet went up from year X to year X 1″ which might be literally true…but irrelevant to the actual long term trend, especially if there was some other smaller cycle (El nino, La Nina) involved.

Of course, I agree that Politifact is not doing this responsibly; they sure appear to be bending to conservative pressure to be “balanced” because, well, the conservative are lying so much.

Note: this is from my comment.

Science/Evolution

Genes and evolution (by Jeremy Yoder )

Does evolutionary change happen in big jumps, or a series of small steps? The question may seem a little esoteric to non-scientists—how many mutations can dance on the head of a pin?—but it has direct implications for how we identify the genetic basis of human diseases, or desirable traits in domestic plants and animals.

That’s because the evolutionary path by which a particular phenotype, or visible trait, first evolved in a population is closely related to the genetics that underlie the trait in the present. Phenotypes that arose in a single mutational jump will probably remain connected to one or a few genes with large effects; phenotypes that evolved more gradually do so because they are created by the collective action of many genes. So what kind of evolutionary change is most common will determine which kind of gene-to-phenotype relationships we should expect to find.

In an excellent recent review article for the journal Evolution, Matthew Rockman, a biologist with the Department of Biology and Center for Genomics and Systems Biology at New York University, makes the case that the era of genomics has, so far, been much too focused on finding genes of large effect. Fortunately, Rockman also sees the beginnings of a new movement towards acknowledging the importance of small-effect genes—one which may ultimately make genomic association studies more useful.

He goes on to talk about Genewise association study (GWAS). Here is the idea: some evolved traits are Mendelian (a mutation of only a few genes, possibly only one are involved). Some involve the mutation of many genes with all of these genes working together to get the given effect (ability to tolerate heat is one such trait). Since these genes didn’t mutate together, this track is far more difficult to find.

I recommend surfing to the blog and reading the rest.

If you believe that capital gains taxes should be low, make the argument and show your data and give evidence of why it helps the economy. If you want to cry about “double taxation” because of corporate taxes…do you REALLY want to go there? That implies that corporations aren’t “people” but rather exist to make the shareholders rich.

You’ll have to answer questions like this one, and you’ll have to admit that capital gains were not always low.

Note the Republican attempt to refute his argument: it is basically that many people make money off of capital gains.

That doesn’t mean that Krugman is wrong; Krugman points out that the FACT that most of the capital gains go to the very wealthy, not all of it. Note that this “rebuttal” is thin on actual data and it basically unsubstantiated ranting.