# blueollie

## Whining, politics and science

Gee, when people dismiss crackpot ideas (e. g. engage in global warming denialism) it gives Charles Krauthammer the sadz. No, Mr. Krauthammer: ideas have no inherent right to respect, including…well, some academic ideas like this one (forbidding “triggers”).

Speaking of dumbness: a few of the “in the future predictions” made by the film “Idiocracy” have come true. But…I should point out that some of these predictions were already commonplace prior to the movie. Remember how humans in “civilized” countries used to amuse themselves: public executions, burning animals alive, making people fight to the death, etc.

Politics
Yes, keeping control of the Senate will be an uphill fight for the Democrats, even if some of the “head to head” polls look ok now. There is the problem of the “drag” on the ticket due to the unpopularity of the President in the states in question, many of which are “red” to begin with.

But there is time, and the recent news for Obamacare has been good.

And maybe, just maybe, there is some attention being paid to inequality. Ok, that book by Piketty is rather highbrow.

Science
It is interesting, but being slightly underweight and undereating seems to help with longevity. Is there an evolutionary reason why this is so? There is a new conjecture about this, but the conjecture has detractors:

Why did creatures evolve such a mechanism in the first place? Researchers have declared the most popular theory doesn’t make evolutionary sense, and they’ve proposed a new explanation in its place.

The most prominent theory involves what happens physiologically during times of food scarcity. When the living is good, natural selection favors organisms that invest energy in reproduction. In times of hardship, however, animals have fewer offspring, diverting precious nutrients to cell repair and recycling so they can survive until the famine ends, when reproduction begins anew. Cell repair and recycling appear to be substantial antiaging and anticancer processes, which may explain why underfed lab animals live longer and rarely develop old-age pathologies like cancer and heart disease.

Margo Adler agrees with the basic cellular pathways, but she’s not so sure about the evolutionary logic. Adler, an evolutionary biologist at the University of New South Wales in Australia, says this popular idea relies on a big assumption: that natural selection favors this energy switch from reproduction to survival because animals will have more young in the long run—so long as they actually survive and reproduce. “This idea is repeated over and over again in the literature as if it’s true, but it just doesn’t make that much sense for evolutionary reasons,” she says.

The problem, Adler says, is that wild animals don’t have the long, secure lives of their laboratory cousins. Instead, they’re not only endangered by famine but by predators and pathogens, random accidents and rogue weather as well. They also face physiological threats from a restricted diet, including a suppressed immune system, difficulty with healing and greater cold sensitivity. For these reasons, delaying reproduction until food supplies are more plentiful is a huge risk for wild animals. Death could be waiting just around the corner.

Better to reproduce now, Adler says. The new hypothesis she proposes holds that during a famine animals escalate cellular repair and recycling, but they do so for the purpose of having as many progeny as possible during a famine, not afterward. They “make the best of a bad situation” to maximize their fitness in the present. “It’s an efficiency mode that the animal goes into,” she says. Adler and colleague Russell Bonduriansky published their reasoning in the March BioEssays.[...]

Mathematics
This Scientific American article discusses “modular forms” and notes that a current mathematician appears to have solved a riddle proposed by a famous mathematician from yesteryear. As articles about mathematics go, this one is pretty readable.

April 18, 2014

## On knowing what you are talking about….

First: this is how some discussions about religion appear to me. Comments to the effect of “I don’t see how it could be otherwise” are not convincing.

Economy
When people talk about raising the retirement age, remember that there is a big spread in “years lived after 65″ between wealthier white collar workers and poorer blue collar ones.

See here:

I was pleased to see this article by Annie Lowrey documenting the growing disparity in life expectancy between the haves and the have-nots. It’s kind of frustrating, however, that this is apparently coming as news not just to many readers but to many policymakers and pundits. Many of us have been trying for years to get this point across — to point out that when people call for raising the Social Security and Medicare ages, they’re basically saying that janitors must keep working because corporate lawyers are living longer. Yet it never seems to sink in.

Maybe this article will change that. But my guess is that in a week or two we will once again hear a supposed wise man saying that we need to raise the retirement age to 67 because of higher life expectancy, unaware that (a) life expectancy hasn’t risen much for half of workers (b) we’ve already raised the retirement age to 67.

Ms. Lowrey’s article is here.

Here is one of my pet peeves: all too often, a non-specialist will attempt to claim that the mainstream view/theory in a different profession is wrong because it doesn’t make sense to them. Here Larry Moran takes on a chemistry professor’s (at Rice University, no less) claim that evolutionary theory is flawed. Professor Moran concludes:

I suppose I’m going to be labeled as one of those evil “Darwinists” who won’t tolerate anyone who disagrees with me about evolution.1

I’m actually not. I just don’t like stupid people who think they are experts in evolution when they have never bothered to learn about it. Here’s my advice to graduate students in organic chemistry: if you want to know about evolution then take a course or read a textbook. And remember, there’s nothing wrong with admitting that you don’t understand a subject. Just don’t assume your own ignorance means that all the experts in the subject are wrong too.

It isn’t just “experts at a different field” though. Right now, we are hearing more and more from people who think that vaccines are bad and contain lots of harmful chemicals. One scientist had enough and made an epic drunken rant:

No, this is not a partisan issue; there are plenty of liberal anti-vaccination types out there, and they are a disgrace.

March 16, 2014

## Science is hard and subtle…genetic drift and neutral mutations in evolutionary theory

Disclaimer: my Ph. D. and publications are in mathematics; I am not a scientist. But I was having a discussion with someone who has an MD/Ph. D. and he seemed to indicate that evolution, at least the basics, should be understandable to the general public. I disagreed; I thought that the nuances might be difficult to grasp though something like “natural selection” might be, at least at the “broad framework level”, easier to understand.

So, here is a post by Larry Moran (biochemist) about genetic drift and the neutral theory.

Here is what is going on, at least as far as I can tell. A new allele is formed by mutation; the mutation can be roughly classified as “beneficial” (enhances reproductive success), “neutral” (doesn’t change reproductive success) and “deleterious” (harms reproductive success). The theory of Natural Selection would posit that the beneficial alleles would have a HIGHER PROBABILITY of becoming fixed in the population.

The theory of Genetic Drift shows that we are still talking about probabilities here: beneficial mutations can still be taken out of the population for randomness reasons; there is no guarantee that beneficial mutations will survive to be passed on. Genetic Drift theory has nothing to do with the benefits of a particular mutation.

The argument is really over probabilities: how big is the effect of natural selection and how much is really due to random factors? You sometimes see this as a debate between the Darwinists (the natural selection is the primary driver) versus the pluralists (NS plus many other factors, with randomness playing a bigger role).

I don’t have the credentials to have a valid opinion on this debate, but it is interesting to me.

## One question for creationists:

I can’t claim my question is original; it isn’t. I shamelessly stole it from Katha Pollitt (one of the The Nation columnists that I respect):

Do you really think that scientists from physical anthropology, anthropology, geology, biology, cosmology, astronomy and physics are engaged in some massive fraud to hide the truth? Or, do you really think that (just about) ALL of them are making some elementary mistake that YOU are catching? Really?

February 6, 2014

## Different start and a couple of thoughts…Good Old Days and Bill Nye’s debate

Today, I woke up, checked some e-mail and yes, did some math. That might be a way to start my Tuesday/Thursday when I start to teach late: get up, start my duties and THEN break for a run/walk as I’ll take in a few moments.

It will be indoors, again:

Our neighborhood streets are solid compressed snow and ice.

What I am working on: it is somewhat technical. But imagine you want to find solve $f(x) = 0$ where the solution is impossible to solve “in closed form” (e. g. solve it like you did in algebra class). There are numerical techniques that you can use a computer for. If you’ve had calculus, you might recognize Newton’s method where if $x_{n}$ is an approximation to the solution, $x_{n+1} = x_n -\frac{f(x_n)}{f'(x_n)}$ where $f'(x)$ is the derivative of $f$. Never mind that; the point is that one generates a series of approximations to the solution (provided certain conditions are met): $x_1, x_2, x_3, .....x_n, x_{n+1}, ....$ which are hopefully getting closer to the desired solution. If you met the correct “starting requirements” and the solution exists, this sequence of numbers WILL get close to your desired solution.

One problem though: “how many times do you have to do this?” is an important question. One reason: the computer can’t store every number exactly; hence there is round off error, and that error grows with each calculation.
So, if it is the case where each approximation $x_n$ has error inherently built in, it might be possible (if certain conditions are met) to take your series of approximations and manipulate them so that the larger “inherent errors” subtract off and one gets close to the solution in a fewer number of steps. One adds calculation early (adding round off error) to save many more calculations later (greatly reducing round off error).

One such process is called the Aitken Delta-squared process and that is what I was working on.

Two thoughts

Thought one: the Good Old Days:

Okay, I’m just going to say this once more: No, I don’t miss the days when gas was 15 cents a gallon, and your curfew was “when the street lights came on,” and kids were more afraid of their parents than of the cops…..
Because back then, women, minorities, gays, and other marginalized people had even fewer rights than they have now. Crime is not really significantly worse now than it was then. It’s just than when a man beats his wife to a pulp, he can be convicted and jailed for it now, whereas back then, it was just seen as a domestic issue and no business of anyone else. People are still killing other people. People are still loving other people. People are still dying of curable diseases. People are still committing random acts of kindness.
And what a lot of conservatives don’t like to admit, but what the facts support, is that even the white, male, heterosexual population is better off when non-whites, females, gays, and any marginalized segments of society gain strength and power. Power is a renewable resource, increasing for the whole when it increases for a part; not a finite, limited supply.
In general, more of us are better off than we were 20, 40 years ago. I wouldn’t trade my penny candy memories for gas-guzzling over-poluting cars and institutionalized misogyny, not ever.

She is right, of course. I think that when we remember the past, we remember the good but not the bad. And change is NEVER all good; for example we live longer (most of us anyway) but that means there are more elderly who live long enough to lose their minds through dementia and Alzheimer’s disease.

What was curious though was one of the replies she got (she is religious and has religious friends):

In matters of the flesh, it certainly does seem things are better than they were.

But in matters of the Spirit, we are not better off, we are worse off and it is deteriorating from there.

We are abandoning God. That is never a sign that things are “better”, no matter the outward appearance that they are.

That leads to the next point. There are those who use religion to better their own lives in the hear-and-now, but to all too many, there is an inherent virtue to accepting some woo-woo supernatural claim (THEIR claim, of course) and rejecting it is a type of evil.

I can’t have an intellectual discussion with someone who is that delusional.

Which leads me to discuss the Bill Nye “The Science Guy” (educator) versus Ken Ham (owner of the creation museum).

I might watch the debate later

There are two schools of thought:

1. Bill Nye didn’t understand that this was an exercise in politics: hence he lost by merely showing up.

2. Bill Nye won the day by presenting some science to people who don’t see a lot of it. Maybe, just maybe, he planted a seed of science that might later germinate in a young mind.

Ok, there is a third, less popular school of thought: show up and insult the creationist as a charlatan. Here, the scientist started off by making some blunt accusations against the creationist and then offered the creationist a chance to electrocute himself:

Prior to the debate, I was in camp 1, but after the debate (which I didn’t watch), I thought ….well…remembered as a kid I once believed that superstitious nonsense….maybe? Then again, I kind of “evolved” out of it by basically living among more educated people. I have deep respect for those who manage to find their way out while staying in the same environment.

Ok, time to get it….

February 6, 2014

## No, I am not watching the Science Guy debate Ham

Seriously: why would I? If I got to ask Mr. Ham on question, it would be: “do you seriously believe that physical anthropology, geology, biology, astronomy and physics are involved in some major conspiracy to hide the truth?”

No, creationists deserve no more intellectual respect than any other woo-woo. This is the way you deal with them:

## unexpected “snow” day

We had the day off due to weather; I suppose the university felt pressure to make a “night before” decision and there *might have* been white out conditions the next day.

Still, from my point of view it was sort of comical; I live only a walk away, there was hardly any snow and I ended up going to the public gym (which WAS open) and lifting (as usual) and walking 5K OUTSIDE. Yes, it WAS cold (close to 0 F) but not that bad if you were dressed for it.

What made this weather interesting is that there was a 40 degree drop (F, about 22 degree drop in C) over an 8 hour period. Now something like this has happened in 1836 in Illinois, back before we had forewarning of such events. I can recommend climatologist Jim Angel’s report on this; it is very interesting.

Other posts
Bruce Schneier has an interesting post on how income inequality can be seen as a security threat of sorts (think: a more equitable society might need fewer resources devoted to security). Paul Krugman points out how unhinged some of the super wealthy have become; some are equating having to pay more tax with…the start of the Nazi lead holocaust?

Why might they become unhinged? Well, when you are that rich, who are going to tell you that your idea is nuts? There is some value to not living in a bubble of “yes people”.

Evolution
Larry Moran directs us to an excellent post called “Seven things about evolution“. It is a non-technical post; a non-scientist should be able to understand all of it.

Then some scientists describe their trip to the Creation Museum. There is some laughter but some sadness. My wife had no desire to go; she didn’t want to give them money.

I admit that I mostly laugh at them…but then I had to remember that *I* started early life believing that BS. How many will start with that and NOT break away?

So I suppose I ought not laugh too hard even if I am tempted to dismiss most of the visitors as “the hopeless who’ll never amount to anything.” They might be ruining some potentially fine minds.

January 28, 2014

## A bit of science

Well, calm before the storm…we had a long…and productive search committee meeting. All I can say is that there are some smart, accomplished mathematicians looking for jobs.

Workout notes Full weight workout followed by snow shoveling (about 1/2 an inch due to a very brief but intense snow squall last night).

Supplemental: planks, McKenzie, hip hikes, rotator cuff, Achilles
pull ups: 5 sets of 10 (strong)
bench: 10 x 135, 4 x 180, 7 x 170 (not that bad)
abs: 3 sets of 10 of: twist, sit back, crunch, v. crunch.
super set with dumbbells: 3 sets of each exercise:

seated military (supported) 12 x 50
upright row: 10 x 25
bent over row: 10 x 65
curl: 10 x 30

Also 2 sets of 10 x 160 pull down, then 10 x 130 (different machine: without the cable)

It was ok, though my shoulders were a bit sore afterward.

A bit of science:

dogs and wolves: the new theory is that modern dogs and modern wolves had a common ancestor; the earlier theory was that dogs came from wolves. The path wasn’t as simple as had been previously believed.

The team of scientists sequenced the genomes of three grey wolves – one of which was from China, one from Croatia and another from Israel – to represent the three regions where dogs are believed to have originated.
They produced genomes for two dog breeds – a basenji, which originates in central Africa and a dingo from Australia – as both areas that have been historically isolated from modern wolf populations.
The researchers also sequenced the genome of a golden jackal to serve as an ‘outgroup’ representing earlier genetic divergence.

Their analysis of the basenji and dingo genomes, plus a previously published boxer genome from Europe, showed that the dog breeds were most closely related to each other.
Likewise, the three wolves from each geographic area were more closely related to each other than any of the dogs.
Dr Novembre said the findings of the study tell a different story than he and his colleagues anticipated.

Instead of all three dogs being closely related to one of the wolf lineages, or each dog being related to its closest geographic counterpart, they seem to have descended from an older, wolf-like ancestor common to both species.
‘One possibility is there may have been other wolf lineages that these dogs diverged from that then went extinct,’ Dr Novembre said.
‘So now when you ask which wolves are dogs most closely related to, it’s none of these three because these are wolves that diverged in the recent past.
‘It’s something more ancient that isn’t well represented by today’s wolves,’ he added.

Upshot: science is hard and can’t be reduced to a bumper sticker or a slogan.

New discovery about the Tiktaalik (fish to tetrapod species) Enjoy:

The fossilized pelves and a pelvic fin of Tiktaalik roseae reveal that the evolution of hind legs actually began as enhanced hind fins, according to the scientists. This challenges existing theory that large, mobile hind appendages were developed only after vertebrates transitioned to land.

“Previous theories, based on the best available data, propose that a shift occurred from ‘front-wheel drive’ locomotion in fish to more of a ‘four-wheel drive’ in tetrapods. But it looks like this shift actually began to happen in fish, not in limbed animals,” said Prof Shubin, who is the lead author of the paper published in the Proceedings of the National Academy of Sciences.

Discovered in 2004 by Prof Shubin, Dr Edward Daeschler of Drexel University, and the late Dr Farish A. Jenkins, Jr., of Harvard University, Tiktaalik roseae is the best-known transitional species between fish and land-dwelling tetrapods.

Neil Shubin, of the University of Chicago and the Chicago Field Museum, discovered the Tiktaalik. I highly recommend his first book Your Inner Fish and can recommend his other book The Universe Within as well.

January 17, 2014

## Tribalism, values, philosophy and what science you accept….

I can say that one of the hardest things to do is to give up a preconceived notion based on new data and science.

So, I am seeing all sorts of “oh, hah, hah, where is your “global warming now” posts and articles.

(side note: here is an interesting article about so called “wind chills”. Yes, 10 F with a strong wind feels worse than 10 F with no wind, but I’ve always thought the wind chill stuff was a bit bogus. Remember that the wind makes it feel colder as this enables heat to be transferred from out of your body; in engineering class you learned that $\frac{dQ}{dt} = k \Delta T \frac{dm}{dt}$ where $\frac{dm}{dt}$ is the mass flow rate of the fluid and the $\Delta T$ is the difference between the ambient temperature and the temperature of the object. You know this if you’ve taken a hot bath: in the tub if you are still, you might be ok, but you feel hotter if you move…..because if you move you are increasing the flow rate of the water around your body.

Well, wind does the same thing.

Back to the main argument:

So, people say “we’ve had record cold; how can the earth possibly be warming up?”

Well, for one, “global warming” is talking about a long time trend of average temperatures:

You can see the upward trend, but there are also ups and downs. For example, the next several years after 1998 were cooler years compared to 1998, mostly because 1998 was so blasted hot.

In fact, I took a similar graph, and started it in 1998 to “show” that the earth is really cooling!

I can easily see this being convincing to some.

Then one has to understand that warming means only small change in temperature per year and that how cold we are in winter largely depends on where the jet stream is, as it holds back that arctic air mass. And even if the arctic air mass is a degree or two “warmer”, it is still brutally cold (by our standards).

So, as you can see, the issue is a bit complicated. And yet, many conservatives deny it, just as they deny evolution.

Part of it is tribalism in action.

But part of it is philosophical; conservatives desperately want to believe that their deity is in charge:

They deny evolution for similar reasons: how can one believe that “every hair on your head is numbered by God” if you are the outcome of a stochastic process? (NOT a purely random process!)

So, one might say that philosophy matters. It certainly does to liberals; just look at the so-called “pro-science” liberals (so they tell you) who foam and the mouth about GMOs though, on the science issue part (whether the GMO foods are safe or not), they are dead wrong (more here)

Question them and once you get past their nonsense (IF that is even possible), you’ll find out that what they are really objecting to is the business practices of companies like Monsanto…and some are bound to an appeal to nature. Hey these mushrooms are natural; maybe we can get these woo-woos and crackpots to eat them?

So my frustration grows. It is ridiculous to resist facts (as currently understood) due to some philosophical point of view…..or is it?

This made me think of my post about Copernicus and the scientific objections to the Copernican theory of heliocentric astronomy.

My first reaction: why in the world would we view the earth as being special or different from the rest of the universe?

Oh oh…that is a PHILOSOPHICAL point of view. That is, the “null hypothesis” should be that the laws of science are basically the same everywhere; there are no “special” areas.

Yes, there is evidence that suggests that this is true, but why should this be the “null hypothesis”??? In fact, there is evidence that an aspect of this might not be true (albeit with tiny variations in our observable horizon)

I suppose that I should rethink my disdain for philosophy and point of view (lens of viewing things, if you will).

Of course, an expression of humility (we only know a little) does NOT open the door to wholesale crackpottery, woo-woo and nonsense.

January 7, 2014

## Some halftime stats and science

Yes, I am blogging at halftime of the Oklahoma versus Alabama game. OU leads 31-17 but Alabama has the type of team that can overcome adversity…and I remember the Chick-Fil-A Peach Bowl where Duke lead 38-17 at the half only to lose to the (ugh) Aggies.

The quality of this blog has suffered recently due to…well, increasing business. First it was the super busy semester and then it was vacation.

Hopefully, I can talk about a few things of substance this time.

Weather: yes, it is very cold in Illinois this “winter”. The jet stream has dipped and we are paying the price as the Jet Stream holds back the Arctic Air Mass.

Now of course, Republicans deny global warming…and now an increasing number are denying evolution:

There also are sizable differences by party affiliation in beliefs about evolution, and the gap between Republicans and Democrats has grown. In 2009, 54% of Republicans and 64% of Democrats said humans have evolved over time, a difference of 10 percentage points. Today, 43% of Republicans and 67% of Democrats say humans have evolved, a 24-point gap.

Paul Krugman says that this reflects increasing tribalism (“what does a good conservative believe?”) which, of course, has consequences in other public policy matters (e. g. macroeconomics). Hence Republican candidates have to be very careful not to present the unvarnished truth if they want to keep their base (e. g., Mitt Romney walking back his statements about cutting spending during a recession limiting growth)

Now, there is peril for liberals here too: this is one reason those of us who are scientifically literate must speak out for science, even when it goes against what many of our liberal political allies might think:

What this tells us is that elite opinions matter a lot in public discourse. The gap between liberals and non-liberals is not really there on this issue (GMO) at the grassroots. That could change, as people of various ideologies tend to follow elite cues. This is why the strong counter-attack from within the Left elite is probably going to be effective, as it signals that being against GMO is not the “liberal position.”

The same applies to woo-woo, “alternative medicine”, the irrational attacks against “fracking” (some attacks about it being improperly or inappropriately used ARE legitimate), etc.

I don’t want liberal leaning media to be at the point where it makes the reader more ignorant than before; here is an example of the Wall Street Journal doing exactly that (on income inequality).

Aging and time to failure curves
It is well known that as we age, the probability of dying in a given year goes up. In fact, the probability of dying in a given year doubles with every 8 years of life. Example: if you are married to someone who is 16 years older than you are, they are 4 times more likely to die in a given year than you are.

This article discusses the various mechanisms of why this might be true; it makes for interesting reading.

The bottom line: the model of the attacks on the body being produced at a constant rate, but the body’s ability to fight those attacks being reduced at a linear rate DOES fit this model.

Now as far as the bathtub curve, the lead in to this reliability engineering blog post gives a nice introduction to it, though this article deals with how current reliability engineering deals with “burn in failures” and how “time to obsolescence” affects the curve.

January 3, 2014