# blueollie

## This is one reason you should CHECK instead of relying on memory

I ran a 5K (3.25 mile actually; the course is “long”) run this morning; I ran the same race on the same course last year.

The difference: I REMEMBERED that last year was not as cold but windier. I was wrong on BOTH counts when I checked via Weather Underground:

This year (via Weather Underground)

Last year (via Weather Underground)

I think this is what happened this year: this time, I went in knowing the course and expecting that long, difficult stretch toward the end (.8 miles against the wind). And as far as the wind: the winter has sucked almost the entire time, so we are more used to it.

## No whining, some science/philosophy issues

It is has been a while since I linked to anything but “winter sucks” and “here is my workout”.

Jerry Coyne has a couple of interesting articles.

One: he talks about an article that claims that we “should study history to understand science”:

Alejandra Dubcovsky, an assistant professor of history at Yale, thinks that it’s essential for scientists to study history (she doesn’t specify what kind of history, or if she means the history of science), for another reason: because it gives us scientists “a sensitivity that only the humanities can teach.”

Or so she maintains in a new piece at The Chronicle of Higher Education, ”To Understand Science, Study History.”

Like the reader who sent me the link, Dubcovsky seems not only defensive about her discipline, but stretching a bit to make her point. To show how history informs our scientific sensitivities, she uses the examples of Rosalind Franklin, which will teach us that science is not gender-blind (she says Franklin is “largely forgotten,” which is simply untrue); of Rebecca Skloot’s wonderful book about Henrietta Lacks (donor of the HeLa cells), which should teach us that science and race have an “uneasy history;” and about Oppenheimer and the atomic bomb, which should teach us that “we find deep, sometimes unforeseen, and often devastating consequences, even from the most theoretical of projects.”

Yep. I am often amused to hear a non-specialist tell me what “I don’t know about” in my own discipline.
Frankly, the humanities ARE under fire and are really stretching to stay relevant. Why? My guess: higher education is getting more and more expensive, and there simply isn’t a great demand for humanities majors. The market for humanities Ph. D.s is also terrible.

And yes, science IS blind to sex; for example, if you get the laws of science wrong, what you build with them won’t work. I doubt that there is a feminist interpretation of quantum mechanics.

Note: the humanities ARE valuable IMHO…and even have practical value. Steven Pinker’s book Better Angels of Our Nature, gives a bit of credit to fiction in helping humans become less violent (e. g. reading a novel better helps us “walk a mile in another person shoes”).

In this day of a smaller globe, the study of language and culture is essential! And knowing some history is extremely helpful, especially given some of the turmoil we are seeing now. Much of it has ancient roots. For example: had we remembered that Vietnam and China were traditional rivals and enemies, we might have reacted better to the situation in Vietnam rather than escalating that horrible, wasteful war.

Professor Coyne has another article about Whole Foods (the store) and about how it promotes woo-woo (beyond the usual woo-woo stuff about “natural” and “organic”). Here, he goes off on Whole Foods pushing homeopathic remedies (placebo really). This might be seen as a “liberal” type of creationism, though conservative sites like NewsMax also pushes woo-woo “cures” and the like. If you get on their e-mail lists, you’ll see adds for them. Hey, there is nothing more Republican that cheating the gullible out of their money!

Sandwalk (Larry Moran’s blog) takes on the “argument from evil” response that some atheists attempt to use against theists (e. g. if your loving God exists, then why did horrible thing X, Y, or Z happen?)

I agree: this is a waste of time. The response by the theist (who believes in a specific deity) is something like “we don’t know God’s ways” or “this is in this life, which is just a microsecond in all of eternity…even the worst possible suffering in the here and now doesn’t compare to ETERNAL bliss that we are going to get (some of us anyway), blah blah blah.”

It is weak medicine, IMHO> And of course, there could be an Evil God. Here is my favorite:

February 28, 2014

## The midwest winter will stay and stay and stay…

The weather here will suck for quite a while longer…until April. Here is why…and this also shows that while WE have been getting pounded, well…the rest of the planet…not so much. The arctic air mass has decided to spend some time with us and neglect its other duties.

February 27, 2014

## More on outliers…cold and science…talking past one another

No workout this morning (up too late for the basketball game and I needed sleep). But I’ll lift after my 9-10 class and maybe catch a quick swim at 1100 (1000 yards?). I’ll take my lunch to the gym locker so I HAVE to go to the gym.

Yes, MORE snow and cold on the way (6-10 inches are forecast for the weekend, though that is a few days out):

Basically, we are having a (junior varsity) Canadian style winter this year, and I don’t expect relief until sometime in April.

A bit of science (I need cheering up)

Religion

Why do some people continue to insist that “it is in the Bible” means anything at all?

Talking past one another
Paul Kurgman’s mini essay made me think:

James Surowiecki makes an important point: if you want a society in which everyone has a decent life, you need to construct a society in which everyone has a decent life — not a society in which everyone has a small but equal chance of living the lifestyle of the rich and famous.

Not that we’re anywhere close to the second condition, anyway — the most important factor in whether you can become rich is whether you chose the right parents: Most people are going to end up with socioeconomic status close to where they started. But even if that weren’t true, those moving up the ladder would be matched by an equal number moving down. Since anyone could find himself or herself downwardly mobile, social mobility arguably actually strengthens the case for a strong safety net.

But many conservatives are just fine with a society that heavily awards winners and lets the losers flounder; this is the high risk, but high potential society which perhaps is left over from the old “frontier mentality”. Either you have some success, or die.

And statistically, the vast majority of us (myself included) are pretty average (despite what you read on the walls of Facebook; from the glowing reports of parents, you’d think that the off spring of my FB friends are all bound for the National Academy of Science!).

Having a society that caters more to the average might well be more realistic, but it might well crush the dreams.

February 26, 2014

## This tough winter…and the why….

Now there is a dispute as to the role that the diminishing sea ice and warming arctic air has in the erratic behavior of the jet stream.

What isn’t in dispute is that the jet stream is behaving erratically and that the planet is warming:

Just when weather weary Americans thought they’d found a reprieve, the latest forecasts suggest that the polar vortex will, again, descend into the heart of the country next week, bringing with it staggering cold. If so, it will be just the latest weather extreme in a winter that has seen so many of them. California has been extremely dry, while the flood-soaked UK has been extremely wet. Alaska has been extremely hot (as has Sochi), while the snow-pummeled US East Coast has been extremely cold. They’re all different, and yet on a deeper level, perhaps, they’re all the same.

This weather now serves as the backdrop—and perhaps, as the inspiration—for an increasingly epic debate within the field of climate research. You see, one climate researcher, Jennifer Francis of Rutgers University, has advanced an influential theory suggesting that winters like this one may be growing more likely to occur. The hypothesis is that by rapidly melting the Arctic, global warming is slowing down the fast-moving river of air far above us known as the jet stream—in turn causing weather patterns to get stuck in place for longer, and leading to more extremes of the sort that we’ve all been experiencing. “There is a lot of pretty tantalizing evidence that our hypothesis seems to be bearing some fruit,” Francis explained on the latest installment of the Inquiring Minds podcast. The current winter is a “perfect example” of the kind of jet stream pattern that her research predicts, Francis added (although she emphasized that no one atmospheric event can be directly blamed on climate change). [...]

So why don’t scientists like Kevin Trenberth accept it?

On Inquiring Minds, Trenberth outlined a number of scientific criticisms. One of them is simply that there is a great deal of change in the jet stream anyway, and more wavy patterns just happen from time to time. “The main counterargument to Jennifer at the moment is that a lot of this can simply happen through natural variability,” Trenberth explained. As he noted, there have been winters in the past with wavy jet streams and very cold mid-latitude “polar vortex” excursions. “In some years, the Arctic air gets bottled up, and it doesn’t penetrate into middle latitudes much,” says Trenberth, “and in other years, it has more waviness, outbreaks of cold occur.”

“A lot of this can simply happen through natural variability,” according to Trenberth.
And there’s an additional reason for skepticism. Trenberth thinks that if a process as important as the one described by Francis were occurring, then climate models—complex computer simulations of the atmosphere under climate change—would have picked it up. But when scientists run these models, he says, “it takes a really long time, 50 years or something like that, to see a big change in the atmospheric circulation in association with climate change.” Francis is thus postulating a change much more rapid than what the models show.

This is a legitimate science debate and not the bogus “it is cold here ergo global warming is a hoax” nonsense you hear in some media outlets.

February 22, 2014

## Yes, it WAS a warm January 2014…..globally….

Yes, we got pounded with snow; even if it doesn’t snow another flake for the rest of the season (yeah right) we have had the 3′rd snowiest winter; the snowmaggedon of 2011 is still a bit ahead. But we are just at 50 inches (probably over given today) and we’ve been cold too.

But….globally:

The combined average temperature over global land and ocean surfaces for January was the warmest since 2007 and the fourth warmest on record at 12.7°C (54.8°F), or 0.65°C (1.17°F) above the 20th century average of 12.0°C (53.6°F). The margin of error associated with this temperature is ± 0.08°C (± 0.14°F).

The global land temperature was the highest since 2007 and the fourth highest on record for January, at 1.17°C (2.11°F) above the 20th century average of 2.8°C (37.0°F). The margin of error is ± 0.18°C (± 0.32°F).

For the ocean, the January global sea surface temperature was 0.46°C (0.83°F) above the 20th century average of 15.8°C (60.5°F), the highest since 2010 and seventh highest on record for January. The margin of error is ± 0.04°C (± 0.07°F).

I know; if you live here it seems hard to believe. But it is a big planet and we are just a tiny bit of it.

February 22, 2014

## Science is hard, part II

This is the type of thing that can drive a non-specialist nuts. There was a study that doubted the effectiveness of mammograms.

Experts called on to review the CNBSS confirmed that the mammography quality was poor (2). The trial used second hand mammography machines, which were not state of the art at the time of the trial. The images were compromised by “scatter,” which makes the images cloudy and cancers harder to see since they did not employ grids for much of the trial. Grids remove the scatter and make it easier to see cancers. Also, technologists were not taught proper positioning. As such, many women were not properly positioned in the machines, resulting in missed cancers. And the CNBSS radiologists had no specific training in mammographic interpretation. The CNBSS own reference physicist stated that “…in my work as reference physicist to the NBSS, [I] identified many concerns regarding the quality of mammography carried out in some of the NBSS screening centers. That quality [in the NBSS] was far below state of the art, even for that time (early 1980s).”(3)

In this latest BMJ paper, only 32 percent of cancers were detected by mammography alone. This extremely low number is consistent with poor quality mammography. At least two-thirds of the cancers should be detected by mammography alone (4). In an accompanying BMJ editorial, Kalager and Adami admit that “The lack of mortality benefit is also biologically plausible because the mean tumour size was 19mm in the screening group and 21mm in the control group… a 2mm difference.” The documented poor quality of the NBSS mammography screening alone explains these results and should disqualify the CNBSS as a valid scientific study of modern mammography screening. Yet, the CNBSS trial was even more troubled (5).

To be valid, randomized, controlled trials (RCT) must employ a system to ensure that the assignment of women to the screening group or the unscreened control group is random. Nothing can/should be known about participants until they have been assigned to one of these groups. The CNBSS violated these fundamental rules (6). [...]

The lesson: when a “ground breaking” study is announced in public, wait for the fall out before drawing conclusions. Science eventually gets it right, but don’t jump the gun. Let the community as a whole take a look first.

February 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