blueollie

Evolution in my own back yard

Workout notes: NOTHING.

Main street mile tonight; my heat leaves at 7:20. I hope to do better than I did last week. It will be hot, but to improve, all I need to do is to hold back for the first 1/4 and not go crazy in the second 1/4.

Yardwork
I was in the back cutting and dealing with some of the weeds and weed trees. What I’ve noticed: since I started to pull more and more weeds by the roots, a type of weed with a prickly stem has become more prominent. It has a very shallow root; I saw one growing in an old pile of dirt near the garage. Clearly, these prickles act as a defense against being eaten or being otherwise destroyed. Reproductive success is what matters.

Then I had quite a few rabbits in the back yard as I worked. Formerly, rabbits were very, very shy, running away before I could get near them. Now their comfort distance is much, much shorter than it used to be. In fact, I asked one to move so I could pass the power cord to my mower beneath it. I am not saying that they are completely comfortable with me; they aren’t. But they are comfortable getting much, much closer to me than they ever did before.

June 27, 2014 Posted by | biology, nature, Peoria, Peoria/local, science | , , | Leave a comment

Nature Friday: GMOs, Chernobyl animals, energy, frogs, exercises and fisheries….

Exercise There is some evidence that exercise can clear unnecessary stuff in the short term memory. Tests on mice have shown that treadmill running helps them forget electric shocks. But there is more in this article:

Adult mice that exercised on a running wheel after experiencing an event were more likely than their inactive mates to forget the experience, according to a paper from researchers at the University of Toronto, published in Science today (May 8). The results suggest that the production of new neurons—neurogenesis—prompted by the exercise wiped out the mice’s memories. They might also explain why human infants, whose brains exhibit abundant neurogenesis, do not have long-term memories.

“In general, hippocampal neurogenesis has been thought to be the basis for memory and they’re suggesting that it’s the basis for amnesia,” said Thomas Insel, director of the National Institute of Mental Health. “That’s a very controversial and provocative concept.”

Infantile amnesia is common to all humans. Children typically do not develop long-term memories until age three or four. But why is that? Sheena Josselyn and her husband Paul Frankland, who are both neuroscientists at the University of Toronto, pondered precisely that question after noticing that their two-year-old daughter could easily remember things that happened within a day or two, but not several months in the past.

More specifically, they wondered whether it might have something to do with neurogenesis in the hippocampus—a brain region involved in learning and memory. Hippocampal neurons are produced rapidly during infancy, but neuronal generation in the region slows to a trickle in adulthood. “This inverse relationship between the levels of neurogenesis and the ability to form a long-term memory got us thinking that maybe one is due to the other,” said Josselyn.

Surf to the link to read more.

Energy: this photo was captioned: “How windfarms RUIN landscapes – shocking illustration of the destruction wrought by wind industry fanatics” (via @Jonathan_Leake on Twitter)

windmillsruinlandscapes

Government intervention and fisheries: Via Paul Krugman:

Brad Plumer tells an important, little-known tale. It begins with things going badly:

Back in the 1980s and ’90s, many fisheries in the US were in serious trouble. Fish populations were dropping sharply. Some of New England’s best-known groundfish stocks — including flounder, cod, and haddock — had collapsed, costing the region’s coastal communities hundreds of millions of dollars.

So the government got involved. But we know that government is always the problem, never the solution; so you know what came next.

Or maybe you don’t. In fact, government intervention has been a big success. Many fisheries have rebounded, to the benefit of the fishermen as well as consumers.

Fighting climate change isn’t really all that different from saving fisheries; if we ever get around to doing the obvious, it will be easier and more successful than anyone now expects.

Frogs
There are types of frogs whose males dance to attract mates (surf to the page to see the video) but, unfortunately, these frogs are endangered. These are small, walnut size frogs.

dancingfrog

Animals of Chernobyl
Since background radiation is too high for humans to live there, the exclusion zone around Chernobyl is like a wild habitat. So, scientists are seeing some interesting developments in the animals of the region.

GMO issues Here is a guide to looking at some of the anti-GMO stuff that is out there.

May 9, 2014 Posted by | biology, energy, environment, frogs, nature, science | , , , , | Leave a comment

Don’t let facts get in the way…

Yes, under President Obama, the number of public workers went DOWN and the number of federal workers…in sheer numbers…increased slightly (140-160 K) since 2008 (remember: a fair way to measure workforce growth is to take into account the population growth and the US population grew about by about 15 million during that period…I am estimating about 2.5 million per year from here)

Republicans still insist that government is “growing out of control” under President Obama.

Science
There is a type of cave insect in which the female has a penis like object which she inserts into the male to GATHER UP sperm from the male. The science itself is fascinating. But…wait for it….some “feminist” is “offended” that the scientists used the term “penis”.

Sometimes, I think that some people see the ability to extract offense as a type of virtue.

April 19, 2014 Posted by | biology, economy, science | , | Leave a comment

Epigenetics: Science is hard.

Of course, a short video will be a gross over simplification; see the discussion here.

March 25, 2014 Posted by | biology, science | | Leave a comment

Science, new 538, Putin and Oil….

Science here is an interesting development in life science: 1500 year old moss (that had been frozen) has returned to life upon being thawed!

Researchers have demonstrated that, after over 1,500 years frozen in Antarctic ice, moss can come back to life and continue to grow. For the first time, this vital part of the ecosystem in both polar regions has been shown to have the ability to survive century to millennial scale ice ages. This provides exciting new insight into the survival of life on Earth.

Rachel Maddow: has an interesting segment on how the large oil companies can be used to pressure Putin on Crimea.

Nate Silver’s 538.com: back, up and running. Reviews are mixed:

Here is a piece on economic data. What it says is fine, but it won’t interest me. I wished this piece on hockey goalies had been longer and more analytic. The same is true for this piece on corporations hoarding cash, which also could use more context. Maybe it is I rather than they who is misjudging the market, but to me these are “tweener” pieces, too superficial for smart and informed readers, yet on topics which are too abstruse for the more casual readers. I want something more like the very good Bill Simmons analytic pieces on Grantland, with jokes too, and densely packed narrative, yet applied to a much broader range of topics. Barring that, I am happy to read one very good sentence or two on a topic.
Here is a piece on whether guessing makes sense on the new SAT. It is fine but presents material already covered in places such as NYT.

I love seeing pieces on how statistics are used in real life, and his political poll analysis was spot on. But forecasting results from polls is one thing; trying to use raw data in place of understanding a nuanced discipline is quite another.

And right there you have an important lesson about what it means to take data into account. It very much does not mean changing your views all the time — if you have a model of how the world works, and the model is working, stability in what you say reflects respect for the data, not inflexibility. If I have spent the past 5+ years insisting, over and over again, that in a liquidity trap budget deficits don’t crowd out private spending and expanding the Fed’s balance sheet doesn’t cause inflation, that’s because they don’t. And if I return to those points many times, it’s because too much of the world still doesn’t get it.

Now, about FiveThirtyEight: I hope that Nate Silver understands what it actually means to be a fox. The fox, according to Archilocus, knows many things. But he does know these things — he doesn’t approach each topic as a blank slate, or imagine that there are general-purpose data-analysis tools that absolve him from any need to understand the particular subject he’s tackling. Even the most basic question — where are the data I need? — often takes a fair bit of expertise; I know my way around macro data and some (but not all) trade data, but I turn to real experts for guidance on health data, labor market data, and more.

What would be really bad is if this turns into a Freakonomics-type exercise, all contrarianism without any appreciation for the importance of actual expertise. And Michael Mann reminds me that Nate’s book already had some disturbing tendencies in that direction.

March 19, 2014 Posted by | biology, blogs, economics, economy, science, world events | | 1 Comment

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.

February 16, 2014 Posted by | biology, evolution, science | Leave a comment

GOP governor’s debate, math and science

Workout notes
short version: weights plus elliptical: elliptical was 30 minutes, much of it on “butt” setting.
weights: did the rotator cuff series and McKenzie set afterward; hip hikes and Achilles during.
pull ups: 5 or 6 sets of 10; lost count.
bench: 10 x 135, 4 x 180, 7 x 170 (more challenging than expected)
military press (dumbbell): 3 x (12 x 50)
upright row (dumbbell): 3 x (10 x 25)
dumbbell curl: 3 x (10 x 30)
pull downs: 3 x (10 x 160)
rows (Hammer): 3 x (10 x 220)
abs: 3 sets of 10: crunch, v. crunch, sit back, twist.

Posts
It is still cold (3 F, or -16 C) , and the neighborhood streets are still mostly the type of ice that comes from cars driving over snow. The city plows do just enough to bury the sidewalks in ice but not enough to really plow the streets to pavement. Peoria, IL is a nasty city during wintertime.

But while this is one of the two really bad recent winters, it isn’t out of the ordinary by HISTORICAL standards:

Based on preliminary data, the average temperature statewide is 20.0 degrees. That is 6.3 degrees below average and ranked as the 17th coldest January on record. Of course, if the forecast holds for the rest of January, we would end up colder. Here is a list of the 20 coldest monthly average temperatures in January. The column marked “Temperature” is for the January statewide temperature and the column marked “Departure” is for the departure from the 1981-2010 average of 26.3 degrees.

Surf to the link to see the rest; note that 1994, 2009, 2010 make the list.

And yes, we are hearing “global warming is a hoax”:

cold

(hat tip: Why Evolution is True)

More science
There is a type of shrimp that has eyes with more color receptors (12) than human eyes have (3). But:

It’s tempting to think that with 12 color receptors, mantis shrimp see a rainbow humans can’t even conceive. But Marshall and his colleagues found the opposite. They trained mantis shrimp to associate certain wavelengths of light with food. As the wavelength of light defines its color, this meant that the shrimp saw certain colors as harbingers of treats.

They then showed the shrimp two colored-lights and let them choose the one that would get them treats by grabbing or tapping at it with their claws. By altering the wavelength of the lights, the researchers could figure out how good the shrimp were at telling one hue from another.

As it turned out, the shrimp could differentiate wavelengths that were about 25 nanometers apart, essentially the difference that separates orange and yellow. In comparison, humans can discriminate shades that are as little as 1 nanometer to 4 nanometers apart.

“They’re definitely not seeing the world of color in as much detail as other animals,” Marshall said of the shrimp.

So why keep the 12-receptor system? Marshall and his colleagues aren’t sure how it works yet, but they suspect the shrimps process color very quickly by setting up patterns of receptor excitation that correspond to certain colors. Imagine, for example, that every receptor is an empty bucket. If a couple of buckets on one end of the spectrum appear full, the shrimp knows it’s seeing red. On the other end of the spectrum, the buckets represent blue.

In other words, mantis shrimp might not so much process colors in the brain as recognize them in the eye, a technique that could help the animals quickly pick out colors in their brilliant reef environment.

Note: some internet memes get this wrong. Surprised?

Speaking of coloring: this blog post discusses an aspect of knot theory and, by mathematics standards, is very readable. So if you want a glimpse of what I think about from time to time, surf there.

Now on the opposite end of the intellectual scale

The Republicans had a governor candidates debate last night; it was 90 minutes and I saw about 65 minutes of it.

The line up: treasurer (Rutherford) (won his race when Gov. Quinn got reelected), political novice BUT A BUSINESSMAN (Rauner) (and the leader in the polls ..), the state senator that Gov. Quinn beat last time (Brady, a creationist) and another double chinned state lawmaker (Dillard).

From my point of view, this was the quote of the day:

In one of the few barbs during the debate, Rutherford pledged he wouldn’t have need “training wheels” to start running the state — a veiled shot at Rauner, who has never run for political office.

“I’m a reasonable Republican. I’m not a Republican with a horn and a tail,” Rutherford said.

But Rauner didn’t back down, proudly portraying himself as a government outsider.

“I’m the only one who hasn’t been in Springfield for decades,” he said.

Since Rutherford stressed his reasonableness and openly said that diversity (racial, religious and cultural) is a good thing, and stressed that knowing what one is doing is a good thing, he has no chance in the GOP primary.

Most of the debate: “Chicago sucks, marijuana is bad, we need more educational funding but lower taxes”, etc.

Before too long, this race might devolve into “which candidate will execute more witches”.

If that remark seems too snarky, you might be underestimating how dumb the Republicans in Illinois are.

Susanne Atanus, one of two Republicans taking aim at U.S. Rep. Jan Schakowsky’s seat representing Illinois’ 9th congressional district covering Chicago’s Far North Side and the North Shore suburbs, spoke out about the incumbent’s liberal reputation during an interview with the Daily Herald this week.

“I am not in favor of abortions, I am not in favor of gay rights,” Atanus, who has staged two previous unsuccessful runs for Congress, said during a videotaped portion of the interview, before going into more detail with the paper.

“God is angry. We are provoking him with abortions and same-sex marriage and civil unions,” she added, blaming natural disasters like tornadoes and diseases including autism and dementia on recent advances in the LGBT movement. “Same-sex activity is going to increase AIDS. If it’s in our military it will weaken our military. We need to respect God.”

David Earl Williams III, Atanus’ primary opponent, can be seen smirking through much of Atanus’ statements in the Herald video and said he was offended by her comments, though he also does not support marriage equality for same-sex couples.

Yes, these remarks have drawn rebukes from some Republican leaders, but they are not that far off what many of the GOP primary voters believe.

January 24, 2014 Posted by | biology, Illinois, mathematics, Republican, republican party, republicans, science, weight training | , , | Leave a comment

There ARE snow frogs….

alps-snow-frogs-615

The upshot: these frogs only have a brief window in which to mate; hence they are out, even when it is cold. And they can stay in amplexus for months (the fertilization takes place outside of the body; the female releases the eggs and the male fertilizes them):

Though egg laying takes place in spring, frog pairs in mountain ponds can begin hibernation in amplexus—a months-long embrace that may provide a breeding advantage by allowing mating as quickly as possible once warm weather arrives. Eggs of high-elevation frogs may be 30 percent larger than those of lowland females, giving tadpoles a head start. Eggs and tadpoles of mountain frogs have developed resistance to genetic damage from ultraviolet radiation, a component of sunlight that is more intense in the thinner air of high altitude.

And yes, frogs (at least many of them) have a type of antifreeze to protect against frostbite and to keep the vital organs alive.

December 19, 2013 Posted by | biology, frogs, science | Leave a comment

Misconceptions, sensationalism and science

Economics Austerity: does it work? Evidence is scant.

We are adding jobs. All isn’t rosy but things are somewhat better:

Still, unlike some other months that presented decidedly contradictory signals, many of the underlying factors identified by government statisticians at least pointed in the right direction. Hourly earnings, as well as the length of the typical workweek, both increased. The overall labor participation rate, while still low by historical standards, rose two-tenths of a percentage point to 63 percent.

At the same time, jobs were added to a broad range of sectors, rather than restricted to a few, lower-paying areas.

Manufacturing, closely watched because its ups and downs serve as a bellwether of the overall economy, added 27,000 workers. Besides that jump, Mr. Gapen of Barclays said he was also glad to see that the construction sector gained jobs for the third month in a row, indicating that housing continues to rebound.

Physics
Protons, of course, are made up of subatomic particles. It turns out that the total mass of a proton doesn’t change over a superlong period of time. One might ask: “well, why would it?” But this is one of those fundamental questions that should be asked.

Evolution
Lots of times, authors of pop-science articles and books will take a routine fact, loudly proclaim that this fact “kills well known theory/hypothesis/metaphor X” (even if all it does is kill a simplistic caricature of it) and then get blistered by other scientists. Here is such a case; here someone claims that the “Selfish Gene” metaphor is dead. Richard Dawkins says: “Really? I think not.”:

Over at Richard Dawkins’s own site, he’s responded to Dobbs’s misguided critique of the “gene-centered” view of evolution as described in The Selfish Gene. Richard’s piece is called “Adversarial journalism and the selfish gene.“ He’s remarkably polite for a man who’s been trashed in such an unfair (and erroneous) manner, and politely though firmly explains that, yes, he knows about regulatory genes and that, as we know, they’re simply selfish genes that regulate other selfish genes. He compares the toolbox of regulatory genes (a simile the biologist Sean Carroll also uses) to the subroutines of a Macintosh. and then notes:

Does Dobbs, then, really expect me to be surprised to learn from him that:

“This means that we are human, rather than wormlike, flylike, chickenlike, feline, bovine, or excessively simian, less because we carry different genes from those other species than because our cells read differently.”

Does Dobbs really think the existence of genes controlling the expression of other genes is either a surprise to me or remotely discomfiting to the theory of the selfish gene? Genes controlling other genes are exactly the kind of genes I have in mind when I speak of “selfish genes” as the “immortal replicators”, the “units of natural selection”.

Jerry Coyne (a biologist) says more here.

Larry Moran (a biochemist) mostly likes Coyne’s critique, but has some quibbles with it.

The upshot: a biochemist looks, of course, at the molecules and is apt to characterize evolution (a change in the frequency distribution of alleles with time) at the molecular level; the biologists tend to look more at the bodies, organs, etc.

In this case, Moran is more from what I’d call “pluralistic mechanisms for evolution” camp (assigning heavier weight to thinks like random genetic drift, in which neutral mutations (no effect on reproductive success) account for much of the variation) whereas Coyne has been called a neo-Darwinian (Natural Selection is the overwhelming factor, though other factors (such as drift) influence evolution).

This is the type of thing smart accomplished scientists argue about.

Speaking of evolution and biology This is an interesting result in cancer research.

The rough idea is this: cells use something called a “replication fork” when they reproduce. Sometimes this fork breaks. Healthy cells use one mechanism to repair a damaged “replication fork” whereas cancerous cells use a different one.

This might provide insight on how to fight some cancers.

December 8, 2013 Posted by | biology, economics, economy, evolution, physics, science | , , | 1 Comment

Science fact: stranger than science fiction

Remember Chernobyl? Some fungi have been found to be living inside the highly radioactive containment building….and…using gamma radiation the way that plants use sunlight:

There has been an exciting new biological discovery inside the tomb of the Chernobyl reactor. Like out of some B-grade sci fi movie, a robot sent into the reactor discovered a thick coat of black slime growing on the walls. Since it is highly radioactive in there, scientists didn’t expect to find anything living, let alone thriving. The robot was instructed to obtain samples of the slime, which it did, and upon examination…the slime was even more amazing than was thought at first glance.

This slime, a collection of several fungi actually, was more than just surviving in a radioactive environment, it was actually using gamma radiation as a food source. Samples of these fungi grew significantly faster when exposed to gamma radiation at 500 times the normal background radiation level. The fungi appear to use melanin, a chemical found in human skin as well, in the same fashion as plants use chlorophyll. That is to say, the melanin molecule gets struck by a gamma ray and its chemistry is altered. This is an amazing discovery, no one had even suspected that something like this was possible.

Surf to Doug’s Darkworld to read more.

November 30, 2013 Posted by | biology, evolution, science | , , | Leave a comment

Follow

Get every new post delivered to your Inbox.

Join 653 other followers