13 August 2011 Posts (non-jock)

Ok, today posts will be all over the place. I’ll clump all of the science/math/medicine/geek stuff together, the political “facts” stuff together and the political/social commentary stuff together.

This is very promising: evidently there is now a way to chemically “train” our antibody cells to target and kill leukemia cells:

A step toward a new possible treatment for leukemia, one that uses patients’ own immune cells to target and destroy cancer is getting a lot of media attention.

It should be noted, however, that the therapy, however promising, has been tested in only three patients, who had varying side effects such as fevers as high as 104 degrees, heart dysfunction and breathlessness. Most of the side effects resolved themselves within a matter of weeks.

A year after the therapy, two of the patients had complete remission of leukemia and one had a partial response to the therapy (meaning the patient still has cancer, but a less severe case). All three were suffering from chronic lymphocytic leukemia, one of the most common types of the disease that affects blood and bone marrow.

Published Wednesday in both the New England Journal of Medicine and Science Translational Medicine, researchers reported that they had been able to engineer the patients’ own white blood cells into “serial killers” to destroy the cancer cells.

The research team from the University of Pennsylvania’s Abramson Cancer Center and Perelman School of Medicine extracted white blood cells from the patients and genetically reprogrammed them to attack tumor cells.

They programmed the T cells, which are a blood cell type that protects the body from infection, to bind to a protein that is expressed in chronic lymphocytic leukemia tumor cells. Doctors infused the modified T cells back into the patients’ bodies.

“Within three weeks, the tumors had been blown away, in a way that was much more violent than we ever expected,” said Dr. Carl June, senior author of the study, in a university press release. “It worked much better than we thought it would.”[…]

There is more there; of interest is how the patient feels just after a success. It has been described as being like a terrible flu.

For those who know medicine and biology, here is a technical review of the paper.

Yes, I know, n = 3 and this is too early to draw a firm conclusion. And yes, those pesky statistical tests can be a problem. It is entirely possible for one to run a biological experiment honestly and competently, analyze the data honestly and competently, and still end up with a “false positive” result.

Example: one can say, test a “cure for a disease” against a placebo group in a controlled study. It is possible to find out that one group (the treated group) recovers and the other doesn’t and to calculate that the probability of this result happening by chance is less than, say, 5 percent (we say p = .05). But if you run this experiment 100 times, well, you can expect 5 false positives. And given that there are thousands of experiments being run…well, you get the idea.

Here is one of the worst cases of that:

Many scientific papers make 20 or 40 or even hundreds of comparisons. In such cases, researchers who do not adjust the standard p-value threshold of 0.05 are virtually guaranteed to find statistical significance in results that are meaningless statistical flukes. A study that ran in the February issue of the American Journal
of Clinical Nutrition tested dozens of compounds and concluded that those found in blueberries lower the risk of high blood pressure, with a p-value of 0.03. But the researchers looked at so many compounds and made so many comparisons (more than 50), that it was almost a sure thing that some of the p-values in the paper would be less than 0.05 just by chance.

The same applies to a well-publicized study that a team of neuroscientists once conducted on a salmon. When they presented the fish with pictures of people expressing emotions, regions of the salmon’s brain lit up. The result was statistically signif­icant with a p-value of less than 0.001; however, as the researchers argued, there are so many possible patterns that a statistically significant result was virtually guaranteed, so the result was totally worthless. p-value notwithstanding, there was no way that the fish could have reacted to human emotions. The salmon in the fMRI happened to be dead.

Evolution in Action
Schneier’s security blog isn’t a place that most would expect to find interesting stuff on evolution, but it is. However, when one thinks about it, Nature is in an arms race of sorts and therefore living things are constantly evolving ways of attacking and ways of defending.

He points us to an article that talks about an orchid that lures wasps to pollinating it…by mimicking a meat smell!

A common wasp on a foraging mission catches an enticing scent on the breeze. It’s a set of chemicals given off by plants that are besieged by hungry insects and it means that there is food nearby for the wasp’s grubs – caterpillars. The wasp tracks the smell to its source – a flower – and while it finds nectar, there are no caterpillars and it leaves empty-mandibled. The smell was a trick, used to dupe the wasp into becoming a unwitting pollinator for the broad-leaved helleborine.

The broad-leaved helleborine (Epipactis helleborine) is an orchid that grows throughout Europe and Asia. It is but one deceiver in a family that is rife with them. About 10,000 species of orchids trick pollinators into visiting their flowers. Some attract males by mimicking the sight and smells of females. Others resemble orchid species that provide rich nectar rewards, while providing none themselves. But while thousands of species offer the potential for sex or food, only the broad-leaved helleborine advertises itself by promising fresh meat.

Darwin himself noted that even though the helleborine packs a substantial reservoir of nectar, it is pollinated by only two species of insects – the common wasp and the European wasp. Until now, no one knew how the orchid was attracting its pollinators. Jennifer Brodmann from the University of Ulm in Germany solved the mystery by testing how wasps responded to the smells and sights of orchids.

She found that the smell of the helleborine alone attracted just as many wasps as the whole flowers. In contrast, the sight of a flower in a glass box that didn’t let any scents through was far less attractive. Luring wasps with odours makes sense for the helleborine, for it grows in shady parts of dark coniferous forests, where they are difficult to see. […]

Mr. Schneier also points to an interesting article about rats that have somehow learned to apply a poison to their hair:

A porcupine-like rat turns its quills into lethal weapons by coating them with a plant toxin, a new study says. Neighboring African hunters use the same substance to make elephant-grade poison arrows.

No other animals are known to use a truly deadly external poison, researchers say.

Scientists have long suspected that the crested rat might be using poison because of stories of dogs becoming ill or dying after encounters with the rodent, and because it has a distinct black-and-white warning coloration seen in other species.

It was unclear until now, however, where the nocturnal rat got its poison.

The researchers made their discovery after presenting a wild-caught crested rat with branches and roots of the Acokanthera tree, whose bark includes the toxin ouabain.

The animal gnawed and chewed the tree’s bark but avoided the nontoxic leaves and fruit. The rat then applied the pasty, deadly drool to spiky flank hairs. Microscopes later revealed that the hairs are actually hollow quills that rapidly absorb the ouabain-saliva mixture, offering an unpleasant surprise to predators attempt to taste the rat. […]

There is more here about the rat and other animals that use toxic or repelling stuff. Note: yes, poison frogs are made so by their diets in the wild (they lose their toxicity when in captivity). But the frogs themselves are poisonous; a predator gets sick (or dies) when they eat the frog.

Of course, Mr. Schneier still has the interesting technical stuff too; here he leads us to an article about two engineers who made a drone that can fly and hack into computer systems. It is horribly sophisticated but…home made.

Bottom line: if the professionals really want to hack you, they can. Your precautions will help keep the amateurs away, and yes, that is worth doing.


Keep the pressure on, Mr. President.

Now the President is under fire from some liberals. I am not talking about that principled criticism that points out that the policies that he is pushing for is inadequate or that he has adopted the Republican narrative. Example: Paul Krugman has hammered him over his too timid stimulus package; while this was probably the biggest one we could get through for political reasons, it would have been helpful for him to be on record as saying that it was too small. But Krugman also urged the House to pass the Senate health care bill, even that was way too watered down for liberal tastes (e. g., my taste).

But there are some who want liberal members of Congress to, well, act like the Tea Party caucus. Fareed Zakaria tells such people to “grow up”:

Over the last week, liberal politicians and commentators took to the airwaves and op-ed pages to criticize the debt deal that Congress reached. But their ire was directed not at the Tea Party or even the Republicans but rather at Barack Obama, who they concluded had failed as a President because of his persistent tendency to compromise. This has been a running theme ever since Obama took office.

I think that liberals need to grow up.

As the New Republic’s Jonathan Chait brilliantly points out, there is a recurring liberal fantasy that if only the President would give a stirring speech, he would sweep the country along with the sheer power of his poetry. In this view, writes Chait, “Every known impediment to the legislative process – special interest lobbying, the filibuster, macroeconomic conditions, not to mention certain settled beliefs of public opinion-are but tiny stick huts trembling in the face of the atomic bomb of the presidential speech.” […]

Obama passed a large stimulus package within weeks of taking office. Perhaps it should have been bigger, but despite a Democratic House and Senate, it passed by just one vote. He signed into law an unprecedented expansion of regulations in the financial-services industry, though one that did not break up the large banks. He enacted universal health care, through a complex program modeled after Mitt Romney’s plan in Massachusetts. And he has advocated a balanced approach to deficit reduction that combines tax increases with spending cuts.

Maybe he believes in all these things. Maybe he understands that with a budget deficit of 10% of GDP, the second highest in the industrialized world, and a debt that will rise to almost 100% of GDP in a few years, we cannot cavalierly spend another few trillion dollars hoping that will jump-start the economy.


He might understand that Larry Summers and Tim Geithner are smart people who, in long careers in public service, got some things wrong but also got many things right. Perhaps he understands that getting entitlement costs under control is in fact a crucial part of stabilizing our fiscal situation, and that you do need both tax increases and spending cuts-cuts that are smaller than they appear because they all start with the 2010 budget, which was boosted by the stimulus.

I am going to make trouble by posting this on Daily Kos, where I am certain to get flamed. 🙂

Newest Republican Entrant
Governor Rick Perry is making all sorts of claims about jobs in Texas. Here are a couple things to remember:
1. A state can “poach” jobs from another state; that doesn’t help the job rate in the United States.
2. Some claims are, well, misleading (at best):

As Paul Krugman writes:

Funny how Deval Patrick isn’t running for President on the strength of the Massachusetts economic miracle.

Yes, Texas has added more jobs — but it has to, to keep up with population growth. And bear in mind that if you lose your job in Texas, there isn’t much of a safety net.

OMG: I agree with Rush Limbaugh!!!! (sort of)

Rush Limbaugh shredded Fox News over their questions for the Republican presidential candidates in the debate on Thursday night.

Speaking on his radio show on Friday, Limbaugh blasted the network, which co-hosted the debate in Iowa. He blamed the candidates’ attacks on each other on what he believes was the hosts’ attempt to gain the approval of mainstream media.

“My gosh, does nobody on this panel remember that we’re running against Obama?” he thundered. “What is this business that these guys are trying to tear each other up?”

Then, he alleged, “Fox wants these people to tear each other up. Cause they want approval from the mainstream media, cause that’s what the mainstream media would do.” He added, “You never see the Democrats pitted against each other, not like this was.”

Uh, ok, yes you do see Democrats pitted against each other; witness the 2008 Democratic debates. But yes, while some of the questions were pretty stupid (e. g., the one where Ms. Bachmann was asked if “she was submissive to her husband”) and some were contrived for entertainment purposes.

BUT…notice that Mr. Limbaugh seems to assume that Fox News would have an interest in making the Republicans look good. “Fair and Balanced?” 🙂

Social Commentary
9-11 remembrances: I agree that Ted Rall has a point.

Liberals vs. Conservatives: they are NOT mirror images of each other; as Paul Krugman says, this misconception leads to misunderstandings:

I’m not the first person to notice this, but whenever you read conservatives trying to critique what they think the other side believes, you find them assuming that their opponents must be mirror images of themselves. The right believes that less government spending is always good, regardless of circumstances, so it assumes that the other side must always favor more government spending. The right says that deficits are always evil (unless they’re caused by tax cuts), so they assume that the center-left must favor deficits in all conditions.

I personally get this a lot, of course. Not a day goes by without someone blithely asserting that I have never called for spending cuts on anything, and that I have never called for action against budget deficits. A few minutes searching this blog would disabuse them of these beliefs, but they don’t need to check — they know.

What seems beyond their intellectual range is the notion that other people might have subtler beliefs than their own. Keynesianism, in particular, is not about chanting “big government good”. It’s about viewing recessions through the lens of an economic model under which temporary increases in government spending can, under certain circumstances, help reduce unemployment. Indeed, not all recessions call for fiscal stimulus; it’s the special conditions of the liquidity trap that make it essential now — which is why the Bush deficits, run under non-liquidity trap conditions, say nothing at all about the desirability of deficits now.[…]

I’ve seen this in my own interactions. For example, many of my conservative friends see taxes as nothing more than taking from the hard working and giving to the slackers. Because I think that we should have some safety nets, they think that I am ok with cheaters and slackers (I am not).
What they don’t seem to understand is that I see taxes as a way to pay for government services (military, roads, police, public education, NSF, NASA, FAA, etc.) and I know that the safety net programs are but a tiny percentage of what we pay for.

That does NOT mean that I think that we shouldn’t look for waste and inefficiencies; we should. That does NOT mean that I think that we shouldn’t do some reforms to Medicare and Social Security (especially Medicare); we should.

Talking to them can be so frustrating; there are times where it would just be simpler to dismiss them as evil and stupid though in reality, they are neither. Many give generously of their time and money to charity, and many of them have found successes in business and in the military that I’d never find.

Still, it is hard to talk to them; it is almost as if they are from different planets.

Humor: here is one way to get guys to read the newspaper:

click on the photo to see it at its source in full size.

(the above from here)


August 13, 2011 - Posted by | 2012 election, biology, evolution, human sexuality, humor, political/social, politics, politics/social, Republican, republican party, republican senate minority leader, republicans, science, spandex, Spineless Democrats, technology

1 Comment »

  1. September Wild Flower Society Classes…

    September 2011 Listings Adult Classes, Gardening, Horticulture, Field Trips in Eastern MATuesdays, September 6, 13, 20, 6:30-8:45 p.m. and Sundays, September 11, 18, 9 a.m.-1 p.m. Native New England Shrubs, Garden in the Woods, Framingham, MA, and fie….

    Trackback by | August 14, 2011 | Reply

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