The Physics Police

The Physics Police

Thursday, June 27, 2013

GMO Pig Stomachs

Bad science is actually quite uncommon. I browse through dozens of new papers each week. That's why, even though I post about bad science a lot, reading it still shocks me. It's shocking because the authors think know they can get away with it. Nobody reads the study.

Instead, people read headlines like GMO feed turns pig stomachs to mush and get scared. They post hateful, ignorant comments along with these news articles. They share the links on Facebook, where group think deepens hatred towards the out-group of scientists, and reinforces fear of an imagined conspiracy of greed to make people sick.

The statistical rebuttal to this pig paper has already been done. Go check out what Weed Control Freaks, Random Rationality, Farm Progress, Mark Lynas, and The Progessive Contrarian have to say.

The bottom line is, no statistical significance. It's more fake science.

But wait, there's more!

Do you remember Howard Vlieger, from my post titled Don't Eat Soil? This guy spoke out against GMO. He also said:
[GMO] is causing a tremendous disruption, and a wide array of digestive problems.
He couldn't be more biased, right?

Well, he's the 2nd name on the pig paper, and the farmer who's pigs were studied, on his own farm.

Yes, this kind of stuff still shocks me...

Monday, June 24, 2013

Plants Can't Do Math

I saw this funny article titled Plants do sums to get through the night. It claims:
The John Innes Centre scientists show that to adjust their starch consumption so precisely they must be performing a mathematical calculation – arithmetic division.
I probably don't need to tell you that this claim is false. The author of the article has confused a mathematical model for its subject. The two are not the same!

After all, rocks don't compute parabole when tossed in the air. We use pen and paper to compute rock trajectories, and starch consumption in plants. But rocks and plants just do what they do, with no need for computation.

That said, this claim could have been true. A plant could start with two molecular concentrations, representing the numerator and denominator, then end up with one concentration of molecules, equal to the quotient. Such a biological system would be, in effect, an analogue calculator; and that would be awesome!

Sadly, this is not the case. The paper cited by this article, titled Arabidopsis plants perform arithmetic division to prevent starvation at night, appears to have been written by plants, for plants. It hardly deserves to be called a paper. It is disorganized, overcomplicated, and does not support its conclusions.

The paper was published in some open-access journal called eLife, which has no established track record. Well, now it has a track record of publishing garbage...

In the paper, there are three models, which each use hypothetical molecules S and T. These represent the starch storage and estimated time until dawn, respectively. Basically, T inhibits S, while S breaks down starch, so that the rate of starch consumption is equal to S divided by T.

Even if this is how plant metabolism worked, this wouldn't be called calculation. It would be called behavior. This model lacks a third molecule to encode the quotient. Instead, the quotient is inherent in the rate of starch degradation. It's a controlled enzymatic reaction. This is how all inhibitors work, in all living things. It's not a calculation. It's not arithmetic. It's not even novel biochemistry.

Even worse, there is one jaw-dropping flaw in the paper. The reported evidence does not support any of the over-complicated models.

Essentially, the models attempt to explain why the starch concentration is always (so close to) zero at dawn. In other words, why is the right hand side of this graph a strait line? How does the plant know what slope to make that line?

You don't need the T molecule to accomplish this. The smooth slope can already be accomplished by their definition of S. Specifically, that S is proportional to the quantity of starch stored during the proceeding period of light.

More intense light (or more daytime) leads to more starch, and therefore more S. More S leads to speedier consumption of starch, during the next dark period. In other words, the starch degradation rate is encoded in the quantity of S, by the action of starch generation during daylight.

See? No complicated models (or division) necessary.

Sure, you can throw several variables into a pot, stir them up, and boil on best-fit for 30 pages.

You'll get a tiny-ass p-value.

But that's not science.

Friday, June 21, 2013

Hollow Earth

Today I heard about an hypothesis from the 18th century called Hollow Earth, which supposes the Earth to be hollow. I figured such a space vessel would be possible to construct, with air on the inside, and a hard shell around it. Here is what I discovered...

G is the gravitational constant.
P is Earth-normal Atmospheric pressure.
ρshell is the mass density of the shell, assume solid iron.
ρair is the mass density of the inner, Earth-like atmosphere.
r is the radius of the world.
s is the thickness of the iron shell.
The Air pressure is balanced by weight of shell is:
(1) P = (m * g) / 2
Why did I divide by two, you ask? Well, the force of gravity falls off, linear, from g gravity at the surface, to 0 on the inside of the shell, so the average weight is half g.

Mass of a square meter slice of the shell is:
(2) m = ρshell * Vslice
Assume that one meter is small compared to the curvature of the shell.
The volume of a square meter slice of the shell is:
(3) Vslice = (1 meter)2 * (s)
Surface gravity on Hollow World is:
(4) g = (G * M) / r2
The total mass of the planet, shell plus atmosphere, is:
(5) M = ρshell * Vshell + ρair * Vair
The volume of the metal shell is a difference of two spheres:
(6) Vshell = Vworld - Vair
The volume of the world is:
(7) Vworld = (4π/3) * r3
The volume of the atmosphere is:
(8) Vair = (4π/3) * (r - s)3
Putting it all together, we have an equation with only two variables:
(9) P = (ρshell * s * ((G * ((4π/3) * ((ρshell * (r3 - (r - s)3)) + (ρair * (r - s)3)))) / r2)) / 2
Graphing this last equation shows us the possible configurations of Hollow World.

The horizontal axis is the r, the radius of the world, in meters.
The vertical access is s, the thickness of the iron shell, also in meters.

Notice that upper left is desaturated, because it's meaningless for the thickness to be larger than the radius. The function quickly drops down to around 5 km thick shell around a world with radius between 100 km (that's no moon) and 10,000 km (super-Earth).

For an object as large as the sun, the thickness would be 0.684 km. It keeps getting thinner because the surface gravity gets stronger, pulling down more on the shell, while the inside pressure stays the same. As a result, less and less thickness is required to do the job.

It's mostly the air inside that's responsible for the increased gravity, too!

Due to the Shell Theorem, people on the inside would experience free fall, no matter the size. Cities could be designed like rafts, lashed together.

Just don't let your world spring a leak. Too much decrease in air pressure would put too much load on the shell. Enough inward force could cause the metal to buckle, and the whole world to collapse in on its self.

You could set up a fusion reactor to act as a miniature sun in the center. It could use exhaust to maintain it's position in the center. At night, it could power down, and condense water on its cooling surfaces to acquire hydrogen for the next day's sunshine.

Sounds like a fun science fiction world to explore!

Thursday, June 20, 2013

Success of the HPV Vaccine

HPV is a sexually transmitted disease that causes ovarian cancer in women. A vaccine for many variants of this virus has been out for a few years. It's shown to be quite effective at preventing infection. You might even say...

In fact, prevalence of HPV decreased 56% since 2006, among females aged 14 to 19.

This is surprising, because only about 1 in 3 girls in this age group have received the full three doses. Half of them have received at least one dose, which seems to be 82% effective.

The effectiveness of the vaccine is also boosted by something known as herd immunity.

This is good news for women, because ovarian cancer is the fifth leading cause of cancer death in women.

Not for long!

Monday, June 17, 2013

Glyphosate vs. Soy

A study published in Food and Chemical Toxicology this month suggests that glyphosate may act as an endocrine disruptor in very small concentrations, as little as:
10-12 M = 10-12 mol/L = 10-12 * (169.07 g/L) = 1.6907 * 10-7 mg/L
I find it easier to comprehend very small concentrations in parts per million (ppm). We can assume the Glyphosate is dissolved in water, so mg/kg = ppm, then:
(1.6907 * 10-7 mg/L) / (1000 kg/m3) = 1.6907 * 10-13
That's less than 0.16907 parts per trillion; a very small concentration, indeed!

So, what does this mean about the human health risk from glyphosate?

(Figure 6B: The effect of glyphosate and genisterin on cell growth; from page 23.)

The study equates the estrogenic activity of glyphosate to that of genistein. This phytoestrogen is found in soy, and is infamous due to pernicious myths about its effect on breast cancer. In reality, cancer patients who consume soy foods after their diagnosis actually fare better than patients who do not consume soy foods.

The myth comes from the methodology used to test chemicals for their estrogenic activity. Human breast cancer cells have been very well studied. The hormonal pathways that lead to cell viability are well understood. Therefore, these cell lines are ideal laboratories for testing certain types of estrogen hormone regulation. But this is an in vitro effect, and implies nothing about in vivo cancer cause or growth.

By the way, phytoestrogens aren't just found in soy, but in other foods, too. Flax seed, sesame seeds, wheat, oats, barley, beans, lentils, yams, rice, alfalfa, apples, carrots, pomegranates, rice, coffee, mint, ginseng, beer, and marijuana are all sources of phytoestrogens. Everything that was once alive; i.e. everything we eat, has hormones in it.

If anything, this study shows that the glyphosate residue on your soy bean can be no worse for your body than the soy bean its self.

Friday, June 14, 2013

Pollen in Honey

Today I found an ironic article that claims:
More than three-fourths of the honey sold in U.S. grocery stores isn’t exactly what the bees produce, according to testing done exclusively for Food Safety News.
The testing examined samples of honey for the presence of pollen grains.

Absence of pollen in honey is evidence of ultra-filtration (at ~50 microns). This is a common industry practice meant to help prevent crystallization. The pollen grains can seed the formation of sugar (sucrose) crystals.

Another way to prevent crystallization is adulteration with fructose from corn syrup, etc. A small amount of fructose is enough to impede the formation of sucrose crystals.

The FDA standard does not exclude either of these practices. The question is, which do you consider more authentic? Ultra-filtered, or corn syrup adulterated?

The folks at Food Safety News argue that ultra-filtration results in a product that isn't exactly what the bees produce. By that logic, low fat milk isn't exactly what the cows produce, and egg without shit on it isn't exactly what the chicken produces.

In any case, I think you will agree that ultra-filtration is less deceptive than adulteration. This contradicts the claims in the article, that honey without pollen in it isn't real honey.

The way I see it, in order to prevent crystallization, honey with pollen is more likely to have been adulterated using corn syrup than the ultra-filtered honey.

So, really, that pollen you see, under the microscope, in a sample from a jar of gooey, runny honey, implies corn syrup adulteration.

Pollen is reason to suspect it might NOT be 100%, "real" honey.

Supreme Court on DNA

Steven Salzberg has expressed some criticism regarding the recent, mixed ruling of the Supreme Court on the issue of patenting DNA.

He claims that the Syllabus contains numerous factual errors, for example:
The nucleotides that code for amino acids are exons, and those that do not are introns.
Saltzberg says that, on the contrary:
The nucleotides that code for amino acids are contained within the exons, but they are not the same thing.
But, according to the NIH, an exon is:
Coding sequence of DNA present in mature messenger RNA.
I fail to see any difference in these three descriptions. In common parlance, the term exon refers to both the DNA sequence that is excluded from mature RNA, and the RNA that is transcribed but later cut out. The Supreme Court's description seems fine to me.

Saltzberg also takes issue with this quotation from the Syllabus:
...synthetically create exons-only strands of nucleotides known as composite DNA (cDNA). cDNA contains only the exons that occur in DNA, omitting the intervening introns.
He says that this definition is wrong, because:
cDNA stands for complementary DNA, because the DNA produced is the complement of the original strand.
He's got a point. Since 1973, cDNA has been short for complementary DNA, where you start reading from the 3" instead of the 5" end.

But in this court case, we have a NEW term, called "composite DNA". The document defines this term, and uses parenthesis to define a shorthand. It's confusing, but fair!

Of course, I suspect that "composite DNA" is a bullshit term cooked up by Myriad's lawyers to confuse the issue and sound credible.

I think this is the part of the Syllabus that scared people:
cDNA is patent eligible because it is not naturally occurring.
As it happens, you won't find their "composite DNA" in in nature. If such a molecule has application in the medical field (I can't think of any), then a process to manufacture such a molecule is deserving of patent protection.

On the Human Genome Project website, genetic tests are described like this:
... researchers design short pieces of DNA called probes, whose sequences are complementary to the mutated sequences. These probes will seek their complement among the three billion base pairs of an individual's genome. If the mutated sequence is present in the patient's genome, the probe will bind to it and flag the mutation.
This goofy "composite DNA" stuff wouldn't make a good probe, because the patched together sequence of exons won't match the patient's DNA, and so won't bind to it.

But neither Myriad nor any company holds any patent for this (presumably) useless stuff. No test for breast cancer requires licensing of this hypothetical stuff.

This isn't really a mixed verdict at all. Gene patenting is now a thing of the past!

What does this mean for the average person? The cost of genetic tests, like the one for breast cancer, will cost less.