The Physics Police

The Physics Police

Sunday, December 7, 2014

Michael Greger on Flavonoids


Michael Greger posted a YouTube video titled Cancer, Interrupted: Garlic & Flavonoids in which he offers a dubious summary of a paper from 2012 on the protective effect of the flavonoids.

This paper studied two phytochemicals, quercetin and rutin, at doses from 100μM. Greger presents the results as if they're relevant for humans eating diets rich in these chemicals. While the study is interesting, it's preliminary and the dosages studied are not in the least environmentally relevant.

We can use the molar mass of the two flavonoids studied to understand this dose in parts per million:

(302.236 g/mol) * (100μM) = 30 ppm quercetin
(610.520 g/mol) * (100μM) = 61 ppm rutin

Notice these concentrations are similar to the doses found in the foods high in these phytonutrients.
Red onions contain 32 ppm quercetin and buckwheat contains 100 ppm rutin.

How much of each food would a 70kg human need to consume to match the doses in this study?

(70 kg) * (30 ppm) / (32 ppm) = 144 pounds of red onions
(70 kg) * (61 ppm) / (100 ppm) = 94 pounds buckwheat

That's a lot of red onions and buckwheat! It's clear that these doses aren't achievable through diet.

The lesson here is not to mistake food for medicine. Eating a varied diet containing lots of fruits and vegetables is a good idea for many reasons. The effects of high doses of phytochemicals are not among those reasons.

Wednesday, November 26, 2014

Chugging Triclosan Soap

A paper was published last week in the Proceedings of the National Academy of Sciences demonstrating that the commonly used antimicrobial additive triclosan is a liver tumor promoter. That's actually the title of the paper! Hilda Bastian at Scientific American wrote a good article on the study, calling out its authors on their hype and fear-mongering. She also points out the study's small sample size and that the positive results came at very high dosages.
... mice received less than 28.6 mg/kg TCS daily through water ... [1]
So, how much triclosan liquid soap would I have to drink daily in order to achieve this dose?

First, we need to know the concentration of triclosan in your average bottle of hand soap:
... most of the popular liquid hand soap brands contain between 0.1% and 0.45% weight/volume ... [2]
I'll be generous and assume that all of the 0.45% triclosan in our liquid soap is absorbed.

For your average 70 kg human the daily dose can now be calculated!

(70 kg) * (28.6 mg/kg) / (0.45%) = 445 g

Just shy of 16 oz. That's a lot of hand soap to use, much less drink. Daily.

You can't even bring that much on an airplane!
Unless you're actually drinking the stuff (don't), environmentally relevant doses from normal are measured in parts per billion [3, page 13], i.e. orders of magnitude lower concentrations than in this mouse liver study. In particular, absorption through the skin is very low, maybe 6.3% [3, page 11]. It's biological half-life is measured in hours [3, page 13].

Preventing antibacterial resistance is reason enough to avoid products with triclosan.

Argument from chemophobia isn't how we get people to use antimicrobial products responsibly.

1. http://www.ncbi.nlm.nih.gov/pubmed/25404284
2. http://www.ncbi.nlm.nih.gov/pubmed/17683018
3. http://ntp.niehs.nih.gov/ntp/htdocs/chem_background/exsumpdf/triclosan_508.pdf

Saturday, September 27, 2014

Measles Vaccine Efficacy in China

For whatever sick reasons, anti-vaccine activists try to use fear to dissuade parents from vaccinating their children. Make no mistake. This is an act of pure evil. Not only does it leave unvaccinated children at a higher risk of catching serious, sometimes fatal contagious diseases, but it puts everyone around them at increased risk of catching these diseases too. This is what drives many people to fight against the misinformation, myself included.

The name of the game is science denial for the anti-vaccine activist. They have their work cut out for them. Concocting a worldview where a health measure that prevents between 2 and 3 million deaths every year is a bad thing takes a lot of work.

Thankfully, sometimes all we need to do is give them enough metaphorical rope to hang themselves.

Here's an example!

Earlier this year, a study was published to the Bulletin of the World Health Organization on the progress towards the elimination of measles in China.

Sayer Ji, infamous for misrepresentation of scientific articles, in a blog post about the study, says:
China has one of the most vaccination compliant populations in the world. In fact, measles vaccine is mandatory. So why have they had over 700 measles outbreaks from 2009 and 2012 alone? The obvious answer is the the measles vaccines are simply NOT effective.
While the study's conclusion states unequivocally that:
In 2013, most of the resurgence seen in measles cases was the result of the susceptibility of unvaccinated or incompletely vaccinated children...
Which directly contradicts the central claim of Ji's blog post. This is typical of Ji. He consistently references scientific studies in an attempt to lend credibility to his argument despite the fact that the contents utterly refute his argument. He relies on the laziness and lack of education among his readers. If any of them simply read the study, they'd notice that it says the opposite of what he claims.

His biggest mistake was using the word "effective" which, in the study of vaccines, has a rigorous mathematical meaning. The efficacy of a vaccine is defined as:

E = 1 - (V / U)

Where U and V are the "attack rates" in the unvaccinated and vaccinated population, respectively. We calculate these attack rates by dividing the number of sick people divided by the population size. So the first question is, who got sick? The cited study shows 53% of measles sufferers were unvaccinated, while 47% were fully vaccinated.

The anti-vaccine activist might say, "but those percentages are almost the same! It looks like the vaccine hardly made a difference. You've got almost a 50% chance of getting sick either way, right?"

Wrong. And we just need one more piece of information to prove it.

According to the title of Ji's own blog post, "99% are vaccinated." Now we can calculate attack rates:

V = 0.47 / 0.99 = 0.475
U = 0.53 / 0.01 = 53

Which means the efficacy of the measles vaccine in China is:

E = 1 - (0.475 / 53) = 0.991

Or, 99.1% effective, consistent with efficacy noted on the CDC website.

So why is the anti-vaccine activist wrong to suppose you've got a 50% chance of getting sick either way? I like to think of it from the point of view of the measles virus. If I spread randomly from person to person, it will be hard for me to find that one unvaccinated person in a crowd of 100 people. If I do manage to find that person more than 1% of the time, I've done better than chance. That means it was easier for me to infect this person than the other 99 vaccinated people.

It only takes grade school math to expose the likes of Sayer Ji.

Friday, September 12, 2014

Solar Power and Birds

The Ivanpah Solar Power Facility is a "thermal tower" solar plat in the Mojave Desert, California. Rather than converting sunlight directly into electricity as do photovoltaic solar panels, thousands of mirrors reflect sunlight at a central tower. Water in the tower is heated to 1,000 degrees Fahrenheit. The resulting steam runs an electric turbine. Storing solar energy in the form of heat allows the plant to generate electricity 24 hours a day. Latent heat used overnight is replenishing the next day.

This feature allows the plant to avoid the major drawback of other renewable energy production systems, like wind farms and photovoltaic arrays, which only output energy when the wind is blowing, and the Sun is shining, respectively.

Ivanpah Solar Power Facility (No, it's not Burning Man.)
Criticisms of this pilot plant include the cost, and environmental impact. As for the cost, pilot plants are always expensive. Huge savings are typically seen when a technology is scaled up. The facility cost about $5,561 per kW, only one and a half times the cost of building a new coal facility which runs about $3,500 per kW. Anyway, cost is a concern for the economists. I'm interested in the environmental impact, because I'm an environmentalist.

Unforeseen in the Environmental Impact Statement and prior to construction, some birds were found to have been burnt by when they flew into the area of focused sunlight. US Fish and Wildlife Service (FWS) began an investigation in July, 2012.

Shortly after the plant formally opened in February, 2014 the Wall Street Journal ran an attack piece by Cassandra Sweet with accompanying correspondent interview.
A giant solar-power project officially opening this week in the California desert is the first of its kind, and may be among the last, in part because of growing evidence that the technology it uses is killing birds.
This WSJ article leaves out the fact that all buildings with windows kill some birds, and that all methods of generating power harm the environment. The question is, how many birds are killed by this facility due to heat damage from fling into the focal range? And, how does the environmental impact of this facility compare to other types of facilities?

By the time the FWS published a preliminary report of their investigation in April, 2014, the news story was long forgotten. The report got little attention until August, when Ellen Knickmeyer and John Locher published an egregiously misleading article in the Associated Press.
Federal wildlife investigators who visited the BrightSource Energy plant last year and watched as birds burned and fell, reporting an average of one "streamer" every two minutes, are urging California officials to halt the operator's application to build a still-bigger version.
Here's what report actually says about the "streamers":
... these events represent the combustion of loose debris, or insects.
In reality, the report investigation found only 47 birds injured by solar flux in the 1-year study period. So, at least 47 of the "streamers" might have, in fact, been birds. But not all of them. The article attempts to fool its readers by knowingly conflating the streamers with bird deaths. I trust my readers know better than to fall for such an obvious syllogistic fallacy.

Credulous readers of the AP article would walk away thinking that the report showed 5,591 times more bird fatalities than were actually reported. That's misleading by 3.7 orders of magnitude!

How does this compare to some other anthropogenic sources of avian mortality?
  • An estimated 1.4-3.7 billion birds are killed each year by cats.
  • As many as 980 million birds crash into buildings annually.
  • 174 million birds die from power lines every year.
  • Up to 340 million birds perish from vehicles/roads.
  • Approximately 6.8 million birds die flying into communications towers.

And how does this compare to other types of power generation?

Avian Mortality from different types of power generation.

One study compares estimates of the number of avian fatalities per GWh by energy sector.
  • 0.27 for Wind
  • 0.60 for Nuclear
  • 9.40 for Fossil Fuel
Whereas I calculate the total (solar flux + other causes) fatalities per Gigawatt-hour:
  • (141 birds per year) / (1000 Gigawatt-hours per year) = 0.141 for Ivanpah

That's right. The Ivanpah plant costs the least number of bird's lives per Gigawatt-hour. It's terrible to measure electric power in terms of dead birds. But if you really care about protecting birds, you must question whether the benefits outweigh the risks, not to your own political ideology or world-view, but to the birds.

Moral and environmental consideration of a technology must include the cost of the alternatives!

Solar thermal towers help protect birds by replacing more hazardous means to generate power.

Sunday, August 10, 2014

Sugar in a Caesarean Section

Last Week Tonight with John Oliver is plagued by the same problem as other comedy news shows like The Daily Show and The Colbert Report. They sometimes get things wrong because the writers are comedians trying to be funny, not skeptics trying to think critically.

In this week's episode, while discussing our broken prison system, John brought up the story of Regan Clarine. While an inmate in Perryville State Prison inmate underwent a C-section operation. Her mother Lori was interviewed for Al Jazeera.
Lori said the medical staff didn't stitch the wound shut. Instead, they dressed it with butterfly bandages.
It sounds like Clarine was treated with BioWeld, a new way to seal wounds without staples or stitches. The machine uses plasma to bind skin to a biological film based on a naturally occurring sugar.

Clarine developed an infection in the wound site, and sent to the prison hospital. According to Lori:
... they decided that the best thing to do for this would be to pack it with kitchen sugar … we're talking sugar that you get from, because they donate it from McDonald's from Burger King, you know? They're standing there ripping open these little packs of sugar and filling that wound.
It sounds like Clarine was treated with Multidex powder, a moist wound filler useful for reducing purulent exudate (or "oozing" as described in the Al Jazeera article). Some of these powder packets do sort of resemble McDonald's sugar packets in shape and size. The mistake is easy to make, especially for an anesthetized person, but they aren't from a fast food joint. They're medicine.

Multidex powder packets.

This medicine approved for use in 1997. It's main ingredient isn't "kitchen sugar" (sucrose) but a different polysaccharide called maltodextrin.

Even Lori's brother, who's a doctor, said:
It's probably just a nickname of something. Nobody would pour sugar in a wound. So don't worry about it.
But the article says:
Sugar was used to treat wounds before the advent of antibiotics in the early 1900s, but it's no longer accepted medical practice.
Which is false! As we've seen, sugar is used in modern medicine to both seal and pack wounds.

I don't question that this poor inmate was mistreated. It seems likely she developed these complications as a result of inadequate care. Neither do I blame anyone for misunderstanding their doctors bedside explanation of the treatment they receive.

I blame Abigail Leonard and Adam May, authors of the article, for not checking their facts, and for printing the opinion of the mother of an inmate as fact despite all common sense, and without the least bit of skepticism. America Tonight is not supposed to be a comedy show, right?

The claim that privatization of the penal system leads to poor inmate treatment is a serious one, and needs to be backed up with evidence. In this case, the sugar is not evidence. The wound re-opening and subsequent infection is evidence.

Another issue is that a 18-year-old woman was sentenced to 2.5 years for intent to sell prescription painkillers. We can argue for reform of drug laws without exaggerating the problems that face inmates. We already knew prison is terrible before this story. Drug offenders belong in rehab, not prison.

I think John Oliver (and his writers) really care about the topics they talk about on the show. I want them to know that they can better serve their audience with the truth than with half-truths and lies. This can only be accomplished by checking facts and applying critical thinking, which is hard work.

I leave you with this quote by John Oliver from 2009:
... Someone came up to me and asked me a question about a news story, and I didn't know anything about it so I just lied and they listened to me and believed me. The feeling of power that I got from that lie infecting their head made me think, "Yes, this is what I want to do for a living." (1:40)
I know this was said with irony. Let's not make it double-irony.

Sunday, June 15, 2014

Fukushima's Children are Safe

posted an op-ed on EcoWatch with the outrageous title Fukushima's Children are Dying wherein he claims:
More than 48 percent of some 375,000 young people—nearly 200,000 kids—tested by the Fukushima Medical University near the smoldering reactors now suffer from pre-cancerous thyroid abnormalities, primarily nodules and cysts.
These blatantly misrepresented and severely up-rounded numbers come from a recent health survey conducted by the Japanese government. In the survey, kids from the Fukushima area underwent ultrasound thyroid screening.

Only 2,070 of the 295,511 participants had significant thyroid nodules. This is consistent with the worldwide average prevalence of such nodules in children, between 0.2% and 5%.

These poor kids had a follow-up screening. Those that still had nodules underwent biopsy. In the end, only 91 cases were found to be malignant or suspicious.

This rate is very low when you consider upwards of 50% of children with symptomatic nodular thyroid enlargement end up diagnosed with thyroid carcinoma. In this Japanese health survey, the ratio was 4.4%, ten times lower.

Why was the false positive rate so high in this screening? Because of something called selection bias.

Whenever a healthy population is screened for disease you get a higher rate of false positives than for an unscreened population, who aren't tested unless they come to their doctor with symptoms. This is because the rate of disease is higher among patients with symptoms than it is for the entire screened population.

If we screened everyone as thoroughly as the Japanese government screened these kids from Fukushima, we'd expect to find the same high rate of false-positive nodules, and the same low rate of true-positive carcinomas. Luckily, childhood thyroid cancer is very rare and has a long-term survival rates greater than 95%.

The Japanese government is screening kids for safety. They have NOT found an elevated rate of precancerous thyroid abnormalities. Many of Fukushima's children have been displaced from their homes to keep them safe.

They're safe. Not dying.

Wednesday, May 28, 2014

The Universe Is Not Math

Max Tegmark has this crazy theory called the Mathematical Universe Hypothesis. He first published a paper on the topic in 2007. It made very little impact in the physics community, for reasons we shall see later on in this post. Then in 2008 he managed to get a piece published in Discover Magazine. Shortly thereafter he began work on a book finally published in 2013 titled Our Mathematical Universe which he managed to plug on Physics World, Scientific American and Science Friday.

He's even a guest on a this week's episode of Minute Physics in which he asked the leading question Is the Universe Entirely Mathematical?

The answer, of course, is a resounding and obvious NO!

His Mathematical Universe Hypothesis (MUH) states that the External Physical Reality (EPR) is a mathematical structure if it can be described by a Theory of Everything (ToE). He's not only saying that a ToE perfectly describes how the EPR works, he's saying that they are one in the same thing! He makes this unambiguously clear on page 280 of his book.
Whereas most of my physics colleagues would say that our external physical reality is (at least approximately) described by mathematics, I'm arguing that it is mathematics (more specifically, a mathematical structure).
Well, Max, your most of your physics colleagues would be right. One of the first things they teach you in grade school science is that theories are models of the universe, not to be mistaken for the real thing. The MUH might remind some of my readers of a strong version of Platonism.

In other words, the MUH is one giant exercise in equivocation, which can be demonstrated by analogy. Maps correspond to, but aren't the same as the territory they represent. Even a perfect scale-model replica of some territory must be built at some location other than the territory in question, and so is a distinct entity unto its self. Mistaking this replica for the real thing is demonstrably false, and not simply because you can walk right off its edge.

For example, imagine if Max were to claim that, since the design of the Eiffel Tower in Las Vegas is identical to the design of the Eiffel Tower in Paris, they are one in the same tower.
Whereas most of my architecture colleagues would say that the Eiffel Tower in Las Vegas is (at least approximately) described by the Eiffel Tower in Paris, I'm arguing that it is the Eiffel Tower in Paris...
Taking the fancy physics jargon out of the argument exposes it as semantic doggerel.
On the same page 280, in a footnote no less, Max tries to justify this argument from isomorphism.
From the definition of a mathematical structure, it follows that if there's an isomorphism between a mathematical structure and another structure (a one-to-one correspondence between the two that respects the relations), then they're one and the same. If our external physical reality is isomorphic to a mathematical structure, it therefore fits the definition of being a mathematical structure.
Did you notice the GIANT CIRCULAR ARGUMENT?!

Isomorphism is a tool that can only be applied to two mathematical structures. Max expects us to believe that we can use this tool on the ToE and EPR. But this begs the question of whether the EPR is a mathematical structure in the first place!

I find it astounding that buried in a footnote at the bottom of a single page in a 397 page book is one feeble attempt to use circular reasoning and fancy math words to sell abject nonsense to the reader.

I can't for the life of me understand why anyone takes Mad Max seriously.

Friday, April 25, 2014

The Electrolytes Plants Crave

Phosphate is a bad-ass little molecule. It plays the central role in plant and animal metabolism.

For example, plants use the sun's energy to stick a third phosphate onto ADP to form ATP, rightfully called the "molecular unit of currency". In animals, muscle contraction consumes a ton of ATP. All aerobic organisms, including humans, form ATP using chemical energy from caloric sources such as fat, protein, and sugar. Even anaerobic respiration, thought to happen in the most ancient bacteria, is just a different way to turn ADP into ATP by adding one more phosphate.

I would go so far as to define life on Earth as a very complex mechanism for making ATP by somehow gluing a phosphate molecule to the end of ADP!

Phosphate, the metabolism molecule.
Sodium phosphates are formed by sticking sodium atoms on those dangling oxygen atoms. When you have all three oxygen atoms paired up with sodium in this manner, it's called trisodium phosphate (TSP) which is used as a food additive (acidity regulator and emulsifier), cleaning agent, and was in the past an ingredient in some soaps and detergents.

That may sound like a scary chemical, but it's just the salt of phosphate, the metabolism molecule. Biologically, it's harmless. Table salt is more toxic than trisodium phosphate, presumably because it has higher molecular density of sodium!

In addition to having the electrolytes plants crave, TSP has been studied as a sports supplement.

TSP has the electrolytes algae crave, too. Prolific algal blooms can deplete the water of oxygen, killing fish and other animals. In an effort to reduce the risk of algal blooms, TSP was taken out of dish soap because it was thought the electrolytes might be causing too much algal growth by raising the biological supportive capacity.

People crave electrolytes, too. TSP is approved as a food additive by the EU, and is generally recognized as safe by just about everyone who passed High School biology.

Nick Brannigan and Vicky LePage of Health Conspiracy Radio seem to disagree. I'm not saying these two didn't pass High School biology, but such news wouldn't come as a big surprise.

They posted a man-on-the-street video shot on the Las Vegas strip where they hassled passers by about the (imaginary) dangers of this food additive.

This popular children's cereal also has an ingredient that is the main ingredient in degreasing paint, trisodium phosphate. We wanna know how many people know that this toxic chemical is in their favorite children's cereal... (0:08)

... it says "warning, harmful if swallowed." Does that look okay to eat? (1:57)
If you watch the video, you can see them liberally sprinkling crystalline TSP over a bowl of cereal. It's a white powder that resembles sugar. Mixed with water (i.e. when swallowed) high concentrations of TSP form an alkaline solution. Alkaline means high pH, whereas acidic means low pH. In other words, concentrated TSP can give you a chemical burn, not due to toxicity, but due to alkalinity.

I don't have to tell you that the concentrations of TSP found in cereal are small. Does cereal cause chemical burns? Does it bubble when you dump it into lemon juice? No, I didn't think so. The acidity of food is seldom of dietary concern. Lemons are highly acidic with a pH of 2.4, where a pH of 7 is neutral, and the pH of your typical TSP-based cleaning agent is 12.

Let's forgive the conflation of alkaline with toxic. The amount of TSP in cereal doesn't significantly change the pH of the food. Therefore, a tall glass of lemonade, being very acidic, poses a greater threat to your stomach lining than does TSP in cereal. Baking soda is also alkaline, with a pH of 9. Do you know what they use baking soda for...?

The alkalinity of TSP is an ironic complaint coming from Nick Brannigan who did an hour long show on the "alkaline diet" with some quack doctor! Aside from deceit, the only only explanation I can think of for Branniga's duel hatred and love for alkaline foods is that he doesn't know what alkaline means or how it matters to human health.

Anyway, here's the appeal to nature fallacy in all it's glory.
If you look on the ingredients in this, you can understand all the ingredients, you know what you're eating... It's a lot healthier for you, it's got no chemicals in it... These have all ingredients you can read... (2:36)
So long as airheads like Vicky LePage keep using the word "chemicals" as a synonym for "bad", I'm going to keep reminding people that everything is made of chemicals. Also, this idea that chemicals which you don't know how to pronounce are bad for you is one of the most blatantly ignorant things I've ever heard.
People have been asking us if we work for Nature's Path. We don't. (3:51)
No, but you work for NaturalNews, which is the worst anti-science website and supports Nature's Path because of their dedication to GMO labeling, all-organic ingredients.

Let's put on our Health Conspiracy glasses and take a closer look at these "healthier" ingredients in Nature's Path Leapin Lemurs Cereal:
Organic corn meal, organic whole grain corn meal, organic evaporated cane juice, organic peanut butter, organic molasses, organic cocoa, sea salt, organic soy oil, natural flavor, tocopherols. (Source)
All peanut butter, even certified organic, contains traces of aflatoxin, produced by the fungus Aspergillus flavus. It's LD50 (a measure of toxicity) is 1.2 mg/kg, which is 6,167 times more toxic than TSP!

Whether it's certified organic or not, molasses can contain sulfur dioxide, which according to NaturalNews is not so good for most human consumption. Even worse,
When fed in large amounts, and incorrectly, molasses may be toxic... The remedy is to immediately give them a solution that is rich in phosphorus and sodium. (Source)
You read that right. Molasses is toxic sludge, and trisodium phosphate is the only cure!

Did you know that caffeine is a natural pesticide? It's LD50 is 265 mg/kg, which is 30 times more toxic than TSP. Do you still want to eat that cereal which has organic cocoa that's loaded with toxic pesticides?

According to NaturalNews, soy oil, even certified organic soy oil, contains traces of hexane, a constituent of gasoline! Eww!

Even the cinnamon in Cinnamon Toast Crunch contains the chemical coumarin, which has an LD50 of 275mg/kg, which is 27 times more toxic than TSP. Coumarin have been used as rodenticides, too! Ever heard of Warfarin?

See how easy it is to play this trite little game? Notice also how many contradictions pop up once you decide to vilify something against all reason?

TSP is an extremely safe food additive. Health Conspiracy Radio is aptly named, because Nick Brannigan and Vicky LePage have conspired to mislead people about TSP using fear tactics and the appeal to nature fallacy.

Thursday, April 3, 2014

STAP In The Name Of Love

Back in January, Nature magazine published what is now an infamous paper claiming discovery of:
... a unique cellular reprogramming phenomenon, called stimulus-triggered acquisition of pluripotency (STAP) ... In STAP, strong external stimuli such as a transient low-pH stressor reprogrammed mammalian somatic cells, resulting in the generation of pluripotent cells.
If true, this would herald a revolution in stem cell research. Potential medical applications of a technique for transforming somatic cells into stem cells cannot be overstated. Sound too good to be true? Well, that's likely the case.

The paper, and in particular its lead author Haruko Obokata, have come under scrutiny due to alleged image manipulation and what has so far been a lack of reproducibility.

This week, Riken published the results of their internal investigation which found two instances of research misconduct by Obokata:
In manipulating the image data of two different gels and using data from two different experiments, Dr. Obokata acted in a manner that can by no means be permitted. This cannot be explained solely by her immaturity as a researcher.
... Dr. Obokata had used images in Paper 1 that very closely resembled images in her doctoral thesis. Yet the experimental criteria for the two papers were different ... this data was extremely important in showing the pluripotency of the STAP cells, and the actions taken by Dr. Obokata completely undermine the credibility of the data. There is no doubt that she was fully aware of this danger, and we therefore conclude that this was an act of research misconduct involving fabrication.
The report goes on to disclaim that verification of the STAP phenomena can only be done through scientific inquiry by third parties. This is true, but STAP is an extraordinary claim which, now that the paper's credibility is completely undermined, is supported by no credible evidence. I think Paul Knoepfler put it best:
There's still a chance that STAP is real, but if I were in Vegas or at the race track I'd put the odds in the single digits at this point. (Source)
A STAP cell begs Obokata-san to STAHP falsifying images.
One bizarre outcome of this fiasco has been a tide of allegations (by know-nothing Internet trolls) that the Riken investigation was motivated by sexism or other such prejudice.
My feeling is that this woman is taking the brunt of this because of her age and gender, and less because she (probably) needs work on her research skills ... From the very beginning of this whole thing they focused on her age and gender and what color her lab was rather than the science. (Source)
A panel of Riken males, who could have several motives for defaming this young woman, have ALLEGED that in their opinion she did something improper. (Source)
I think it is more that Japanese culture agains women. (Source)
This is ridiculous, because concerns over the images and results originally came from the worldwide community. True, the media, especially in Japan, showed a lack of professionalism by obsessing over age, gender, and what color her lab was. Lack of professionalism in science journalism should hardly surprise anyone, least of all those familiar with my blog.

Ironically, those know-nothings crying sexism are the ones guilty of prejudice. By assuming the Riken committee members are motivated by sexism they are buying into the stereotype of Japanese male chauvinism.

In reality, maintaining the institution's reputation is the obvious motivation for the investigation. The threat this paper poses to their reputation is due both to the extraordinary claims, and also the media circus. Recall that the latter is arguably due to some sexism, but on the part of the media who flocked to cover this story of a young female scientist.

I might also point out that panel of committee members is not all male. Bizarre conspiracy theories like this are only able to exist when rooted in poorly researched assumptions.

Misconduct aside, the thing I find the most fishy about STAP is the inconstant protocol. The original paper in the January edition of Nature laid out a protocol for creating STAP cells. Labs used this protocol, but failed to replicate the results. Early in March, Obokata published a more detailed protocol which seems to indicate that STAP cells are difficult to make. The new protocol also contains steps that look like after-the-fact manipulation and back-peddling.

Later in March, Charles Vacanti independently published a still-different protocol. Vacanti is co-author on the original paper, and namesake for that mouse with an ear growing on it's back. Despite his claims that this new protocol of his is able to create STAP cells easily and in just 2 days, no labs have yet claimed replication.

Thursday, March 27, 2014

Thomas Bøhn Biased

Thomas Bøhn is an anti-GMO activist. He's calls himself the "Senior Scientist", which is to say program coordinator, for a Norwegian non-commercial foundation called GenØk. They claim their vision is of the safer use of biotechnology. This reads to me as the disuse of biotechnology.

Bøhn is the lead author on a paper to be published in Food Chemistry which claims to reject the hypothesis that GM soybeans are "substantially equivalent" to non-GM soybeans. This conclusion is based on miniscule nutritional differences they consider statistically significant.

Their analysis is incorrect because it misuses a statistical test called one-way ANOVA. This test requires that the responses for a given group are independent and identically distributed normal random variables. In other words, this test requires the only difference between the GM and non-GM soybeans is their management practice. This assumption is incorrect.

Farmers do not randomly adopt one management practice over another! They do so with careful consideration. As a result, many important confounding variables are unaccounted for in the Bøhn paper, including soil quality, available water, local whether, and all other conditions a farmer might deem important to selecting a management practice.

The small variations in nutritive content between the samples is easily explained by variations in farm conditions, and cannot be attributed to any one management practice.

You can read about many other systemic and emblematic flaws in this paper in an extensive review by Amelia Jordan on Skepti-Forum.

Tetanus Vaccine in Kenya

Neonatal tetanus is a preventable and often fatal infection among infants in Kenya. Vaccinating women of child-bearing age is effective at preventing this disease. Antibodies pass from the mother through the placenta to the fetus. This protects both mother and child from tetanus infection as a result of injury during childbirth. Sadly, this results in 110,000 deaths per year in Africa.

A vaccination campaign lead by the Kenyan Ministry of Health in collaboration with the World Health Organization was undertaken last week. This program aimed to vaccinate two million women of reproductive age in sixty high-risk Kenyan districts.

Meanwhile, head of the Catholic Church in Kenya John Cardinal Njue was busy sewing deadly paranoia. During his xenophobic rant to news reporters, he had this caution for his congragation.
Let us be very careful, and weight very carefully the agendas -- I mean the proposals -- that come or be sent by people from elsewhere. (Source)
Nice Freudian slip, there, Cardinal. Seemingly unbeknownst to this feckless monster, that agenda had by people from elsewhere is to save babies from dying.

This media circus seems to have started when Catholic Health Commission of Kenya Chairman Paul Kariuki Njiru sent a letter to Kenyan newsrooms asking these frantic, leading questions.
Is there a tetanus crisis on women of child-bearing age in Kenya? If this is so, why has it not been declared? Why does the campaign target women of 14 - 49 years? Why has the campaign left out young girls, boys and men even if they are all prone to tetanus? In the midst of so many life-threatening diseases in Kenya, why has tetanus been prioritized? (Source)
My readers should already know the banal answer to all these foolish questions. Cabinet Secretary for Health Mr James Macharia met church leaders to explain, you know, why all those babies have been dying, and how the vaccination campaign is designed to stop all those babies from dying.

Njue has since expressed he is not opposed to the tetanus vaccine program, he just wanted a clarification on why it was taking place. I don't believe this excuse for a damn second. He sent his letter to Kenyan newsrooms, not the ministry of health! The questions he asked in that letter were dripping with distrust and ignorance on a topic that, if he was truly curious, could be resolved by five minutes searching on the Internet.

Not only that, but check out this excerpt from the same letter.
Information in the public domain indicates that Tetanus Toxoid vaccine (TT) laced with Beta human chorionic gonadotropin (b-HCG) sub unit has been used in Philippines, Nicaragua and Mexico to vaccinate women against future pregnancy. Beta HCG sub unit is a hormone necessary for pregnancy ... The ongoing tetanus vaccination campaign bears the hallmarks of the programmes that were carried out in Philippines, Mexico and Nicaragua. We are not certain that the vaccines being administered in Kenya are free of this hormone.
This pernicious myth about forced-sterilization was dreamed up by pro-lifers back in 1995 and was roundly refuted at the time. No HCG vaccine was ever tested on humans without their consent.

The idea that HCG is being secretly tested in Kenya is easily dispelled by Professor Gursaran Prasad Talwar of the Indian National Science Academy. In 1992 he worked to develop an HCG-based family planning vaccine, and flatly rejects the despicable conflation of his work with the WHO tetanus vaccination program.
It had some sort of similarity with the tetanus vaccine. The birth control vaccine I developed was the beta sub-unit of hCG that generated anti-bodies that prevented pregnancy in women, but also, protected them against tetanus...

In our new vaccine, we have replaced tetanus toxoid by another carrier LTB, which would avoid the misinformation that has been associated with the valuable tetanus vaccination. (Source)
Clearly, some "information in the public domain" should not be blindly trusted.

Friday, March 7, 2014

Pierce Brosnan and the Navy

Let me preface this post by saying that I like whales. Star Trek IV, and all that. I like cetaceans, too. Pretty much any mammal that lives in the water full time has my respect.

Now, I recently saw this video where Pierce Brosnan says:
Together, we can save the whales.
Sounds good to me! So how are we going to accomplish this? Well, the video is paired with a Natural Resources Defense Council (NRDC) petition which asks the Secretary of Defense to:
Protect whales during the Navy's routine training and testing exercises
Well, that sounds reasonable and in line with the NRDC mission statement:
We strive to protect nature in ways that advance the long-term welfare of present and future generations.
The NRDC claim go on to claim that sonar and explosives testing kill whales, and that:
The Navy's Environmental Review concedes it could kill nearly 1,000 marine mammals.
That may sound like a lot, but one should also consider the big picture. More than 650,000 marine mammals are killed by commercial fishing each year.

Anyway, this number of 1,000 marine mammals seems to come from a 2011 NBC article by Miguel Llanos. For reference, he lists the hstteis.com website, which is an entire website dedicated to hosting information about the Training and Testing Environmental Impact Statement. This makes sense because the report is truly humungous. Just section 3.4 on marine mammals is 394 pages long!

Strangely enough, you won't find the number 1,000 marine mammals anywhere in this long document. Hmm, suspicious. Instead, the synopsis at the very beginning says that:
The use of sonar and active acoustic sources are not expected to result in mortality, although the potential for beaked whale mortality coincident with use of sonar and other active acoustic sources is considered. The Navy has requested two annual beaked whale mortality takes under the MMPA as part of all training activities combined to account for any unforeseen potential impacts.
So that number was only exaggerated by 500 times, no big deal. But wait, if he didn't get the number from the document, where did it come from?

Well, the NBC article has it wedged in with a bunch of hyperbolic remarks from one Zak Smith, an attorney for, you guessed it, the NRDC! Apparently, this guy has been spreading this false claim about the Navy's report for years.

Neither Miguel Llanos nor Pierce Brosnan seem to have cared enough about saving the whales to check the facts. Not even a little. They got duped into making a 100-mile mountain out of a 2-foot mole hill.

In other words, the Navy's annual take authorization of 2 accounts for only 0.0003% of the 650,000 marine mammal deaths each year.

Clearly, there are bigger fish to fry!

But seriously, this episode amounts to nothing more than a political attack on the Navy. Now, I don't much like military spending, myself. Put me in charge and I'd give half the pie to NASA in a heartbeat. My goal isn't to fight against political viewpoints that I'm opposed to. I share both environmentalism and anti-military-industrial-complex viewpoints with Zak Smith and the NRDC.

Where I part ways with these activists is the lying lies they tell in order to gain attention. Not to mention donations to their contrived cause.

Some people might ask, what's so bad about a little white lie?

I'll tell you what's so bad about it. People can tell. People who aren't on board can sense the self-righteous denial. By telling lies, you miss the chance to get them on board which you might have with a reasoned argument. They may not literally be able to do the math, but emotionally, people can detect the red flags of rhetoric and phony activism. It's a turn-off. It doesn't help save the whales.

Antagonizing and making ignorant demands at the Navy doesn't help save whales, either. It gives them less reason to care if they feel like they're being treated like the enemy. Clearly, they've put a lot of time and effort into this report. Why make an enemy out of a potential ally?

I'm sick of this nonsense.

I want people to be better environmentalists, dammit! Mindlessly clicking on hollow petitions makes a mockery of environmentalism. The popularity of this particular scam betrays a grievous lack of skepticism in the movement.

If we want to follow the NRDC mission to protect nature in ways that advance the long-term welfare of current and future generations, we're going to need to stop mindlessly believing celebrities, and start thinking for ourselves.

Check your facts, Mr. Bond!

Monday, March 3, 2014

Kepler Past, Present, and Future

The Kepler mission is one of most interesting things that has happened in science in my lifetime. The spacecraft was launched in 2009 and spent its first 4 years staring, unblinking, at a tiny patch of stars in the constellation Cygnus.

Before this mission, we didn't know for sure that planetary systems were common around other stars. True to the Copernican principle, once it started looking, Kepler caught all sorts of planets transiting in front of their host stars. These transits cause the stars light to dim slightly, and the Kepler team reports these as candidate exoplanets.

Follow up on these candidates is performed by ground-based telescopes, which carefully measure the redshift of the starlight from the candidate's star. Changes in the redshift can betray small changes in velocity due to the gravitational tug of the planet on its star.

The sensitivity of these ground-based telescopes is quite impressive. For example, the HARPS spectrograph in Chile can identify radial-velocity shifts as small as 0.3 m/s. For comparison, the Earth's gravity perturbs the Sun by only 0.1 m/s. This puts us right on the edge of being able to confirm Earth-like planets.

Last week NASA announced the confirmed identification of 715 "confirmed" exoplanets. This announcement is huge because, before it was made, the list of confirmed exoplanets numbered only 975. In fact, Kepler now accounts for 57% of all confirmed planets.

However these 715 exoplanets were not confirmed by spectroscopy. The paper in which this list was published calls them "confirmed" citing a false-positive rate less than 1%. They were able to rule out false positives by looking for systems with multiple planet candidates.

Because planetary systems tend to form in a tight disk, we sometimes see the whole system edge on. This means that we're likely to see multiple planets transiting in front of the star. This fact helps distinguish multiple planet systems, busy with lots of transit events, from false positives, where spurious data look like single, isolated transit events.

Part of what makes this technique possible is how common are multiple planetary systems, like ours. In other words, the Copernican principle makes hunting exoplanets a little bit easier.

One of the greatest things about this new planet list is that it includes over 100 Earth-size planets.
Geoffrey Marcy has predicted that the Milky Way galaxy contains something like 40 billion Earth-sized planets within their star's habitable zone.

You may ask, how do you get 40 billion Earth-like planets from just 100 Earth-sized planets? One thing to keep in mind is that, by chance, we only see a few of the Kepler stars edge on to their planetary ecliptic. Most planets orbit in an ellipse that doesn't eclipse their star in our line of sight.

Also, the Kepler viewing area is only a tiny fraction of the sky. I couldn't find this number anywhere else, so I calculated it myself:

115.6 / 41,253 = 0.28%

So there are still plenty of planets out there, just waiting to be discovered! And visited...?

Sadly, last year Kepler suffered failure the second of four reaction wheels. With only two working reaction wheels, it can no longer keep oriented in space, which requires three wheels, one for each dimension of space. This mechanical failure caused an early end to it's planet-finding mission.

Or so it seemed, until NASA came up with what they're calling the K2 mission. By keeping the sun in the X-Y plane, they can do a pretty good job keeping the space craft on balance using just two reaction wheels. The catch is, Kepler will be limited to the field of stars in our ecliptic. It will also have diminished precision, but will still be able to discover lots of new planets.

Let me explain why I think this is a good idea!

So far, we've been finding exoplanets in a patch of the sky where, if there was anybody home, they couldn't easily see our planetary system, because our ecliptic is pointed in a different direction.

But Kepler will now be pointed at stars who see our ecliptic edge on.

If anybody's home around these stars, they could detect Earth by the same transit method.

Neighbors worth knowing something about, right?

Thursday, February 27, 2014

Fukushima Lying Liars that Lie

There's a scare post by Turner Radio Network making its way around the Internet. The piece is called SURPRISE: You're Eating Fukushima Radiation and Bloody, Cancerous Tumors in Fish Contaminated By Radiation.

This ignorant bit of fear-propaganda relies on yucky pictures stolen from all over the Internet to convince readers that there are tangible effects of Fukushima radiation far away from Japan.

Of course, no such thing is happening. None of the pictures are of animals made sick from Fukushima radiation. Most of them were taken years before the nuclear disaster! The rest have just as little to do with Fukushima.

There are two lessons here regarding laziness.

First lesson, the people who make up these scare posts are super lazy. You don't have to get up very early in the morning to expose them as lying lairs that lie. Google image search did most of the work for me.

Second lesson, the suckers who read these scare posts are super lazy. They don't bother to do a simple fucking Google image search, which takes five fucking seconds. This is why the people who make up these scare posts put in so little effort; they aren't afraid of getting caught.

Scaring fraidy-cats is easy. It's like irradiating fish in a barrel!





(Warning: gross pictures below.)








Salmon caught in 2009, before the Fukushima disaster.
The post claims this salmon was caught by Brian Holter. In fact, it's a fish caught by someone named Morty who attached it to his 2009 post on a discussion forum, long before the Fukushima earthquake! The white stuff was caused by a parasite and is called Tapioca Disease.

Dr. David Schindler holding a fish from an inland river.
This fish is from the Athabasca River in Alberta, 500 miles from the Pacific Ocean! It's from a news article about the environmental impacts of oil sands, and has nothing to do with Fukushima. The coward who posted this scare piece cropped out the guy's face.

Pike caught in 2008, before the Fukushima disaster.
This pike was caught in 2008, long before the Fukushima earthquake! The picture is from a forum post by Barbwire asking about the infection, which was probably result from a rival fish bite.

Herring with an unknown infectious disease.
These bleeding herring were identified by Vancouver Island marine biologist Alexandra Morton as likely having some viral or bacterial infection. As she says in the article this picture is from, whatever the disease, it is clearly infectious, not caused by radiation.

Pickled herring from a food website.
This one is of a pickled herring, stolen from a cooking website! I think we, much like this fish, have more urgent problems than an infinitesimally increased lifetime risk of cancer from Fukushima radiation, which is vanishingly insignificant compared to background levels.

Chinook salmon from 2004, before the Fukushima disaster.
Here's yet another fish caught before the Fukushima earthquake! This one is from a website all about various fish pathogens. Oh, they have a nice (gross) section on that Tapioca Disease from earlier! Take my advice and finish eating before you check it out, though. You're welcome.

Point Lay walrus with skin lesions. Poor thing.
The sick walruses are from Point Lay. First of all, nobody in the scientific community thinks for a moment these skin sores are from radiation. Just to be sure, though, testing for radionuclides was added to the joint effort by NOAA and FWS to discover the cause of the illness. A 2013 update reported that:
... preliminary results confirm cesium 137 levels in one healthy and four UME seals are similar to cesium 137 levels in Alaskan seals sampled during the mid-1990's.
It will be interesting to see what the final results show. If "radiation" does have anything to do with it, then it will be UV from the ozone hole, not radionuclides from Fukushima.

First documented case of a great white shark with cancer.
The photo above is from a Discovery News article in 2013 about how sharks do in fact get cancer. The picture is important because it's the first time a tumor has been documented in the species. And no, I don't think many people are out eating great white sharks, even the ones with cancer.

Wednesday, February 19, 2014

The Lighthouse Nebula

Today I read an ABC Science article by Stuart Gary titled Runaway pulsar has astronomers scratching their heads which starts off:
A newly discovered fast-moving pulsar streaking across the galaxy with enormous x-ray jets, defies the laws of physics, according to scientists.
There are two red flags here.

First, things don't defy the laws of physics. Something can defy explanation within some particular model or theory. When this is the case, a journalist should just say which observation defied explanation by which model or theory!

Second, there is no such group as scientists to which things can accord. When reporting on a published paper, a journalist should name at least the lead author and include the title of the paper as a link to the paper. Here's how it's done:

The paper in question is titled The long helical jet of the Lighthouse nebula, IGR J11014-6103 by Lucia Pavan et al.

I've found that tantalizing and vague language doesn't earn the reader's trust or attention. It only serves to alienate readers who would take the article seriously. I think that should include just about all of them! Why would anyone bother reading the science section unless they are ready to take it seriously?

Red flags aside, the statement is also false. This pulsar, known as the Lighthouse Nebula (designated IGR J11014-6103) was discovered back in 2011! It's no more newly discovered than the first Thor movie. Oh, and in the article, its name was mistyped the star's designation! (UPDATE: I sent a letter to the editor and they promptly fixed this typo.)

Anyway, the article goes on to quote Miroslav Filipovic, coauthor on the 2011 and 2014 papers:
One of the biggest mysteries is that we only see these jets in x-rays, there's no radio signature, that's totally shocking to us ... this is extremely difficult to explain through any theories we have at the moment.
Okay, two things.

First, there most certainly is a radio signature, that's what the whole paper is about!


Left panel shows the Lighthouse Nebula's X-ray signature.
Right panel shows the Lighthouse Nebula's radio signature.
It's right there. In the paper. The paper you published. Come on bro! I can't imagine how this quote came about. It doesn't seem out of context or anything. Maybe Filipovic was referring to the 2011 paper? But no, that paper's abstract says quite clearly:
A possible radio counterpart positionally coincident with the source was also identified.
That doesn't sound like "no radio signature" to me. If the quote isn't taken out of context, or entirely fabricated, then Filipovic might have been showboating. Either way, someone is being dishonest.

Second, the data are not at all difficult to explain. That's the whole point of the paper! You see, a 2012 paper proposed that this pulsar was propelled to a high velocity by its neighbor that went supernova. What's new in this 2014 paper is fitting both X-ray and radio data to a model of the pulsar's spin and velocity.

The radio and X-ray profiles peak at different positions.
This can be explained by the cooling of the emitting particles.
Alignment favors a pulsar high velocity greater than 1,000 km/s.
There's no unexplained, shocking mystery at all! The data easily fit a model where the pulsar is flying away from its companion at high velocity. Not only that, but the spin axis of the pulsar is perpendicular to the direction it's moving.

Think of the jets like the smoke coming from a train's smoke stack. It's really hot when it first shoots out, then expands and cools, forming a slowly fading tail as its source zips on ahead.

This is a great paper. It shows how subtle clues can reveal the nature of an incredibly distant object. You don't have to see the pulsar in detail to know which direction its jets are facing, or how fast it's moving. Science rules!

But this spectacular deductive reasoning is utterly lost to readers of the news article. It's a tragedy of incompetence. Sure, readers get a puff of mystery that alights their human urge to discover. But they won't be given the satisfaction of actual discovery.

Even after reading all three papers, I feel similarly unsatisfied by a question that keeps coming back to me. Why does this news article go out of its way to make Filipovic sound oblivious to the paper's very thesis?

This question really has me scratching my head.

UPDATE: As you can read in the comments below, Miroslav has kindly explained to me that the first picture above is actually the pulsar wind nebula, not one of the the pulsar jets. The pulsar wind nebula is a standing shock wave of charged particles accelerated by the magnetic field, but is an independent feature from the pair of jets. This wind shows up clearly in the radio spectrum. More importantly, Miroslav was correct that there's no radio source of the jets, themselves! My bad.

Though I'm yet to be convinced that a missing jet radio signal is truly unexpected, since the paper seems to indicate otherwise. Also, this quote from the ABC article seems to conflate the radio signal from the jets with any signal from the pulsar itself:
Pulsars were first discovered because of their characteristic radio signals, so this is extremely difficult to explain through any theories we have at the moment.
These quotes have me scratching my head, too:
It's impossible to easily explain all these crazy things we've seen in this object.
Not according to the paper!
One of the problems is, it's impossible to prove any of these ideas.
Not something you do in science!

Friday, January 24, 2014

Ironic Iron Impoverishment

Mighty Morphin Power Ranger Mike Adams of Natural News reports Wheaties cereal ... can be levitated with magnets.
Adding shards of metal to a cereal is not nutritionally equivalent to nutritive minerals formed during the growth of grain-producing plants...
To understand this issue it helps to know why the body needs iron in the first place. Hemoglobin is the protein that our red blood cells use for oxygen transport. This protein contains for Heme B groups. These four organic molecules contain one iron atom at their center.

Heme B, an iron-containing compound found in hemoglobin.
Fe is the chemical symbol for iron.
According to the CDC, Iron deficiency is the most common nutritional deficiency and the leading cause of anemia in the United States [1]. This disease is easily preventable via fortification of foods like breakfast cereal with iron.

There are two basic kinds of iron used to fortify foods, elemental iron powder, and salts like iron sulfate. The iron enrichment in question must be ferromagnetic because it is attracted by a magnet. This means it is iron powder, which is ferromagnetic, not iron salts, which are paramagnetic.

In general, the powders have lower bio-availability than iron salts [2, 3]. This is not to say the powders are bad. You have to use a few times more substance, some of which passes through the digestive system without being absorbed. That's fine, because they are still less expensive. Also, powder may be preferred to salts because the later can contribute an undesired taste.

The differing bio-availability is well known [4] and  has been taken into consideration when they print the label since 1973 [5]. Iron atoms taken up from powders are nutritionally equivalent to any other source.

Anyway, finding iron in breakfast cereal is not news. It's a popular kids science experiment!

I'm sure Mike's parents are really proud of him.

I was curious why the bits of iron were large enough to see, because particles in food-grade iron powder range in size from 0.5 to 10 micrometers [4]. That's smaller than a red blood cell. This small size increases bio-availability [5].

Presumably the flecks in this kids science experiment are clumps of the powder that have stuck together due to magnetism, or were not fully dissolved when added to the cereal mixture.

As if this story weren't bizarre enough, it has one final twist. You see, I know someone who would really get upset that Mike Adams is telling cereal manufacturers to put less nutrition in their product.

His name is 2004 Mike Adams.

Friday, January 17, 2014

The Nature of Responsibility

In his blog post titled Rim-Laid Eggs Gary Patton writes about the black robin. This endangered species was saved from extinction by a breeding program starting with a single female bird.

This heroic effort had one side effect, though. As explained in a National Geographic article, many females laid eggs on the rim of the nest, where they were not properly incubated, and failed to hatch. Faced with a decision:
The team repositioned the ones on the rims... Under normal circumstances, natural selection would have quickly weeded out the alleles (versions of a gene) behind the behavior...
Gary argues that:
... by interfering with the normal rules of natural selection, the recovery effort increased the predominance of a gene that led to the rim-laid egg tendency, and that meant that the recovery was actually establishing a genetic characteristic that would guarantee species failure in the long run.
... It seems to me that it is a cautionary tale, and that the story of the black robin should make us think again about our often presumptuous ideas that human beings can properly run the natural world.
Gary seems to imply that interfering was a presumptuous, bad move. But as the article states:
Without this move, it’s unclear if the species would have made its dramatic recovery...
Clearly, survival for the not-so-fit is better than no survival at all! Saving the rim-layer's eggs was the right call. This isn't a cautionary tale, it's a victory thanks to the hard work of Don Merton and his team of conservationists.

The true cautionary tale is about a bird allowed to become severely endangered in the first place. After all, the closer a species is to extinction, the harder it is to save, and the longer its recovery.

The genetic origin of rim-laying does demonstrate the importance of genetic diversity within a species. Now that the population has grown to a safer level, natural selection will quickly reduce the rim-laying allele back to a normal level. If the non-rim-laying allele had been lost, the black robin would have been in real trouble. Luckily, no such recessive disease thwarted the recovery effort.

It's wrong to say human beings should not run the natural world. First of all, it's poor philosophy of science to erect an artificial distinction between homo sapiens and their environment.

We're a part of the natural world, and the case for conservation is made much stronger as a result. When a species goes extinct due to habitat loss or hunting, it proves we are connected. The same goes the other way around. When our game animals or fish are hunted to extinction, we starve. When we vanish biodiversity by clear-cutting a million acres of rainforest, some potential medical boon, some scientific discovery, and much beauty is lost forever.

We are part of nature as nature is part of us.

Like Don Merton and his team, we have decisions to make. That doesn't mean we must become presumptuous masters of some imaginary world of nature. The "let them rule over the fish in the sea and the birds in the sky" anxiety comes strait out of Genesis. This Old Testament thinking only makes sense if you believe man is meaningfully separate from nature.

In the bible, mankind has a soul, setting him apart from the beasts. In nature dualism, human beings lift themselves out of nature with their culture and technology. This is less supernatural, but also false. It's also inherently dangerous.

A dualist way of thinking leaves the door wide open for discrimination. If you're not of my religion, then you're going to hell. If you're not of my race, then you're inferior. If you're not of my species, you're going extinct. Gary is clearly not one to discriminate like this, but his philosophy leaves us impoverished when dealing this type of discrimination.

Now, I'm neither a member of PETA nor a vegetarian. I don't think all species are the same, and therefore deserve equal treatment. I just think setting aside human beings as dual to the rest of the world is wrong and ethically dubious.

Don Merton wasn't playing god by choosing to save the black robin. His program was conducted from compassion, not some biblical imperative to run the natural world.

He had an opportunity to save a species from extinction, so he took it.

That's the nature of our responsibility. To nature.