Wednesday, April 30, 2008

Quote of the Day

Yep, Ben Stein has finally jumped the shark. Just when you thought he couldn't get more ridiculous:

Ben Stein: … Love of God and compassion and empathy leads you to a very glorious place, and science leads you to killing people.
Wow. And I can hardly even remember the last time I killed anybody.

Hat tip: Friendly Atheist.


Friday, April 25, 2008

Friday beautiful science

Today's Friday beautiful science was inspired by the obituary of Edward Lorenz:

In discovering “deterministic chaos,” Dr. Lorenz established a principle that “profoundly influenced a wide range of basic sciences and brought about one of the most dramatic changes in mankind’s view of nature since Sir Isaac Newton,” said a committee that awarded him the 1991 Kyoto Prize for basic sciences.

Dr. Lorenz is best known for the notion of the “butterfly effect,” the idea that a small disturbance like the flapping of a butterfly’s wings can induce enormous consequences.

As recounted in the book “Chaos” by James Gleick, Dr. Lorenz’s accidental discovery of chaos came in the winter of 1961. Dr. Lorenz was running simulations of weather using a simple computer model. One day, he wanted to repeat one of the simulations for a longer time, but instead of repeating the whole simulation, he started the second run in the middle, typing in numbers from the first run for the initial conditions.

The computer program was the same, so the weather patterns of the second run should have exactly followed those of the first. Instead, the two weather trajectories quickly diverged on completely separate paths.

At first, he thought the computer was malfunctioning. Then he realized that he had not entered the initial conditions exactly. The computer stored numbers to an accuracy of six decimal places, like 0.506127, while, to save space, the printout of results shortened the numbers to three decimal places, 0.506. When typing in the new conditions, Dr. Lorenz had entered the rounded-off numbers, and even this small discrepancy, of less than 0.1 percent, completely changed the end result.
The photo above is a demonstration of chaos theory. It's a Mandelbrot set, that is seen to contain the same patterns at large and small magnification. You can zoom and explore a Mandelbrot set here. For more on Chaos Theory (written for non-mathematicians), see:


Thursday, April 24, 2008

85th Skeptics' Circle

The 85th Skeptics' Circle is up at Andrea's Buzzing About: Go have a gander.


Exposed: the great GM-food scare made up by the Independent

The Independent recently published an article with the startling headline:

Exposed: the great GM crops myth
Major new study shows that modified soya produces 10 per cent less food than its conventional equivalent
Wow. That's a pretty bold statement. Let's look further into it, shall we?
Genetic modification actually cuts the productivity of crops, an authoritative new study shows, undermining repeated claims that a switch to the controversial technology is needed to solve the growing world food crisis.

The study – carried out over the past three years at the University of Kansas in the US grain belt – has found that GM soya produces about 10 per cent less food than its conventional equivalent, contradicting assertions by advocates of the technology that it increases yields.
Professor Barney Gordon, of the university's department of agronomy, said he started the research – reported in the journal Better Crops – because many farmers who had changed over to the GM crop had "noticed that yields are not as high as expected even under optimal conditions".
I've noticed in the past that news organizations don't always do the best job with science stories, so let's look at the original citation, shall we?

But first, some background (yes, yes, I know that the Independent wouldn't require any background, but they also wrote a factually wrong, irresponsible, scaremongering article, so we'll do some background). Soybean plants have been genetically modified in recent years to be resistant to a broad-spectrum herbicide called Roundup (aka glyphosate). This provides a neat trick for farmers, because they can grow their Roundup resistant soybeans, and spray them with Roundup to kill any weeds (without killing the soybeans). This is a neat trick, because Roundup isn't very toxic to people, and breaks down pretty readily in the soil, providing a neat way for farmers to decrease weeds in their fields, without having to use more expensive and toxic compounds.

Ok, so what was the question that Dr. Gordon asked? From the paper:
There is evidence to suggest that glyphosate may interfere with Mn metabolism and also adversely affect populations of soil micro-organisms responsible for reduction of Mn to a plant-available form. Manganese availablity is also strongly influenced by soil pH. As soil pH increases, plant-available Mn decreases. It is unlikely that Mn deficiencies will occur on acid soils. It stands to reason that the addition of supplemental Mn at the proper time may correct deficiencies and result in greater GR soybean yields.
Ok, so he wanted to ask if there are manganese deficiencies in plants that are treated with glyphosate. And what did he see?

He sees that he can increase yield of soybeans by applying manganese to the soil. Cool, huh? Now, if you're a journalist at the Independent, you may look at that graph and say, "Hey, wait, the conventional soybeans have higher levels of production than the Roundup resistant soybeans!". Well, you could say that, but you'd be wrong. You can't ask that question from these data. Firstly, these strains aren't isogenic. Meaning that their genetic content isn't just differentiated by the fact that the GM strain is Roundup resistant, so increased growth could be due to different genetic content. Secondly, the Roundup resistant strain was sprayed with Roundup. And the other one wasn't. That's a rather large difference. Indeed, the conventional strain of soybean is really only a control to show that increasing manganese levels doesn't increase yield in the absence of Roundup. Thirdly, both these crops were worked over by hand to remove weeds, as they were interested in only studying the effect of manganese on the experiment, not on the effect of weeds in the crop. So this experiment simply can't be used to ask "Do Roundup resistant crops produce more or less than conventional crops?" The experiment wasn't designed to ask that question, and you can't use these data even incidentally to ask that question. And what does the Independent say?
The GM crop – engineered to resist Monsanto's own weedkiller, Roundup – recovered only when he added extra manganese, leading to suggestions that the modification hindered the crop's take-up of the essential element from the soil.
Hmmm.... but they applied Roundup to the Roundup resistant plants. That's another pretty huge difference.

Indeed, the author of the study, Dr. Barney Gordon, concurs. From an e-mail he wrote me:
The article you saw in the Independant was a total distortion of the research. My research concerned manganese application on soils that are known to respond to Mn application. We used one conventional variety and a glyphosate-tolerant near isoline (not genetically identical). The objective of the research was to improve soybean yields under optimum management conditions, not to make any statement about GM crops.
Now, I can almost hear the anti-GM crowd crowing now, "Just because he didn't ask that question, doesn't mean you can't extrapolate from the data he gathered", but as I've outlined above, you can't even extrapolate. The experiment isn't properly controlled to ask that particular question, just to ask the question about manganese suplementation.

And it's rather disingenuous of the Independent to say otherwise.


Tuesday, April 22, 2008

I don't support torture.


Friday, April 18, 2008

Friday beautiful science

Today's Friday beautiful science is a shot of bacteria spreading across a petri plate, with false color added to make them more beautiful. This looks like a Bacillus mycoides type of growth, but I couldn't find the identity on the original website.

Go on over to Eshel Ben-Jacob's website, where there are all kinds of beautifully rendered shots of bacterial growth.




Thursday, April 17, 2008

Quote of the Day

MaryAnn Johanson:

In a parallel universe even crazier than our own, Ben Stein is making a documentary about how the Nazis utilized the controversial theory of gravity to make bombs that fall from the sky to the earth, and so the theory of gravity must be wrong.


Wednesday, April 16, 2008

Just a theory

Via freethoughtpedia.


Tuesday, April 15, 2008

On doubt.

I am a scientist. I am unable to separate the doubting part of my scientist training from the rest of my daily life. Take this little anecdote:

When my son was about 9 months old, Mrs. Factician was playing with some little plastic animals on the coffee table with him. When she said, "Where is the giraffe?" he reached for the giraffe. We were astounded (he was 9 months old, mind you, and hadn't shown an indication that he knew which animal was which prior to this point). She put the animal back, and asked him again, "Where is the giraffe?". Again, he picked up the giraffe.

Mrs. Factician and I started to talk about this. She was of the opinion that he had now learned which animal was the giraffe.

I was a bit more skeptical (perhaps not a good thing for a father, to be skeptical of his son, but like I said, I am unable to turn off doubt when I go home from the lab).

So I tested him. I moved the animals around. "Where is the giraffe?". Again, he reached for the giraffe. Wow, 9 months and he's already demonstrated an ability to identify animals. I was absolutely floored. Every test so far had shown that he could identify the giraffe. But still, I had nagging doubt.

I moved the animals around again. "Ok, now where is the monkey?" He reached for the giraffe. He hadn't identified it with the sound "giraffe" at all. A few repeats of the experiment verified it. The giraffe was merely his favourite animal. It would be weeks still until he positively understood the word "giraffe".

A scientist's life is like this. Constant doubt. Constant testing. Constant experimentation with appropriate controls. Re-evaluating old data. Talking about experiments with other scientists.

The new movie "Expelled" will try to make the point that we have stopped testing evolution by natural selection, and have (as scientists) accepted it as some gospel truth. This is total and complete nonsense. We have continued to doubt it, to test it, and to run experiments with controls. But every test, for over 150 years, has come back confirming that evolution by natural selection is true. That's a boatload of data. That's an amazing amount of confirmation.

While it remains possible that there is another, better explanation, but data suggesting that has not been forthcoming. For now, evolution by natural selection is the best description of the data.


I care about your health

And that's why I bring you this important health update, courtesy of Stephen Colbert.


Monday, April 14, 2008

What can one blogger do?

Whenever I feel powerless to change anything, something like this comes along. I can help put Expelled high in the rankings. And get some real information out there. As Carl Sagan says:

"Science is more than a body of knowledge; it is a way of thinking. I have a foreboding of an America in my children's or grandchildren's time ... when awesome technological powers are in the hands of a very few, and no one representing the public interest can even grasp the issues; when the people have lost the ability to set their own agendas or knowledgeably question those in authority; when clutching our crystals and nervously consulting our horoscopes, our critical faculties in decline, unable to distinguish between what feels good and what's true, we slide, almost without noticing, back into superstitions and darkness."


Friday, April 11, 2008

Friday beautiful science

Today's Friday Beautiful Science is a photo of the moon Phobos. Phobos orbits Mars, and is orders of magnitude smaller than Earth's moon (compare Earth's moon at 3400 km in diameter to Phobos at 19-21 km in diameter). As you can clearly see in the photo, Phobos is not regularly shaped. From the Planetary Science blog:

Mars Reconnaissance Orbiter approached to within 6,800 kilometers (4,200 miles) of Phobos to capture this enhanced-color view of the Martian moon on March 23, 2008. The color is from infrared, red, and blue-green channels on the camera, so it represents light shifted slightly longer in wavelength than human eues can see, which emphasizes subtle colorations on the moon. The color view shows that the material surrounding the giant crater Stickney (on the left side of the moon) appears gray while the rest of the moon appears reddish. The grayer material is likely fresher material.
Click on the photo to get a large majestic view of Phobos.


Wednesday, April 9, 2008

A creationist, a scientist and a lawyer walk into a bar...

Go here for the punchline. This just cries out for massive linkage.


Tuesday, April 8, 2008

Quote of the Day

" If you are in possession of this revolutionary secret of science, why not prove it and be hailed as the new Newton? Of course, we know the answer. You can't do it. You are a fake."

-Richard Dawkins

h/t Pal MD


Saturday, April 5, 2008


Expelled, the Musical is about to hit theaters! In theaters across the country! Well, in a few theaters. This has inspired creationist mathematician and philosopher William Dembski to fire up his prognostication machine!

Hmmm... try these predictions on for size.

A controversial documentary set for release nationwide April 18 could foster a cultural shift "equivalent to the fall of the Berlin Wall," says William Dembski, research professor of philosophy at Southwestern Baptist Theological Seminary.
Wow! The fall of the Berlin Wall, that's huge! Bill Dembski has a long run of predictions. He made a prediction during the trial in Dover, Pennsylvania. What did he say about that?
As a consequence, this [court] case really could be a Waterloo for the other side.
Waterloo! Berlin Wall! Hmmm... He might do well to read a little more Twain:
The reports of my death have been greatly exaggerated.
Mr. Dembski, please get back to work, and publish some papers that have data in them. Really. Movies and court cases don't make creationism intelligent design a science. Data, Mr. Dembski. Data. If you're interested in what it looks like, try this little search on evolution.


Friday, April 4, 2008

Westboro Baptist Church Rickrolled!

The Westboro Baptist Church is a group of hatemongers, frequently written up by the Southern Poverty Law Center. They're quite a nasty group of folks. They show up at any prominent funerals, saying that the death of these people is due to America's tolerance of homosexuals. The odd part is that these hatemongers seem to not care whether the deceased people are homosexual or not. It just matters whether or not the news media are there to cover it. They've made themselves notorious by promoting their slogan "God hates fags", and by suing anyone who offends them. I try to avoid calling whole groups of people nasty, but these folks are really hideous. To get an idea of the lengths these weirdos take, see this article:

The [Westboro Baptist Church family] don't just picket, they also fax. And what faxes. Sent out to dozens of government offices, law firms, businesses and homes across Kansas several times a week, the faxes are grotesque, non-stop political commentary lambasting local and national figures.

Minnesota Sen. Paul Wellstone is a "bug-eye faggy baby-killer." Sailors in the U.S. Navy are "blasphemous fag beasts." Jerry Berger, the Vintage owner, is a "[b]loody Jew... merchant of anal copulating."

Joe Lieberman, Al Gore's Democratic running mate last fall, is "an anti-Christ Jew" who "has sold his soul to fags." Elizabeth Taylor is "an evil woman" who led a "wicked, Christ-rejecting, Satan-worshipping life." Jesse Jackson is a "fag" and a "black Judas goat leading his people to hell."

Thanksgiving was established as a "pagan feast" so the Massachusetts governor could "lust after the semi-naked bodies of the Indians he invited." Poet Maya Angelou is the "filthy face of fag evil."

Maya Angelou as a face of evil? What? Wow. Okay, so if you find that offensive, please donate money to the Southern Poverty Law Center. (Mrs. Factician and I give them money twice a year). And after you're done, watch this guy do an in-person Rickrolling of a Westboro Baptist Church protest. Bravo, dude.

Westboro Baptist Church gets Rick Rolld - Watch more free videos


Tuesday, April 1, 2008

Lab meeting

So I just had lab meeting. A 5th year graduate student was presenting her work on mutational analysis of one of the proteins we study. An interesting lab meeting, but not normally noteworthy for the blog. (I reserve this blog for only the most important events in my exciting life - see Death Star Troofers, below).

So I'm quietly enjoying my coffee, my mind wandering away from the introduction (I've heard it too many times over the last five years) and I hear a voice from the back of our darkened conference room, "Balderdash! I'm going to Expel you from science, because I think your model for DNA rearrangments is absolute crap! Consider yourself Expelled!"

I just couldn't believe it! Apparently PZ Myers gatecrashed our lab meeting! He really does have a problem!