Monday, July 30, 2007

Get fired up about science!

I just discovered Neil deGrasse Tyson on a repeat of the Daily Show. If this guy doesn't get you fired up about science, no one can. Watch here:


Your civic re-shelving duty.

Callooh! Callay! Pharygula points out today a biologist on a mission. Go check him out, you have to love his cause. His first post explains:

I'm not sure if you've noticed, but some bookstores seem to have a little problem discerning science from non-science. I'm specifically talking about biology books vs. creationist books. Sometimes, you will find psuedo-scientific rubbish such as "intelligent design" books next to such authors as Darwin, Mayr, Gould, et al...

...Realise just how successful creationism has been in blurring the lines of what science actually is in the public's eye. So successful, in fact, that books whose main argument is that "God did it" enjoy shelf-space with some of the finest minds ever to grace humanity.

This is unacceptable, and something must be done...

...It is my mission to correctly re-shelve books to the appropriate section of the bookstore.

For example, "Darwin's Black Box", the famous psuedo-science book by the non-evolutionary non-scientist Michael Behe, should not be in the "Evolutionary Biology" section, but something more appropriate, such as "New Age", "Religion", "Christianity", or even "Fiction". You get the idea.

I call on all readers of this blog to follow my example. Help your local bookstore correctly stock their science section. Spread the word.

Thank you, Ste. You just made my day.

via Pharyngula


Saturday, July 28, 2007

My travels

Orac at Respectful Insolence has a neat toy up that shows everywhere he's traveled in the U.S. I thought it might be fun to map out everywhere I've traveled in the world (I confess, I'm less well traveled than he in the U.S.).

Neat toy, you should give it a try.

create your own visited countries map

EDIT: Hmmm... It seems to cut out everything east of Africa. Ah well, I've never traveled there, so it's all good.


Friday, July 27, 2007

Sadly, this is me.


Astronauts gone wild!

Oy. From the New York Times:

NASA’s astronauts have flown while intoxicated on at least two occasions, according to reports of an internal NASA investigation, and the astronauts involved were warned that their drunkenness constituted a safety risk to the flight. But it is unclear whether this is a current problem and whether the incidents involved space shuttle flights.
NASA? Meet Nissan. Nissan, meet NASA. From CNET:
[Nissan] this week announced that it had started testing an in-car Breathalyzer system that disables a car's ignition if it senses that the would-be driver is over the legal limit.


Friday beautiful science

Today's Friday beautiful science comes from the Imaging Technology Group at the University of Illinois. From the caption:

Image of a Xenopus Melanophore stained to reveal the microtubule cytoskeleton (green) and the nucleus (blue). The pigment granules in the cell were imaged using back-scattered light. Image by Steve Rogers. (Confocal)


Thursday, July 26, 2007

How ignorance can kill a child.

I have people in my family who have said things like, "If I ever get cancer, I will show how you can cure it with a good attitude and eating lots of carrots." When I tell my colleagues stories like that, they tend to think that I'm exaggerating.

Take this Canadian family:

Anael L'Espérance-Nascimento was being treated at the Children's Hospital of Eastern Ontario in Ottawa for cancerous cells in his brain and in bone marrow, which are currently not life-threatening.
Doctors recommended chemotherapy for the boy, but his parents have decided instead to treat him by feeding him on a diet of almost exclusively organic vegetables, without sugar or animal products.
Organic vegetables as a cancer cure. Their child will certainly die from this cancer. Why have his parents chosen this path?
[The child's mother] said earlier treatment at the hospital during almost the entire winter took its toll on Anael, who grew small and whose complexion grew green.
Chemotherapy is awful. Really and truly awful. But consider the alternative:
Anael's mother, Marie-Élise L'Espérance, said Tuesday the treatment is based on the idea that the body can heal itself if given the right nutrition.
Great idea, why didn't I think of that? Too bad that most great ideas turn out to be wrong. This woman is experimenting with her child without controls, and with no reason to think that it will work. My heart breaks for her, that her child is suffering through cancer at such a young age (he's only a year older than my son). But my heart breaks even more for her son, who will certainly die under her "care".
[Canadian government] officials asked the province's child protection agency to intervene, but it declined.
One wonders if the reason they're not protesting is that the child is already terminal. I feel sick.

via Eamon Knight


Wednesday, July 25, 2007

Evolution. Not just a theory anymore.

It's true. You can read it here.

Via Bad Astronomy.


Friday, July 20, 2007

Friday beautiful science

Today's Friday beautiful science is a hybrid photo of 4 photos taken by the Cassini space probe on New Year's Eve 2004. They show Saturn's moon Iapetus. This week, scientists at the Jet Propulsion Laboratory unveiled a model for how it is that Iapetus ended up with the ridge running across the moon:

"We've modeled how Iapetus formed its big, spin-generated bulge and why its rotation slowed down to its present nearly 80-day period. As an unexpected bonus, Iapetus also told us how old it was," said Dennis Matson, Cassini project scientist at JPL. "You would expect a very fast-spinning moon to have this bulge, but not a slow-spinning moon, because the bulge would have been much flatter."

Scientists calculate Iapetus originally rotated much faster -- at least five hours, but less than 16 hours per revolution. The fast spin gave the moon an oblate shape that increased the surface area (in the same way the surface area of a round balloon stretches when the balloon is pressed into an oblate shape). By the time the rotation slowed down to a period of 16 hours, the outer shell of the moon had frozen. Furthermore, the surface area of the cold moon was now smaller. The excess surface material was too rigid to go back smoothly into the moon. Instead, it piled up in a chain of mountains at the equator.

"Iapetus' development literally stopped in its tracks," said Castillo. "In order for tidal forces to slow Iapetus to its current spin rate, its interior had to be much warmer, close to the melting point for water ice." The challenge in developing a model of how Iapetus came to be "frozen in time" has been in deducing how it ever became warm enough to form a bulge in the first place, and figuring out what caused the heat source to turn off, leaving Iapetus to freeze.

The heat source had to have a limited life span, to allow the moon's crust to rapidly become cold and retain its immature shape. After looking at several models, scientists concluded that the heat came from its rocks, which contain short-lived radioactive isotopes aluminum-26 and iron-60 (which decay very rapidly on a geologic timescale). Since these elements decay at a known rate, this allowed scientists to "carbon date" Iapetus by using aluminum-26 instead of carbon. Scientists calculate the age of Iapetus to be roughly 4.564 billion years old.
Via Bad Astronomy.


Thursday, July 19, 2007

65th Skeptics' Circle

The 65th Skeptics' Circle is up at NeuroLogica. Go have a gander.


Tuesday, July 17, 2007


Looks like we're not the only ones to be getting free creationism tracts in the mail. The New York Times reports that they've been sent all over the country (our department got several last week). Harun Yahya has been mailing it all over.

Kenneth R. Miller, a biologist at Brown University, said he and his colleagues in the life sciences had all received copies. When he called friends at the University of Colorado and the University of Chicago, they had the books too, he said. Scientists at Brigham Young University, the University of Connecticut, the University of Georgia and others have also received them....

While they said they were unimpressed with the book’s content, recipients marveled at its apparent cost. “If you went into a bookstore and saw a book like this, it would be at least $100,” said Dr. Miller, an author of conventional biology texts. “The production costs alone are astronomical. We are talking millions of dollars.”
Quote of the day?
As the scientists ponder what to do with the book — for many, it is too beautiful for the trash bin but too erroneous for their shelves...


Friday, July 13, 2007

Friday beautiful science

The lab across the hall from me just got a confocal microscope (for the low, low price of $200,000). In honor of that, I'm presenting these confocal shots of a developing mouse embryo, taken from the Wellcome Images site, a storehouse of biomedical images available free to the public. Check them out.

These embryos are at the 8 and 16 cell stages, only a few cell divisions after fertilization.


Wednesday, July 11, 2007

An oldy but a goody...


Dr. Egnor, can I have a unicorn?

Okay, so I had so much fun with my little exercise yesterday, that I thought I'd do it again. But this time, I'm going to include unicorns!

So, I'm reviewing Michael Egnor's review of Dawkins' review of, wait, what? Let's start again:

So Michael Egnor, of Rushing River of Stupid fame, also wrote a review of Dawkins' review of Michael Behe's new book. Clever Dr. Egnor writes:

According to Darwin’s theory, cockroaches really did evolve from ‘bacteria-like’ ancestors over billions of years. So, what’s the threshold of time after which I could plausibly infer that random mutation and natural selection was an adequate explanation for the cockroaches, starting with bacteria?
Dr. Egnor? Meet Dr. Pace. Dr. Pace, meet Dr. Egnor. It seems Dr. Egnor really doesn't understand evolution by natural selection at all. Evolution doesn't posit that cockroaches evolved from bacteria. The theory of evolution by natural selection suggests that bacteria and cockroaches have a common ancestor from which both evolved. Cockroaches aren't more highly evolved than bacteria , Dr. Egnor. They are both highly evolved for their niche.
So I ask Dr. Dawkins:1) How long could I leave the bacteria in the incubator before I could reasonably infer that the cockroaches evolved from the bacteria by random mutation and natural selection? Please provide me with the experimental evidence (data and journal references) that you use to arrive at your answer.
You really don't get it, do you? Please, sir, you're embarrassing yourself. One wouldn't predict bacteria to "evolve into cockroaches". Likely over millions and billions of years they would evolve into all kinds of new organisms, but not cockroaches. This is one of several fundamental differences between creationists and scientists. Creationists assume we (and the world around us) was inevitable. Scientists assume this is what happened, and investigate how it happened. Cockroaches aren't inevitable, Dr. Egnor. Whatever does evolve out of your experiment, it wouldn't be cockroaches.
2) If you can’t tell me, then why isn’t Dr. Behe’s question- what are the limits to what Darwinism can accomplish- a fair question?
It's because your thought experiment is a stupid one. Let me design a similarly stupid experiment. How many years would I have to keep a container filled with air, earth, fire and water before God would create a unicorn for me? If you can't answer that question, how do you think Creationism (erm, I mean intelligent design) explains anything?


Tuesday, July 10, 2007

Review of Pat Sullivan's review of Dawkins' review of Behe's "Edge of Evolution"

So here's the back story. Michael Behe writes a book, called "The Edge of Evolution". Richard Dawkins (not Dawkin's, Mr. Sullivan) reviewed "The Edge of Evolution". And Mr. Sullivan reviewed Dawkins review. Here, I will review Mr. Sullivan's review of Richard Dawkins' review.

Yep, I'm really going to do it. Just because it'll make me laugh.

Exactly my point in my post here in number 2 and 3... Always say ID scientists are creationists and always say they are not real scientists. In other words, demean them which is my point number 1.
Beg pardon, your point number what?

Honestly, if you folks insist on using the word "Darwinist", I think it's only fair if we use the word "creationist". Really, we could be using "bronze age mythicist".
Here is a review of Dawkin's review written by Logan Gage. A quote from this review: "Dawkins is a master of rhetoric. Only he could take a clear example of intelligently designed evolution (dog breeding) and offer it as a convincing “proof” of Darwinian evolution."
Now, who's review? *heavy sigh* Ok, bud. I'll spell it out for you, as slowly as I can possibly type. Behe claims that we could never expect in all the time on earth that random mutation could produce the variety of organisms seen on earth. Never in a billion years. That's Behe's claim. Dawkins shows that random mutation is sufficient to produce all the variety seen in dogkind. He is not using this as an example of evolution via natural selection. The only point he's trying to make is that random mutations happen, and happen frequently. He's merely pointing towards random mutations as a source of the change in all the varieties of dogs on earth.

Unless you're suggesting that the mutations that produced dogs were made by genetic Egyptian and Chinese genetic engineers in the bronze age, can we agree these were randomly produced mutations? And they are sufficient to produce every size and shape of dog on earth, in a matter of a few thousand years. Get it? Now multiply that time period by about 1,000,000. Might be enough time to account for all life on earth? Maybe?

From Pat Sullivan's comments:
I found his comparison of very intelligent dog breeding to be a rather silly argument for blind, random, slow evolution, especially for new species.
Really? You find it silly? That's good, because he's not arguing that. He's arguing that random mutations can happen sufficiently frequently to produce massive changes in an organism. That is all. Mutations happen. Alot of 'em.
Even [another commenter] cite[s] it as proof something can evolve really fast. Sure, if it is be guided intelligently!
Oy. Are you trying to be obtuse? This is just an argument for frequency of mutations. That is all. Please stop. Mr. Sullivan, you're clearly not ready to understand natural selection, so we can skip that lesson for today. Just try to comprehend that random mutation is sufficient to produce change. Again, unless you're positing bronze age molecular biologists making directed changes in the genome...

But fortunately, Mr. Sullivan clears it all up with this quote from a wise philosopher:
I said to someone over 30 years ago, "I fear a man's science is guided and governed by his underlying philosophy." I believe it even more now.
Oh. Never mind, you're quoting your own wise wisdom of wiseness. Thanks for sharing.


Monday, July 9, 2007

Creation Comic

From Saint Gasoline.

via Pharyngula.


Friday, July 6, 2007

On the creation museum.

“I am patient with stupidity but not with those who are proud of it.”

-Dame Edith Sitwell


Friday beautiful science

Today's Friday beautiful science comes from the lab of Julie Theriot. These are sped up movies of Listeria bacteria inside human cells. Listeria actually attaches to the actin filaments inside the cell, and uses the actin to force itself around through the cell (and to force its way into neighboring cells). On the left side of the human cell, you can see some bacteria stretching the cytoplasm. If there had been another human cell adjacent to this one, the Listeria cell likely would have punctured the membrane of the human cell, and moved directly into the adjacent human cell. Super cool.

From the Theriot lab website:

Listeria monocytogenes is a small rod shaped gram-positive bacterium that is ubiquitous in the environment, in the soil, on plants and animals. Listeriosis (the state of Listeria infection) is associated with eating of unpasteurized cheese or dairy products, or consumption of contaminated vegetables. Infection occurs primarily in newborns and infants, elderly or immunocompromised individuals, or pregnant women (mother is asymptomatic or has influenza-like syndrome, but the newborn can acquire it during birth, or infection can cause abortion or premature delivery). According to the CDC about 1500 cases are reported in the United States each year, mostly in the aforementioned high risk groups.

Listeria enters the host along with infected food. Most of the bacteria will be killed by acid in the stomach, but the surviving bacteria invade the cells of the intestinal tract, going from cell to cell and thereby spreading the infection laterally. Intracellular movement of the bacteria is essential for this lateral infection to occur, and Listeria has been described to move with a "comet-tail" or like an "actin rocket". The Theriot Laboratory is studying how Listeria moves within cells, and results of this research may someday be used to generate vaccines or other means to prevent infection by Listeria. Currently, the only preventive measures are thorough cooking and cleaning of food, as well as pasteurization of dairy products. Treatment of Listeriosis primarly depends on antibiotics.
Check out this part of Dr. Theriot's site for more cool movies.


Thursday, July 5, 2007

64th Skeptics' Circle

The 64th Skeptics' Circle is up at Skeptical Alchemist. Go have a gander.


Tuesday, July 3, 2007

Free Atlas!

This week, my advisor received a free book in the mail. The Atlas of Creation, Volume I, by Harun Yahya. In the accompanying letter he writes:

While Darwin asserted his theory, he suggested that living beings evolved from one another and that we would see the emergence of intermediate forms as more and more fossil records emerge- with the hope that they might be found in the future--, but since then not a single intermediate form has been uncovered. On the contrary every unearthed fossil has refuted Darwin and carried the characteristics that prove the fact that "SPECIES HAVE NEVER CHANGED".
It's an enormous book, with large decent-quality photographs of things like mosquitoes in amber, and other demonstrations that organisms that were on the earth a few million years ago are similar to organisms that are on the earth today. And it asserts, over and over, (and often in full caps), that EVOLUTION IS FALSE. It's quite a read.

How did my advisor warrant such a gift? Is she a creationist? Well, from the scorn in her voice when she put it on the lunch table, I'll take it as a "No." Is she an evolutionary biologist? No. Well, when talking about this book with one of the grad students in the lab, I discovered that all of the principal investigators in our department have received this book in the mail. It's got to be worth $200 just for the photographs (though it retails for between $100-250, depending on where you find it), so our department alone makes it about $2000 spent on creationist books. So watch for your copy in the mail, apparently this guy has some cash to spend.

And who is Harun Yahya? Well, based on this photograph, I'd say he's in hiding, and only showing his wax body double. But from his website:
Born in Ankara in 1956... ...His intellectual activities opposing materialism and atheism began to elicit reactions from wider circles. Certain groups, alarmed by Adnan Oktar's nationalist and religious activities, set up a major conspiracy against him. Their plot coincided with the publication of his work Judaism and Freemasonry, which provoked an enormous response.
I'll bet it did. According to Wikipedia (take that for what it's worth):
The publication of Soykırım Yalanı sparked much public debate. [13] This book claims that “what is presented as Holocaust is the death of some Jews due to the typhus plague during the war and the famine towards the end of the war caused by the defeat of the Germans”[14].
I know that those of you in labs will be waiting with bated breath for your free copies of this page-turner.


Monday, July 2, 2007

Why good science matters.

The folks at Answers in Genesis are upset, apparently, about a column in USA Today that is critical of their little museum. To be fair, it doesn't single out Answers in Genesis (and they noticed it two years after the fact). It takes a broadside at all anti-intellectual tripe. I quite enjoyed it. My favorite bits:

It's so important that we protect and improve the science education in this country.

I say that because I like technology, and because I want to see more of it stamped (literally or figuratively) "Made in America."

That's why we need to worry about the state of American science education. If we can't give our kids an accurate understanding of the world, we can't expect them to give us better technology. The brains and products and jobs will be elsewhere, because good technology requires good science.
then there are national embarrassments like Cincinnati's Answers in Genesis Museum (to be fair, located just outside the city). Such institutions use fake "science" to convince gullible people of silly things. They show petrified wood (a few thousand years old) next to old bone (millions of years old). The objects look similar, so they'll say "See, dinosaurs were here a few thousand years ago!"

Gullible people believe them. Worse, every kid whose parents take him to places like that can probably be scratched from the list of 'America's Future Scientists."
That's why we develop theories to explain the evidence we have: Evolutionary theories (steady state, punctuated equilibrium, etc.) explain all the evidence we have for evolution; gravitational theories (general relativity, quantum gravity) explain the ton of evidence we have for gravity.

And when we have new information, we say, "Ah, that theory is wrong." And science gets better. That's why we can fit the entire Library of Congress on a few plastic platters, and why my father can come home from open-heart surgery after less than a week. Science learns. Science improves.

(Low-intelligence folks try to twist that, not surprisingly. They say, "Ha ha! Science has been wrong!" as opposed to "Oh, science corrects its mistakes.")

So we question our knowledge, refine it, and change it. And that doesn't mean questioning something for no good reason, it means questioning something because of new facts (not just old ideas rehashed or renamed).

A good indicator: When people have to resort to lies and distortions to promote their point of view — are you listening, Cincinnati? — it probably means they're wrong. A healthy argument is one thing; ignoring data, or trying to put bad research on par with good research, is another.
And finally a warning:
We're no longer a manufacturing economy; a quick count of all the "Made in China" labels in your house will probably confirm that. We're a service economy, and an economy based on intellectual property. If we want to dominate that market — in technology, in software, and in ideas — we need to make sure tomorrow's leaders have the best education they can get.
Thank you, Mr. Kantor.


Mark this day in 2007, the day that gene networks were discovered

There are at least two major ways that science articles in newspapers can fail.

The first is the "No, duh." coverage. That is, the article is presenting things that scientists have known for years if not decades, but presenting it like it's a major new discovery that will require major rethinking of how that area is studied. The second is the "the goblins will get you!" coverage, that is that if it weren't for the genius working at PETA, we wouldn't know that we're all going to die, when in fact the data say nothing of the sort.

Denise Caruso managed to hit a double this weekend in the New York Times entitled (stupidly): A Challenge to Gene Theory, a Tougher Look at Biotech. Let's start with her grandiose opening statement:

The $73.5 billion global biotech business may soon have to grapple with a discovery that calls into question the scientific principles on which it was founded.
Gee whiz! That sounds exciting! If only it were true...
Last month, a consortium of scientists published findings that challenge the traditional view of how genes function... (snip) ...To their surprise, researchers found that the human genome might not be a “tidy collection of independent genes” after all... (snip) ...Instead, genes appear to operate in a complex network, and interact and overlap with one another and with other components in ways not yet fully understood.
*gasp!* Really? They operate in networks? Sort of like this paper by Jacob and Monod suggested in 1961? The statement that "genes appear to operate in a complex network" is like saying that "the liver operates in a complex environment". Of course the liver works with other organ systems. This is not news. We've known about networks for a really long time, and with each year we're understanding more and more of these networks, and finding more and more spokes to them. In the last ten years, the study of networks has even become a discipline of its own, called systems biology. This is not new.
Biologists have recorded these network effects for many years in other organisms. But in the world of science, discoveries often do not become part of mainstream thought until they are linked to humans.
Or at least, in the world of newspapers. This has been mainstream for years.

Unfortunately, Francis Collins (director of the National Human Genome Research Institute) gave a misleading quote on their website, which is quoted in the New York Times article:
Because of the hard work and keen insights of the ENCODE consortium, the scientific community will need to rethink some long-held views about what genes are and what they do, as well as how the genome's functional elements have evolved.
While Ms. Caruso seems to think this means that he's discovered that gene networks exist, it seems more likely that he means that they have discovered particular networks that will make it easier to understand particular diseases. I admit, he's not being clear, and she bases the first half of her article off of this quote. (And I find it hard to believe that Francis Collins is stupid enough to think this study marks the discovery of gene networks).

So where does she take this credulous party off to next? Why not fearmongering?! (I've covered her scaremongering here in the past). Enter fearmonger Jack Heinemann, (director of the Center for Integrated Research in Biosafety):
“Because gene patents and the genetic engineering process itself are both defined in terms of genes acting independently,” he said, “regulators may be unaware of the potential impacts arising from these network effects.”
They're also unaware of the possible interactions between cheese and tomato sauce, and yet we don't test these in combination (and cheese is a living food product, after all!). This is yet another case of someone demanding that testing be done of every possible interaction between different genes and the food that they are placed in. Why? Knowing that your food has a complex network of genes that may be changed by the introduction of a foreign gene doesn't change the fact that the constituents of that food don't change.

Here's an analogy. If you remove someone's kidneys, you will find that they now require dialysis because they can no longer process out the urea from their blood. Without dialysis, they will eventually poison themselves and have multiple organ failure. However, you can say for sure that they will not grow wings and breathe fire, just because you messed up their organ homeostasis.

In the same way, adding foreign genes to plants, you can only get what you put in. You may increase the amount of protein, or decrease the amount of carbohydrate, or make the plant grow slower, but you won't get a corn plant with wings that is poisonous to humans merely by inserting the BT-gene. You can only get what you put in.

From Denise Caruso:
Now that the consortium’s findings (that there are gene networks) have cast the validity of (the gene) theory into question, it may be time for the biotech industry to re-examine the more subtle effects of its products, and to share what it knows about them with regulators and other scientists.
Oy. This just makes me cringe. Please, Ms. Caruso. Please. The stupid. It burns...