Wednesday, July 27, 2005

Tangled Bank #33 -- 27 July 2005

Tangled Bank – Table of Contents Alert

A New Issue of the Tangled Bank has been made available:

27 July 2005; Vol 1, No. 33


Submissions to this issue of the Tangled Bank come from the physical sciences, biological sciences, biomedical sciences, and other related fields. They have been organized, for your convenience, according to research areas.

Journey Through Time
Pat Hayes at Red State Rabble
Pat Hayes goes to the Grand Canyon and uses the evidence he finds there to refute creationist claims.


What’s the Deal With Fluoride?
Steve Pavlina at Steve Pavlina’s Personal Development Blog
A critical look at fluoride in your drinking water. The author questions the use of fluoride, much like Gen. Ripper speaking to Mandrake in Dr. Strangelove, and comes to the conclusion that the addition of fluoride to water supplies does more harm than good.

Systems Biology – Biology of the Future or Newest Fad?
Alex Palazzo at The Mad Scientist
Biologists have an inferiority complex, or so the author claims. They look up at physicists with envy as studies of atom smashing and telescopes garner attention from the popular press, while insights into cell division only see publication in scientific journals. What’s a poor biologist to do other than go interdisciplinary and create Big Biology?

Dr. E. Fuller Torrey, M.D., Wanker
Heinrich Gompf at She Flies With Her Own Wings
A U.S. Congressman attempted to de-fund an NIH grant because he does not believe that the National Institute of Mental Health should support research on pigeons. Dr. Torrey’s Wall Street Journal op-ed inspired this defense of studying neurobiology and behavior in model organisms and the peer-review process in general.

Go Practical
Adam Ierymenko at Grey Thumb
The author presents an alternative approach to going after anti-evolution groups. He suggests that instead of debating creationists, scientists should take advantage of what evolution does for the non-scientists. One such approach is to market technologies that take advantage of evolutionary theory as such.


Super-Adequate Structural Homologies, or The Ornithorynchus Shuffle
Scott Eric Kaufman at Acephalous
Charles Darwin was not the only person writing about evolution in the nineteenth century; he simply had the best mechanism – natural selection – for the evolutionary process. Inspired by a recent review of a book about another book published prior to On the Origin of Species, the author compares Robert Chambers’s Vestiges of the Natural History of Creation with Darwin’s more legendary work.


Deep Impact (Live): Much Cooler Than a Mediocre Blockbuster
Millagan at EGAD
An astronomer’s play-by-play account of the Deep Impact probe’s collision with the comet Tempel 1. He provides images of what happened along with descriptions of what to look for in those images.

Physics and Chemistry

Two cheers for string theory
Sean Carroll at Cosmic Variance
A physicist, “who is not personally identified as a string theorist,” gives us some insight into an often misunderstood realm of physics. We learn that string theory explains quantum gravity better than any other approach. The author proceeds to defend the theory explaining that it does have applications despite what some critics claim.

Moral Relativity
Matt at Pooflingers Anonymous
Einstein came up with the theory of general relativity (E=mc2) and was the first person to relate the energy and mass of an object in a simple equation. The author offers a similar equation for moral relativity complete with a derivation and application.

Not All Things Freeze
Jeff Shaumeyer at Bearcastle
Spurred by an offhand remark in a book, the author questions the idea that “all things freeze when they get cold enough.” The discussion centers on helium, the only element that will not freeze under its own vapor pressure, and the physical characteristics of the different states of matter.


Dynamic Forces
Rock of Ages
Pat Hayes at Red State Rabble
A journey through the Grand Canyon reveals insights into the formation of rock strata and how geologists use inference to reconstruct earth history.

Cellular and Developmental Biology

The History of Tubulin Detyrosination
Alex Palazzo at The Mad Scientist
Discoveries over thirty years ago revealed that the alpha-tubulin protein is modified in nerve cells. The author discusses the history of these discoveries as well as how they were interpreted and future directions in tubulin modification research.

Development, medicine, and evolution of the neck and shoulder
PZ Myers at Pharyngula
The development of neck and shoulder bones has confused biologists long after they solved the major developmental patterns in the hindbrain and spine. A new study uses transgenic mice to follow the fate of neural crest and mesodermal cells in order to unravel the mystery. The findings also shed light on a bone that has gone missing in most tetrapods, but is found in fish.


More Pelican Puzzlement
Mike at 10,000 Birds
One of the nation’s largest American White Pelican nesting colonies is losing members and at a rapid pace. This piece explores a few possible hypotheses, but none of them can explain the phenomenon. Maybe there’s too much fluoride in their drinking water.

Close Encounters
Pamela Martin at Thomasburg Walks
The author writes about an encounter with a deer and a fawn when visiting a region near Thomasburg, Ontario. This particular encounter may explain previous observations of deer in the wild.

Formicidae Imports: The Argentine Ant
Chris at Organic Matter
The common, household ant found throughout the southern United States is actually an invasive species from Argentina. Eradicating this invader has been problematic as different environmental factors exist in the native and ancestral populations.


Ancestral Magnitudes
DarkSyde at Unscrewing The Inscrutable
The author intertwines genealogy with evolution to determine how many grandparents it takes to get from humans to different human ancestors, such as early primates, primitive mammals and early vertebrates. The article attempts to trace human ancestry back to the beginnings of the universe.

The Genotype and the Phenotype and How to Measure Divergence
RPM at evolgen
While calculating percent divergence from molecular data is a fairly straightforward procedure, morphological measurements are tainted with subjectivity. The author argues that comparing sequence level estimates of divergence to phenotypic estimates can only lead to faulty conclusions about the relative roles protein sequences and regulatory elements play in anatomical evolution.

Sleeping the summer away 2: converging in on an epiphragm
Aydin Örstan at Snail’s Tales
Two distantly related families of snails close their apertures with calcareous epiphragms, whereas close relatives of these families have a membrane-like epiphragm. The article describes these physiological differences in snails, and the author argues that they arose independently via convergent evolution in the two taxa.

Information From Randomness?
Jim Clark at JC’s Blog
In Richard Dawkins’s The Blind Watchmaker the author uses a computer algorithm to change a random string of letters into a predetermined sentence by selecting for letters that match the target string. This article argues that Dawkins’s “Weasel” algorithm does not accurately simulate the origin of information from a zero information state.


Andrew at Universal Acid
A recent study on how your brain processes images while you blink leads to this discussion of how the human brain interprets visual input.

Immunology and Medicine

Infectious Disease Genetics
Hsien-Hsien Lei at Genetics and Public Health Blog
Despite improvements in disease prevention and treatment, many people still die from infections. An epidemiologist suggests that new developments in the field of pathogenomics will provide the next step forward in combating infectious disease.

Andrew MacGinnitie at Dr. Andy
In the earliest days of anti-microbial treatments, some researchers tried developing bacteriophages to combat infections. These attempts went by the wayside with the advent of penicillin and other antibiotics. With the increase of antibiotic resistance amongst virulent strains of bacteria, researchers are once again turning to phages to treat bacterial infections.

Dealing with conflict
Orac at Respectful Insolence
Dr. John Ioannidis, M.D. recently examined high profile, highly cited medical trials and their follow-up studies and determined that at least 1/3 of the original publications were refuted by subsequent papers. Orac explains what this means for medical research and how to interpret the results in the light of alternative medicine.

Applied Biological Sciences

Rediscovering Nature
Ironman at Political Calculations
Car designers at DaimlerChrysler turn to the sea with their newest concept car. Using the boxfish body plan as guidance, they came up with a vehicle that had low drag coefficient and a lightweight yet sturdy structure.

Agricultural and Plant Biology

Science can be tasty!
Kitty O’Neil at Science and Sarcasm
New potatoes are young tubers that are not fully mature. The author describes the differences between these and regular potatoes, and why she enjoys them as a summertime delicacy.

The Poetry of Leaves
Nuthatch at Bootstrap Analysis
A look at how leaves are arranged on a stem. A mathematical view of leaf arrangements focusing on similarities and patterns found amongst different plant taxa, and why they are arranged that way.


Human Habitation of the Canyon
Pat Hayes at Red State Rabble
The earliest human settlers in the Grand Canyon arrived over ten thousand years ago. The author explores some of the evidence for these humans on the walls of the canyon.


The Wizarding Apprentices' Surprising Discovery
GrrlScientist at Living the Scientific Life
A university instructor deals with scheduling an exam that conflicts with the release of the newest Harry Potter book, only to discover that the lecture professor is also a Harry Potter fan.


Hybrid vs. Hybrid and how the Times gets it wrong
Joel Shurkin at …Of Cabbages and Kings
The New York Times recently ran a front page article on hybrid cars in which they claim hybrids “improve performance but don’t save gasoline.” The author takes umbrage at this claim, arguing that pure hybrids do, in fact, improve gas mileage, and the Times did not consider pure hybrids in their article.

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The next issue of the Tangled Bank will be at Creek Running North on 10 August 2005. The editors invite you to submit your entry directly to or


At 12:07 PM, Blogger Bora Zivkovic said...

Wow - this looks great! Again, a day when I get nothing else done, I expect...

At 1:21 PM, Blogger Bora Zivkovic said...

Yup, I was also struck by those two... looks more like stuff that would be debunked in the Skeptic's Circle.

Still, as much as I read science blogs, I was amazed at how many of these posts I have not read yet prior to today.

At 3:28 PM, Blogger RPM said...

A bit of clarification about the anti-evolution post and the anti-fluoridation post:

I included them despite despite my initial reaction to do otherwise.

Basically, I didn't feel I could fairly (with my limited knowledge in the subject matter) disregard the fluoridation post. I'll leave it up to those with a more comprehensive knowledge of the material to refute the claims made in the post -- just because I'm the messenger does not mean I endorse the message. Some people have already pointed out that he attacks straw men and does not use well regarded data.

The "anti-evolution" post only refutes Dawkins's example, not all of evolutionary theory. It's more on whether or not the genetic code could have arisen from nothing. Once again, I'll leave it up to the reader to decide whether or not the Dawkins analogy is appropriate and if the author adequately refutes it.

At 5:10 PM, Blogger Sunil said...

absolutely outstanding edition of the TB. Great job....and it's better than this week's nature issue :-)

At 11:56 PM, Blogger Bora Zivkovic said...

Are you sure Creek Running North is the next host? Tangled Bank homepage says it is Cognitive Daily.

At 8:21 AM, Blogger RPM said...

The schedule had to be updated (again). I guess the Tangled Bank page is yet to be updated.

At 12:30 PM, Anonymous Anonymous said...

Wow. Something useful on weblog -- so obviously it must a science and not politics blog. Great collection!

(I also read the Dawkin's argument, btw, as more over the example than the premise).

Looking forward to the next.

At 1:34 PM, Anonymous Anonymous said...

The fluoride article is full of misrepresentations, partial truths and quotes out of context. Even if you don't know the specifics of the evidence, a casual reading (and look at other articles on that site) should have been sufficient to know that this is pseudoscience at its worst.

The evidence that fluoride prevents dental caries is overwhelming.

Please educate yourself if you're going to reference ridiculous article like this.

For shame.

At 8:40 PM, Blogger jqb said...

"Basically, I didn't feel I could fairly (with my limited knowledge in the subject matter) disregard the fluoridation post."

But statements such as these should have been enough:

"Essentially, fluoride makes you a bit less intelligent."

"the bottom line is that fluoride is an industrial pollutant which became a serious problem several decades ago, and this problem was essentially solved by devising ways to feed the stuff to humans."

"So what are the health reasons for water fluoridation? There aren’t any."

"By reducing the acidity of your diet, you can safely prevent your teeth from dissolving."

At 9:04 PM, Blogger jqb said...

> The "anti-evolution" post

Why the scare quotes, when the post starts "Those who ascribe to the faith called Evolution ... They would like to believe that somehow information can arise out of randomness, but we who design computers know better."?? What could be more anti-evolution than that? I mean, c'mon. The fellow is explicitly a creationist, and he's offering the standard creationist argument against Dawkins's program, an argument that has been refuted by Dawkins and others numerous times.


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