October 2, 2005 - October 8, 2005 Archives

Drawing a Line in the Academic Sand

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Two recent articles in Inside Higher Ed News are presenting a good overview as to how academics view Intelligent Design.

Drawing a Line in the Academic Sand and Common Ground on Intelligent Design

The first article discusses the statement by the President of the University of Idaho.

President White Wrote:

“Because of the recent national media attention on the issue,” reads President Timothy P. White’s letter, “I write to articulate the University of Idaho’s position with respect to evolution: this is the only curriculum that is appropriate to be taught in our bio-physical sciences.” The short letter goes on to allow for the teaching of “views that differ from evolution” in other courses, like religion and philosophy, but not as a scientific principle, which is “testable and anchored in evidence.”

They quote Harold Gibson, a University of Idaho spokesperson

Gibson said that if he were a faculty member interested in “intelligent design,” he would actually feel better because of the letter. “It clearly states there is a place for teaching of views that differ from evolution, as long as they’re in faculty approved curricula,” he said

Thus far this week, I’ve discussed the history of pandemic influenza in general, and avian flu in particular. I’ve discussed some issues that must be addressed to prepare us for a pandemic, and the groundbreaking resurrection of the Spanish influenza virus. Today I want to end the series with a look at how prepared we currently are as a nation, and highlight some personal preparedness steps you can take.

If you recall from Tuesday, the first outbreak of H5N1 was back in 1997. The anthrax attacks were in 2001. Surely by now we’re prepared for some kind of serious, large-scale, biological event, right? Well…

The Feds: “um, er, the dog ate my homework?”

The U.S. is still working on finalizing its Pandemic Influenza plan, which it keeps promising will be done “soon.” But scientists are a bit skeptical…

“We need more than just a plan; we need the resources to actually activate it,” said Jeffrey Levi, a pandemic specialist at the Trust. “The real test of the plan will be whether it comes with dollars attached.”

The current draft of the administration’s plan fills several hundred pages. It describes the role of the federal government in coordinating the response to a flu pandemic and outlines steps to be taken at all levels of government before and during an outbreak.

In addition to production and stockpiling of vaccines and antivirals, the plan seeks to conduct research, prepare public education campaigns and develop ways for hospitals to handle large numbers of patients.

Continue reading (at Aetiology)

As we’ve pointed out before on the Panda’s Thumb, the proposed intelligent design textbook Of Pandas and People indicates that intelligent design was simply a rebadging of creationism. In view of that, let’s look at the short chapter of the 1993 edition of Pandas which discusses human evolution. Here are some quotes from that chapter:

Does the fossil record provide any evidence for either the Darwinian or the intelligent design view of man? (p.107)

Homo erectus had a larger brain (950cc) than Homo habilis, and walked with an upright posture, like man…. It had significant anatomical differences from modern man that have prevented its classification as Homo sapiens. (p.110)

Design adherents, however, regard Homo erectus, as well as the other hominids discussed in this section, as little more than apes, and point instead to the abrupt appearance of the culture and patterns of behavior which distinguish man from apes. (pp.112-3)

Who are these “design adherents” who regard Homo erectus as “little more than apes”?

From the York Daily Record we receive the following article how desperate the defense was to discredit Forrest.

Various ID organizations have been active trying ‘muddle the water’, underlining how afraid they must be of the scholarly evaluation of the Wedge Strategy and of Pandas and People.

HARRISBURG — Along about the 658th hour of Dr. Barbara Forrest’s stay on the witness stand, during Day Six of the Dover Panda Trial, I started looking for her horns.

Never did see them.

It was right about the time that defense lawyer Richard Thompson was repeatedly asking about her various memberships in such seditious, treasonous and just plain evil organizations as the New Orleans Secular Humanist Association and the ACLU that it occurred to me to look for her horns.

They weren’t there.

Now, it could be that she was hiding her tail under her trim black pantsuit, but frankly, I didn’t really look.

Supreme Court nominee Harriet Miers has

given 10 percent to 12 percent of her earnings – “if not more” – to the evangelical Valley View Christian Church in Dallas, where she has been a congregant for about 25 years

according to Judge Nathan Hecht of the Texas Supreme Court, who has dated Miers. This Newsday article has the details.

What has this to do with Panda’s Thumb? A lot!

I know I said I was going to discuss a bit more about pandemic preparedness today, but I think I’ll hold off on that to discuss this story:

It sounds like a sci-fi thriller. For the first time, scientists have made from scratch the Spanish flu virus that killed millions of people in 1918.

Why? To help them understand how to better fend off a future global epidemic from the bird flu spreading in Southeast Asia.

Researchers believe their work offers proof the 1918 flu originated in birds, and provides insights into how it attacked and multiplied in humans. On top of that, this marks the first time an infectious agent behind a historic pandemic has ever been reconstructed.

Continue reading (at Aetiology)

With the recent Amicus Brief, it has become even more relevant to address claims that there is a scientific controversy or discussion about intelligent design. I argue that from a scientific perspective the discussion is already over. ID has shown itself to be scientifically vacuous, based on flawed premises.

I am not alone.

It would ‘become the death of science’. Ker Than reports on the ‘controversy’ surrounding intelligent design, pointing out that a new scientific theory must offer something compelling.

But in order to attract converts and win over critics, a new scientific theory must be enticing. It must offer something that its competitors lack. That something may be simplicity, which was one of the main reasons the Sun-centered model of the solar system was adopted over the Earth-centered one centuries. Or it could be sheer explanatory power, which was what allowed evolution to become a widely accepted theory with no serious detractors among reputable scientists.

So what does ID offer? What can it explain that evolution can’t?

To answer this, it is necessary to examine the two main arguments — irreducible complexity and specified complexity — that ID proponents use to support their claim that a Supreme Being is responsible for many or all aspects of life.

Based on an evaluation of the two main arguments, the author comes to a conclusion similar to that of various others who have asked very similar questions.

nodal in zebrafish

Do vertebrate embryos exhibit significant variation in their early development? Yes, they do—in particular, the earliest stages show distinct differences that mainly reflect differences in maternal investment and that cause significant distortions of early morphology during gastrulation. However, these earliest patterns represent workarounds, strategies to accommodate one variable (the amount of yolk in the egg), and the animals subsequently reorganize to put tissues into a canonical arrangement. Observations of gene expression during gastrulation are revealing deeper similarities that are common in all deuterostomes—not just vertebrates, but also the invertebrate chordates (tunicates and cephalochordates) and echinoderms.

What does all that mean? If you think of development as a formal dance, the earliest stages are like the prelude; everyone is getting out of their chairs around the ballroom, looking for partners and working their way towards the floor. The dispositions of the dancers are variable and somewhat chaotic, and vary from dance to dance. Once they get to their positions, however, we're finding that not only is there a general similarity in their arrangements, but they're all dancing to the very same tune. In this case, one of the repeated motifs in that tune is a gene, Nodal, which is active in gastrulation and shows a similar pattern in animal after animal.

Continue reading "The evolution of deuterostome gastrulation" (on Pharyngula)

Tangled Bank #38

The Tangled Bank

It's here! Yet another feast of science blogging is available for your delectation at Living the Scientific Life.

The scientific community is all too familiar with the dangers an influenza pandemic could bring. The politicians and general public are starting to become aware of the issue as well; indeed, one can hardly open a newspaper or turn on the television without hearing about “bird flu.” So, what’s actually being done to prevent an influenza catastrophe? What are the issues? What can be done?

These are the questions that keep public health officials awake at night, because the answer is always that we’re not doing enough. While we may be resigned to the fact that a future pandemic can’t be completely prevented, the damage can be minimized. Today, I’ll discuss the problems we face, and the proposed solutions to counter them, when it comes to pandemic influenza preparedness.

Continue reading (at Aetiology)

Allies of ID creationism have filed a friend-of-the-court brief in the Kitzmiller case which you can read here. It essentially argues that the court should not address the scientific validity or invalidity of ID; "[T]he scientific theory of intelligent design [sic] should not be stigmatized by the courts as less scientific than competing theories," the brief argues. (p. 5) Of course, determining that a set of assertions is not scientific is not necessarily to "stigmatize" those assertions, but simply to understand their nature; it's not stigmatizing a duck to say that if it quacks and waddles and has feathers, it's a duck. ID is not science because it is not a testable explanation of natural phenomena in terms of other natural phenomena. Instead, it's an assertion that phenomena can only be explained by invoking non-rational, non-testable, non-repeatable magical phenomena.

More Zany Young Earth Creationism

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Many readers and posters to PT are well versed in the sheer zaniness of Young Earth Creationism. But even after reading YEC literature for over 10 years, every now and then I’ll come across something that makes me burst out laughing and saying to myself, “No, these guys cannot be serious.”

You really have to exercise some pretzel logic (just to work in a reference to a pretty cool Steely Dan album) to buy into a 6,000 year old earth, and a boat floating around for about a year with 16,000 animals taken care of by 8 people.

A perfect example of this double-jointed mind game came to me in an email from AiG a few days ago containing a link to a PDF pamphlet penned by Ken Ham, AiG’s President. (http://www.answersingenesis.org/Home/pdf_notice.as…)

Aside from offering a series of sheerly absurd explanations of how they fit that many animals on board (they took babies), fed them all (a lot of them hibernated, so they didn’t eat), ventilated the ark (without smelling like their heads were shoved into a gorilla’s armpit), and shoveled up all the poop (probably done by undocumented workers, hence not mentioned in Genesis for tax purposes), Ham also wrote a short section regarding the building of the Ark.

Cardinal backs evolution and “intelligent design”

A senior Roman Catholic cardinal seen as a champion of ”intelligent design” against Darwin’s explanation of life has described the theory of evolution as ”one of the very great works of intellectual history”.

Vienna Cardinal Christoph Schoenborn said he could believe both in divine creation and in evolution because one was a question of religion and the other of science, two realms that complemented rather than contradicted each other.

Schoenborn’s view, presented in a lecture published by his office today, tempered earlier statements that seemed to ally the Church with United States conservatives campaigning against the teaching of evolution in public schools.

Anyone working in the area of influenza virus epidemiology is familiar with the name Robert Webster. A virologist at St. Jude’s Children’s Hospital in Memphis, the native New Zealander has been leading the charge against influenza for well over 40 years. Barely out of graduate school, Webster hypothesized that something like genetic reassortment (which had not yet been discovered) occurred to cause the big changes that appeared among human influenza viruses, driving pandemics. He performed a simple experiment that cemented the course of his career: he found that serum from patients who had survived the 1957 influenza pandemic reacted with avian influenza viruses. Later genetic analyses showed that the “Asian flu” virus had indeed received 3 of its 8 gene segments from birds. It happened again in 1968: the pandemic virus was the result of a reassortment between human and avian influenza viruses. These observations led to more than 30 years of surveillance of waterfowl in many different countries, and the revelation that these waterfowl constitute a reservoir of all known subtypes of influenza virus.

Webster’s worst fears seemed to be coming true in 1997. Hong Kong was experiencing an influenza outbreak in chickens so severe it had been nicknamed “chicken Ebola.” Humans were also affected. The first case was in a 3-year-old boy from Hong Kong. Though doctors knew he had died of the flu, they were uncertain of the strain, and sent samples off to several high-level laboratories for further testing. When it came back H5N1, the Centers for Disease Control and Prevention sent Keiji Fukuda to Hong Kong to investigate. After a month of searching, he and his team found no further evidence of infection with this avian virus in the human population—so they left, writing off the boy’s illness as a “freak occurrence.” They were premature. By the end of the year, 18 cases had been confirmed; 6 died. Clinical features often included a primary viral pneumonia and death quickly after onset of symptoms. The route of transmission in all cases appeared to be direct bird-to-human contact. Fearing a public health crisis, officials ordered the culling of Hong Kong’s entire poultry population. Analysis of the virus showed it to be a serotype H5N1 virus.

Continue reading (at Aetiology)

The Tangled Bank

Today is the day to get your links in for the Tangled Bank appearing tomorrow at Living the Scientific Life. Send them in to GrrlScientist, me, or host@tangledbank.net.

The Holy Grail of biochemistry is what’s known as the “protein folding problem“. We’ve long known that most proteins’ function is based on their 3-dimentional structures (i.e. their folds), and that these structures are dependent on their linear amino acid sequences. What we haven’t known is how exactly their amino acid sequences determine their structures. This would be an extremely useful thing to know, because currently the only way to determine a protein’s 3D structure is through X-ray crystallography or NMR, both of which are expensive, time-consuming, and aren’t even guaranteed to work. If the protein folding problem were solved, the thousands and thousands of proteins that we’ve sequenced could have their structures deciphered almost overnight, revolutionizing our understanding of how proteins function. Of course it probably won’t happen that way; the protein folding problem will probably be slowly chipped away at rather than solved in one fell swoop, and crystallographers and NMR spectroscopists will remain gainfully employed for the foreseeable future.

But two papers published in a recent issue of Nature from the lab of Rama Ranganathan knocked a chip out of the protein folding problem. Their results show us that protein folding might be simpler than we think.

PT Lauded by Scientific American

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Since no one else has done it, on behalf of my colleagues here I’ll immodestly draw attention to Scientific American’s selection of Panda’s Thumb for one of its 25 “Science & Technology Web Awards 2005”.

If it’s in the media and related to evolution, you’ll find it posted, dissected and debated on this lively and informative watchdog blog. Devoted to debunking all existing and nascent theories related to the anti-evolution movement, the site’s contributors comprise a passel of the world’s most vigilant and passionate biologists, geneticists, students and concerned citizens, for whom stemming the tide of creationism and its offshoots is a fulltime job. The general public can join the fray in the “After the Bar Closes” forum, where political, religious and personal evolutionary arguments are given a full dressing-down by the site’s rowdy, articulate devotees.

The Loom, where Carl Zimmer holds forth on the biological sciences with clarity and erudition, was also selected along with 23 other excellent science and technology sites in whose company we’re honored to find ourselves. Go read ‘em all!


Eureka Alert

The largest-ever experimental analysis of duplicated genes provides insight into mechanisms of evolution

Zürich, Switzerland – When Mother Nature creates an identical copy of a gene in an organism’s genome, the duplicated copy is usually deleted, inactivated, or otherwise rendered nonfunctional in order to prevent genetic redundancy and to preserve biological homeostasis. In some cases, however, gene duplicates are maintained in a functional state. Until now, the biological and evolutionary forces behind the maintenance of these duplicates as functional components of the genome have remained unclear.

But I thought biologists were too “close-minded?”

Australians Barry J. Marshall and Robin Warren won the 2005 Nobel Prize in medicine Monday for showing that bacterial infection, not stress, was to blame for painful ulcers in the stomach and intestine.

The 1982 discovery transformed peptic ulcer disease from a chronic, frequently disabling condition to one that can be cured by a short regimen of antibiotics and other medicines, the Nobel Prize committee said.

Thanks to their work, it has now been established that the bacterium Helicobacter pylori, which the new Nobel winners discovered, is the most common cause of peptic ulcers.

Woodward and Pitts on ID

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In an article published October 1 in the New York Times, “Evolution as Zero-Sum Game”, Kenneth Woodward makes an interesting observation:

The danger in intelligent design is not just that it is bad science but that it seeks to enlist evidence from science in the service of religious truth…. But the designer God of intelligent design is no more necessary to Christianity (or other monotheisms) than was the deistic God of Newtonian physics. In both cases, God ends up being made in the image of an intellectual system.

And in a column in the Lawrence Journal World today, Leonard Pitts writes,

I would argue that faith and science are in some ways more complementary than contradictory. But it’s telling that where they do conflict, as in the question of human origin, it’s always people of faith who beg for validation…. There is an unbecoming neediness about these constant schemes to dress religion up as science. Why are some people of faith so desperate for approval from a discipline they reject? …

We inhabit a universe vaster than human comprehension, older than human wanderings, more wondrous than human conception. And in the face of that, we do the natural thing. We ask questions and seek answers.

That’s not a denial of God. It is evidence of Him.

It’s hard to avoid hearing about influenza virus these days. In all the noise, it’s tough to sort out the facts from the rumors and conspiracy theories. I’ve already discussed a bit about the basic biology in this post, so I’m not going to review that here (though a good overview can be found here for those of you who need to bone up on your influenza virus virology). So, this week, as a part of Pandemic influenza awareness week, I’ll be writing a 5-part series about various issues regarding influenza. Today, I’ll discuss the history of influenza, focusing on past pandemics. The rest of the week will address the following topics, with the goal of presenting a review of the facts without the scare-mongering:

  • “Avian flu” and H5N1, 1997-present
  • Where we are now—are we ready for a pandemic?
  • How do we prevent/control a pandemic? What models and surveillance can tell us
  • Other issues in influenza

So, without further ado, let’s dive into today’s topic:

A quick trip through the history of pandemic influenza (on Aetiology)

Link Sunday, October 02, 2005 BY MARY WARNER Of The Patriot-News

Darwin and God seem irreconcilable to many Americans. That’s why evolution remains a flashpoint in public schools.

Many others see no conflict, though. And that reconciliation has been a subtext of a closely watched federal trial in Harrisburg about teaching evolution.

”Faith and reason are not only compatible. They are complementary,” testified Ken Miller, a biologist who took the stand to affirm Charles Darwin’s theory as established science.

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