Archive for December, 2006

A nice discovery on neurons from UF

Friday, December 29th, 2006

GAINESVILLE, Fla. — Scientists analyzing the genomics of a marine snail have gotten an unprecedented look at brain mechanisms, discovering that the neural processes in even a simple sea creature are far from sluggish.

At any given time within just a single brain cell of sea slug known as Aplysia, more than 10,000 genes are active, according to scientists writing in Friday’s (Dec. 29, 2006) edition of the journal Cell. The findings suggest that acts of learning or the progression of brain disorders do not take place in isolation — large clusters of genes within an untold amount of cells contribute to major neural events.

“For the first time we provide a genomic dissection of the memory-forming network,” said Leonid Moroz, a professor of neuroscience and zoology at the University of Florida Whitney Laboratory for Marine Bioscience. “We took advantage of this powerful model of neurobiology and identified thousands of genes operating within a single neuron. Just during any simple event related to memory formation, we expect differences in gene expression for at least 200 to 400 genes.”

Researchers studied gene expression in association with specific networks controlling feeding or defensive reflexes in the sea slug. To their surprise, they identified more than 100 genes similar to those associated with all major human neurological diseases and more than 600 genes controlling development, confirming that molecular and genomic events underlying key neuronal functions were developed in early animal ancestors and remained practically unchanged for more than 530 million years of independent evolution in the lineages leading to men or sea slugs.

Moroz and his collaborators uncovered new information that suggest that gene loss in the evolution of the nervous system is as important as gene gain in terms of adaptive strategies. They believe that a common ancestor of animals had a complex genome and different genes controlling brain or immune functions were lost independently in different lineages of animals, including humans.

Until now, scientists have been largely in the dark about how genes control the generation of specific brain circuitry and how genes modify that circuitry to enable learning and memory. For that matter, little is known about the genes that distinguish one neuron from the next, even though they may function quite differently.

Molecular analyses of Aplysia neuronal genes are shedding light on these elusive processes. In 2000, senior author Dr. Eric Kandel, of Columbia University in New York shared the Nobel Prize in Physiology or Medicine for his work using Aplysia as a model of how memories are formed in the human brain.

Despite its simple nervous system — Aplysia has about 10,000 large neurons that can be easily identified, compared with about one hundred billion neurons in humans — the animal is capable of learning and its brain cells communicate in many ways identical to human neural communication.

In the new findings, scientists identified more than 175,000 gene tags useful for understanding brain functions, increasing by more than 100 times the amount of genomic information available for study, according to Moroz and 22 other researchers from UF and Columbia University. More than half of the genes have clear counterparts in humans and can be linked to a defined neuronal circuitry, including a simple memory-forming network.

“In the human brain there are a hundred billion neurons, each expressing at least 18,000 genes, and the level of expression of each gene is different,” said Moroz, who is affiliated with UF’s Evelyn F. and William L. McKnight Brain Institute and the UF Genetics Institute. “Understanding individual genes or proteins is important, but this is a sort of molecular alphabet. This helps us learn the molecular grammar, or a set of rules that can control orchestrated activity of multiple genes. If we are going to understand memory or neurological disease at the cellular level, we need to understand the rules.”

Scientists also analyzed 146 human genes implicated in 168 neurological disorders, including Parkinson’s and Alzheimer’s diseases, and genes controlling aging and stem-cell differentiation. They found 104 counterpart genes in Aplysia, suggesting it will be a valuable tool for developing treatments for neurodegenerative diseases.

“The authors have assembled a tremendous amount of data on gene transcripts associated with neuronal signaling pathways in Aplysia that sheds new light on evolutionary relationships of this very ancient and highly successful marine animal,” said Dennis Steindler, executive director of UF’s McKnight Brain Institute, who did not participate in the research. “A very important part of this study is the discovery of novel genes not formerly associated with the mollusk genome that include many associated with neurological disorders.”

The findings are especially important for scientists using mollusks in experimental systems, according to Edgar Walters, a professor of integrative biology and pharmacology at the University of Texas Medical School at Houston, who was not involved in the research.

“Few animals other than Aplysia allow scientists to relate a molecular pathway directly to the function of a cell, all in context with an animal’s behavior,” Walters said. “In a mammal, it’s hard to identify and manipulate a single cell and know what its function is. With Aplysia, there is direct access to whatever cell you’re interested in with just a micropipette. As a scientist who wants to know which molecules are present in Aplysia for experimental manipulation, I am very happy to see this paper come out.”

Holiday Time!

Saturday, December 23rd, 2006

Happy Holidays (or Merry Christmas if you prefer) from Florida Citizens for Science to all of you! If I could send out a card to you, I think this would be my choice. Enjoy.

What a pitiful year

Wednesday, December 20th, 2006

John Lynch at his Stranger Fruit blog gives us a rundown of creationist activity over the past year. Summary of the creationist effort? Full of crap, defeated and “no one cares.” Hopefully, they’ll stay the course.

Georgia stickers lose

Tuesday, December 19th, 2006

A suburban school board that put stickers in high school science books saying evolution is “a theory, not a fact” abandoned its legal battle to keep them Tuesday after four years.

The Cobb County board agreed in federal court never to use a similar sticker or to undermine the teaching of evolution in science classes.

In return, the parents who sued over the stickers agreed to drop all legal action.

Science Teachers Selected for Grant Participation

Monday, December 18th, 2006

Wakulla County High science teacher Ann Kennedy was selected by the district’s superintendent for a unique training opportunity made possible by a $25,000 grant from Progress Energy. The timing of this training is critically important because, in 2006-2007, student FCAT science scores are tied to school grades.

“Because science is a field that changes daily due to research, it is important to stay abreast of new developments,” said Brenda Crouch, a consultant with the Panhandle Area Educational Consortium (PAEC). “One of the best ways to stay current is to attend a national conference that offers pre-conference institutes and more than 1,200 concurrent sessions for science educators. Professional development of this caliber is expensive, and our small, rural districts cannot afford to pay for teachers to attend the conference and for travel costs associated with attendance.” 

That is, until now. Kennedy joins eight other science teachers from northwest Florida who will attend the 55th Annual National Science Teachers Association National Conference March 29-April 1 in St. Louis, thanks to Progress Energy. 

Hunting for pythons

Monday, December 18th, 2006

Here’s a good story about the threat exotic species (pythons) pose to the Everglades and what scientists are doing about it. Notice the creative ideas for catching the elusive pythons.

After slipping, sliding and tumbling down a rocky embankment, Snow, a wildlife biologist, grabbed one of the creatures by the tail. The python, Oberhofer says, did not care much for that.

“It made a sound like Darth Vader breathing,” she says, “and then its head swung around and I saw this white mouth flying through the air.”

Snow saw the mouth, too – the jaws open 180 degrees, the gums an obscene white, the needle-sharp teeth bared in an almost devilish grin.

Yet, as vast and threatening as these wetlands may appear, they have been so drained and abused by humans in the last century that a population of pythons, if left unchallenged, could take down this fragile web of life within a generation.

“It’s a now-or-never thing,” Oberhofer says. “We still have a chance, with the python’s numbers being so limited, to do something. But if we let this go, we don’t know how far the pythons will migrate, how much they will reproduce.”

One thing is certain, Snow says. “They’ll eat just about everything that’s warm-blooded.”

“I’ve walked right by pythons and not even known they were right next to me,” he says. “Most times, you can’t see the enemy until you stumble across it.”

Crunching his way back to the off-roader, eyes darting this way and that, he described tactics to control pythons. One idea, recommended by snake management experts, has produced results: implanting captured pythons with radio transmitters and releasing them into the wild to track their movements, habitat use and breeding patterns – and to betray the locations of other pythons.

“It’s all based on the Judas concept,” Snow said, noting that four “tagged” pythons had led to the capture of 12 others through October and that three more pythons with transmitters have since been released.

Snow suspects that female pythons lay down trails of chemical scent “cues” for suitors. If scientists could develop synthetic cues, he says, the chemicals might be used to draw pythons into one of his traps.

A conversation with creationist John Baumgardner

Saturday, December 16th, 2006

I ran into John Baumgardner here at the American Geophysical Union meeting here in San Francisco. He was talking to a couple of people telling them that ‘we have new data showing decay rates aren’t constant’. They slinked away and John said ‘Can we chat for a moment? I’ve been reading your papers and thinking about how they apply to the flood story. I said please don’t misuse my papers and then I said, before we get to my stuff can I ask you a few questions. I list my questions and John’s responses:

1. John, I’ve always been critical of you for signing on to papers that discuss old earth mantle evolution or old moon. In my view these are completely antithetical to your beliefs and I think you are either a hypocrite or you are being deceiving. I know I would not co-author a paper that was so at odds with my own scientific views.

Baum: That has bothered me a bit. In some cases I’ve asked to be taken off, but my co-authors insist that the work could not have been completed without my input. So, I simply said to myself that ‘the physics used in the paper were fine’ and I agree with the physics in the papers.

2. But John, the physics in those papers are based on an old earth that you don’t believe.

Baum: Perhaps I should have been more careful.

3. It also bothers me that creationists like John woodmorappe (aka jan Peczkis) writes young earth articles under one name and old earth evolutionary articles under another.

Baum: That bothers me too.

4. Can I ask you a question that no young earth creationist will answer?

Baum: Sure.

5. Assuming that the geologic column was laid down in 6000 years, what deposits mark the onset of the flood, the peak flood and the post flood?

Baum: I think that we all agree that the flood started at the ‘great unconforrmity’? Somewhere around the Cambrian explosion of life.

6. John, it can’t be an explosion of life for you. It’s a death event right?

Baum: Right.

7. What about peak and post flood?

Baum: Peak flood would be Paleozoic and post flood is very hard to pin down.

8. I know that, but your group (young earth creationists) have had more than 150 years to figure this stuff out, what’s the problem? There are people like Jon Davison who argues that your onset is his post-flood recolonization.

Baum: Yes, I know. I don’t like that model.

9. Northrup argues for something in between Davison and your model.

Baum: I’ve talked to Northrup about that. It’s a shame we can’t agree.

10. The bible is your guidebook on the flood, surely the answer can be found there and there should be no need for such disagreement?

Baum: The flood story is only briefly mentioned. we have to fill in the gaps and that’s why it’s hard to answer your questions with specific.

11. So in fact, you don’t “all agree”. I have a different take on why nobody wants to answer these questions, there are things in the geologic record that are anathema to flood advocates. How do you explain the ubiquitous occurrence of paleosols in the geologic record (specifically in the Paleozoic since that’s your flood.)

Baum: I think paleosols have been misidentified.

12. On what basis?

Baum: I live in the southwest and I see a lot of rocks that remind me of a flood. Rocks like nowhere else in the geologic record.

13. Let’s get back to paleosols. What specifically makes you think that people like Greg Retallack has misidentified paleosols?

Baum: Well I’ve seen a lot of rocks.

14. So have I and so has Greg. Furthermore, both of us are trained as geologists and spend a lot of time looking at the same rocks you have. Paleosols (http://gondwanaresearch.com/hp/paleosol.htm) have burrow stuctures, root structures etc that make them hard to dismiss with a handwave.

Baum: There are rocks in the Paleozoic that are unlike any at any other time.

15. Ok, paleosols you are not going to answer. What rocks in the Paleozoic are unique?

Baum: Large bodies of sandstone that cover many many square miles.

16. Have you ever been to Mississippi, Louisiana and parts of Texas? The Mississippi river has left thousands of square miles of sand and silt in those states and in the gulf of Mexico. The rivers draining the Himalayas are creating absolutely huge plains of sand and silt (Gangetic plain and the Bengal fan).

Baum: Well, I’ve seen things that don’t look like anything else.

17. John, you’re a great geophysicist and Terra was a revolution in code-writing, but you’re not a geologist and perhaps a few courses in geology might help.

Baum: I’m not a geologist, but I see a lot in the southwest. let’s get back to the flood. Remember it’s going to be very fast movement. The oceans are going to open quickly with lots of eruptions and steam.

18. John, don’t you have a heat problem?

Baum: Yes, we know that.

19. John, it’s not a small heat problem.

Baum: Yes, we recognize that we have cooling problems to solve. Specifically how are we going to cool all that oceanic lithosphere.

20. I know John, I wrote up a small web page discussing the cooling profiles in the ocean floor that would be generated by your model (http://gondwanaresearch.com/oceans.htm. Have you seen it?

Baum: No, but I’ll have a look.

21. So how are you using my research?

Baum: Well, I’ve got a radical new idea.

22. John, flood geology is a very old idea (more than 200 years old at least), so nothing you propose can be considered radical. Creationists like Agassiz went out and studied the rocks and realized that a global flood was inconsistent with the biblical account.

Baum: Well, yes but think about going from your Rodinia to Pangea in a short amount of time. That’s just what inertial interchange true polar wander says.

23. Not really John but it sounds fascinating. Why don’t you send me your article and I’d be happy to critique it. I will obviously not agree with the premise, but I might be able to help you avoid some egregious errors in your analysis. It was nice to meet you and i’d be happy to chat further anytime.

Baum: Nice to meet you too.

Note: Any errors in recollection of these events is mine and mine alone. John also told me of some more ‘groundbreaking research’ coming from ICR, but I promised not to discuss it. I can tell you that it is neither groundbreaking or research. I also reminded him that he knows the science game really well and if he wants to be taken seriously he has to publish his models. He asked me if I’d seen his article in “New Scientist”. I haven’t, has anybody here? I mentioned that’s not exactly a peer-reviewed journal. Anyway, we parted there and i went to get another beer.

Cheers

Joe Meert

William Dembski shows the depth of research at Discovery Institute

Saturday, December 16th, 2006

One of the major criticisms leveled on the Intelligent Design movement is their lack of scientific research.  One wonders about how much time the fellows at the Discovery Institute spend conducting research.  I was surprised (well, not really) to find out that William Dembski (senior fellow at DISCO) is spending most of his time blogging and making cartoons.  Here’s his latest slam on Judge Jones (Dover judge):

http://www.overwhelmingevidence.com/id/JJ_school_of_law/

Dembski admitted that this is his voice and, in fact, the site is Dembski’s site.  I’m sure that this is sure to be played in any future court cases and illustrates the vacuous and sophomoric nature of the current intelligent design movement.  This video should be viewed as an embarrassment to the Discovery Institute and Dembski should be viewed as a liability to the ID movement.

Cheers

Joe Meert