Monthly Archives: October 2006

Nature 2006/10/12

Hmm. Lot’s of cool stuff in the Nature issue of 2006/10/12.

There’s the article on the use of ketamine to treat depression, and how its mechanism of action has got researchers rethinking what depression really is. Ketamine is a drug primarily used (legitimately) as an anesthetic agent in animals and young humans, and recreationally by adult humans as a psychedelic. Two-thirds of a study group of depressed people scored 50% on a quantitative assessment of depression, some of them finding themselves less depressed within two hours of treatment with ketamine. Ketamine’s target, unlike most anti-depressants currently prescribed that influence serotonin re-uptake, are receptors for glutamate in the brain. The resulting hypothesis is that in some patients, depression is the outcome of a brain that is over-producing glutamate, possibly as an abnormal response to stress. And there’s at least part of the rub. Depression may be a grab-bag of similar symptoms that patients may come to in a variety of different ways. It is certainly the case that patients with clinical depression may have to try several different anti-depressants before finding one that works well for their particular case; diagnostics do not yet make it easy to test a patient and determine the drug treatment of choice directly. Of interest was the sidebar item on John Lilly, the dolphin researcher with a thing for mind-altering drugs. My advisor, Bill Evans, had some anecdotes to tell about Lilly.

On the cosmological front, research reports that the transition from a quark-gluon plasma to hadronic matter was smooth rather than an abrupt phase transition, based upon high-performance computational analysis of the usual quantum chromo-dynamics (QCD) equations.

An article on the eyes of flies discusses how dipterans achieve higher visual resolution by subdividing their rhabdoms. Beyond the structure of the compound eye, it turns out that the rhabdom split plus some neural wiring leads to better visual acuity for dipteran flies.

Another item on vision concerns the co-option of plant photosynthetic chemistry by vertebrate species to transduce red light. This apparently happens in the wild in some fish. The brief communication shows that adding chlorin e_6, a chlorophyll derivative, to salamanders also boosted red light receptivity in vision. The article concludes that these results “highlight a potential for spectral enhancement by accessory chromophores in all opsin-based photoreception systems.”

While under the heading of ‘Developmental Biology’, a report on how signalling changes can lead to the growth of a two-chambered heart in the normally single-chambered tunicate Ciona intestinalis. This obviously has application to evolutionary questions about how changes in organs involving discrete numbers of sub-parts may come about. Evo-devo apparently comes up trumps for explaining such things as increasing the number of chambers in hearts.

A report on populations of pike in a lake with two almost completely separated basins shows that the populations match the “ideal free distribution” very well indeed. In animal populations, there are density-dependent effects, so high densities reduce overall fitness for members of the population. Different environments, such as different basins of a lake, can have their own and separate effect on fitness. The result is that there is an ideal free distribution such that members of a population cannot improve their fitness by changing from one environment to the other, and it turns out the the real-world pike populations match the ideal free distribution in the lake under study. This included a three-year period where human intervention changed the usual relationship in fitness between the two basins to make the one that generally had less fitness normally had higher fitness during that period. The pike population levels changed accordingly.

Of course, there is a clinker, the news item titled, “Intelligent design gets political”. Nature is years late with that assessment. ID always was political as socio-political movements can be. That it continues to be pushed politically hasn’t surprised those of us watching the antievolution movment.

Spam as DoS

The server here handles several WordPress weblogs. I have Akismet running, so they weren’t filling up with spam being served. What I hadn’t realized was just how much bandwidth and resources spammers were sucking out of the server. Reed Cartwright and I worked on the issue last night. Reed got a per-IP connection limiting module working with lighttpd, and I installed a basic “captcha” plugin for the various WordPress installations on the server. Sorry to make entering comments a little more difficult, but the spamming traffic was making it hard for real users to get near sites served from here.

Darwin Online

Darwin Online

Dr. John van Wyhe has been on a mission for years now to collect and make available the text of Darwin’s work online. The web site has been up for at least a couple of years, but now apparently has attracted the attention of Nature, so there is now a bit of a buzz. One thing that looks new-ish on the site, or at least I overlooked it before, is the availability of 2nd through 5th editions of the Origin of Species. Something that has been a long-term idea of mine is to produce a variorum of OoS, and now there is at least a resource to get the text of all versions from. There is another site that has a list of Darwin’s correspondence, but last I checked, they simply allow a search on an index, and do not provide the actual text of the correspondence.

So far as I can tell, no one has published an algorithm for production of a variorum version of three or more source works. This is in itself a neat little problem to work out. Certainly, if I do fit that in somewhere, I’ll get in touch with Dr. Wyhe to contribute something back to his project.

Photo Daydreaming

It seems unlikely that whatever insurance covers in the end will be sufficient to replace the photographic gear that I lost: a Fuji S2 Pro DSLR, a Nikkor 70-200mm f/2.8 VR lens, a Nikkor 28-105mm f/3.5-4.5 lens, and a Promaster 12-24mm lens. So I likely will have to compromise on something, somewhere.

But at the moment I’m indulging some fantasies, not looking at the far more dismal reality. If I could set about buying something within range of the original purchase price of the Fuji S2 ($2,400 in 2002), what would I be getting? I still have various other Nikon lenses, so I’m likely to remain with a Nikon system. About the only circumstance that might alter that is if some combination of Canon gear matching the feature set of what was stolen from me was significantly cheaper, while matching or exceeding the image quality. If somebody has some info on that, enter a comment.

So here are some of the choices I see…

Continue reading

Science and Modeling the Mind

The October 6th issue of Science had a special section of articles on “Modeling the Mind”. This is something that I enjoyed reading, having concentrated on the computational side of these techniques in studying for my master’s degree. For some time during my Ph.D., I was developing background to explore modeling the mental processing of biosonar in dolphins. Although my dissertation topic changed to something more clearly within physiology and bioacoustics, the techniques and approaches still are of considerable interest to me.

The first article concerns research by Jeff Hawkins, the inventor of the PalmPilot PDA. Hawkins developed a theory of action for the cerebral cortex, positing that the single functional operation that cortical neurons perform, as explicated by Mountcastle in the 1970s, was prediction of events. And Hawkins aims to convert theoretical knowledge into practical applications, having founded a software company, Numenta, to develop applications based upon theories of neuroscience.

Maybe once I calm down from the recent theft of our stuff, I will take up commenting on some of the other articles. It really is good to see this topic getting some exposure.

I’ve Been Robbed

Yesterday, we went out hunting. I fought a headache all day long. We got home about 6 PM, parked the van in the driveway, stumbled inside, and went to bed.

Apparently while Diane and I tried hard to knit the ravelled sleeve of care, other folks were busy. They ripped off various and sundry things that we somehow hadn’t had the gumption to remove from the van. My vest, with prescriptions and checkbook. A pair of pants with my PDA and full set of keys. My Fuji S2 Pro digital SLR, three lenses, flashes, and other photo accessories. A Marshall Stealth II telemetry receiver. We’re still trying to figure out what exactly they made off with.

Fortunately, they didn’t steal the van itself. We had left Rusty and Shelby in there, too. The birds are safe now.

The police say I need to close my checking account, call in a locksmith, and find as many serial numbers on gear as I can. My insurance company says I’m covered… for depreciated value on everything over 1 year old, and a $500 deductible. This, I can tell you, is no fun at all.

Update: This would be a longshot, but longshots are about all that burglary victims have in retrieving their stuff. I am going to list serial numbers of the camera gear here. If anyone happens to run across one of these, please drop me a note.

  • Fujifilm S2 Pro DSLR camera, SN 23A03478. The cover of the topdeck LCD is cracked.
  • Nikon Nikkor EDIF AFS VR 70-200mm f/2.8 G lens, SN 217315
  • Promaster AF 12-24mm f/4 lens, SN 7116783
  • Nikon Nikkor AF 28-105mm f/3.5-4.5 D lens, SN 508516

Luskin Gets Something Right

In a long and tedious response to my article pointing out that Casey Luskin had experience in “flying under the radar” himself, Casey got one point right. It’s a heading that he used:

“There Is No Comparison Between My Situation and Celeste Biever’s Deception”

That’s correct, I did not compare Luskin and Biever to try to figure out whether one was more “wrong” than the other. I’ll leave that sort of casuistry to the pros at the IDEA Center and Discovery Institute.

Getting Cozy with Drupal

Recent software upgrades on the server here busted the xtemplate themes that I had set up for three domains running CivicSpace. CivicSpace is based on the Drupal content management system, so a perusal of the Drupal themes page led me to the “interlaced” and “argeebee” themes that I’m using as-is at the moment.

I’ve been learning about Drupal themes, though, and I hope to be able to apply that to some of my sites soon. Of course, I’m making use of a lot of good info on the web to get acquainted. Here are some of the sites that I am finding useful: base documentation for PHPTemplate

Information on “front page” theming with PHPTemplate

Developing separate themes for different website sections

Comment has a method for custom block positioning in 4.6

Nick Lewis’s excellent tutorials on CSS horizontal menus in Drupal

That horizontal menu tutorial, by the way, is a slick piece of work. Retrieving the menu sub-tree from Drupal takes just two lines of PHP code. Making it behave with CSS takes about a dozen lines in a “menu.css” file. While it isn’t quite a “dropdown” type menu in the end, it does have the advantage of not needing any Javascript at all to get things done. As security issues make it more common for people to turn off scripts on untrusted pages, this sort of consideration will become more important.

Ohio Ditches the Discovery Institute

As reported on the Panda’s Thumb, the Ohio State Board of Education killed off Resolution 31 on Tuesday. The apparent Intelligent Design advocate strategy was to keep the Achievement Committee pondering the issue assigned to it last February until after the November elections. This strategy backfired when the full board met and decided to take direct action. They moved to close discussion on Resolution 31 permanently and remove the Achievement Committee’s authority to do anything about it. They then voted to take up the motion as an emergency measure. That passed by a substantial majority. Then they voted on the motion itself, again passing by a wide margin. The margin would not have been quite so wide but that two of the ID advocates on the board were absent from the meeting.

For too long, the ID advocates in Ohio have taken it as a given that they can manipulate the system at will to advance their agenda. The action by the full board today shows that they are no longer willing to extend that sort of benefit of the doubt to the ID advocates. If the Discovery Institute had advised the ID advocates on the board to wait for a better time, they took a large misstep.

For three years, Ohio was a showpiece for the Discovery Institute, with a state Board of Education that had given the DI what they wanted in terms of “compromise” language in the science standards to be exploited in getting the same old bogus antievolution arguments into the classrooms. That started to go sour for the DI when the BOE last February removed the compromising language from the standards and the deficient “critical analysis” lesson plan from its list of approved curriculum materials. The BOE had given the ID advocates something in return, though, in the form of Resolution 31, which gave the ID advocate dominated Achievement Committee the mandate to suggest whether some further change to the science standards should be made because of the removal of the “critical analysis” indicator. As usual in ID advocate land, the public was not welcome to peek at the progress of the Achievement Committe on this issue. When ID advocate Deborah Owens-Fink for the first time found herself in a real election race for her SBOE position with an accomplished and experienced politician, ex-Akron mayor Tom Sawyer, the wait-until-after-the-elections strategy seemed to be adopted. Perhaps the ID advocates thought that if the evolution/creation issue was not active in the weeks leading up to the election, the voters would simply forget about it. This seems rather doubtful, but I expect that there was a certain amount of desperation in the Fink campaign driving that assessment. The action by the SBOE yesterday both removes the remaining wedge the ID advocates had and raises the evolution/creation issue to prominence in the SBOE election campaigns just a few weeks prior to the elections.

Voters in other places have consistently removed ID advocates when given an informed choice on the matter. In 2004, citizens of Darby, MT voted out a set of ID advocates there. The new school board rejected the ID policy considered by the former board. The reason that most people know about Dover, PA and not Darby, MT lies in the timing of the school board elections: in Darby, the election occurred before the board could implement an ID policy and trigger a lawsuit. In Dover, PA, the voters narrowly turned out all eight ID advocates running for re-election to the board. The election was held just days after the close of the trial about the Dover ID policy. Primary elections in Kansas this past summer are a harbinger of a probable shift in the composition of the SBOE there from creationist dominance to moderate majority, and a likely rejection of the Minority Report science standards that treat antievolution arguments credulously. The ID advocates’ reliance on populist rhetoric somehow has not translated into actual votes in the booths on election day. American voters by proponderance are Christian believers, just as the Discovery Institute often reminds us, but Christian believers also often see passing off untruths to children as just plain wrong. They seem to have in significant measure wised up to the sham that ID’s marketing comprises and the sub-standard science education that ID advocates peddle as their sole product.

We Have a Winner!

We all knew that she had it in her to do this. Former U.S. Representative Helen Chenoweth-Hage had demonstrated her cluelessness before with “endangered salmon bakes” and assertions that government “black helicopters” were harassing Idahoans over compliance with the Endangered Species Act. She rebutted the report that salmon were endangered with the observation that she could buy cans of salmon in the supermarket. Such idiocy surely could not all be directed at subjects outside her personal safety, could it? On October 2nd, Chenoweth-Hage proved to the world that she had the “right stuff” by going seatbeltless as a passenger holding a baby in her lap, and in a single-car crash earned the Darwin Award that we all suspected must be awaiting her. The baby, though thrown from the vehicle, survived with minor injuries.

Taming Wild Water

The New York Times reports on a cheap new device to help people get good drinking water in places where clean water simply isn’t available.

The invention is called Lifestraw, a plastic tube with seven filters: graduated meshes with holes as fine as 6 microns (a human hair is 50 to 100 microns), followed by resin impregnated with iodine and another of activated carbon. It can be worn around the neck and lasts a year.

Lifestraw isn’t perfect, but it filters out at least 99.99 percent of many parasites and bacteria, the demons in most fatal cases of diarrhea.

Vestergaard Frandsen, a Danish company, has invented this device, which costs about $3 per unit, as well as various other items aimed at parasite control in the developing world. The article notes that about 100,000 of the LifeStraws have been distributed so far.

It also notes that the device is ineffective against viruses and the parasite Giardia, which makes its use for US hikers, campers, and hunters not quite as appealing as it might otherwise be. If there were a version that could be used to pre-treat water that could then be hit with one of the Giardia treatments available, it might sell here in the US. A premium price here could help subsidize distribution to developing countries.

If It Worked for Columbus…

The Eclipse That Saved Columbus

The article by Ivars Peterson recounts a tale we know today from a variety of literary sources that took the experience of Columbus and ran with it. The voyage of Columbus in 1502 to the New World wasn’t going well. He and his crew were stranded on Jamaica, and the crew’s depredations on the local population had caused those locals to stop rendering them aid. Things were becoming critical in 1504.

Weary and ill, Columbus had withdrawn to his ship. There, he pondered his precarious situation. Returning to the stained pages of the Ephemerides, he noted Regiomontanus’s prediction of a total eclipse of the moon on Feb. 29, 1504.

Yeah, that’s right, we have Columbus to thank for the “I am going to make the {large heavenly body of your choice} disappear” cliche’ that has become a part of popular culture.

Such a dramatic episode didn’t escape the attention of novelists, who later used eclipse occurrences in a similar way to further their own plots. You’ll find the device in H. Rider Haggard’s King Solomon’s Mines, Mark Twain’s A Connecticut Yankee in King Arthur’s Court, and even in Hergé’s Tintin adventure Prisoners of the Sun.

Something the article notes is that the predicted eclipse that saved Columbus’s skin was made via the Ptolemaic geocentric model of the solar system. The Copernican revolution of a heliocentric model of the solar system was still off in the future, adding spice to the new century. This can be a difficult concept for some to grasp, that a scientific idea can be wrong, yet productive and leading to many correct predictions and practical applications. The heliocentric replacement meant that predictions of astronomical events could be made with greater ease, accuracy, and at longer times from the present. Of course, within the history of the heliocentric model, one has various refinements (going from an assumption of circular orbits to circular orbits with epicycles to elliptical orbits) and the fostering of new ideas, like Newton’s laws of motion and universal gravitation, which helped explain why the model worked at all. Placing these events within a physical framework marked a distinct change from the ready assignment of phenomena to direct supernatural intervention and maintenance.

Luskin, Undercover Agent

The Cornell University IDEA Club web site, The Design Paradigm, offers up a story about New Scientist reporter Celeste Biever requesting information about the club via an assumed identity as a Cornell student. They close with the following:

We’re simply a forum for civil, informed discussion, and we like having various points of view. If you think you’ve got a strong argument supporting either side, we’d love to hear it. And if you just want to come and listen to the arguments you’re welcome too.

We do prefer, though, if you don’t lie to us.

Going undercover, though, is not something solely practiced by ID critics. UCSD IDEA Club and IDEA Center co-founder and current Discovery Institute spokesperson Casey Luskin has his own experience in flying under the radar. Back in 2000, there was a seminar series at UCSD about combatting creationism. Casey Luskin was a participant in the seminar. Some of Casey’s summaries and responses that circulated on the closed “Phylogenists” email list were copied to a Finnish-language Usenet discussion group. It is interesting to read Casey’s take on these. In his summary of Russell Doolittle’s presentation to the seminar group, Casey talks about how he held back on what he might otherwise have said in defense of Behe. There isn’t something explicit there, but the implication seems to be that Casey was reluctant to state to his classmates that he was in the opposing camp. That interpretation is bolstered by Casey’s description of my outing of him (see previous link).

So, if it is wrong to incompetently take on a false identity to ask a few questions, is it also wrong to avoid telling a seminar organizer and other seminar participants about having an antithetical stance to the course’s intended purpose, perhaps resulting in the exclusion of another student who might have had a direct interest in participating?

Two Reported Antidotes from the University of Wisconsin

‘Failed’ experiment yields a biocontrol agent that doesn’t trigger antibiotic resistance

New drug blocks influenza, including bird flu virus

The two press releases linked above report work with broad claims for the control of disease.

The first discusses the production of a bacterial plasmid that undergoes lethal runaway self-replication. The researcher also has developed a bacterial host organism for the plasmid, such that the benign host is able to suppress the runaway self-replication. Bacteria with which it conjugates and transfers the new plasmid to do not receive the suppression property, and thus are killed by the new plasmid. It sounds to me like this technology will likely require specific targetting of disease agents, since the generality of each host will be limited by how picky the actual disease agent is in recognizing other bacteria for conjugation. The press release doesn’t give details about how the suppression of the plasmid is accomplished, so it isn’t clear that this property would always remain safely behind in the host organism. Nor is it clear that the obvious optimism of the researchers that the suppression property is unevolvable in disease organisms is well-founded. Another thing to consider is whether in conjugation, the host organism could be made virulent by what it receives from a disease agent. It is possible that answers to these concerns have already been made, but were not communicated in the press release.

The second discusses a broad treatment antiviral agent against influenza viruses, one that blocks the virus from entering cells in its host. The agent in this case is a peptide. The researchers noted 100% protection against infection with various influenza, including the H5N1 viruses (aka “bird flu”). As an “entry blocker”, the new agent differs from vaccines, which prepare the immune system to mount an effective response on infection with a pathogen. A note at the end of the article speculates that it might be possible to generate vaccine-like action with this entry blocker, if the entry blocker could be tuned to block only most instead of all viruses from entry to cells. The idea here is that the patient would get enough viral load to trigger an immune response, but not so much as to make them more than mildly sick. Vaccine production currently requires quite a lot of work to produce a specific vaccine, and given the rapid evolution observed in influenza, by the time a vaccine is produced, the disease agent in the wild may be considerably different, reducing the effectiveness of the vaccine. Being able to produce vaccine-like action on a short time scale and with a cheaper process could help considerably with response to emerging viral disease agents.