Monthly Archives: February 2009

More About the Behe Talk

Michael Behe gave a talk at the University of North Carolina at Wilmington, as mentioned in a previous post here. The news report had this very interesting snippet, where Behe expounds on the standard he holds others to in doing research. Behe was discussing Judge John E. Jones III and his 2005 decision in the Kitzmiller v. Dover Area School District case, and is credulously believing the DI’s subjective text analysis.

“It wasn’t the judge’s opinion. He showed no independent thought,” Behe added. “If you want to understand this (the debate about evolution), you can’t rely on somebody else, you’ve got to look at it yourself and come to your own conclusion.”

Emphasis added.

Let’s zip back to 2005, when Michael Behe was on the witness stand, under oath, and being thoroughly impeached by Pepper Hamilton attorney Eric Rothschild. Behe’s own methods of coming to a conclusion about a topic were themselves the subject of interest, and Behe seemed to be singing a different tune when it was his own behavior that was on the line:

[164]Q. And here we’ve got chapter called “Evolution.” Then we’ve got Fundamental Immunology, a chapter on the evolution of the immune system.

[165]A lot of writing, huh?

[166]A. Well, these books do seem to have the titles that you said, and I’m sure they have the chapters in them that you mentioned as well, but again I am quite skeptical, although I haven’t read them, that in fact they present detailed rigorous models for the evolution of the immune system by random mutation and natural selection.

[167]Q. You haven’t read those chapters?

[168]A. No, I haven’t.

[169]Q. You haven’t read the books that I gave you?

[170]A. No, I haven’t. I have read those papers that I presented though yesterday on the immune system.

[171]Q. And the fifty-eight articles, some yes, some no?

[172]A. Well, the nice thing about science is that often times when you read the latest articles, or a sampling of the latest articles, they certainly include earlier results. So you get up to speed pretty quickly. You don’t have to go back and read every article on a particular topic for the last fifty years or so.

So Michael Behe’s conclusions should be considered golden, even though it turned out that his “search” was on a very particular turn of phrasing and he only “sampled” some recent publications in any case, relying entirely upon those few people whose work he skimmed, and not bothering to inquire of them whether they agreed with his interpretations. But Judge Jones, having listened closely to the testimony of experts and having the benefit of extensive cross-examination on the very points in contention, can’t be credited with having come to his own conclusion legitimately. Behe, and pretty much everybody else at the Discovery Institute, can’t seem to understand, or perhaps can’t bring themselves to admit, that a judge utilizes proposed findings of fact and law only when the advocates have made their case in the courtroom. The conclusion is not held simply because it appears in the proposed findings, but because the evidence and testimony provide the justification for coming to that conclusion.

Does Michael Behe deploy a consistent standard for depth of research in coming to a conclusion?

I don’t think so.

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Movie List

Picked up from Facebook… If I’ve counted correctly, I’ve seen 84 out of the following 232 movie titles. (Counts via use of “cat | grep pattern | wc” to get watched and unwatched numbers. The original on Facebook said it had 239 titles, which I think is wrong. I even added a couple where a series list was obviously incomplete.)

Continue reading

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Kirk Durston and Misrepresentation of Avida

Kirk Durston wrote in his “Introduction to Intelligent Design”:

Recent computer simulations have failed to generate 32 bits of functional information in 2 x 10^7 trials, unless the distance between selection points is kept to 2, 4, and 8-bit steps.

The 2003 Lenski et al. paper on Avida is cited by Durston as supporting the quoted statement. The 2e7 number comes from the section describing how 50 runs failed to evolve the EQU function if no less complex functions were rewarded, and the 2e7 number refers to the 2.15e7 unique genotypes evaluated in those 50 runs (p.143). But the remaining numbers don’t match up to stuff in the paper. 2, 4, 8, and 32 are mentioned in the paper as values of merit awarded to organisms based on the number of NAND operations required for the task completed. Those aren’t measures of “functional information”. Durston also left out the “16″ number, which corresponded to the level of merit of two other tasks that were not rewarded in that experiment, and thus their absence is misleading.

Getting to bits isn’t difficult. I’ll be using a simple approach since the Avidian programs at issue all utilize a set of 26 instructions. Any instruction could be in any position in an Avidian genome, so each instruction in an Avidian genome can be considered to contribute

- log2 (1/26) = 4.70

bits to the Avidian.

If one were trying to express “functional information” of an Avidian in bits, one might assert that five NAND instructions being necessary out of an instruction set with 26 instructions in it would give you 23 bits, or that the minimal number of instructions needed for EQU of 19 gives 89 bits, or that the reported value of 35 instructions that were necessary for EQU in the knockout experiments reported yields 164 bits, or that the 60 instructions in the first Avidian to perform EQU yields 282 bits. None of those match the “32 bits” Durston mentions, and trying to assert the 23 bit figure would require using an idiosyncratic measure. All the other possible assertions yield more bits than Durston’s quote states.

If one is trying to specify how high the bar was that Avida failed to clear in that experiment, the lowest that one might reasonably argue for would be the 89 bits that one may derive from the minimal known program using 19 instructions. That’s a lot more than the 32 bit figure asserted by Durston.

If one is trying to figure out how large an informational difference exists between programs that accomplish the various logic tasks in Avida, Durston’s statement about “distance between selection points of 2, 4, and 8-bit steps” doesn’t seem to correspond to anything there. Any single insertion or deletion changes the information content of an Avidian by 4.7 bits (when one uses the standard instruction set of 26 instructions), not the even powers of two stated by Durston. Further, there is a handy table of the shortest known hand-coded Avidian programs.

Task Shortest known program length Bits Size of Merit Reward
NOT 6 28 2
NAND 5 23 2
OR_N 6 28 4
AND 9 42 4
OR 15 70 8
AND_N 10 47 8
NOR 19 89 16
XOR 15 70 16
EQU 19 89 32

Based on the minimal program lengths, all the logic tasks are substantially more complex than Durston admits. The “32 bit” barrier Durston discusses was not reported in the experimental results that he cites. NOT and NAND tasks, at 28 and 23 bits, evolve exceedingly rapidly in Avida populations whether they are rewarded or not. I just pulled up Avida-ED, turned off all rewards but EQU, and let a 3,600 max population run go. AND_N, at minimum a 47 bit task, turned up by update 196 in the very first run I made. That it was unrewarded does not mean that it did not evolve. The only task reported not to have evolved without other tasks being rewarded was EQU, an 89 bit task. Besides not being based on anything in the cited paper, it is easy to do some runs of Avida or Avida-ED and see that Durston’s primary claim of that sentence is demonstrably false: logic tasks of greater complexity than 32 bits do evolve in Avida even if less complex tasks are unrewarded. I tried that directly in Avida-ED by turning off rewards for all sub-32-bit complexity logic tasks (NOT, NAND, and OR_N) and running it. My first run had AND_N and AND evolve by update 800, OR by update 1200, XOR by update 1345, and NOR by update 1549. A second run fixed on a population mostly doing ANT and NOR. My third run showed evolution of EQU by update 2400. All the logic tasks rewarded were over 32 bits in complexity in those runs, and none of the less complex tasks were rewarded as “steps”. There isn’t a handy tally of unique genotypes, but it can’t possibly hit 2e7 such until after 5555 updates, anyway.

Expanding on Durston’s erroneous discussion on functional distance rewarded, the differences between minimal length programs for different tasks are in {0, 5, 14, 19, 23, 24, 28, 42, 47, 61, 66} bit distances, not “2, 4, and 8 bits” as Durston mistakenly asserts. The knockout experiment reported in the paper discusses the case where a single point mutation changed an Avidian program that had previously performed the AND task into one that performed EQU instead:

Besides EQU, this genotype performed five of the eight simpler logic functions; AND was lost as a side-effect of the EQU-producing mutation, and NAND had been eliminated by the one-step-prior mutation.

Based on minimal program lengths, the step from AND to EQU is a distance of 47 bits. The Avidian also performed the NOR task both before and after the mutation that permitted it to perform EQU. A transition from performing NOR to performing EQU could be claimed to be a 0 bit distance, given that both have shortest program lengths of 19 instructions, but that was not what was observed in that case. The very source Durston cites as support rebuts his assertions.

The implication of Durston’s “unless” phrasing is incorrect as well. The 50 run experiment where only EQU was rewarded did not try out an alternative reward structure to get to EQU. Durston cannot be referring to the outcome of experiments where all nine logic tasks were rewarded because he specifically used the unique genotypes figure from the “only EQU is rewarded” experiment, and not the significantly smaller number of unique genotypes explored in getting to EQU in the main experiment (1.22e7) where all nine logic tasks were rewarded.

So about the only thing Durston managed to get right in that sentence was copying one number from the original paper, where he limited himself to one significant digit. That seems excessively non-functional.

The Lenski et al. paper does a lot more than repudiate Durston’s dolorous-but-derelict assertions, though. It demonstrates via evolutionary computation that complex functions can arise from modification of simpler precursors. Avida removes the usual mainstay of antievolutionist argumentation, that there isn’t enough information about a lineage of interest to demonstrate that only evolutionary processes need be invoked as efficient causes to get to the result. Durston essentially gives us an instance of response #4 from my 1998 essay on objections to evolutionary computation:

Natural selection might be capable of being simulated on computers, and the simulations may demonstrate good capacity for solving some problems in optimization, but the optimization problems are not as complex as those in actual biology.

This objection typically appears once the first three above have been disposed of. Computer simulation, once held to be either a potential indicator of merit or an actual falsifier of natural selection, is then treated as essentially irrelevant to natural selection. It is certainly true that computer simulations are less complex than biological problems, but the claim at issue is not that EC captures all the nuances of biology, but rather that EC gives a demonstration of the adaptive capabilities of natural selection as an algorithm.

Durston’s attempt to misrepresent a single Avida experiment of modest extent and use that misrepresentation to make a proscriptive negative claim about evolutionary processes in biology is risible.

A point to be made, though, is that evolutionary processes don’t have to be good at “poofing” things together all at once; that’s the special creation hypothesis. Many religious antievolutionists get stuck on this, thinking that unless evolutionary processes have the asserted capabilities of omniscient, omnipotent creative deities that they can’t be credited with the history and diversity of life on earth.

Update: Other places Google thinks Kirk Durston’s erroneous conclusions have propagated:

Evolution under fire? — Part 1

Mathematically Defining Functional Information In Biology

Does God Exist? – Part 2 of 3 (about 6:20)

Re: Kirk Durston on information theory

Intelligent design question

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Origins of “Intelligent Design” … Again

The traveling Discovery Institute roadshow featuring a double bill of John West and Casey Luskin got some attention when ERV and others attended the proceedings at the stop in Oklahoma.

At After the Bar Closes (the online bulletin board that itself was featured in the talks), “carlsonjok” also attended and is delivering a set of annotated notes from the event. Here are excerpts that caught my eye.

“carlsonjok”‘s annotations are in square brackets.

Center for Inquiry has ID timeline – it starts in 1983 (after McLean v. Arkansas?) Not true, ID goes back to the Greeks and Romans like Socrates and Cicero. [Hold this thought because we are going to hit Casey Luskin over the head with it a bit later on. Don't these guys coordinate their messages? Srsly.]

[...]

He seems to accuse Darwinists of taking an anti-intellectual view of Western Civilization by not allowing questions. [I'll get a little more into West's tactics in the Q&A session that belie the notion that West is interested in questions. Also see comments above about why doesn't EN&V allow comments.]

[...]

Ron Numbers, distinguished anti-ID scholar thinks the ID=creationism equivalence is a rhetorical device to de-legitimize ID and is nothing more than a smear so people won’t look at evidence. [West talking about rhetorical equivalences as smears conjures up images of pots and kettles. Making such equivalences will become a recurring theme in the rest of West's talk.]

And my response:

The “intelligent design” timeline… is irrelevant.

The issue isn’t whether somebody put “intelligent” next to “design” before 1987, like the old Reese’s commercials discussed putting “chocolate” next to “peanut butter”. The issue is about the use of “intelligent design” as if that meant a field of human inquiry. Plenty of people before had used “intelligent design” as a descriptive phrase about a property that they attributed to certain phenomena. That sloppy, unfocused sort of rhetoric does indeed have a long, long history.

But “intelligent design” meaning a field of study, a scientific field of study that would have a place in a K-12 science classroom? That usage uniquely first appears in the just-post-Edwards v. Aguillard decision period in the draft manuscript that eventually got published as Of Pandas and People.

West may be able to handwave fast enough in front of a debate audience to obfuscate the vast difference there, but in a courtroom this will be developed at length and such that there is no confusion left for the IDC advocates to hide behind.

So far as I can tell, the Thaxton claim that anybody in the movement had a notion to push “intelligent design” rather than creationism in the pre-Edwards run-up to OPAP is completely lacking in substantiation. If they actually had that, do you suppose they would not have presented it during the Kitzmiller trial?

No, neither do I.

Ron Numbers does think that there is a distinction between creationism and “intelligent design”. It’s becoming an increasingly fringe position. For almost everybody else who actually studies the antievolution movement, the evidence from the Kitzmiller case completely demolished the notion that “intelligent design” represented a legitimate field of scholarly inquiry. And it wasn’t “the Darwinists” that put them in that position; it was the record of their actions, painstakingly analyzed and presented to the court. They only have themselves to blame. They could have taken their own rhetoric in the Wedge document seriously and convinced the scientific community first, if they were going to. They chose to give that a pass and push on with the culture war. It’s not our fault that they did their own cause damage that way, and it is not our fault that they absolutely make it necessary to lay all this out in the plainest of terms.

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Poles of the Conflict Model Are Self-Reinforcing

The conflict model of the relation between science and religion is polar, with doctrinaire religious people at one pole and adherents of evangelical atheism at the other. Each time one stakes out an even more extreme position, it elicits, in almost Pavlovian stimulus-response fashion, an equally extreme rejoinder.

Take, for example, Carol Iannone’s piece in NRO, taking a recent set of book reviews by Jerry Coyne as a jumping-off point. And, boy, does Carol jump.

Remember this when you see a version of Inherit the Wind, with its fradulent implication that the Bible and Darwin are perfectly compatible, and its closing scene with the Clarence Darrow character exiting happily with both in his briefcase. Generations of schoolchildren have been misled by this lie. Now at last we have the truth and can begin again to build on that.

According to the polar extremes, any middle ground doesn’t actually exist, so one may as well migrate to a pole right now… the one the particular person writing happens to reside at being the only reasonable choice, of course.

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Project Steve by the Numbers

Over on the Panda’s Thumb, there’s a thread about NCSE’s Project Steve hitting the kilosteve mark, that is, the 1000th signatory. A commenter there wished to register her annoyance with Project Steve, and to do it with numbers:

Louise Van Court said:

I realize that the whole Project Steve thing is a spoof on the Dissent From Darwin statement and that the NCSE is just having fun with it, but 1,000 signatures is not a very impressive number really. I am more impressed by the lack of signatures to either of these statements considering the bureau of labor statistics on the www.bls.gov/ocoso47.htm#outlook site of a total of 173,000 biological scientists (apparently using some rounded figures) including “biological scientists, biochemists and biophysicists, zoologists and wildlife biologists and biological scientists all others.” The number of signatures is not even 1% of the total number even with Steve and derivations of that name being fairly common in the US. Perhaps there are many scientists that prefer not to put their names on a public list and just want to stay away from the culture war. Good for them.

James F. immediately pointed out that 1,000 * 100 = 100,000, so a goodly percentage of the eligible people had in fact signed on. It’s always amusing to see antievolutionists joining innumeracy to ignorance.

But Louise Van Court is even worse off than James F. noted. If one goes to the link she provided, one gets a 404-style message. If one does some looking, one can find the actual link. There, “Biological Scientists” are said to have numbered about 87,000 in 2006. Indented entries in four categories split that out. Louise arrived at the 173,000 number by adding up the rounded-off figures for biological scientists and the categories of biological scientists. She counted everyone twice and presented that as a figure. If what she had come up with by inflating the population number to double its actual size was, as James F. put it, an “EPIC FAIL”, one wonders how to express just how badly off she was given the actual numbers from her cited source.

Project Steve has been somewhat more open to Ph.D.s from outside the stated categories, but it is primarily pitched to them. The numbers indicate that for the biological sciences, Project Steve may be close to complete saturation.

That’s what I call shooting oneself in the foot; nice job, Louise!

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200th Anniversaries

Today is the 200th anniversary of the births of Abraham Lincoln and Charles Darwin. I’ll be adding things to this post through the day.

Google has taken note of the day. If you go to their website, they have a Darwin’s finches-themed logo:

There are lots of Darwin Day activities going on around the country. And Evolution Weekend is coming up.

Check out the SSE video birthday card:

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Florida: Reliving the Past

State senator Stephen Wise plans to introduce a bill requiring balanced treatment for “intelligent design” whenever evolutionary science is taught in Florida’s science classrooms.

Of course, “balanced treatment” and “equal time” bills for “creation science” led to the 1987 SCOTUS decision in Edwards v. Aguillard that ruled “creation science” as unconstitutional. Wise’s bill, if worded as stated in the article, is likely to provide a complementary court case for “intelligent design”.

Wise said that if the Legislature passes the bill, he wouldn’t be surprised if there’s a legal challenge.

“You just never know. They use the courts all the time. I guess if they have enough money they can get it in the courts,” he said. “Someplace along the line you’ve got to be able to make a value judgment of what it is you think is the appropriate thing.”

Sen. Wise, just a note… if “intelligent design” creationism were able to make a convincing case to the scientific community, there wouldn’t be any issue about it being suitable as accountable science content for the public school science classrooms. But IDC is clearly religious antievolution, a narrow sectarian viewpoint without scientific standing or accountability, that you are inappropriately trying to insert by the political process rather than having it demonstrate its merit. People end up using the courts because of the bad behavior of people like you. It is where they can get redress for what you’ve done. It is not unseemly behavior on their part to take up the only route for redress that you have left open to them.

And if it comes to it, I hope to render my assistance to those who will oppose you in court, much as I did in 2005 for the Kitzmiller v. DASD case in Pennsylvania.

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Josh Rosenau Drops By

Josh Rosenau, Public Information Project Director at the National Center for Science Education and blogger at Thoughts From Kansas, was in Michigan this past week to give some talks. Diane and I met Josh and Rich Lenski at MSU’s International Center yesterday for lunch. After lunch, Josh squeezed in a trip out to our house, where he got to meet the hawks, Shelby and Rusty. Here’s Josh with Shelby…

wre 0489 ws

Josh will be at the AAAS meeting in Chicago next week.

Here’s a pic of Josh at the panel discussion on Feb. 3rd at the East Lansing Unitarian Universalist Church:

wre 0442 ws

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Tilting at Windmill (Cookies): Trans Fat Math

Diane and I like certain snacks. But maybe those snacks don’t like us. Take, for example, Voortman Windmill Cookies. They taste excellent. Now, the FDA allows manufacturers to use a “Zero grams Trans Fats” label on packaging if the amount of trans fat per serving is less than 0.5 grams. But that leaves considerable ambiguity as to the healthiness of this snack.

The American Heart Association recommends that one restrict trans fact consumption to 1% or less of one’s total daily caloric intake. That translates to around 2 grams. The page helpfully notes that various foods naturally contain some trans fats, thus additional trans fat exposure in manufactured foods will likely lead to excess trans fat consumption.

The Windmill cookie package does have a prominent label on the front of the package saying, “Zero grams Trans Fat! Non-Hydrogenated! Per Serving”. What this tells me is that for FDA compliance, each serving has less than 0.5 grams of trans fats. Now let’s look at the nutrition label. There I find that Voortman defines a serving of Windmill cookies as two cookies. I think I have eaten as few as two cookies at a sitting, but I don’t think I’ve done that often. Voortman says that there are about thirteen servings in the package. Now, it is possible that Windmill cookies have no trans fat at all. That isn’t excluded by the labelling. However, if that were the case, they could make that stronger claim on the packaging. The use instead of the weaker “per serving” claim is an indicator that some trans fat is likely still in the recipe. In the worst case, how much would that be? Given the data on the label and assuming it is accurate, that would be just under 6.5 grams trans fat per package of cookies. Even if you were to allocate your entire daily trans fat experience to Windmill cookies, you’d want to restrict yourself to less than a third of a package per day.

In the trans fat nutrition game, zero is not really zero. Small numbers add up, especially when delicious cookies are the vector.

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Doctor in the House

Jill Biden earned her Ph.D. Ed.D. in 2007 in education. Robin Abcarian, reporter for the Los Angeles Times, must be having a tough time finding material to write about, given the article attacking Biden for being identified as Dr. Jill Biden. The level of research Abcarian undertook is exemplified by this erratum in the online version:

FOR THE RECORD:
The headline in an earlier version of this article incorrectly stated that Jill Biden had a doctorate in English. She has a doctorate in education.

Media Matters has an excellent response to Abcarian, taking apart many of the slights that Abcarian had worked into the article. One of the most annoying moments in the Abcarian article was its quoting of a newspaper staffer about policy:

Newspapers, including The Times, generally do not use the honorific “Dr.” unless the person in question has a medical degree.

“My feeling is if you can’t heal the sick, we don’t call you doctor,” said Bill Walsh, copy desk chief for the Washington Post’s A section and the author of two language books.

Bill Walsh is confused. While doctor as a description of what someone does for a living is tied to the medical profession by modern usage, the “Dr.” title of address is accurately applied to any holder of a terminal research or professional degree that is a doctorate. That is inclusive of medical doctors, but not exclusive of doctorates in the arts, sciences, and other professions.

The hypocrisy issue raised by Media Matters was particularly telling: would the LA Times demur from calling LA Lakers owner Jerry Buss as “Dr.”, and go so far as to publish articles attacking him for using his earned title? Certainly the “policy” cited by Walsh is inconsistently applied. The LA Times has published articles that do use “Dr.” to refer to people other than medical doctors. Like this article that includes a reference to “Dr. Jerry Buss”.

Of course, the low point in the Abcarian article as pointed out by Media Matters has to be the implication that someone using “Dr.” as a title might be guilty of a criminal offense, “title fraud”:

German investigations of “title fraud” don’t have anything to do with Jill Biden. Nobody – nobody except the LA Times, that is – is suggesting that Jill Biden is guilty of “fraud.” And Germany doesn’t prohibit non-medical doctors from using the title doctor; it prohibits people who didn’t earn their doctorate in Germany or the EU to call themselves doctor. Again: this has absolutely nothing to do with Jill Biden. It’s just a cheap shot; a clumsy effort to suggest there is something fraudulent about her use of the title “doctor,” even though there is nothing wrong with her doing so – by American standards or German.

It’s probably a safe bet that Robin Abcarian doesn’t hold an earned doctorate. The sort of anti-intellectualism that comes through that article doesn’t usually come from a background in graduate studies.

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Social Networking Annoyance at Reunion.com

I signed up at “reunion.com” some time back, and occasionally I get email from them. I went over to the site and eventually got logged in. I tried the people search function, and apparently a grade school friend was in the system, but clicking on “View Profile” merely popped up a page saying I could upgrade my account by paying them money. Not yet done exploring the system, I spent some time entering data on my profile, including the nine places I’ve lived and the three universities I’ve taken degrees at. One thing I had done was that I entered “R.” in the “Middle Name/Initial” field on the first page of profile editing. Umpteen pages later, I hit the “Done” button, and got a page informing me that I had entered an invalid character in the “Middle Name” field… and all my other data went away, too.

I went to the “About” page, and it has a link to allow email to the Reunion.com people about various issues. I thought that I would send them a suggestion:

Suggestion:

I just spent thirty minutes filling in data on where I’ve lived, gone to school, etc., only to have it ignored because I had entered “R.” in the “Middle Name” field, which apparently hates periods. I’m not inclined to spend that time again providing information for your system.

If you have “drop dead” error checking, you should partition it off so that an error there does not put the user’s effort in filling out the rest of the data at risk.

Wesley

I hit the “Continue…” button, and the next page requires filling out a bunch of fields to “register for user support”. Uh, not likely, dudes.

Reunion.com… is it a good use of time? I don’t think so. The underlying idea is good, but the user interface needs vast improvement to make it even marginally pleasant.

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Biosonar Turns Waspish

Nature (7228, p.361) had notice of an article in Biological Journal of the Linnean Society (96, 82-102, 2009) that demonstrates the use of biosonar in several species of parasitic wasps. These wasps seek out beetle larvae in trees, using hammer-like ends of the antennae to produce sound.

So far as I know, this is the first group of invertebrate species to be shown to use biosonar.

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