Monthly Archives: January 2006

Procrastination

Projects with deadlines invite work applied elsewhere. Thus the new-fangled drop-down lists in the sidebar, with code taken from the Neuron theme. Meanwhile, I am getting some work done towards my presentation for this coming Saturday and for a revision of a paper. Busy, busy. Tomorrow, we’re also picking up Diane’s trailer for her field season in Wyoming. Since her season starts in about two weeks, selection favored an all-seasons type rig. I’ll try to get some pictures up. Also, Diane will be starting her own weblog shortly. I don’t know whether she will be making frequent entries from the field or not, but she will have the option.

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Dogs and Cancer

A Science Daily item notes that an experimental cancer treatment for dogs with melanoma shows some promising results. The technique involves making a vaccine by culturing melanoma cells, turning off the runaway reproduction of those cells, then adding DNA to also have those cells make proteins that stimulant the immune system.

As is usual, funding is an issue. There is a lot of demand for the vaccine treatment, though, so perhaps this will become a commercially viable product.

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An “ID” Survey in the Blogosphere

I got a request to respond to a survey, the survey group being those who run pro-science websites and weblogs (though not referred to in quite that way), the particular answers to remain anonymous, and the results to be posted to an “intelligent design” weblog when completed.

The survey has but one question:

On which points are intelligent design and creationism identical? [...] (Please check all that apply.)

The options given are, as often happens in amateur surveys, wretchedly incomplete. Here they are:

A. Both creationism and intelligent design require one to have a particular interpretation of the Biblical creation account.

B. Both creationism and intelligent design require one to accept a particular age of the Earth and of the universe.

C. Both creationism and intelligent design require one to reject evolution.

D. Both creationism and intelligent design identify the Christian God as the creator.

E. Both creationism and intelligent design hold that there is an intelligence behind certain features of nature.

F. There are no points of similarity between creationism and intelligent design.

G. None of the above options accurately describe the relationship between creationism and intelligent design.

I hope that others responding to this question, if sticking with the options above, simply respond with “G”.

If nothing else, the author of this survey has managed to overlook the option recently taken by Judge Jones in the decision for the Kitzmiller v. DASD case:

“Intelligent design” (or other labels on the same argument content) is a sham designed to insert the same arguments that were ruled impermissible in previous cases.

Another live option that encapsulates the same relationship without bringing in the legal term “sham” would be:

“Intelligent design” is a subset of the arguments previously labeled “creation science”.

Consider Henry M. Morris of the Institute for Creation Research, who criticized “intelligent design” thus: “It is not really a new approach, using basically the same evidence and arguments used for years by scientific creationists but made to appear more sophisticated with complex nomenclature and argumentation.

I think that people who answer within the current framework, but don’t take option “G”, are likely to respond with option “E”. And I think that the useful rhetoric for “ID” to be gained thereby is to say that even pro-science people don’t see overlap between the religious content of “ID” and SciCre. For various other options given, the “ID” rhetoric is likely to be that the respondents simply “don’t understand ID”, and “how can they make such false criticisms?” The option likely to be touted as the “honest” answer would be “F”, though anyone picking that would have to be pretty much completely ignorant of the argument content of the two labels.

As given, the whole thing looks phonier than a street game of three-card Monte. And like that venerable con, the mark either cannot give the right answer, or is likely to get mugged for doing so.

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The Welcome Mat

Hi. If you are dropping in from “Unscrewing the Inscrutable” or “DailyKos“, this message is for you.

I got into the whole evolution/creation thing by being a little too curious. In 1986, I attended an antievolution lecture at the University of Florida and spoke to the lecturer afterward. I asked if there were further materials I might look at. He gave me a copy of Henry M. Morris’s “The Scientific Case for Creation”. As I read it, my disappointment grew and grew. The sheer mendacity which suffused that book, and which apparently pervades the antievolution movement in general, spurred me into action to counter it.

I did not attend that lecture as a “dogmatic Darwinist” or “atheist” or whatever scare words might be popular. I was willing to be persuaded by a well-founded apologetic. What I found, though, were falsehoods peddled as if true. As we found out last year, the content of the antievolution materials has definitely not gotten better on that score; just check out the cdesign proponentsists.

If there’s one recent post here that you ought to read to find out where I’m coming from, then it must be The Galvanic Response.

I’m going to make a capsule summary of links related to websites I’m associated with.

Continue reading

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Progress in Advertising?

Well, here’s a note for the culture wars: Evolution sells.

Or, at least it seems that recognizable bits of cultural iconography associated with evolutionary biology do not, in the minds of advertising types, raise a red flag for at least one segment of conservative culture.

In the February 2006 issue of the National Rifle Association’s American Hunter magazine, there is a two-page spread advertisement for Elcan’s “DigitalHunter” riflescope. This adds digital still and video capability to a scope, with an LCD on top for review of images. I can only recall one time in my youth when I went deer hunting with a rifle, and I don’t know precisely what the process of sighting something, snapping a picture, and then bringing the rifle into an upright position to review the image is supposed to do. Perhaps it’s meant to settle those old arguments: “I swear, he had ten points if he had a nubbin!” Perhaps the next craze in fishing will be a digital video/still camera that would capture images of whatever comes near the hook.

I digress. The real reason that I am discussing this ad at all is the artwork that goes with it. Click on the image for a larger version.

That’s right, it’s a derivative of the famous “March of Progress” painting. The message seems to be that if you are a hunter, anything but Elcan’s DigitalHunter riflescope is hopelessly primitive.

Continue reading

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Rusty At Dusk

Yesterday, while returning from looking at RVs for Diane’s upcoming field season , we stopped at a place that had a small patch of brushy cover around a streambed. It was just past sunset. While we don’t usually like to start hunting Rusty so late, it was either take this opportunity or simply not have her out at all. Diane went to get permission from the property owners, while I got some boots on. Diane indicated that they had said, “Yes”, so I let Rusty out of the van. She popped out and up to the top of the van.

A woman and two young children came over to watch us. As we prepared ourselves, Rusty moved from spot to spot on the van. She may have been looking for an opportunity to steal food, as she had managed to snag a bag of sliced summer sausage from our cooler earlier when I opened it to get a soft drink out. Fortunately, Rusty doesn’t like the taste of summer sausage and Diane was able to retrieve it from her without too much difficulty. Anyway, Rusty was paying attention to our movements in and around the van, which meant that the other people got a nice up-close look at her.

We let Farli, our 12-year-old Vizsla, out of the van. As Farli started to work the small field, Rusty launched off the van and headed for the stream bed. I directed our onlookers’ attention to this, and so they got to see Rusty pitch up, do a wingover, and drop into the streambed. She missed a cottontail there that time, but it was a nice flight.

Rusty had another five flights, connecting with a cottontail on that last one. It was getting pretty dark by that time anyway. I thanked our hosts for letting us hunt there, and answered various questions about Rusty and falconry. Diane had some discussion of things with the children. One of them was a vegetarian, so Diane was explaining that Rusty did not have the option of going vegetarian, that she needed animal prey to survive. That’s probably a tough short lesson to get across. In any case, the people there invited us to come back in the future to let Rusty hunt some more, noting that they have more rabbits and mice than they want around their property.

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“Evolution Makes a Mockery of Fishing Policy”

Over on the Science A GoGo site, they have an article titled, “Evolution Makes a Mockery of Fishing Policy”. The study used strong selective pressure on fish populations mimicking the policy of taking the largest fish in the population. What they found was that the populational response was an evolutionary one, that part of the populational variation was in body-size traits, and that the new population with much smaller frequency of large body size individuals reflects new population characteristics:

Walsh said that removing the large fish in each generation caused declines in many traits spanning the life history, physiology and behavior of the fish. “We know that commercially exploited populations of fish often are slow to recover when fishing pressure is reduced. Our research indicates that the over-harvested fish stocks are slow to rebound because fishing selects for evolutionary changes in the life history of the fish. Because the changes in the fish are genetic, they don’t immediately go away when fishing ceases,” he concluded.

Not surprising, really, given the classic studies of John Endler on guppy evolution in Trinidad streams. Guppy populations under strong selection by predators tend to have smaller, more drab males, as the larger, more colorful males are more attractive to both females and predators. What we have in commercial fishing is a situation that can be cast in much the same way, with humans as the predators.

Unfortunately, it would be unusual for an insight from biology to actually make a difference in setting fish stock management policy. Where biological concerns have been raised in the past, it has been all too common that political concerns overrode them. Perhaps a smaller fishery many years ago on various over-fished stocks could have prevented the precipitous declines that have been seen in recent years. The management decisions that permitted continued higher levels of take than were supported by the biological data emphasized the short-term benefit of higher employment in the fishing industry, ignoring the long-term cost that is now presenting its bill. The resulting unemployment rate is, I think, going to be far higher than the projected reductions that caused policymakers to set aside the relevant biology.

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Sight and Sound

There’s notice in Scientific American Online of a neurological study of owls showing that the coordination of sight and sound processing in the brain modulates attention: there is increased attention given to sounds that correlate with the direction of gaze. The article notes that this is the first nonprimate species in which this sort of phenomenon has been seen.

There is speculation mentioned that this sort of system may be common to all vertebrates. If so, that will be an interesting finding, since the underlying brain anatomy is not the same across all vertebrates. While the lateral superior olive is implicated as a part of the brain that links sight and sound in primates, those renowned sound processors, bats and dolphins, entirely lack the structure. I’m not sure what the neural architecture of the owl brain is, and a brief Google search doesn’t shed immediate light on whether owls have the lateral superior olive, either.

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Turning a Card, Part 1

I want to take up an issue out of an essay by Orson Scott Card on “intelligent design”. While Card usefully concludes that “intelligent design” is not yet science and thus does not merit attention in science classrooms, he unfortunately is behind the times on the issue of the identity and continuity of antievolutionary argumentation that flows from natural theology through creationism, scientific creationism, creation science, into intelligent design, and on to whatever the next convenient label may be, “teach the controversy”, “strengths and weaknesses”, “sudden emergence”, “intelligent evolution”, etc. There is ample evidence that “intelligent design” is simply a subset of arguments made by the advocates of “creation science” before it, and that in the instance of the supplemental high school textbook Of Pandas and People one finds a nexus between advocacy of “creation science” that morphed into “intelligent design”. This goes so far as to link even many of the high-profile advocates of “intelligent design” to earlier advocacy of “creation science”.

First, I’d like to note something good and serviceable that Card wrote in his essay:

Intelligent design uses the evil “must” word: Well, if random mutation plus natural selection can’t account for the existence of this complex system, then it must have been brought into existence by some intelligent designer

Why? Why must that be the only alternative?

Just because the Darwinian model seems to be inadequate at the molecular level does not imply in any way that the only other explanation is purposive causation.

There might be several or even many other hypotheses. To believe in Intelligent Design is still a leap of faith.

But even in this the student of antievolution can recognize a parallel between the argumentative structure of “intelligent design” and “creation science”. Creation science’s bid for legal standing to enter public schools was based upon the concept of “two models”, known as the “two model approach”. Creation science advocates told the public, and the courts, that there were only two possible models: creation or evolution. Thus, in this approach, evidence against evolution must and only could be evidence for creation. Card’s reaction to having this “logic” show up in “intelligent design” is just the reaction Judge William Overton had in the McLean v. Arkansas case. There, he called the “two model” approach a “contrived dualism”, and rightly scorned it. As is evident, “two model” reasoning underlies both “creation science” and “intelligent design”. It was also noted by Judge John E. Jones III in his decision in the Kitzmiller v. Dover Area School District case late in 2005:

ID is at bottom premised upon a false dichotomy, namely, that to the extent evolutionary theory is discredited, ID is confirmed. (5:41 (Pennock)). This argument is not brought to this Court anew, and in fact, the same argument, termed “contrived dualism” in McLean, was employed by creationists in the 1980′s to support “creation science.” The court in McLean noted the “fallacious pedagogy of the two model approach” and that “[i]n efforts to establish ‘evidence’ in support of creation science, the defendants relied upon the same false premise as the two model approach . . . all evidence which criticized evolutionary theory was proof in support of creation science.” McLean, 529 F. Supp. at 1267, 1269. We do not find this false dichotomy any more availing to justify ID today than it was to justify creation science two decades ago.

More later.

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Quantifying Spin

With the most fiercely fought Canadian election in more than a decade taking place on Monday, the crossfire of political rhetoric between the incumbent prime minister and his Conservative Party challenger is becoming heated – but which one is more trustworthy?

According to a new computer algorithm, Prime Minister Paul Martin, of the Liberal Party, spins the subject matter of his speeches dramatically more than Conservative Party leader, Stephen Harper, and the New Democratic Party leader, Jack Layton.

Spin, in this case, is defined as “text or speech where the apparent meaning is not the true belief of the person saying or writing it”, says the algorithm’s developer, David Skillicorn at Queen’s University in Ontario, Canada.

He and his team analysed the usage patterns of 88 deception-linked words within the text of recent campaign speeches from the political leaders. They then determined the frequency of these patterns in each speech, and averaged that number over all of that candidate’s speeches. Martin received a ranking of 124, while Harper and Layton scored 73 and 88, respectively.

“I think it’s expected that any party in power is going to use spin more than the challenging party,” Skillicorn says. “They have a track record to defend.”

(New Scientist article)

Prof. Skillicorn is an expert on data mining, and is especially interested in applying matrix decomposition techniques to the topic. I looked up his home page and found this article on applying the same technique as mentioned in the New Scientist article to a collection of over 289,000 Enron emails. The utility of the technique in this case is to have an automated process that can indicate which smaller number of documents should receive human scrutiny. This is pretty cool stuff, and I’m thinking this could be a good technique to have in the toolkit.

Update: It appears that Prof. Skillicorn’s methods specify the use of two commercial products, the “British National Corpus” and the “Linguistic Inquiry and Word Count” software. I had been hoping that the actual software might be open source, but that appears to be out of the question.

I’ve corresponded with Prof. Skillicorn, and he suggests the Coredge “Logik” knowledge discovery product. He is working with Coredge to incorporate his algorithms into their product.

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There Is No Substitute

When it comes to conservation research, a study suggests that surrogate or model species do not “stand-in” for endangered species.

An article in the latest issue of Conservation Biology examines the use of surrogate animals to predict or target what is endangering another species. Researchers often use similar, often called umbrella or flagship, species to identify the cause of endangerment to others. These substitutes may be chosen because they are biologically similar representatives of the troubled species, or they may be used to develop a predictive model to which the original species can be related. The authors find that using these substitutes cannot create reliable information about population responses; human induced disturbances will not always affect common and rare species in the same fashion. “After all, target species are the ones that are doing poorly, whereas other taxa continue to persist or even thrive despite human disturbance,” authors Tim Caro, John Eadie, and Andrew Sih state.

The authors suggest three criteria that must be met in order to use substitute species with confidence. The first is to establish the relationship between the level of the disturbance and vitality rate of the substitute. Second, the trait(s) that affect both species’ viabilities must be identified. Third, the trait value and the disturbance threshold must be established for the substitute. The authors see these hurdles as almost insurmountable, especially in a field as cautious as conservation. “Where at all possible, we advocate making every possible effort to examine the target species directly before resorting to substitute species,” the authors conclude.

This study is published in the December issue of Conservation Biology.

The sensitivity of specific taxa to environmental stresses is illustrated in the recent recognition that military mid-frequency sonars under certain circumstances have a history of injuring and killing certain species of beaked whales, while other toothed whale species and baleen whales in the same areas are little affected.

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Another Credit Card Call…

This time another of my credit card banks calling to let me know that they’d be sending out a free credit report to me to check for anything untoward, and, by the way, they would simply love to help monitor my account for signs of identity theft and credit card fraud, completely free. For the whole first month.

Well, I scorched the guy’s ears a little, accused him of aiding and abetting in a scam, and he told me that I just didn’t understand. And that’s about where we left it.

In his own words, he said that ten million people have become victims of identity theft. If all the credit card companies are doing about this is coming up with ways to milk the consumers for more money, that number is going to get a lot larger in a hurry. Asking consumers to voluntarily buy into a program that offers no guarantees that anything of value will be gained is no answer to the bigger picture. Maybe I’m completely off-base and there is no threat to consumer credit, but ten million victims sure hints that this is a job that needs cooperation and coordination at very high levels, not telemarketing scare tactics aimed at terrorizing individual consumers.

Continue reading

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Rusty Bags a Big Bunny

Or, more precisely, a smallish jackrabbit.

Diane had Rusty out today, and Rusty went missing. The battery in the transmitter seemed to be a bit weak, so Diane was only getting an intermittent signal. But eventually Diane tracked Rusty down, where Rusty was munching on the second jackrabbit that she has caught, the first having happened in about 1992. I think Rusty may have gotten tired of not seeing cottontails and decided to go for the larger, but available, prey item. Remember what I said earlier about our little two pound predator? The jackrabbit weighed about five pounds.

There was some difficulty in getting Rusty back on the glove. By the time Diane located her, she was already stuffed, and not cooperative about coming to the glove. So I left work and headed in her direction to see if Rusty would prefer to come to me. Before I could get there, though, Rusty changed her mind and came to Diane’s glove for another leg of rabbit. A successful hunt is where you come back with all the birds you started with, and this one had a bonus of a jackrabbit on top of that.

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“The Hawk Is Dying”

There’s media buzz about a new low-budget drama film being screened at the Sundance Film Festival, “The Hawk Is Dying”.

Paul Giamatti stars as a guy who continues to pursue his interest in “falconry,” despite the fact that he’s simply no good at it, and has even killed a few birds in the process. Perhaps I’m going only on the great cast and the enjoyably bizarre-sounding premise, but this is one I’ll be looking out for. Co-starring in the Julian Goldberger film are Michelle Williams, Michael Pitt, Robert Wisdom, Rusty Schwimmer and Ann Wedgeworth. (Yes, “Lana” from Three’s Company.)

(JoBlo)

Ouch.

I’d like to say that “falconry is not therapy”, but that would be a lie. I know of someone whose doctor has prescribed falconry as an activity.

But I think that falconers do take note of apprentices whose birds, in general, don’t seem to live long, and the tendency is not toward a supportive, “Hey, that could happen to anyone.” If there is some group of people who get more critical of others in the same pastime, I haven’t encountered it.

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Raptors and Human Evolution

Raptors munched on human ancestors, the headlines could well say. The American Journal of Physical Anthropology is publishing research by Lee Berger saying that damage to the skull of the Taung child shows a pattern similar to monkey skulls that have been worked over by eagles.

The Ohio State study determined that eagles would swoop down, pierce monkey skulls with their thumb-like back talons, then hover while their prey died before returning to tear at the skull. Examination of thousands of monkey remains produced a pattern of damage done by birds, including holes and ragged cuts in the shallow bones behind the eye sockets.

Berger went back to the Taung skull, and found traces of the ragged cuts behind the eye sockets. He said none of the researchers who had for decades been debating how the child died had noticed the eye socket damage before.

Berger concluded man’s ancestors had to survive not just being hunted from the ground, but from the air. Such discoveries are “key to understanding why we humans today view the world the way we do,” he said.

Diane and I have noted that at two pounds, Rusty, our Harris’ Hawk, is capable of taking prey several times her weight. And given the pattern of behavior that we’ve seen (bascially, if it isn’t another Harris’ Hawk and looks remotely susceptible to attack, eat it), we have no doubt that a raptor several times larger of the same temperament would have no compunction in dining on us rather than hunting with us.

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Speaking of Archiving

One of the things that would be good to do would be to keep track of changes to my web pages over time. If everything I did went through a content management system, one way would be to keep some sort of transaction log. But that’s not the situation I want to consider. Many of my pages go back to 1994 and 1995, well before CMS. So given a set of pages without access to some backend, how best to track changes over time?

There are open source programs to mirror websites. To name a couple, there’s HTTrack and w3mir. I’ve used w3mir for quite some time on Unix hosts, and the Windows port of HTTrack. w3mir provides an option to only download changed items given a previous directory of mirrored pages. So here’s what I am thinking about…

Start with a full mirror of a site. I don’t think that a mirroring operation should happen more than once a day, so I’m thinking that a directory named for the site and subdirectories named for the date of mirroring should be sufficient. If I’m wrong on frequency, certainly the subdirectories could be named by both date and time of mirroring.

For subsequent checks of the site, copy the most recent mirror, then invoke w3mir in “update” mode. This should minimize bandwidth use, as only the header information will be needed for many files. I need to see whether the w3mir logging output would be useful for post-processing, but even if not, a comparison of the files in each directory would shortly yield a record of which files changed between visits.

There’s the issue of browsing a set of mirrors with possible changes. This is a problem that the Internet archive has previously solved, but so far as I can tell, they don’t make their software available to others for use. And that’s about where I’ve gotten to in musing about this. I’m hoping to be able to use symbolic links on a Unix host to patch up each mirror, allowing full browsing while only keeping unique files, so as to minimize hard disk space usage.

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A Personal Tragedy

Back in December, I visited my friend, Mark Perakh, author of “Unintelligent Design” and the fellow behind the TalkReason website. He lived with his wife and two dogs in a two-story home a bit north of Escondido, California. He sent an email earlier today to say that his house has burned down. Everyone got out fine, but the house is a total loss. They are staying in a hotel until a rental house is available.

So why do I say “tragedy” when everyone made it out OK? There are some material things that are not easily replaceable, no matter how much money you have. And Mark’s collection of his papers certainly qualifies on that score. While I was there, Mark showed me a sampling of his papers and his two dissertations. While I don’t read Russian, I know that the dissertations had the elegance that follows from function, with many fold-out hand-drawn illustrations, and each equation hand-inked in the text (and there seemed to be equations on most pages). Mark had many letter-file boxes holding reprints of articles that he had published, and showed me some of the hundreds of papers to his credit. I’m not sure whether Mark will try to re-assemble such a collection again, but I know that it was difficult to obtain publications from the Soviet Union in the past, and I suspect that things have not gotten much easier in that regard with the breakup of the USSR.

This has got me thinking about my own collection of “stuff” and what to do about disasters. There aren’t that many “things” that I would be too broke-up over, but I hate to think of the computer files I’ve got becoming lost forever. So I think one project to bump up in priority is making a set of DVDs with the irreplaceable data such that I can send copies elsewhere: to parents, to friends, to anyone living under different circumstances who would be unlikely to suffer the same disaster.

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Federal/State Permitting

One of the things that George Allen brought up was that the joint federal and state permitting system for falconry is planned to go away, to be replaced by permits issued by each state.

While some falconers and NAFA have urged getting the federal permits out of the picture, my personal experience has been that having the federal permit is a plus when travelling or moving. Most law enforcement personnel are not well acquainted with falconry regulations, and with the proliferation of traffic checkpoints, one can easily see how an encounter that goes well given paperwork that clearly shows that falconry is controlled at the federal level might not go so well if the paperwork only shows a state other than the one where one meets up with local authorities.

So I’m going to be making a couple of arguments to Allen (and FWS) on this matter.

First, the individual states are not signatories to the Migratory Bird Treaty Act of 1918. It is because the USA is a signatory to this international treaty that falconry permits are even necessary. The states cannot offer a “permit” under MBTA because they have no part of it. So I see a simple dichotomy here: either we need a federal permit showing our compliance with MBTA, or no permits at all are needed to be in compliance with MBTA.

Second, if there is something about the law in this case that renders the above invalid, it is still the case that FWS has to certify state programs for compliance with MBTA. I think, then, that part of that compliance would be to have any permits issued by states say something to this effect: “United States Falconry Permit, issued under the authority of the state of X”, with specific language on the permit itself saying that falconers have the right to travel through any state where possession of the species of raptor is legal. (Some states, like Hawaii, don’t allow raptors entry, but Hawaii is not a big potential problem, either.) The FWS should ensure that any state issuing permits guarantees reciprocal recognition of permits from all other states, and this should be spelled out on the permit that each falconer carries. It is only with this sort of pre-emptive language that falconers will be able to avoid untold unpleasantness when travelling to national meets or moving to a new state.

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Presentation at Falconry Meet

I made these notes on the PDA during the presentation on Friday night. Unfortunately, I couldn’t successfully post with my connection.

George Allen of the US Fish and Wildlife Service presented on falconry take. He gave the results of population modeling for eight species with good data, showing species specific differences in maximum sustainable yield. This primarily is due to different ratios of breeding adults to ‘floaters’.

He illustrated this with the past problem with peregrines and pesticides. For years, the decline in population was masked because floaters became breeders. Once the floater population is exhausted, the population is in danger of crashing.

There will be a draft EA published soon that will have a 90 day comment period.

Falconers need to work with environmental groups in order to educate them about falconry and its relation to conservation, especially with peregrine recovery.

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