The Austringer

I have a bit more information about the connection difficulties I’ve been having with my ISP, Verizon FIOS. I have a residential account in Palmetto, FL with Verizon FIOS. Mostly, it works fine. I can get to a host of web sites without difficulty, and the transfer speeds are great.

I do remote system administration on two servers in the Dallas-Fort Worth Metroplex. Those servers get their connection via a Verizon FIOS Business plan link. (Yes, Verizon, the servers are on an account where serving is usual and expected.) One server provides my regular email, the other serves a whole bunch of web sites via virtual hosting. And things there are mostly working, where the outside world can merrily get pages served on demand.

But…

As of sometime early last Tuesday morning, January 10th, Verizon FIOS stopped reliably talking to Verizon FIOS. I can tell the approximate time of the outage as the last email message my computer here picked up from the server there was at 1:09 AM CT. The problem is very likely to have manifested within a very few minutes after that. And the problem’s characteristics are just plain weird. One expects most ‘problems’ with connections to be user error. Certainly that’s the primary basis of Verizon FIOS’s residential account tech support, who are ready to quit if the problem isn’t solved by having the user clear their browser cache or resetting the router. This problem, though, is more complex and is not localized to my particular account. First, not all connectivity is gone, just *most* connectivity. I can use SSH to log in remotely and use commands that return small amounts of information. Once I try a command that would return a page or more of text, the connection drops with a ‘Broken pipe’ message. There’s a web page that is static and is only a few hundred characters in size that I can successfully retrieve. But none of the web sites that rely on web applications (Drupal, WordPress, and IkonBoard) do anything but spin forever while the browser displays ‘Waiting on …’.

So let me jot down some things I’ve learned about this so far.

* It isn’t a DNS issue, as ‘nslookup’ finds any of the domain names and returns the correct IP address quite rapidly.

* It isn’t a single port failure. Ports 22, 25, 80, and 587 are, at a minimum, included in the affected list.

* It isn’t a complete break, as connections on the scale of a single packet of data at a time work.

* Using traceroute for other websites shows three hops taken within the Verizon routing center in Tampa. Traceroute for the affected servers shows two hops taken similarly, but the third times out.

* My parents live in Lakeland, Florida, a goodly distance away from where I live, and have Verizon FIOS as their ISP. I visited there this past weekend and asked my dad if he had been able to check this blog recently. He said no, not for about the past week. I tried traceroute from their connection, and it behaved the same way as from my home connection. The problem is not localized, it affects other Verizon FIOS customers.

* I’ve heard from Texas where another Verizon FIOS user of the email system cannot connect to the email server. I don’t have a traceroute result from them to compare.

I have two open tickets on this problem with Verizon, FLCP08NT6J and FLDQ090SXY. There are some other people who have posted to the web saying that they are having network difficulties with Verizon FIOS in the same time frame, but I haven’t seen a report that exactly matches what I am seeing. I’m writing this post by the expedient of using a proxy for my browser, which is a nuisance. (While it is on, my Google search results tend to come back in German, which I can’t read.) It’s a bit of a Catch-22, since I’d like to get feedback from Verizon FIOS users, but if the problem is of the nationwide scale that I expect it is, this post will be unaccessible to them from that account. On the other hand, if it is accessible via Verizon FIOS elsewhere, that would be useful information to have. If you are a Verizon FIOS user, I would appreciate it if you could run traceroute from the Verizon account to baywing.net and copy the results into a comment here. I’ll copy my traceroute results into a comment here shortly.

How to invoke traceroute:

Under Windows, open a command prompt. In the command prompt, type in the following:

tracert baywing.net > tr_baywing.txt

It will take a few minutes to complete if you also have the problem I’m having. The result ill be in a text file, ‘tr_baywing.txt’, in that directory. Copy and paste the text in a comment here if you aren’t seeing the problem, or contact me if you are having the problem.

On Mac or FreeBSD, open a terminal window. At the command prompt, type in:

traceroute baywing.net > tr_baywing.net

On Ubuntu Linux, open a terminal window. At the command prompt, type:

tracepath baywing.net > tr_baywing.net

Here’s my email, if you can’t leave a comment here (remove spaces and convert to symbols as indicated): w e l s b e r r at b a y w i n g dot n e t

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My connection to the servers in Texas from my home systems is unreliable. For the moment, my only reliable link to various of my web sites and my usual email is via my Android phone. Fortunately, I’m grandfathered into an unlimited data plan and have a Bluetooth keyboard. But that is still not a long-term solution. I have a trouble ticket in for my Verizon FIOS ISP that has been active since this past Wednesday without resolution. I just got a call from Marc saying that another email user is having much the same connection problem, so he’s also putting in a trouble report from his side. The servers run on a Verizon FIOS business plan, so connection outages are a concern on that basis, too.

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View at St. Pete.

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Upcoming television series on PBS: Inside Nature’s Giants, begins January 18th at 10 PM.

Professor Joy Reidenberg is an unlikely TV star. She’s a comparative anatomist with the Mount Sinai School of Medicine in New York. Physically, she is diminutive, dark-haired and dark-eyed, and not the sort of slender sylph in morphotype that TV producers seem to favor. But Joy has deep anatomical knowledge and a gift for communicating what she knows, and that led the producers of the documentary series, “Inside Nature’s Giants”, to feature Joy in their program.

Diane and I have known Joy for years as a fellow attendee of various biennial conferences hosted by the Society for Marine Mammalogy. At the latest conference, we caught up with her following the conference-end banquet. She spun us a fascinating tale of how she came to star in a television series. Joy said that she received a call from the producers early one Friday afternoon preceding a holiday weekend, asking her if she might be interested in dissecting a stranded fin whale for a television program. Sure, she said, thinking that they were prospecting and planning for a project that would be months, if not years, down the road. So the question following her “yes” response floored her: Could she be on the plane for Ireland at 6 PM? Maybe was the answer, as Joy told us that physically getting to each part of the transportation network she’d need to get her stuff and passport would stretch things. Her husband and daughter decided to join the expedition. To cut things short, Joy and family made it to Ireland, and despite various amusing misadventures, made it to the locality of the whale stranding on time. There, the documentary producers pressed her into service as liaison to the local health authorities, who had to be convinced that permitting a whale necropsy on the spot was the best way forward to safely disposing of the carcass. She also had to try to convince the police to keep people away from the body, and she reported less success on that front. In any event, Joy got to do the dissection there for the cameras, and her innate enthusiasm and ability to draw people into discussion of anatomy impressed the producers so much that she became a regular co-host on the series.

There was also the adventure of traveling back home. Diane and I have attended necropsies of cetaceans, sirenians, pinnipeds, and sea turtles, and one has to take fairly strong measures to deal with the remaining odor that clings to clothes, skin, and hair. Joy had to physically get inside a decaying whale there in Ireland, and that makes for a different scale of olfactory assault. Joy told us of taking a succession of showers with vigorous scrubbing, but in the end even her family opted to stay in a separate room at the hotel. On the plane ride back, Joy was shifted to the very rear of the plane by the flight attendants, who kindly told the other passengers that they were having trouble with the toilets to explain the stench.

The TV series, “Inside Nature’s Giants”, is slated to air six episodes on PBS, starting January 18th, 2012, at 10 PM. The series is all about charismatic megafauna, but concentrates on post-mortem anatomical examination. Check your local PBS affiliate to make sure of the schedule. Another regular on the series who should be familiar to readers is Prof. Richard Dawkins.

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I’m attending the Society for Marine Mammalogy biennial conference this year. The location is the Tampa Convention Center, making this pretty simple to get to.

Saturday and Sunday are when various workshops are held. Today, I’m attending the Sirenian workshop. It is an all-day affair, with 33 speakers and over 200 attendees.

My early connectivity was best with my Facebook account (Wesley R. Elsberry), but I’ve gotten set up with synced Twitter (welsberr) and Facebook status updates, so most of what I’m noting as things proceed will be going out that way.

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The editors of the Tulsa World think that Lawmakers should adopt stronger wildlife laws. That’s fair enough in light of the tragedy in Ohio where exotic predators like lions, tigers, and bears were released by a suicidal keeper. But the editorial’s structure left much to be desired, in my opinion. They do have a good opening:

It’s understandable, and in most instances maybe even OK, for Oklahomans to own and keep certain kinds of unusual critters on their homesteads, even in the city. There’s nothing wrong with a few chickens or an occasional horse or donkey.

But tigers and bears? Allowing people to own and keep large, sometimes-predatory animals on their premises is just asking for a tragedy to occur.

This next part looks all right on first reading, but there is a problem when it is paired with the ending of the editorial:

But in many parts of the state, a tiger can be kept as a backyard pet without the approval of any agency. And too often, the results are predictably tragic.

“These animals are being bought and sold at the hands of people that have no business owning them. I have seen what happens to them in private hands, and the animal loses,” said Dr. Kay Backues, director of animal health and the senior staff veterinarian at the Tulsa Zoo.

“It’s horrifying,” she said. “It’s tragic. And nationally, there are a good number of people that are killed every year or injured by exotic animals they’ve kept as pets.”

Once we get to the end, things have gone from the specific focus and into the completely general:

Micah Holmes, who’s with the Oklahoma Department of Wildlife Conservation, which licenses native-animal breeders, perfectly summed up what ought to be the Legislature’s marching orders: “First thing we’re going to say is that wildlife belongs in the wild.”

This is a potential problem with a simple solution. Let’s address it before another tragedy occurs.

Do they really want to advocate a simple solution of all wildlife belonging in the wild, that is, that no one can be allowed to have any animal considered wild? They don’t clarify what, exactly, their “simple solution” is supposed to cover. I thought of falconry first. Then in composing my response on their site, I discovered that one of their authorities quoted, Dr. Kay Backues, herself owns exotic wildlife that could be at risk under an exceedingly broad wildlife ban. How far might that go? Many people keep aquaria stocked with exotic wildlife, many species of which are obligate predators. It seems to me that the legislative response to the Ohio tragedy either is going to be more complex than the editors claim, or a lot of people are unexpectedly going to find themselves at the wrong end of a simple law.

Here’s my response in a comment left on their site:

As the saying goes, every complex problem has a solution that is simple, neat, and wrong. The editorial starts with a more specific thrust concerning large, predatory exotic animals capable of killing humans, but ends with an incredibly broad statement about all wildlife as the “marching orders” to the state legislature.

Hopefully the “simple solution” eventually advocated is just complex enough to permit falconry to continue to be practiced in Oklahoma. Falconry involves always-predatory and sometimes large animals kept by people for the purpose of hunting. The falconry community acted to conserve endangered raptor species when pollution threatened those populations, which sounds to me like the wildlife won in that case, contrary to the import of the quote in the editorial from Backues. Of course, Backues may have been more circumspect and nuanced in what she said than what the editors chose to pass on to us. In fact, given that Backues herself owns an exotic pet (an umbrella cockatoo, according to Anne Brockman’s article), one would expect that she must have done so. Does Backues agree with Holmes on the exceedingly broad dictum, “wildlife belongs in the wild”? I’m unaware of any successful release into the wild (success meaning that the released animal lives out the remainder of a normal lifespan there) of an umbrella cockatoo, especially one that has spent 25 years in the care of man.

The legislators might want to talk to the folks at the Oklahoma Falconers Association to figure this issue out, at least as far as falconry is concerned. There may be other stakeholders, such as Dr. Backues, who would also be negatively affected by too-broad a “simple solution”. And if the editors want to advocate a simple solution to the problem, maybe a little more care ought to be invested in saying what they think the simple solution is, since “the regulation of exotic wildlife” leaves quite a bit unspecified.

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Some time back, I mentioned getting data off CD-ROM and putting it on hard disk with a second hard disk for back-up. As time passes, this gets more critical. I think archivists start getting antsy about CD-ROM after a decade or so, and I have media that go back to 1996.

And I have run into CD-ROM data disks with various reading errors.

So I thought that I would mention a freeware tool for Windows that addresses getting what can be gotten from a CD-ROM with problems. This is Roadkil’s Unstoppable Copier (RUC). Fortunately, you can stop it in bad circumstances by killing the process in Task Manager. I’ve done this after setting it to work on a CD-ROM with an obvious, visible blemish. In its default setup, RUC will attempt multiple reads of bad sectors in order to recover as much of a file as possible. This leads to it taking a long, lllllooooonnnnngggg, time to get through a patch of damage. Longer than I was willing to wait, anyway. So in the “Settings” tab, I set it to “Auto Skip Damaged Files”. This copies off all the undamaged files from the CD-ROM, and it does so fairly expeditiously. For some CDs, I may decide to let it trundle for a few days to analyze things, but first I want to get as much of the good stuff secured as I can. This tool looks to be a help in that regard.

The lengthy recovery process is probably most useful for large text files, where recovering a majority of a file is preferable to losing all of it due to a possibly small section that is damaged. For binary files, this may not be universally useful. The data files I have are raw integer data, so as long as the reconstituted file preserves the same length, I can recognize the bad patches and leave them out of analysis. That may not hold true for ZIP files and other compressed archives, JPG images, and the like.

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We’ve known for a long time that Casey Luskin has some very odd ideas about what constitutes a technical publication. Casey’s been good enough to document another deficiency of his in this respect for all to see, but no one is allowed to comment. (I wonder what happened to the Discovery Institute’s grand experiment in interactive commentary, anyway?)

Casey thinks I’m a hypocrite for criticizing Granville Sewell on the topic of self-plagiarism. As evidence, he notes that an essay co-authored by Jeff Shallit and I was published on the web and later in the journal Synthese.

The Case of Wesley Elsberry’s Self-Plagiarism

In 2003, Wesley Elsberry and Jeffrey Shallit co-published a paper, “Information Theory, Evolutionary Computation, and Dembski’s ‘Complex Specified Information,’” on the website TalkReason.org. (I wrote a response to the substance of their 2003 article here.)[*]

In 2011, Elsberry and Shallit co-published a paper in the journal Synthese titled “Information theory, evolutionary computation, and Dembski’s “complex specified information.’”

If you’ll notice, the titles of those two papers are identical. That’s not all that’s identical in the papers. A comparison performed by a colleague using the plagiarism-detection software SafeAssign shows that these two papers are ~94% matching.

(Note: The analysis used text files I had prepared using the original PDFs of the papers. For processing, I had to strip out some numbers and mathematical equations which did not translate well into the text files. Also, my colleague’s name has been redacted.)

Isn’t it just a bit hypocritical that Elsberry harps upon Sewell’s supposed mortal sin of “self-plagiarism” when Elsberry himself has taken previously published work and then republished it in academic journals?

Yeah, I’ll stipulate that the essay is mostly the same. But…

Casey, Casey, Casey… Republishing essentially the same thing multiple times in the technical literature is a bad thing. Getting something that’s been released on the web but not yet published in the technical literature is perfectly fine, with a caveat: the authors should make sure that the editors are aware of the prior release. This was done for the essay that was published in Synthese. (The editors also knew of a similar essay published in 2004′s “Why Intelligent Design Fails”, which Casey hasn’t mentioned yet.) This situation is not what “self-plagiarism” applies to. Nor is converting material from a dissertation into technical articles considered self-plagiarism, which is another process that I’m still working on. For another case in point, some time ago Reed Cartwright blogged a criticism of a paper. Another researcher saw that and invited Reed to contribute to a response letter in the technical literature. Does Reed’s previous web publication of the line of criticism used in the letter establish “self-plagiarism”? That’s a clear “No”. Scientists treat the technical literature as a separate source of knowledge from popular sources like blogs and portal sites. Repetition of material in lay outlets is essentially of no concern to the scientific endeavor. When it occurs in the technical literature, it is perceived as a pernicious problem.

But Granville Sewell doesn’t have a situation analogous to mine, where I converted a lay release into a publication in the technical literature. The Discovery Institute itself counts his shtick about the 2nd Law of Thermodynamics twice already in its list of “peer-reviewed” work on ID. I have no doubt that had AML actually followed through on publication of the essay, the DI would have happily counted it three times over in their list instead of just twice. The DI and its spokes-weasels can’t simultaneously claim that each re-publication counts separately and that self-plagiarism that repeats the same arguments in the technical literature is not happening. Of course, Casey knows how weak his position is, else he wouldn’t have added the following to his screed:

So I personally don’t care if Wesley Elsberry plagiarizes himself, and it doesn’t matter to me one bit if he resubmits material he’s already published to any publication he likes.

My point is simply this: it is hypocritical for Elsberry to attack Sewell for “self-plagiarism,” when Elsberry does the same thing. What Sewell (and Elsberry) have done isn’t a crime. Elsberry’s complaint is both baseless, and hypocritical.

Given that IDC advocates are so unproductive, Casey has to defend the line that if they can manage to sneak the same stuff around to multiple venues within the technical literature, there’s nothing wrong with that. Well, there is something wrong with that. Maybe it isn’t high on the lists of academic sin, but it certainly does goes some way to demonstrating intellectual dishonesty to game the technical literature.

[*] Casey, you did not write a response to the substance of our essay. That would have required reading comprehension on your part. What you wrote was an orgy of strawman gouging and delusional codswallop.

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In the Terry Pratchett novel “Witches Abroad”, he sets up an image of “the optimist’s fire”, which he then defines as “two logs and hope”. I bring this up because I’m seeing people who desperately want to be seen as hard-nosed and fiscally responsible proposing the optimist’s economic booster: tax cuts and hope.

Cutting taxes on industry (and regulations, too!), it is said, will finally bring about job creation and get the economic fire burning once again. I am afraid that I’m not seeing the causal link here. Our corporate citizens have plenty of money on hand, various estimates putting those cash reserves in the trillions. It’s not like any tax cuts are contemplated on that scale, so that leads to the vexing question of why jobs aren’t being created now? If they are worried about consumer spending, tax cuts for businesses don’t address that at all.

Well, having said that, I would propose a tax cut for businesses. But I am not proposing an across-the-board tax cut. No, I think that there should be a tax incentive for businesses that create new jobs. If you have a business and are bringing more people into the workforce than you did the year before, your business should get a break on its taxes. If you have a business that is standing pat on jobs or shedding them or outsourcing them, then, sorry, but no tax break for you. Probably this would have to have some metric that ties together both number of jobs and total compensation per job. The right incentive structure will reward companies more for better-paying jobs, and less for low-paying job creation. But that’s a refinement to be considered after getting more people onboard with the big idea.

This puts the right outlook on using the tax code to influence business: it makes clear what behavior is needed to take advantage of the tax incentive, and makes clear that until that behavior is actualized, there is no corporate handout in the offing. It rewards the corporate citizens who are making things better here in the USA, and withholds benefits from those who seek to cut labor corners or send jobs overseas. It means that we aren’t cutting our own economic throats to no better purpose than padding executive bonuses, which seems to be all that we’ve gotten out of corporate tax-cutting in recent memory. It would mean that we are applying a lighter where it is needed rather than hoping that a fire will start on its own somewhere, somehow. And, best of all, even if it doesn’t work and most corporations refuse to create jobs anyway, we haven’t burdened the rest of the taxpaying public unnecessarily.

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Back in 1990, Clayton Williams, Jr. was in the news a lot as he ran for governor in Texas. His campaign famously imploded over insensitive good-ol’-boy comments made to a weekend gathering of media. He was rich, but there didn’t seem to be much else to recommend him. I always thought it odd to go by the “Clayton Williams, Jr. Alumni Center” at the TAMU campus.

But it appears I need to seriously revise my assessment of Williams. The Austin-American Statesman reports that Williams had some extraordinarily good advice for Texas Governor Rick Perry (which Perry obviously and promptly ignored):

Williams, a wealthy Midland oil man, wrote to Perry as the State Board of Education was starting the debate over new science curriculum standards. He warned Perry to stop any effort by the board to include creationism or intelligent design in those standards.
“If Texas enters into a debate on the teaching of fundamental religious beliefs in public schools, it will tarnish our strong academic reputation, set our ability to attract top science and engineering talent to Texas back decades and severely impact our reputation as a national and global leader in energy, space, medicine and other high tech fields,” Williams wrote.
He continued: “Governor, this is a very important issue for Texas. I urge you to quell this issue quietly, firmly and permanently.”

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It’s been a long time coming, but the paper on evidence for multiple sound sources in the bottlenose dolphin appears in the October 15th issue of the Journal of Experimental Marine Biology and Ecology. I’ve been told that the PDF will be freely available soon, hopefully in the next week or so.

The abstract is:

Indirect evidence for multiple sonar signal generators in odontocetes exists within the published literature. To explore the long-standing controversy over the site of sonar signal generation, direct evidence was collected from three trained bottlenose dolphins (Tursiops truncatus) by simultaneously observing nasal tissue motion, internal nasal cavity pressure, and external acoustic pressure. High-speed video endoscopy revealed tissue motion within both sets of phonic lips, while two hydrophones measured acoustic pressure during biosonar target recognition. Small catheters measured air-pressure changes at various locations within the nasal passages and in the basicranial spaces. Video and acoustic records demonstrate that acoustic pulses can be generated along the phonic fissure by vibrating the phonic labia within each set of phonic lips. The left and right phonic lips are capable of operating independently or simultaneously. Air pressure in both bony nasal passages rose and fell synchronously, even if the activity patterns of the two phonic lips were different. Whistle production and increasing sound pressure levels are generally accompanied by increasing intranarial air pressure. One acoustic “click” occurred coincident with one oscillatory cycle of the phonic labia. Changes in the click repetition rate and cycles of the phonic labia were simultaneous, indicating that these events are coupled. Structural similarity in the nasal apparatus across the Odontoceti suggests that all extant toothed whales generate sonar signals using the phonic lips and similar biomechanical processes.

This was a big undertaking, requiring the coordinated effort of a lot of talented and busy people.

Diane Blackwood designed and implemented our acoustic recording layout and the dolphin stationing device and biteplate, and made sure the amplifying equipment was operational and protected from incident. (Incidents with electronics in proximity to sea water are all too common.) I designed and wrote the software that acted as a multichannel digital data recorder, the data reduction program, and the analysis program. Bill van Bonn was our veterinarian who spent our data recording sessions lying prone on the dock as he placed, checked, and positioned the endoscopes and pressure catheters. Our principal investigator, Ted Cranford, operated the video side of things, including the high-speed video capturing the endoscope views. Sam Ridgway and Don Carder consulted with us, helping us with the use of the pressure catheters (which had previously been used in two prior studies they authored). Monica Chaplin and Jennifer Jeffress were the dolphin trainers on the spot during data recording. Tricia Kamolnick and Mark Todd were trainers who helped get the subjects prepared for our data collection process, and Mark Todd implemented the regular video system. It took between two and three hours each data collection day for us to set up, test, and calibrate all the equipment. Breaking down took somewhat less time, but I would still have to run a custom program to demux the data, produce images visualizing the data for each trial, and then shift the day’s data off the hard disk and on to CD-ROM media.

Update: The Marine Mammal Center has put up the PDF of the paper.

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There’s a “Judge Judy” video clip being circulated where Judge Judy is deciding a case over unpaid rent. A young woman is the plaintiff, and is seeking several months of unpaid rent from a young man who shared an apartment with her. The young man is deeply confused about the concept of government aid for the purpose of rent, and Judge Judy unsuccessfully attempts to educate him about that. He asserts that because he could have paid for a hotel with the money, that he is justified in spending the money for other purposes.

But what struck me was the conclusion to the clip. The young man asks whether the plaintiff paid the rent on the apartment, and Judge Judy tells him that is an excellent question. Judge Judy then determines that the plaintiff only actually paid the rent for one month out of the several months that she is suing the defendant over. Judge Judy abruptly dismisses the case.

I’d appreciate feedback from the legally-oriented folks out there. It seems to me that Judge Judy is only justified in a dismissal like that if she is running (or simulating) a court of equity, not a court of law. So far as I can figure it, a court of law would hold it irrelevant to a claim whether the plaintiff was in violation of a contract with a third party. But in a court of equity, the plaintiff must be filing a case with “clean hands”, and it is that standard which the plaintiff in this case failed to meet.

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Casey Luskin has an unenviable track record. Pretty much anytime Casey gets going, you can count on him to shoot himself in the foot someway, somehow.

Yesterday evening’s blog post by Casey is no exception. So if Casey has done it again, why would I give the title I have? Well, because of the way Casey shoots himself in the foot. You see, Casey so often goes off half-cocked because he doesn’t bother to figure out what the person he is critiquing actually said, and here we have Casey not listening to the primary source again, therefore Casey “doesn’t do it again”.

Casey’s target this time was Dr. Eugenie C. Scott of the National Center for Science Education. When Casey is up against a strawman he’s constructed, he pulls no punches, thus his post’s title of “Eugenie Scott Misrepresents the Law on Evolution Education”. What does Casey present as evidence of his claim of the title? Let’s let Casey go on a bit:

Uncommon Descent is reporting that National Center for Science Education (NCSE) executive director Eugenie Scott has stated in a talk: “You cannot teach evidence against evolution. There have been some court decisions that have talked about this including Kitzmiller, but there has not been a really clean test of this idea of teaching evidence against evolution.”

Uncommon Descent? Casey trusts them to get anything right? He shouldn’t, because they didn’t. The snippet Casey gives truncates even what UD managed to relate, and UD was missing a pretty critical word in there. Casey doesn’t note that Genie led into to quote by saying that she had an asterisk on this item, “this item” being text on a projected slide on screen. With the critical text restored, we have this instead: “OK, what else can you not do? I have a little asterisk here that you cannot teach evidence against evolution.” Genie goes on to explain the state of the law concerning this point. It has an asterisk because, as Genie ably explains, the law is not yet settled on this particular point. Casey apparently doesn’t know about this, and about the only way that could happen is if he started foaming at the mouth based only on the UD text and failed to actually listen to Genie’s video presentation. Here’s Casey blowing off a piece of his foot:

Isn’t that convenient for Eugenie Scott that she now claims that the courts have insulated evolution from any form of critique in public schools?

First, Casey fails to note the nuanced presentation Genie made concerning the point of law in question. Second, Casey places religious antievolution argumentation within “any form of critique”. A science classroom is not the appropriate venue for “any form of critique”. Only critiques that themselves have passed scientific muster are appropriate there, and that leaves out the old, moldy religious antievolution argumentation.

In any case, Dr. Scott is misrepresenting the law.

Oh, really? Why didn’t you listen to Genie’s video presentation, Casey? If you had, you would have had the opportunity to not misrepresent Genie.

The Kitzmiller v. Dover lawsuit dealt with the teaching of intelligent design, not teaching scientific evidence against evolution. And even if it had, Judge Jones would have been overruled by a much higher court–the U.S. Supreme Court–which has already ruled that it is legal to teach scientific critiques of prevailing scientific theories like evolution. As the U.S. Supreme Court stated in the 1987 case Edwards v. Aguillard, a case that directly dealt with the topic of origins-education in public schools:

We do not imply that a legislature could never require that scientific critiques of prevailing scientific theories be taught. . . . [T]eaching a variety of scientific theories about the origins of humankind to schoolchildren might be validly done with the clear secular intent of enhancing the effectiveness of science instruction.”

(Edwards v. Aguillard, 482 U.S. 578, 593-594 (1987).)

Eugenie can say whatever she wants but she cannot overrule the U.S. Supreme Court refuting her claims.

Genie claimed that the Kitzmiller decision discussed “evidence against evolution”, not that it provided the final word in law prohibiting presenting “evidence against evolution”. Remember the asterisk Genie mentioned? Oh, of course not, since Casey apparently didn’t bother to listen before making up stuff. Can we find Judge Jones doing what Genie said he did? Of course we can:

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.

ID proponents primarily argue for design through negative arguments against evolution, as illustrated by Professor Behe’s argument that “irreducibly complex” systems cannot be produced through Darwinian, or any natural, mechanisms. (5:38-41 (Pennock); 1:39, 2:15, 2:35-37, 3:96 (Miller); 16:72-73 (Padian); 10:148 (Forrest)). However, we believe that arguments against evolution are not arguments for design. Expert testimony revealed that just because scientists cannot explain today how biological systems evolved does not mean that they cannot, and will not, be able to explain them tomorrow. (2:36-37 (Miller)). As Dr. Padian aptly noted, “absence of evidence is not evidence of absence.” (17:45 (Padian)). To that end, expert testimony from Drs. Miller and Padian provided multiple examples where Pandas asserted that no natural explanations exist, and in some cases that none could exist, and yet natural explanations have been identified in the intervening years. It also bears mentioning that as Dr. Miller stated, just because scientists cannot explain every evolutionary detail does not undermine its validity as a scientific theory as no theory in science is fully understood. (3:102 (Miller)).

Casey’s strawman is taking a pounding, but he still hasn’t demonstrated Genie misrepresenting anything. Casey, though, is plainly misrepresenting Genie’s talk.

More Casey:

Actually, I’ve heard secondhand that Eugenie doesn’t privately believe it’s really illegal to critique evolution. I’m not going to name names, but I’ve spoken with legal scholars who have collaborated with Darwin lobbyists. They’ve told me that what Eugenie Scott fears more than anything is an army of teachers who WILL teach the scientific controversy over evolution because she knows that under current law, it’s legal to do that. There’s a reason why, as Eugenie puts it, “there has not been a really clean test of this idea of teaching evidence against evolution.” That’s because the NCSE and its allies in the Darwin lobby are afraid to file a lawsuit against a policy that requires or permits scientific critique of evolution because they know they will probably lose that case in court.

After all, if the Darwin lobby feels a policy is unconstitutional, they waste little time in filing lawsuits; it took less than two months for attorneys working with the ACLU to help parents file a lawsuit after the Dover Area School Board passed a policy requiring the teaching of ID.

Uh, no, Casey. In the video handily linked in the post at UD, you could have listened to Genie discussing the difference between a “permissive” act and one that is a demand that something wrong be done. For permissive acts, Genie explains that one cannot simply challenge the law on its own, one must instead wait for someone to use the permissive act to implement a curriculum that infringes rights under the Constitution, find out about the infringement, then find someone within the student body who has standing to challenge it and the willingness to challenge it, and all that is much harder than challenging a law that is wrong on its face. Start around 54:50 into the video to hear it. Of course, Casey should have heard it already, but he either didn’t bother … again … or he is lying about what Genie actually said.

But there have been multiple policies requiring or permitting scientific critique of evolution which have remained on the books for years without any lawsuit. For example:

Texas: Students must “analyze, evaluate and critique scientific explanations . . . including examining all sides of scientific evidence of those scientific explanations so as to encourage critical thinking,” and also “analyze and evaluate” core evolutionary claims, including “common ancestry,” “natural selection,” “mutation,” “sudden appearance,” the origin of the “complexity of the cell,” and the formation of “long complex molecules having information such as the DNA molecule for self-replicating life.”

Minnesota: “The student will be able to explain how scientific and technological innovations as well as new evidence can challenge portions of or entire accepted theories and models including . . . [the] theory of evolution . . . .”

New Mexico: Students will “critically analyze the data and observations supporting the conclusion that the species living on Earth today are related by descent from the ancestral one-celled organisms.”

Pennsylvania: “Critically evaluate the status of existing theories (e.g., germ theory of disease, wave theory of light, classification of subatomic particles, theory of evolution, epidemiology of AIDS).”

Missouri: “Identify and analyze current theories that are being questioned, and compare them to new theories that have emerged to challenge older ones (e.g., Theory of Evolution . . . ).”

Alabama: “[E]volution by natural selection is a controversial theory . . . . Instructional material associated with controversy should be approached with an open mind, studied carefully, and critically considered.”

South Carolina: “Summarize ways that scientists use data from a variety of sources to investigate and critically analyze aspects of evolutionary theory.”

Louisiana: Louisiana public schools shall “create and foster an environment…that promotes critical thinking skills, logical analysis, and open and objective discussion of scientific theories being studied including, but not limited to, evolution, the origins of life, global warming, and human cloning.”

Mississippi: “No local school board, school superintendent or school principal shall prohibit a public school classroom teacher from discussing and answering questions from individual students on the origin of life.”

Kansas: “Regarding the scientific theory of biological evolution, the curriculum standards call for students to learn about the best evidence for modern evolutionary theory, but also to learn about areas where scientists are raising scientific criticisms of the theory.”

Ohio: “Describe how scientists continue to investigate and critically analyze aspects of evolutionary theory. (The intent of this benchmark does not mandate the teaching or testing of intelligent design.)”

Each of these policies are still in effect, except for the last two (Kansas’s policy was repealed in 2007 after conservatives lost a majority on the State Board of Education, and Ohio’s policy was repealed in 2006 after its State Board of Education underwent a similar change). The point is this: each of these policies are (or were) on the books for years without any legal challenge from the Darwin lobby. If Eugenie Scott is correct that it’s illegal to teach scientific critiques of Darwinian evolution, why is that?

Genie never said a word about it being illegal to “teach scientific critiques of Darwinian evolution”. What she was discussing was the tendency for religious antievolutionists to present their anti-scientific stuff and try to act as if they have something worth bringing up in a science class. Just because religious antievolutionists call something “evidence against evolution” doesn’t magically change it into something scientific. Scientific critiques have proven to be beyond the capacity of the religious antievolutionists. At best, they present a cargo cult version of critique, adorned with a poor appearance that is, nonetheless, at the limit of what their (mis)understanding of the subject can deliver.

Darwin lobbyists would love to ban scientific critique of evolution in public schools, so why haven’t they filed a lawsuit? It’s simple: They aren’t confident they would win because they know that current law does NOT make it illegal to teach scientific critiques of evolution in public schools.

Sorry, wrong again. Once a bad curriculum turns up and someone with standing to challenge it makes themselves known, then we’ll see how fast off the mark the legal challenge gets going. Casey is trying to equate legal challenges to facially-wrong laws and policies with challenging a law or policy without a facial defect, and that is clearly a misrepresentation of the law. Kinda ironic how Casey ends up doing the bad thing that he claims others do.

What’s most distressing here isn’t just that Eugenie Scott is misrepresenting the law. It’s that in her perfect world, she would apparently prefer that teaching scientific critique of evolution be illegal. What kind of society would we live in if Eugenie Scott and the Darwin lobby had their way, and it was illegal to ask hard questions about scientific theories? Not a good one.

Evolutionary science has a long and distinguished record of asking hard questions about scientific theories. There’s plenty of theories that have been discarded. Casey could read Peter Bowler’s “Evolution: The History of an Idea” to get that background. Or he can continue with not doing it (“it” being due diligence) again… and again.

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Two vehicles in a Bartram Hall (Zoology department building) parking area at the University of Florida were vandalized, apparently because they displayed “Darwin fish” on them. Besides messing up the Darwin fish, the vandal(s) put nails into tires.

Hat tip to Prof. Betty Smocovitis, whose hand appears in the linked video.

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There’s an essay by Randal Rauser at “Christian Post” offering what’s termed a rebuttal to a criticism of an earlier essay. Rauser seems to be a run-of-the-mill “intelligent design” creationism (IDC) cheerleader.

Rauser defends Dembski’s ideas early on.

Joseph H. Axell posted a long rebuttal in the comment section of my article “Unintelligent arguments against intelligent design: A Primer”. There are a number of claims I’d like to challenge in the response. For instance Axell writes: “Dembski’s ‘explanatory filter’ for detecting design has been shown to be inadequate (false positives being but one problem)….” That’s like saying that an umbrella is inadequate because it is ineffectual in a windy rainstorm. Dembski’s explanatory filter, like an umbrella, can still be a useful tool even if it is not perfect. Is Newtonian physics tossed out as illegitimate because it doesn’t work at the quantum level?

Joseph Axell is right. Rauser, not so much. Newtonian physics is useful somewhere, which distinguishes it from Dembski’s “design inference” that has never had a fully-worked out example applied to any non-trivial problem. So much of Rauser’s original essay is based upon the conflation of ordinary and rarefied design inferences that it seems that he must not have read The advantages of theft over toil yet. The deficiencies of Dembski’s CSI are detailed in this essay. In the appendix, we introduced the concept of Specified Anti-Information and demonstrated that it formed an upper bound on Dembski’s CSI and disproved Dembski’s proposed “law of conservation of information”. A concerned reader wondered why we would bother repairing “specification”, and I replied:

The existence of a minimal program/input pair that results in a certain output indicates that there exists an effective method for production of the output. Since effective methods are something that are in common between intelligent agents and instances of natural computation, one cannot distinguish which of the two sorts of causation might have resulted in the output, but one can reject chance causation for the output. We haven’t so much repaired specification as we have pointed out a better alternative to it.

This leads me to a claim about Dembski’s design inference: Everything which is supposedly explained by a design inference is better and more simply explained by Specified Anti-Information.

SAI identifies an effective method for the production of the output of interest. The result of a design inference is less specific, being simply the negation of currently known (and considered) regularity and chance. The further arguments Dembski gives to go from a design inference to intelligent agency are flawed. On both practical and theoretical grounds, SAI is a superior methodology to that of the design inference.

Back to Rauser:

Second, Axell writes: “So you concede that ID proponents have so far failed to achieve even the preliminary goal of establishing that a causal intelligence has been engaged in creating features of the natural world.”

First of all, whether they have or haven’t suceeded in establishing any particular instance of intelligent design is completely irrelevant to the claim that such a project is, in principle, viable. That’s the point! (And philosopher of science / atheist Bradley Monton makes it much better than I ever could.)

I need to reiterate that ordinary design is not the same as rarefied design, and here we have Rauser explicitly trying to ignore that point.

Now for the relation to the title. Here’s Rauser moving in for the rhetorical kill, at least apparently in his mind:

Finally I turn to the main point. Is it true that a person is obliged to provide “a detailed account of the nature of that intelligent cause and of the time, manner and place in which it has engaged with the natural world” if that intelligent cause is one with which we are not “familiar”?

Axell just invented that stipulation but provided no reasoning for it. He just asserts it. But not only is there no reason to accept it. There is also a good reason not to accept it. Consider the following illustration:

Axell’s friend tells him: “Joseph, I fear that there is some kind of intelligence in my house that doesn’t want me here.”

Axell, being a scientifically enlightened denizen of the twenty-first century is skeptical. “What evidence do you have?” he asks.

Axell’s friend then pulls out a ouija board and sets it on the coffee table. Immediately the planchette begins moving across the board and it spells “Get out of here.” Axell can clearly see that nobody is touching the planchette and immediately he picks it up, inspects it closely. There are no magnets: it is only a piece of wood. There are no wires. There is no draft. He puts it back down. Immediately the planchette begins to move again as it spells out “I said get out of here.”

Highlighting added.

Good reason? Excuse me, but all I see here is a pathetic fantasy, one in which Rauser ludicrously inserts his critic. There is no reason, and further, no reasoning, going on in Rauser’s response. It is, rather literally, the demon-haunted world being given as a basis for the legitimacy of IDC. We all knew that already, Randal.

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There’s a row going on about continuing sexism within the skeptical community. Rebecca Watson, a speaker at an international skeptical conference, was propositioned by a male attendee… in an elevator… at 4 in the morning. She turned him down, and later used the incident in calling for better behavior out of the male skeptical community. There’s a lot of other people weighing in over the particulars of how Watson did this, but one of the more puzzling to me is a contribution signed off as from Richard Dawkins.

Posted by: Richard Dawkins Author Profile Page | July 2, 2011 11:11 AM

Dear Muslima

Stop whining, will you. Yes, yes, I know you had your genitals mutilated with a razor blade, and . . . yawn . . . don’t tell me yet again, I know you aren’t allowed to drive a car, and you can’t leave the house without a male relative, and your husband is allowed to beat you, and you’ll be stoned to death if you commit adultery. But stop whining, will you. Think of the suffering your poor American sisters have to put up with.

Only this week I heard of one, she calls herself Skep”chick”, and do you know what happened to her? A man in a hotel elevator invited her back to his room for coffee. I am not exaggerating. He really did. He invited her back to his room for coffee. Of course she said no, and of course he didn’t lay a finger on her, but even so . . .

And you, Muslima, think you have misogyny to complain about! For goodness sake grow up, or at least grow a thicker skin.

Richard

There’s the whole issue of authentication, since this was a comment entered at ScienceBlogs, and you can pretty much sign whatever name you want to something. I hope that the above is the work of a prankster impostor.

If I just have a look at the content, though, it is really troubling to me. We’re talking about social standards of conduct, so there’s going to be differences of context. The really quite horrible levels of sexism and violence toward women mentioned above that are the norm in some cultural contexts do not inform what we should strive for in the cultural context that we live in. Calling for better behavior here is not a repudiation or diminishment of greater suffering endured elsewhere, at least not in my estimation. The line taken in the “Dawkins” missive, if followed consistently and assiduously, would mean a stop to any sort of progressive social change in our culture, as worse examples on just about any topic are bound to be found elsewhere in the world. Karl Kraus put it this way: “The devil is an optimist if he thinks he can make people meaner.”

Yes, we should be activists to improve the human condition around the world. But we have to live in our own culture, and why not try to make things better here, too?

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Years ago, I set up a MyLife profile. Periodically, I get email from them noting that my profile has been searched, and that I should pony up some money so that they will tell me who actually visited my profile. Personally, I find “upgrade” come-ons a disincentive, plus FaceBook and other social networking sites have pretty much removed any remaining utility for sites like MyLife.

Well, I got another MyLife email a few days ago.

Subject: Does Lauri know you? She viewed your profile!

Hi Wesley,

1 NEW person has viewed your profile.

1. [...], York Haven, PA

Upgrade to premium membership and see who!

Well, there’s no mystery in that about who they said visited my profile. I forwarded the message to Lauri Lebo to share in the obviousness of it. Lauri wrote me back to say that it has been years since she used MyLife to visit any profiles. So that “NEW” label they’ve provided in the MyLife email come-on appears to be entirely fictional. This appears to be another good reason to refuse to encourage them with “premium membership” funding.

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I occasionally check out the Tern Micro website. They are manufacturers of controllers and expansion boards for embedded applications. Their controller boards use IAPx86 class CPUs and are programmed in C. A few years ago, I had checked with them about whether they had components suitable for a field acoustic recorder, and given the short time schedule we had, we decided to go with off-the-shelf components instead for that. Things have changed, though, as I found an expansion board of theirs called the GR4 on their page.

Let me set some context. Some years ago, Whitlow Au and Marc Lammers put together a four-element hydrophone array that allowed them to perform acoustic localization. If I recall correctly, their recording system was based upon a National Instruments DAQ card for CardBus hosted in a laptop computer and was capable of 500 kilosamples per second. When multiplexed across four channels, that’s a max of 125 kilosamples per second per channel. With a multiplexed system, you have to account for time offsets between channels as you analyze the data for time-of-arrival estimates of signals. If there is crosstalk at the high acquisition rates, you might have to drop the total sampling bandwidth to give the multiplexing circuitry time to settle to the next channel’s input level. That at least is how I had to work with an NI PCI-MIO-16-E DAQ card back in 1999. The solution to this problem is simultaneous-sampling, where all the channels of interest get their own sample-and-hold circuitry and the conversion is triggered off the same clock input. Simultaneous-sampling hardware is more expensive, since the main sets of circuits have to be multiplied for the number of channels. Around 2001, a project I was involved with bought a couple of simultaneous-sampling DAQ cards for the PCI interface, at a cost of a couple of thousand dollars each.

Of course, lugging a full-up desktop system into the marine environment is not a thing to be undertaken lightly. If one could instead reduce the field recording part to something that could be effectively shielded from the elements and work instead off of straight DC battery power, it would be all-around more convenient. The more remote the field work, the more convenient that gets.

So let’s get back to the Tern GR4. This analog-to-digital expansion board is small, just a bit longer and wider than a business card. It can be provisioned with two ADC chips and 4 MB of memory (and that full configuration is what I’m talking about). The base price is $129, but with the additional features added the cost is $259. The GR4 boards are stackable. There are pin headers that form a communication and data bus with a controller card. Each GR4 permits simultaneous-sampling of two input channels. Each GR4 with two ADC chips aboard can record to its own CompactFlash card continuously by switching between ADC chips and FIFO memory, allowing the just-converted data from one FIFO to be streamed to the CF card while the other is collecting newly-converted data. Because the GR4 units are stackable, you can run several together at once. The Tern page shows a stack of four GR4s and a controller card. The maximum sample rate for the GR4 is 500 kilosamples per second. This means that each simultaneously-sampled channel can be recorded at that 500 kilosamples per second rate. It does 16-bit conversion, which gives good dynamic range to the recordings.

So the technical problem of getting to a four-channel field-deployable data recorder capable of capturing most of the acoustic information from a dolphin click has gotten both easier and cheaper with Tern’s GR4. I had a chat with a technical representative at Tern going over what would be needed for this application, and basically got a recommendation for a couple of different controllers that could do the job with the addition of two GR4 units. Tern offers an evaluation package of a controller board plus the interface hardware and software needed for system development at $249. Add-on options are additional cost. For one of the boards, I’d be interested in an LCD 16×2 readout, RTC clock, CompactFlash interface, and switching regulator, which would add another $100 to the $249 evaluation kit price. So for $349 + 259 + 259 = $867, I’d have that part of the data recorder in hand. Of course, I’d still be looking at a variety of additional costs in development, but this makes contemplating the task that much more feasible.

There are some additional concepts that ought to be broached. For two GR4s, one has to provide CF cards for each. It is pushing the hardware to get continuous sampled data out to the CF card on each expansion card. Trying to move the data over the bus to the controller and out to its CF card just isn’t feasible. There is no file system involved on the CF cards; the data is written to absolute sectors. This makes it a bit more interesting pulling that data off for analysis. In development, it will be up to the programmer to track which sectors go with which recording if multiple recording sessions are used. The signal input range for the ADC circuitry is 0-5V, which means that the output of many amplifiers will have to be conditioned to fit in that range. When recording two channels at 500 kilosamples per second, the total data bandwidth is 2 million bytes per second. So each CF card will receive about 7 gigabytes of data per hour of recording operation. A 32 GB card should be good for over four hours of data recording before needing to be swapped out. The Tern rep estimated that my stack of a controller plus two GR4s would pull around 500 mA of power at 5V while recording. The A-86-P controller at least has on-board power regulation so that it handles DC input from 8.5V to 24V and delivers regulated 5V power to its stack. I figure something like a motorcycle 12V battery would likely provide enough juice for a day’s worth of recording. When not actively recording, though, the controller and its stack can go into a sleep mode that draws only a few mA, which saves a lot on battery power.

I was told by the Tern rep that the GR4 was developed for the needs of a research group doing field work on bat biosonar. It’s no wonder that it caught my eye when I ran across its description.

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Over at the “Uncommon Descent” blog, poster “niwrad” decided to dispute claims of high sequence similarity between human and chimpanzee genomes. “niwrad” posted a statistical test of human/chimp genome comparisons in September, 2010, and a follow-up post this week comparing two human genomes using the metric from the earlier post. These were brought to my attention by “CeilingCat” on the AtBC forum. What the pair of posts demonstrates is another instance of “intelligent design” creationism advocates engaging in mathematical hijinks. The “niwrad” performance has more to do with the style of illusionists than it does actual mathematical and statistical practice. What one has to do with these kinds of things is look for the sleight of hand. Because “niwrad” now has a pair of articles based on the same “trick”, it becomes easier to point out exactly where the prestidigitation happened and why it is reasonable to infer that “niwrad” knows full well that it is a trick.

Let’s review some highlights from “niwrad”‘s initial post:

Supporters of the neo-Darwinian theory of evolution have a strong ideological motivation for minimizing the differences between humans and chimps, as they claim that these two species evolved from a common ancestor, as a result of random mutations filtered by natural selection. Now, I don’t personally believe that humans and chimps share a common ancestry, for a host of reasons that would take me too long to explain in this post. Nor do I attach much significance to the magnitude of the genetic differences between these two species, per se, because in my opinion, the fundamental differences between these creatures lie elsewhere. [...]

[...] The comparison I performed was completely different from those usually performed by geneticists, because was purely statistical in nature. In a sense, it could be described as an application of the well-known Monte Carlo method. [...]

[...] While there is only one possible method of comparing identity between strings of characters (the above pairwise comparison), there are many methods of comparing similarity. In other words, there are many measures of similarity, depending on the rules of pattern matching that we choose. [...]

Any final result for a complete statistical similarity test (especially if it is a unique number) is meaningful only if: 1) the distance function is mathematically defined; 2) the rules for pattern matching and the formulas for calculating the result are explained in detail; 3) it is clearly stated which parts of the input strings are being examined; 4) in the event that computer programs were used to perform the comparison, the source codes and algorithms are provided. My explanations below have the goal to meet the three first constraints. To satisfy the fourth condition, the source file of the Perl script used for the test is freely downloadable here.

[...]

For each pair of homologous chromosomes A and B, a PRNG (pseudo-random number generator) generates 10,000 uniformly distributed pseudo-random numbers which specify the offset, or starting point, of 10,000 30-base patterns that are contained in source chromosome A. The 30BPM test involves searching for all 10,000 of these DNA sub-strings of chromosome A in our target chromosome B. Now let F be the number of patterns located (at least once) in chromosome B. The 30BPM similarity is simply defined as F/100 (minimum value = 0%, maximum value = 100%). The absolute difference between 10,000 and F (minimum 0, maximum 10,000) is the 30BPM distance. [...] It can easily be seen that the 30BPM distance will be zero (30BPM similarity = 100%) if the two strings are identical. In an additional test which I performed on two random 100 million-base DNA strings, the 30-BPM distance was 10,000 (i.e. no patterns on A were located in B). [...]

The results obtained are statistically valid. The same test was previously run on a sampling of 1,000 random 30-base patterns and the percentages obtained were almost identical with those obtained in the final test, with 10,000 random 30-base patterns. When human and chimp genomes are compared, the X chromosome is the one showing the highest degree of 30BPM similarity (72.37%), while the Y chromosome shows the lowest degree of 30BPM similarity (30.29%). On average the overall 30BPM similarity, when all chromosomes are taken into consideration, is approximately 62%. Here we have the classic case of the glass which some people perceive as being half-full, while others perceive it as being half-empty. When compared to two random strings which are 0% similar, 62% is a very large value, so nobody would deny that human and chimp genomes are quite similar! On the other end, 62% is a very low value when compared to the more than 95% similarity percentages which are published by bioinformatics evolutionary researchers. Now, I realize that it may seem somewhat arbitrary to choose 30-base-long patterns, as I did in my test, and indeed it is arbitrary to some degree. However, if the two genomes were really 95% similar or more, as is commonly claimed, also a 30BPM statistical test should produce 95% results, and it does not.

Emphasis added to “niwrad”‘s central claim.

The claim is, of course, poppycock. Anyone with the slightest pretension to an understanding of probability or statistics would recognize that the proposed “30BPM” metric is non-linear and not directly comparable to straight-up sequence similarity numbers. What’s truly ironic is that if “niwrad” were slightly more astute, he might have realized that his “30BPM” metric actually confirms the high sequence similarity results that he claims to have rebutted.

And that brings us to “niwrad”‘s second post, the one that aims to apply his “30BPM” metric to intra-specific genome comparisons, this time done as human-to-human comparison.

One reader suggested applying an identical test in order to compare two human genomes. That sounded like a very good idea to me, so I downloaded another human genome dataset from NCBI and performed a test.

[...]

Finally, the average number of pattern matches per chromosome, shown at the bottom of the table, was very different in the two cases: 9616 for human vs. human comparisons, but only 6173 for chimp vs. human comparisons. The average number of patterns without a match for human vs. human comparisons was (10000 – 9616) = 384, or in percentage terms, 384/10000 = 3.84%. The average number of patterns without a match in human vs. chimp comparisons was (10000 – 6173) = 3827, or in percentage terms, 3827/10000 = 38.27%, which is almost ten times greater.

So the bottom-line question is: if, as many evolutionists say, chimpanzee and human genomes are 99% identical, how “identical” are two human genomes?

“niwrad”‘s final question is interesting for the very salient reason that he did not provide an answer for it, even though his whole trick depends on the conceit that he has developed a better metric for quantifying sequence similarity than that used by actual geneticists. There is a reason why “niwrad” failed to answer, though, and that is that trying to claim that there is only 96.16% sequence similarity between two human genomes is manifestly risible. We know that the “trick” involved here is to confuse genetic sequence similarity with the “30BPM” metric, and that when faced with an obviously nonsensical outcome, “niwrad” punted rather than make explicit the full ridiculousness of his claim.

Above, I mentioned that “niwrad”‘s metric actually confirms high sequence similarity values. Here’s how that happens. First, one needs to realize that one doesn’t need “Monte Carlo” techniques to evaluate “niwrad”‘s “30BPM” metric: we can develop its properties with the usual probabilistic equations. The parameters of interest to us are the rate of change (C), the length of the analysis sequence (K), and the probability of a match (p). If we assume a uniform distribution of changes, then our model is simply the probability p that we do not observe a change within our analysis window K at a particular rate of change C. And that is simply expressed as

Besides being simple, it is obviously also nonlinear. Notice that “niwrad” made quite a fuss about how his metric did what everyone expects for the endpoints of the distribution, where complete sequence identity happened and where complete randomness obtained. Notice that “niwrad” did not go anywhere near calibrating his metric against an expectation concerning a sequence with a known amount of similarity. There’s a reason for that, specifically, that one can’t blather about greater-than-expected dissimilarity if one actual calibrates the technique for known amounts of sequence similarity.

For example, what is the expected “30BPM” result when sequence similarity is actually 99%? We just solve the equation above to yield:

Similarly, when sequence similarity is 99.9%, the “30BPM” expected result is:

So, what about “niwrad”‘s “30BPM” numbers that he obtained empirically? We can convert those back into sequence similarity numbers, which are not the same thing as “30BPM” numbers at all. The equation is simply a rearrangement of the one above:

“niwrad”‘s average “30BPM” value for the human-chimp comparison was 0.6173, giving a sequence similarity estimate of 0.984.

“niwrad”‘s average “30BPM” value for the human-human comparison was 0.9616, giving a sequence similarity estimate of 0.9987.

I should note that “niwrad”‘s “30BPM” metric becomes bloody useless at a point far short of completely random sequences. What point is that? I’m glad that you asked. Given a sample of 10,000 analysis windows, the threshold of usability would be when you have a 50% chance of seeing one match out of those 10,000 samples. That sets p at 0.00005 and gives C as 0.28116. That is, any sequence similarity of less than 0.719 will look exactly the same in “30BPM” terms and be ranked as having 0% similarity.

The “30BPM” metric deployment by “niwrad” does exactly what it was designed to do: exaggerate dissimilarity. It’s a magic trick intended to make an inconvenient fact disappear. It is a fundamentally dishonest exercise.

Update: Fixed the discrepancy between the symbols I defined and what I used in the equations. References to R should have been C, and now are.

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