The Austringer

I’ve changed my bid text to tell an anecdote about penguins and the predatory skua.

I’m not just interested in falcons. I’ve done research on lekking greater prairie chickens. Diane and I were called upon to help researchers test captive-bred prairie chicken response to raptors. We observed the prairie chickens respond to a hawk flying over their pen. These were naive birds, but the whole population hit the deck and stayed put when the hawk flew over the pens, showing that the captive-bred birds still had the instinct to cower intact.

The Antarctic has its own avian predator. The skuas are gulls that will prey upon penguin chicks and even adult penguins. These are large, aggressive birds, described by some as “seagulls from hell”. William Evans told me about an early penguin exhibit, and how people accidentally observed some instinctual behavior in penguins interacting with skuas. A feature that we don’t see in current penguin exhibits was the inclusion of two skuas. The skuas initially spent their time bullying the assembled penguins. A wild penguin can flee from a pursuing skua, and corners tend to be uncommon. It didn’t take long for one of the penguins to find itself cornered by a skua. The cornered penguin pecked back at the harassing skua. One reason penguins don’t often bother with trying to engage a skua attacker is that skuas fly and penguins don’t. But these two skuas had their wings clipped. The skua gave a flap that lifted it momentarily off the ground. Every penguin there suddenly swiveled its head to bear on the skua, then attacked. Within seconds, there were no longer any live skuas in the exhibit.

So I’m interested in seeing what these interactions are like in the wild for myself. Please give me your vote and I’ll enjoy telling you what I learn.

Please give me a hand by voting for my bid and passing that on to other people you know.

There’s a lot of philosophical discussion about what, precisely, constitutes a law or a theory in scientific practice. There’s also a lot of usage of the terms that has come to us over several centuries of not-quite-consistent application of terms.

What I’d like to offer here is not a scheme to try to make past usage fall out consistently; I think that is a task doomed to failure. Instead, I’d like to express a view of the various terms that makes sense to me and is how I have used the terms myself. Hopefully, others will also find it useful, even if only as a spur to discussion.

First, I’ll present a Venn diagram of how I broadly see things, and then add some comments.

I see a qualitative difference between facts and explanations. So the broad non-intersecting categories here are “Facts” on the left, and “Testable Explanations” on the right. I don’t want to go into the qualifier too much at this point, but essentially I see an explanation as delivering knowledge only if it can be tested and applies broadly, that is, inter-subjectively. That’s why I start with “Testable Explanations” rather than an unadorned “Explanations”. You can imagine a further inclusive superset of “Explanations” on the right if you wish, but I won’t spend any more time on that.

Within the realm of facts, one can notice consistent, persistent patterns or interrelationships that occur between facts or classes of facts. These are our “Laws”. One can test a law in the sense that one confirms that the proposed relationship is consistent and persistent. What one does not get from a law is an understanding of why the relationship occurs. Historically, people have received accolades for scientific work in discovering and publishing such patterns, though modern practice seems not to hold such work in good esteem.

When one turns to explanations, things quickly get more complex. “Hypothesis” as shorthand for “scientific hypothesis” is straightforward enough: it is a testable explanation of phenomena, whether or not the tests have occurred yet. But “Theory” is the difficult term to deal with, given that past usage has been so highly variable, confusing and conflating the term not only with hypothesis and the lay connotation of a “guess”, but also where “theory” has been applied to laws or law-like constructions.

It seems to me that when it comes to “theory” it makes more sense to try to make future usage better than to try to reformulate what has gone by in the past. We’d like the usage we settle upon to be broadly applicable to past usage. But we should not be afraid to simply abandon usage that cannot be made to fit a rational view of “theory”, though.

Part of what many people use to distinguish “theory” from “hypothesis” is the status of testing. For hypothesis, testing may not have happened yet. But for “theory” to apply, people generally want testing to have happened already. This seems clear enough to apply as a property of “theory”.

A more problematic property is extent. By that I mean that people will refer to a small-scale explanation as a hypothesis rather than as a theory. One runs into the heap paradox with this, since there is no bright-line rule for where explanations stop being “small” in extent, and thus should be referred to as hypotheses, and where they are “large”, and should be referred to as theories.

It seems to me that a better property to reserve for “theory” is that a theory should be productive, and by that I mean that by application of the theory, one should be able to generate further testable hypotheses.

So for myself, I use theory as a referent for a testable explanation that has been tested and is capable of generating further hypotheses (or has generated further hypotheses). That generally takes care of the problem of “extent” as well, since an explanation that is small in extent is less likely to be productive.

I think this sort of scheme is internally consistent and could be used in teaching, where it should minimize confusion for students. It explains why theories do not become laws (they are in separate categories of concepts) and why laws are more of a starting point for scientific inquiry than an end in themselves, since understanding why the relationships seen in laws happen requires explanation.

It is also why I’m not on board with the move to simply shift terminology around and refer to theories as laws. It seems to me that this is confusing and doesn’t help communication with the public. If we need to deploy different terminology, then make it really different. Where this whole issue of clarifying terms comes to application is in what to call evolutionary biology. At the level of some science organizations, there is a move afoot to simply refer to this as “evolutionary law” as a replacement for “evolutionary theory”, on the grounds (as I understand it) that the reality is closer to the public connotation for law than for the public connotation of theory (the “just a guess” thing). But it seems to me that this essentially is abandoning our responsibility to keep to accuracy if we simply capitulate to lay usage. Another possibility would be to use the insight that what distinguishes theory is that theories provide mechanisms by which things happen, and refer to things as “evolutionary mechanisms”. It at least doesn’t come laden with the baggage of past usage. But evolutionary biology incorporates knowledge that falls into the “facts” category and the “testable explanations” category (as noted by S.J. Gould), so I think a better alternative is simply to make it a broad term and refer to it as “evolutionary science”. This doesn’t permit the easy dismissal of “just a guess” and takes a step away from the whole law versus theory morass.

The Minneapolis-St.Paul Star-Tribune has the story. Norm Coleman’s lawsuit over the recount process in the Senate race with Al Franken was dismissed by Minnesota’s Supreme Court. Coleman finally took this as a sign that maybe it was time to concede, where any of the lower court rulings against his case had not.

The article mentions “gracious” being applied to Coleman’s behavior, and I’ve seen the same in comments to articles elsewhere. I can understand Franken using the word; it’s expected of politicians to emit noises that sound magnanimous when given a victory, even if privately he may think something more in line with standard human experience. But I find it utterly bewildering for anyone not Al Franken to even wander around in associative space near “gracious” to describe someone who spent months doggedly pursuing litigation and having his office issue pointed accusations of wrong-doing all around. It’s like the line from “Apocalypse Now”:

We cut ‘em in half with a machine gun and give ‘em a Band-Aid.

Handing out the Band-Aid counts as a legitimate meaning of “gracious” for some people.

Quark Expeditions has a contest going. They are making a promotion out of sending a blogger to Antarctica on an expedition next year, and have a voting system set up so that each blogger can have people vote for their bid to go on the trip.

I found out about the whole thing a bit late, when PZ Myers on Pharyngula endorsed Grrrlscientist’s bid. So I’m in a bit of a hole at the moment in the voting. Please take a moment to go vote for my bid. You can change your vote later, if you decide to go with another blogger in the running. The voting ends September 30th, 2009.

Back around 1997, Randy Davis at Texas A&M University was putting together an Anatarctic expedition to observe the behavior of diving Weddell seals, including both physiological and bioacoustical measures of what was happening. I got an invitation to go along to assist in the research, but I had to turn that down because of my chronic ulcerative colitis. As my doctor said, though, ulcerative colitis can be cured, and my colon got removed back in 2004. (See the first messages on this blog for the gory details of going through surgery and recuperation.) So now I’m in shape where I can contemplate having an adventure, and I’d like to get the chance to find out part of what I missed due to chronic illness earlier. Please give me a hand: vote for my bid, and pass it on to people you know. And if you do, I’d be grateful to hear from you in the comments here, too.

I should point out that the contest gives the winner a two-person expedition to Antarctica. My partner for the trip is Diane J. Blackwood. Diane’s academic background is also interdisciplinary. She has a BS in zoology, another BS in electrical engineering, an MS in biomedical engineering, and a Ph.D. in wildlife and fisheries sciences. We both went through the same Ph.D. program together at Texas A&M University. Diane has a lot of research experience, from respiratory studies in infants through G-induced loss of consciousness in fighter pilots, from behavior of lekking prairie chickens and sage grouse to reaction times of whales and dolphins in hearing tests. A vote for my bid gets you, the blog reader, an additional expert perspective on the expedition.

Gearing up for Antarctica

It’s a pleasant fantasy to think about what to take along on an Antarctic expedition. One has to balance weight versus value for these sorts of trips, so the first pass will simply be to list off useful things, and later I’ll work on winnowing that down.

Computer gear:

Laptop computer, probably my Gateway MT6458 for me and the old IBM Thinkpad A30 for Diane.
External drive(s), probably one or two 1.5TB USB drives
USB card reader(s)
USB flash drive(s), have one 8GB, will likely stock up on more
Aim to have one or two USB drives pre-loaded with Ubuntu and Knoppix systems for booting and system rescue
CD set of disks for system recovery/reinstallation
GPS with waypoint logging

Toolkit:
Screwdrivers, straight flat blade, Phillips #2, interchangeable tip with tip assortment, miniature screwdriver set
Eyeglass repair kit (2)
Needle-nose pliers
Needle-nose Vise-Grip
Forceps, curved and straight
Dikes, small and medium
C clamps (2)
Gaffer’s tape
2″ PVC pipe tape
Scotch Super-33 electrical tape
Wire-wrap tool
Wire-wrap wire
Hook-up wire, 24 gauge
15W pencil soldering iron
Solder

Photography:
Camera bodies
Nikon D2Xs (digital SLR)
Fuji S2 (digital SLR)
Nikon F2 (manual film SLR)
(May want to get a full frame digital SLR for the trip)
Lenses:
Nikkor VR AF-S 70-200mm f/2.8
Tamron 17-50mm f/2.8
Sigma 12-24mm f/4.5-5.6
Nikkor AI-S 24mm f/2.8
Micro-Nikkor AI-S 105mm f/2.8
Nikkor AI-S 50mm f/2
Sigma AF 18-200mm
(May want to add a 500mm mirror lens or other long lens)
Flash:
Nikon SB-800 (2)
Accessories:
Wireless remote for D2Xs
Gossen Luna-Pro light meter
Compact flash cards
SD to compact flash adapters (2)
Ultrapods (2)
Nikon flash cord
Diffuser for macro work
Custom panorama head
(Need to get a travel tripod)
(More stuff to be listed)

Acoustics:
EDO Western 6166 hydrophone (good for audio through high frequency sound)
Sonobuoy salvage hydrophones, various
Geophone (low frequency and vibration response, has suction cup)
Aiwa miniature stereo mic
Shotgun mic
Olympus WS-320M voice recorder
Archos AV320
Custom hydrophone pre-amps
Battery-powered pre-amps and amplifiers
GT-1000T Amp/monitor speaker
(Will look for flash memory data recorder before trip)

Other:
Hydrometer
Thermometer
Secchi disk
(There are some simple bits of science that can be done with the above tools concerning the state of the sea surface and how the Antarctic peninsula differs from the starting point in Argentina.)

This came across MARMAM just now.

Subject: [MARMAM] Six Beaked Whales stranded in Azores (URGENT)
From: “marc fernandez”
Date: Sat, June 27, 2009 5:47 am

Dear Colleagues,

I want to report an unusual situation occurred during the last week and a
half in São Miguel island, Azores, and ask for help in order to get some
clear conclusions.

During the last two weeks a total of *6 beaked whales stranded* on this
small island, a really unusual fact. Of these *6 two were dead and 4
stranded alive *and returned to the open sea. From the first two animals
(the dead ones) we only can get one identification and it was a Cuvier's
Beaked Whale, probably an immature male. The other four animals stranded on
a beach and they were returned to the sea immediately by the lifeguards and
the coastal guard, for these reason we don't have a lot of information, but
for the pictures they send us probably were Sowerby's Beaked Whales, we only
now that they stranded alive and probably they were immature animals also,
due to the body lenght (about 3.5 meters).

We don't have any notice about military activities in the area, but is
really difficult to get this kind of information, for this reason i want to
ask you for help to find if there is any military or seismic prospection on
the area that could affect these animals.

Thanks for your help.

All the best,

Marc Fernandez Morron
Universidade dos Açores

Marc Morron is asking about military exercises because there is a known correlation between use of mid-frequency military sonar and injury to beaked whales. If anyone has any information, please leave a comment.

I retired my banner that I put together in my hospital bed in 2004 and have set up a set of new banners that get picked randomly with page requests. The original aspect ratio was just too long at 8.84:1, so I shifted it to 8.84:2.

GIMP provides a selection tool for a fixed aspect ratio, which was just what I needed. Rotate, crop, scale, apply levels, unsharp mask, and I can save off another banner image. I’ll try to add more to the mix as time goes by.

Over the weekend, I vacuumed out my video editing desktop machine. It’s been a while since I used it, and it had collected its fair share of dust.

The machine is based on an Asus P4B motherboard and 1.8GHz Intel P4 CPU. This was state-of-the-art when I built the system in 2002. It was built around the requirements of the Pinnacle DV 500 DVD video card. This is a very picky piece of hardware. It only works with a limited subset of motherboards and only has drivers for Windows 98/NT/2000/XP. OK, given all those requirements, what does it offer? It does analog video signal digitization as well as Firewire for DV capture. And it will provide real-time preview for various supported video transitions when paired with Adobe Premiere.

When I was putting the system together, it seemed that hard disks over 40GB were particularly prone to failure. I had gone with a 20GB boot drive and a 40GB data drive originally. A couple of years later, the rough patch in hard disk QC seemed to have passed, and I replaced the 40GB with a 120GB drive. And there the system remained from about 2005 to this past weekend.

Given that Diane and I still are slowly working off a substantial load of debt from grad school and my health issues (see earliest posts here from 2004 for the grisly details), there is now no discretionary budget for computer gear. We get what is needed when it is needed. Our purchases since 2003 include a laptop bought as a replacement under insurance, a $120 laptop bought from surplus at Diane’s college to replace her failing Dell, miscellaneous hard disks for our files, and a desktop upgrade almost completely underwritten by a generous donation from one of my readers here. We are still using daily a desktop computer bought used around 2002.

So doing anything to the video machine had to fit two constraints: I still needed to be using WinXP for the OS, and it needed to cost nothing but a bit of my time. I located two hard disks that had been replaced in other systems by higher-capacity drives, a 60GB and a 200GB drive. I used a partition cloning tool to copy over the 20GB boot disk to the 60GB. This would let me install various new software packages, including the Microsoft C# Visual Studio Express development environment, which uses 1.1GB all on its own. I cleared off the 200GB with a new NTFS format to add it as a second data disk.

Why video and why now? My time at MSU is drawing to a close, so we will be moving shortly. I have a stack of video tapes in DV, Hi-8, and VHS formats. I’ve always intended to get these digitized, and between having little working space and not having a good workflow sorted out, it hasn’t happened. It seemed to me that if I got things squared away, I could be doing a basic video digitization and archiving sequence in parallel with other activities. After all, most of the time is going to be tied up in either playing a video source for capture, or rendering captured video to an archival format.

So given the extra space and some sprucing up of the installed system, I’m ready for moving video bits around. My goal is to have the video available for non-linear editing in nearly-pristine condition. Raw DV is too large to be efficient. After asking around a bit, I’ve started with the aim of rendering to a multiplexed MPEG-2 stream as a format that is easy on storage requirements, but loses little of whatever quality there was in a DV source.

This starts with capture, which for my system comes through the Pinnacle DV 500 DVD. I’m starting with the DV tapes, as this promises to be easiest all around. Pinnacle has their DVTools package that does a fine job of capturing from a DV source. I’ve done about four tapes so far with no dropped frames at all. It does, however, continue past the last actual image from the DV source if the tape isn’t completely full.

When the capture is done, I fire up Sony Vegas and put the capture file on the timeline. It doesn’t take long to snip out various unneeded bits, including the extra stuff at the end of the capture file. If it was all related to one event, I’m ready to render that. If the capture file includes multiple events, I save the Vegas project file for the complete thing and then begin rendering each sub-section separately.

Because these are intended for further editing sometime when I have free time, I’ll just be putting these out to DVD as data. I have ImgBurn installed to handle that. There are at least three tapes in there that I will also author a video DVD for that I know of off-hand. Those will take a bit extra effort, but I’m not doing that for most of these.

Of course, suggestions are welcome. Please do remember the constraints I have, so software package suggestions should be for open source or freeware packages. I do have a laptop that dual-boots Vista and Ubuntu, plus a desktop running FreeBSD 7.2, so video processing on those systems could be done if there’s a suitable benefit.

William Dembski’s No Free Lunch contains the following passage:

The presumption here is that if a subject S can figure out an independently given pattern to which E conforms (i.e., a detachable rejection region of probability less than alpha that includes E), then so could someone else. Indeed, the presumption is that someone else used that very same item of background knowledge — the one used by S to eliminate H — to bring about E in the first place.

[No Free Lunch, p. 75]

Because Dembski’s framework is based upon the elimination of alternative explanations, what we end up with here is the situation that Dembski is attributing the complement of the probability that can be assigned to chance hypotheses to an implicit design conjecture, the one that underlies a particular “specification”. When the “saturated” probability of the alternative is less than 1/2, Dembski says that we should prefer “design” as our causal explanation, and because we have this relationship between the specification and the putative causal story, we thus are adopting that particular causal conjecture.

Some might object that if one considers Dembski’s “Generic Chance Elimination Argument” (GCEA) to simply be in the class of statistical hypothesis tests where one may reject the null hypothesis, in this case Dembski’s definition of a “chance” hypothesis, that there is no indication that any other conjecture becomes accepted as a consequence. But Dembski’s body of argumentation excludes this interpretation, as he at every opportunity insists that having rejected “chance” hypotheses, one must thereby accept that “design” is the causal explanation for the event at issue. If we accept Dembski’s argument, it follows that we are accepting not just “design” in the abstract as a result of a successful design inference (should a non-trivial, non-fictional one ever be instantiated using the GCEA), but also the particular implicit design conjecture that underlies the “specification” used in application of Dembski’s GCEA to that event.

(Original at AntiEvolution.org)

John Lynch has a post critical of the Discovery Institute’s self-serving obfuscation over the phrase “intelligent design” and its history. Lynch makes a great number of cogent criticisms, but it seems to me that the manner in which the conversation goes may still work to the DI’s benefit. I left the following comment there:

The issue isn’t whether the design argument is ancient or even whether the phrase “intelligent design” had been used somewhere, sometime prior to 1987. The issue is that “intelligent design” was first offered as referring to a field of science suitable for instruction in public schools in drafts of the supplemental textbook “Of Pandas and People”. The use of “intelligent design” to mean an alleged field of scientific inquiry was definitely seen in the draft following the SCOTUS decision in Edwards v. Aguillard.

No IDC advocate has ever provided any earlier usage that showed the phrase “intelligent design” as meaning an alleged field of scientific inquiry. End of story.

Why does it matter what meaning is attached to “intelligent design”? Because the courts had already noted that science could not be excluded from classrooms to privilege sectarian religious views. The antievolution movement seized upon that as their ticket to inject their narrow sectarian views into public school classrooms by the strategem of re-labeling the ensemble of arguments as being science, the category of content already noted as approved by the courts. The first tests came when the label of “creation science” was scrutinized, and failed. The switch in label from “creation science” to “intelligent design” occurred in association with the failure of the earlier phrase. The overall strategy remained the same; all that changed was the label to be floated as if it constituted a scientific endeavor that students in public schools should be informed of.

Arguing about prior deployment of “intelligent design” as a descriptive phrase seems to me to be not pointed enough. The IDC advocates aim to sow confusion over this, and allowing them to get people arguing over descriptive uses allows them to make some progress in obfuscation. Every time they trot out the same old BS they should get a uniform reponse that they aren’t dealing with the real issue, that what “intelligent design” was supposed to mean changed significantly in 1987, and did so with the clear intent of permitting the antievolutionists to evade yet another inconvenient outcome in the courts.

George Tiller, a physician who provided late-term abortions to women with high health risks, was fatally shot in his church. Obviously, the shooter has no acquaintance with the concept of sanctuary.

The famous Kevin Bacon site demonstrated that there are less than six degrees of separation between most people. That is, if you know someone who knows someone, etc., in six or fewer such links you can put any two people on the ends of such a chain. I didn’t know it before, but I turn out to be just two degrees of separation from George Tiller; I have a friend who knew Tiller and counted him as a friend.

Responding to the Texas state Senate failing to confirm religious antievolutionist Don McLeroy as chair of the State Board of Education, Sen. Steve Ogden went on the record:

Ogden decried much of the criticism of McLeroy as a “slur.”

“It is not fair to say that if you don’t believe Darwin’s theory of evolution or accept the argument that global warming is occurring, that you should not be on the State Board of Education,” he said.

Mr. Ogden, any concerned citizen could be on a state board of education. Any citizen holding unsubstantiated opinions about empirical research can hold a seat on such a board. However, when a person holding an unsubstantiated narrow sectarian viewpoint who uses their seat on such a board to push to have those views be promulgated as legitimate science, they are not only not doing the job that they are supposed to be doing, they are in malfeasance and have demonstrated by such bad behavior that they do not belong there.

You want kids to learn weird stuff in science classes? Pony up the appropriate ante: show that the arguments you favor have demonstrated their merit under scientific scrutiny and have convinced the scientific community of their worth. Until then, the best approach is to make sure that kids learn what science has to offer in their classes. If it is wrong, the researchers of tomorrow will have a better shot at showing it is wrong if they actually understand it in the first place. Trying to replace instruction with confusion, as McLeroy has consistently advocated, does no one any good.

I ran across this cheat sheet while looking for an answer to setting line spacing of single-spaced within paragraphs and double-spaced between paragraphs in the front matter. While it doesn’t have the answer to that, it does look like a very handy reference for more commonly encountered situations in .

If you are wondering what is, it is a document-processing and typography system. It is to a word processor what a process camera is to a point-and-shoot consumer camera. It’s big, has a steep learning curve, but delivers results far beyond what can be done with consumer-grade word-processing applications, or at least makes it possible to do those tasks with far less hair-pulling.

Technically, is a set of macros originally by Leslie Lamport built on the typography system of Donald Knuth. Documents in are actually programs, so the process of building a document in is much like software development. While there are commercial versions of systems, pretty much everyone I know uses free, open source versions like MikTeX or TeXLive. There are a number of frontends that help users construct and typeset documents using : TeXNicCenter for Windows, TeXShop for Mac, and Kile for the KDE GUI on Linux and FreeBSD.

Why use and not either word processing programs like WordPerfect and Word or desktop publishing packages like Ventura and Quark? First, has excellent mathematics typesetting capabilities. It is the sole format accepted by many journals that often deal with typesetting equations. If you are writing for such journals, there is no alternative. If you want to publish math-heavy text and not spend oodles of your time trying to figure out what went wrong in an “equation editor” for a consumer word processing program, you want . Second, it incorporates a huge amount of typography experience. If you are concerned about making documents that are not just formatted well, but make it easy on the eyes of the reader, provides that for you. It is flexible enough that if you think you know better, you can override just about anything, though most of the time that’s not really going to help your readers. Third, automates just about everything that makes writing large documents a hard task. Let me explain that by example.

When Diane and I were writing our dissertations, we had a task of putting together several chapters of material where the final document had to conform to a long set of rules used by the Thesis Office at our university to assure both consistency across dissertations and to allow micro-filming archives to be able to use the result. In particular, there are rules about the placement of figures and tables relative to where they are first referenced in the text. In word processors, you place your text and you place your figure or table, and there is no effective control over where the word processor finally decides to put the figure or table. I had several chapters of material, and I tried WordPerfect and Microsoft Word, without success. I tried Microsoft Publisher and Corel Ventura, but also ran into difficulties there. It was around that time that I started looking at as an alternative. I found that dissertations in the electrical engineering department were often done in and that there was a thesis class (a sort of configuration or environment document setting a style) for that the EE department made available. This was like an existence proof; people had actually managed to get the thesis office to accept their manuscripts when done with the thesis class. I asked Jeff Shallit for recommendations on books, and he pointed me to the book by Leslie Lamport and the Companion book by Goossens, Mittlebach, and Samarin. What I found back in 2002 was that getting acquainted with definitely took some effort, but it almost immediately was paying off. My figures and tables weren’t going hither and yon willy-nilly, they were pretty much where they needed to be, or could be tweaked to do so.

Then, some of the other benefits started becoming apparent. While word processors have some mechanisms for generating front matter (table of contents, lists of figures and tables), could do this in a very systematic way that basically took the entire load off my back. The other bane of the dissertation writer is references. The Thesis Office wanted all references to be cited in a consistent style, to be formatted in a consistent style, to appear in order, and that every citation in the text would appear in the references, and no reference would appear that was not cited in the text. That last one puts a huge load on someone who is organizing a large set of references for themselves. Let’s say that your committee decides that you should remove some text including a citation that only appears in that text. You have to remember not only to remove the text, but to revamp your bibliography so that the now-uncited reference no longer appears. has a helper program, BibTeX, specifically for handling bibliographic data. Using BibTeX and the natbib style, I was able to address all the concerns of the Thesis Office while keeping things pretty simple for me. BibTeX allows you to set up one or more bibliographic source files containing all the references that you might want to use in your document. Within the document, citing a reference occurs using a “\cite” command. There are variants to allow for various in-text citation formats. The cite command is given a parameter that links to a particular reference in one of your BibTeX files. sets up a file used by BibTeX to pull in just the references that are actually used, and BibTeX applies the desired style to produce the typesetting for the references section. The result is that the references section went from something needing a lot of continuing effort to maintain to needing almost no effort to maintain. That sort of assistance is invaluable when what one wants to be doing is writing content and not worrying incessantly about keeping all the effects of changes one makes to the layout in mind.

Something I didn’t use in writing my dissertation that provides is indexing. If you want to produce a large manuscript with an index, this is something that you can do pretty easily in . Basically, as you go along in the text, you place an index tag next to the text that you want the index entry to refer to. will track the entries and the corresponding page numbers for you. If you re-organize your text, say by swapping chapters 2 and 3 around, you don’t have to re-do all those page number references in an index, will handle it for you.

provides several basic document classes for you, and you can find extensions online. The basic ones include “letter”, “article”, “book”, and “slide”. That last allows you to generate presentations in . Then there are all sorts of styles that one can add on. For example, if you want to write screenplays using the standard formatting rules, the screenplay style can help you. (If, though, you are really intent on screenplay writing, you probably want to look at Celtx. [Addendum: Looking a bit more at the Celtx website, I found this: "TypeSet provides precise automatic formatting of your script to industry and international standards. The Celtx server uses the very powerful LaTex typesetting tool to deliver perfectly formatted scripts."])

There’s a system called LyX that places itself in between full and the usual way one uses a word processor. is used by LyX as a back-end, and you get a display of text that is a bit closer to the usual WYSIWYG experience, but cast by LyX as “what you see it what you mean”. Unfortunately, LyX documents are not simply standard , which to me is a limitation of the system.

Since writing my dissertation, I have relied upon for all my serious writing work, save where a collaborator has insisted upon something else. I use for writing letters and it is the basis for the six or so pending article manuscripts I have. My curriculum vitae/resume is handled in , and I have that set up such that I can generate documents of different lengths and detail, plus tuning the focus of my research statement, all by changing a couple of configuration settings. This means that I have one source text whether I want a CV or a resume, or whether I’m sending the result to someone interested in my biology background, my computer science background, or appreciates my interdisciplinary approach. That also means that I can keep things up to date with changes to just one file, and not about a dozen different ones to handle the most common sets of configuration changes that I use.

If you don’t do equation type-setting, don’t need figures and tables to go where you want, don’t need front matter or bibliographies, and don’t need an index, you’ll probably be perfectly happy using the usual word processor. If you do need any of those things, then you owe it to yourself to check out .

A commenter on Ed Brayton’s “Dispatches from the Culture Wars” asked what I can only assume was meant to be poser question about the use of torture. I responded there, but figure I should also note that here.

It is clear, from all the investigations done to date, that information was gained which saved many lives. So even knowing that, would you all prefer it had not been done?

Yes, so long as “it” is referring to torture.

If we were conducting a moral war, a war on terror, we lost when we failed to conduct ourselves morally.

Taking a moral stance against torture may involve loss of innocent life. Taking moral stances in the past has definitely cost us in terms of lives lost. That hasn’t prevented us from taking such stances. Have we gotten so cowardly recently?

The argument from beneficial results of torture as an intelligence-gathering method has an unstated assumption, that we have adopted a pragmatic or utilitarian stance, where it is merely the cost/benefit ratio of torture use that controls whether we rationally should use torture ourselves. It should be noted that by this standard, the users of torture who stand opposed to us can also justify their use of torture against our citizens. And all that is needed to make that equation tip in favor of torture is that there be no value attached to the life of the “other”, whether them by us, or us by them.

Even if one accepts the implied pragmatic or utilitarian view that can countenance torture, the relation between cost and benefit isn’t as simple as some would have it. Taking an immoral stance, as our leaders have done for us, doesn’t mean that the intelligence gathered that way did preserve the life of some of our citizens. Is there any documented instance where only torture was productive, and no other intelligence methods contributed to our knowledge and response? In any such instance, did the use of torture preclude other methods of intelligence gathering that might have been productive? It is only if torture is cost-free that one may ignore these sorts of considerations. Again, that’s the case when no value is attached to the lives of the others. (I did not say “innocent” in the second instance above, because we can no longer claim innocence for ourselves, thanks to the actions ordered on our behalf.)

If we want to claim the moral high ground for ourselves, we have to give up on pragmatics or utilitarianism on torture. The most effective policy change that could make that clear to the world that I can think of would be treating everyone with the same care, rights, and privileges that we offer our own citizens. Given what a rough deal some of our own citizens get, that’s a low enough ante to show some minimum level of commitment.

I ran across this in the Autobiography of Benjamin Franklin:

In 1736 I lost one of my sons, a fine boy of four years old, by the small-pox, taken in the common way. I long regretted bitterly, and still regret that I had not given it to him by inoculation. This I mention for the sake of parents who omit that operation, on the supposition that they should never forgive themselves if a child died under it; my example showing that the regret may be the same either way, and that, therefore, the safer should be chosen.

The anti-vaccination impulse seems to be ancient, and anciently rebutted.

Conservative commentator Denyse O’Leary has posted an interview with Adnan Oktar at the Uncommon Descent weblog. Oktar is probably better known by his pen name, “Harun Yahya”. He writes prolifically, and has several antievolution books. O’Leary appreciates Oktar’s antievolution. One wonders, though, whether she is as appreciative of some of Oktar’s other contrarian stances, like, say, his Holocaust denial activism. The phenomenon is called “second denial”: those who engage in evolution denial often also take up some other obviously wrong idea.

This isn’t exactly low-profile. The TalkOrigins Archive has had an article up documenting the Holocaust denialism of Harun Yahya as far back as 2003. At the time, it was tough to find the content of Oktar’s “The Holocaust Hoax”, but thanks to “sparc” at AtBC, I now have a link to the full book online. Oktar’s thesis is that Zionists collaborated with Hitler to set up a system to encourage emigration to Palestine; that once hostilities in World War II began, Hitler continued with the policies of segregation previously agreed to by collecting Jews in labor camps; and the whole mass mortality thing was due to “tiffus plague” and the general end-of-war famine. Oktar specifically is in denial that any of the concentration camps utilized gas chambers for mass killings.

How about it, Denyse? What do you think of Oktar’s “second denial”?

The email server I use was having some hardware issues. Marc picked up a new box and disk, and Jeff, who has somewhat more spare time at the moment than I do, suggested we go with Ubuntu Server 9.04 for the new install.

So we switched from a FreeBSD 6.3 box to Ubuntu Server today, and on it the new mail system was Postfix/MySQL/Courier. We spent a bit over four hours copying files and preparing the user accounts to use the new system before bringing the Ubuntu server online in place of the old FreeBSD one.

The rest of my day has been spent in fixing up other issues, like switching over the couple of WWW domains that were served from there and setting up email list software.

I’ve been using Majordomo for email lists since the 1990s. Unfortunately, that’s about the time of the last update for that software, too. So I am getting acquainted with Mailman instead.

Hopefully, most of those issues will be sorted before the end of the weekend.

On a somewhat more personal note, the way that I’ve done email since the 1990s has been disrupted. I’ve used the .forward file in my user account to pipe incoming email into a Perl script I wrote. It uses a whitelist file and a pattern file to sort incoming mail and append it to a file named for the day and with an extension according to the recognized class of email. Most of my email reading has been done using emacs from the command line of an ssh session. Now I’m dealing with using SquirrelMail as a primary interface, at least until I can work out what to do about the setup. I’m looking into Fetchmail, which I’m hopeful may allow me to do much the same thing as I did before, where my script only stuck back into my incoming mail box those items matching my whitelist criteria.

Jerry Coyne lets NCSE know he doesn’t like what they said. Meanwhile, NCSE’s April 2009 fundraising letter includes the following:

At the $100 donation level, we are pleased to offer Jerry Coyne’s Why Evolution is True, a lively and lucid review of the evidence for evolution.

NCSE’s choice of books to use in fundraising promotions and in sales doesn’t seem to have any relation to viewpoint of author except that they fall on the pro-science side of the fence. Nor do I expect that there will be any hard feelings over Coyne’s criticism.

Over at “wattupwiththat”, a commenter opined some time ago:

I remember when I was a kid playing with a bicycle pump that compressing a gas heats it up. Is it possible that some of the high surface temps on Venus are because of that pressure?

Why not have a cold beer to help think that one through?

Philosopher Russell Blackford takes issue with various science advocacy organizations pointing out that many people of faith also manage to accept the findings of science when it comes to evolutionary science. Blackford thinks this is wrong, essentially because the science organizations are infringing on philosophical turf:

This leaves aside the arrogance of science organisations appearing to favour particular religious viewpoints. Of course, it’s true that some religious viewpoints are just irrational, in that they plainly contradict well-established scientific findings. Others, even on my account, are incompatible with science only in relatively subtle ways, and reasonable people with those viewpoints could put some kind of case against my position (even though I might not consider that case to be at all plausible). While this is all true, it’s not up the scientific organisations to be saying it. That’s outside their remit.

Blackford expands a bit on what he sees as acceptable science advocacy organization behavior:

Science organisations should stick to the point that certain findings are the result of systematic, rational investigation of the world, supported overwhelmingly by several lines of converging evidence. In putting that case, they can be “religion blind”; they should present the evidence for the scientific picture, but that’s as far as they should go. They should not comment on what specific theological positions are or are not compatible with science. Leave that to the squabblings of philosophers and theologians, and, indeed, of individual scientists or other citizens. We can think and argue about it for ourselves.

This goes further than just what science advocacy organizations say about the religion and science issue (which I think Blackford mischaracterizes in any case). This makes clear that so far as Blackford is concerned, science advocacy organizations have no business with any aspect of public policy. Blackford at least has provided no qualifying statements that would indicate that talking about science and religion is a special case, and his entire argument is structured in such a way that it does not admit of having special cases: Organizations don’t get to have opinions when those cross over into the intellectual turf handled by people outside the science organization’s particular field of interest.

I think that Blackford misses the point pretty completely. The religious antievolution movement is not something that is primarily about the state of the evidence and the scientific theories about that evidence. Instead, it is a social and political phenomenon. Telling science advocacy organizations to only talk about the evidence and theories is not just shortsighted; it is wrong. Science advocacy organizations need to address both the state of the science (to undercut that false claim to intellectual legitimacy that religious antievolutionists make) and also actively engage in the public policy debate. And that means that there will be discussion of the factors that underlie religious antievolution, whether it offends Blackford’s territorial impulses or not.

Blackford could have a point if science advocacy organizations were also advocating religion, and in fact Blackford implies just that:

This leaves aside the arrogance of science organisations appearing to favour particular religious viewpoints.

It could be a real concern, just as Blackford points out that various counterfactuals asserted by certain denominations could have been true, but are ruled out by the evidence. I don’t see any evidence that science advocacy organizations are favoring particular religious viewpoints. What I have seen done is noting the existence and extent of particular religious viewpoints, which is a rather different issue.

All in all, it is pretty ironic that Blackford has chosen this approach, given how various and sundry evangelical atheists have long complained that they have felt pressured not to emphasize their viewpoint of null compatibility between science and religion in the interest of pursuing the public policy goal of obtaining good science education. Is turnabout supposed to be a good thing now?

The Peoria Journal Star’s opinion page has a couple of recent entries. Here’s a disappointing rant from someone who claims to be a middle school science teacher:

The Texas Board of Education allowing evolutionary theory to be questioned is long overdue.

All science theories should be scrutinized. Otherwise, Einstein would not have proven that time is not constant and that gravity is simply acceleration through space/time. Those school boards that add to their biology books that parts of evolution may not be correct don’t go far enough. No concept in any science book should be absolutely accepted.

Parts of the evolutionary theory are confusing. If survival of the fittest is the standard, then why don’t we let diabetics die instead of weakening the gene pool? Where does compassion fit into this theory?

If brain power propelled man to the top of the food chain, why have all other plants and animals been denied this intelligence? The first time I hear a duck ask a hunter, “Could you please aim that shotgun somewhere else?” I will be impressed.

What explains the enormous complexity of the human body with thousands of processes operating simultaneously that, by themselves, have no purpose? What evolutionary advantage did the first bat have that sent out a sonar signal with no receptors to receive the reflection?

“Teaching students to think is more important than what to think” should be more than just a slogan.

Gary Kutkat

Science teacher

Morton Junior High School

Morton

Karen Bartelt, who many readers may remember from her thorough demolition of the “dissertation” filed by “Dr.” Kent Hovind, responded to Kutkat. She kindly sent me the complete letter she submitted to the Peoria Journal Star with permission to post it.

The first step in being able to scrutinize a scientific theory like evolution is to understand it. This is true whether one is a high school biology student or a junior high science teacher. Gary Kutkatb’s mind-numbingly ignorant caricature of evolution demonstrates that he neither understands evolution nor realizes where science stops and disciplines like ethics begin. His letter says a lot more about his own scientific background, or lack thereof, than it does about evolution and science.

Parts of evolutionary theory become less confusing when one studies the evidence supporting this scientific paradigm. A recent and very accessible book is Why Evolution is True, by Jerry Coyne.

Scientific theories ARE continuously scrutinized. It is by this process that evolution is now recognized, to paraphrase biologist E.O. Wilson, as one of the two universal principles governing our understanding of life. The other principle includes the laws of physics and chemistry. The vast majority of people who work in science see evolution in this light, because they are aware of the evidence supporting it.

Students should be encouraged to question what they learn, but it’s important that they know what they are talking about first.

Karen E. Bartelt, Ph.D.
Semi-retired science educator

As someone who has actually done research on biosonar, let me take up Kutkat’s swipe there:

What evolutionary advantage did the first bat have that sent out a sonar signal with no receptors to receive the reflection?

This rather precisely makes Bartelt’s point. Kutkat is apparently unaware that the hearing apparatus in vertebrates has been described by a researcher with decades of experience, Art Popper, as showing variations on a theme, the theme being established in various fish lineages, and showing modifications of anatomy in amphibians, reptiles, and humans. The receptors are hearing organs or ears, and nobody with half a clue thinks that the last common ancestor of bats didn’t have ears. Humans don’t have built-in active biosonar, but research has shown that humans can perform target discrimination tasks as well as dolphins when a slowed-down version of a dolphin biosonar click train is provided for the humans. Blind humans have taken up echolocation, and have not had any problem using the receptors they still have the use of.

Kutkat may not be aware of how extensively biosonar is used. The most derived systems are those found in some bats and in odontocetes, the toothed whales, but biosonar has also been observed to be used by shrews, voles, badgers, some birds, and most recently a group of parasitic wasps was noted to use it. Most of these other organisms are using biosonar at a very coarse level of resolution, and these sorts of systems make it clear that one need not have the highly-tuned system of some bats in order to derive benefit from active biosonar.

This isn’t the first time a religious antievolutionist has trotted out a claim that biosonar somehow disproves evolutionary biology, and I doubt it will be the last.