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How to get your High School T-Shirt in the News

Posted by tigerhawkvok on September 01, 2009 04:06 in evolution , religion , news , anti-science

It's 3AM, I should be going to bed, and I give my feeds one last look over ... and run into this travesty. In a nutshell? T-shirts are recalled from a high school in Sedalia, Missouri. Why?

Get ready for this. Because they had the stereotyped progression of man iconography.

The offending shirt

Well, it is a pretty wretched image. It goes well with the theme of the band concert (being a band shirt for a concert about the evolution of brass music from the 1960s to the modern day, and called "Brass Evolutions") as a well-recognized image, but that image is bad science. It implies that evolution is a linear process of improvement with no offshoots, and implying that our species is at some sort of pinnacle. I mean, it's a school, so maybe they want better science on their shirt?

Oh, wouldn't that be great. The real answer is, of course, that it offends fundamentalist Christian parents. To quote:

The band debuted the T-shirts when it marched in the Missouri State Fair parade. Summers said he was surprised when he received a direct complaint after the parade.

While the shirts don't directly violate the district's dress code, Assistant Superintendent Brad Pollitt said complaints by parents made him take action.

"I made the decision to have the band members turn the shirts in after several concerned parents brought the shirts to my attention," Pollitt said.

Pollitt said the district is required by law to remain neutral where religion is concerned.
From The SedaliaDemocrat.com.

You're not being religion neutral. You're favoring one particular brand of delusion by denying testable, prediction-generating, bloated in evidence FACT. You know, unless you're actually being consistent and following the brilliant parody of Steven Novella, and actually banning, say, shirts depicting the landing of Apollo 11 since it conflicts with the belief system of Krishnas. And banning iconography of music (goodby sheet music!) since some literalist interpretations of the Koran prohibit that.

Oh wait. You won't.

Sounds like Sedalia needs its own Bobby Henderson, and a good lawsuit.

Ensatina, Taricha, and TTX Resistance

Posted by tigerhawkvok on June 19, 2009 03:17 in evolution , biology , herpetology

Rather than a longish comment on Rachael's latest post, I thought I'd write up a brief entry on Ensatina.

First, the picture:

Ensatina eschscholtzii eschscholtzii

Ensatina eschscholtzii eschscholtzii, or Monterey subspecies of E. escscholtzii. The "Monterey Salamander", found near Monterey, CA.

Ensatina are an interesting species of salamander in that they are a "ring species", or, they have a sequence of morphotypes that gradually change regionally, and these morphotypes overlap but do not interbreed. There are two terminal morphotypes that are too distantly related to be capable of interbreeding (see Wikipedia's discussion of the subject). The beauty of ring species is that they provide a living sample of speciation and evolution.

In particular, Ensatina in the Bay Area differ from the Monterey morphotype in that they are very morphologically similar to the non-terrestrial stage of Taricha torosa, which are highly toxic to ingest. The tetrodotoxin they produce is a neurotoxin that is potent enough to kill most vertebrates (though some Thamnophis (Garter snakes) have evolved modified sodium channels to enable consumption of them as prey items; see this paper and others for more) (DOI: 10.1007/s10886-005-1345-x). Thus, Ensatina in the Bay Area mimic Taricha presumably to avoid predation.

For those of you curious about the diagnostic differences, an Ensatina is generally smoother than a Taricha, with more prominent costal grooves (the grooves along the side), has nasolabial grooves, and has a constricted base at its tail. The Monterey specimen here lacks the yellow eyes of Taricha, though the Bay Area ecomorph has eyes that are quiet similar to those of Taricha.

Suggested Thamnophis/Taricha studies:

Nitrogenous Disposal

Posted by tigerhawkvok on May 23, 2009 02:30 in evolution , biology

Answering a call for a post on ureotelism vs. uricotelism, I thought I'd walk readers through a bit of phylogenetic bracketing that Kit, Rachael, and myself discussed a few nights ago while going through our habitual game of StarCraft.

< !-- SC pic -->

Vertebrates have three primary methods of disposing of nitrogenous waste: excreting ammonia, urea (ureotelism), and uric acid (uricotelism). Of course, all three have their own trade-offs. Excreting ammonia is highly efficient, uses few resources, and little energy, but needs to be done in large amounts of water to avoid toxicity. Of course, as life evolved in the oceans, this was not a problem, and excretion of ammonia is the ancestral/primitive state, exhibited by most actinopterygians (ray-finned fishes, like tuna), and many basal vertebrates. Modern sharks, amphiba and theria (amphibians and mammals), on the other hand, excrete urea, which is less toxic than ammonia, and more energetically favorable than uric acid. However, urea requires a fair amount of water to dissolve it, and uric acid, being virtually insoluble, can be excreted as a solid paste with little water waste.

< !-- uric acid photo -->

So, next follows the question of any self-respecting scientist: between ureotely and uricotely, which would be the derived state? Ureotely has the evidence in its favor urea being more energetically efficient and less toxic than uric acid; uricotely is more conservative with water. However, to believe ureotely is the derived state requires that it was developed convergently in (at least) lissamphibia and theria. It is reasonable for amphibians to be ureotelic, as it is less toxic and less likely to provide problems for thier highly permeable skins, and the excess water is not an issue, given their environmental restrictions. We can therefore postulate that ureotely might have also been favorable for basal tetrapods. How to check, though?

Well, we bracket this entire thing by checking the closest living outgroup to tetrapods -- non-tetrapod sarcopterygians. Doing a bit of research, it turns out that lungfishes (dipnoi) tend to excrete urea, and not uric acid. This then strongly suggests that uricotely is a novel innovation in sauropsida, evolved as a water-conserving mechanism, and what allows reptiles (including birds) to dominate arid environments.

< !-- Centered Tree -->
Uricotely tree

The phylogenetic evolution of traits assuming uricotely to be basal to ureotely

Ureotely tree

The phylogenetic evolution of traits assuming ureotely to be basal to uricotely. An alternative tree would have the only innovation prior to the chondrichtyes/osteicthyes split, with a reversion to ancestral behavior in actinopterygians.

Any other conclusion would require the novel invention of ureotely no less than four times, so the simplest, or most parsimonious, solution would be to have it be the primitive state. The water conservation afforded by uricotely presumably gave sauropsids a leg-up during the arid conditions of the late Permian (and possibly evolved then — I know of no research done in either direction), and thus gave the dinosaurs an advantage.

Evolution of Novel Traits

Posted by tigerhawkvok on May 18, 2009 13:32 in General , evolution

Non Sequitur

Image hotlinked until I update this post from Berkeley

Yes, this ResearchBlogging entry on Panda's Thumb is almost a year old, but I still think it is a great article about a fantastic paper. Essentially, a group of E. coli developed the novel ability to metabolize citrate (Cit+) based on a potentiating mutation earlier in its evolution. Take that, creationists.

Prompted by Pharyngula posts and a high rate of creationist stuff recently. Off to the Burbank Airport to go back to Berkeley ...

Amino Acids and Thermodynamics

Posted by tigerhawkvok on April 13, 2009 20:17 in evolution , physics , biology

ResearchBlogging.org

Now, this is pretty awesome — tying together biology and astronomy in one fell swoop. It turns out that the ten most common (of 20) amino acids are substantially more thermodynamically favorable to form. Now, that's certainly got to take a bit of wind out of creationist sails.

Abstract:

Amino Acid

An amino acid. R represents a functional group. Shamelessly hotlinked from Wikipedia

Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth via meteorites. We combine observational and experimental data of amino acid frequencies formed by these diverse mechanisms and show that, regardless of the source, these ten early amino acids can be ranked in order of decreasing abundance in prebiotic contexts. This order can be predicted by thermodynamics. The relative abundances of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated. The remaining amino acids were incorporated into proteins after pathways for their biochemical synthesis evolved. This is consistent with theories of the evolution of the genetic code by stepwise addition of new amino acids. These are hints that key aspects of early biochemistry may be universal.

The results here hinge on the fact that the ranked amino acid frequencies under various criterion correlate strongly (r=0.96) to ΔGsurf, where ΔG is the Gibbs free energy, which is defined as:

Gibbs Free Energy

Source: Kittel & Kroemer 1980

Which is essentially the enthalpy of a system (loosely, the "thermodynamic potential energy") minus the fundamental entropy of a system

Entropy

Source: Kittel & Kroemer 1980. g(N,U) is more commonly known as the "number of accessible microstates", and is sometimes denoted as W

multiplied by the fundamental temperature (the temperature in Kelvin times Boltzmann's Constant, 1.381 x 10-23 JK-1). In essense, the "sign" of this value (and its magnitude) denote how easy it is for them to spontaneously form. The lower the free energy, the less energy is needed to make a given event occur; thus, something with a negative free energy is spontaneous and releases energy upon its occurance, such as dissolving NaOH in water. Some other events take energy to occur, such as dissolving CaCl2 in water. Thus, in the first example, the beaker gets very hot, and in the second, it gets very cold. So, under the premise of the abiotic origin of life, one would expect the most "entrenched", or common, amino acids should be the easiest to produce. The results from the research support this conclusion:

Group Gsurf (kJ/mol) Err MW (Da) Err ATP cost Err
Early Group 169.342.0 116.220.6 18.56.9
Late Group 285.094.1 157.323.2 36.217.3

Table of values for early and late group amino acids. All errors +/-.

Clearly, the "early group" amino acids, the ones most common in organisms, and that are most simple to form abiotically, have a formation advantage in terms of energy, size, and spontaneity over other amino acids. This is further supported (with some caveats expressed in the paper) in that the amino acid distributions were a bit off for hyperthermophillic bacteria — i.e., the ones living around underwater hydrothermal vents. With the higher energy densities available, differences in amino acid synthesis costs may be a reason for different amino acid preferences in high-expression proteins (though the authors are quick to point out this may merely be an artifact of high temperature stability for proteins).

The remainder of the paper is also quite interesting, but requires a bit more knowledge of biochemistry than I'd like to assume for this blog. The authors touch on the diversity of amino acids, and why the observed diversity in nature is fewer than the maximum number.

Hmmm. A spurt of posting might be coming ...

Paul G. Higgs, Ralph E. Pudritz (2009). A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code Astrobiology DOI: arXiv:0904.0402v1

Not dead!

Posted by tigerhawkvok on April 06, 2009 15:33 in General , evolution , anti-science

Yep, postless for a bit. Suffice it to say things have been hectic and suprisingly full. I have a list of things in my browser that auto open that I want to discuss, like stars in the Pleiades, sauropod neck position, still the Higgs post, and black holes.

However, until those get put up, I will just point you towards a researchblogging article by Grrlscientist (on Living the Scientific Life (Scientist, Interrupted)) about how birds read human eyes.

Also, via Badastronomy, I found out about the Florida Citizens for Science Stick Science competition. The idea is to make a stick-figure comic about a topic that is misunderstood in science (particularly evolution), and "correct the record". For my part, I've submitted the following:

comic

Alternate: large PNG. Disclaimer: Yes, I know that cladograms aren't right for development of an organism. Its a parody. Put the point is you can replace a real transition with the tree development steps here and get the same response.

I amused myself with that one. That's it for now, though. For more random blog entries, Rachael has a cool one up on a caterpillar entering its chrysalis.

Evolution and Language

Posted by tigerhawkvok on March 04, 2009 02:37 in General , evolution , biology

I still have my science posts planned, but I want to spend a moment to comment on biology terminology in the public sphere. I thus give you this declaration:

The use of "descended from" is a subtle, but constant linguistic method of undermining evolutoin and unecessarily seperating species.

What? That sounds high, mighty, obscure and arrogant. However, I think it's true. What of the supposedly innocuous statement: "Humans descended from apes". This has the implicit statement: "Humans are not apes". This enables people to say "We're not monkeys!" Or, "We have ape-like ancestors". This is like saying, "We have primate-like ancestors". Its just as ludricous. We do have primate-like ancestors, and ape-like ancestors, but those are outside of the appropriate splits. For something to be ape-like, it must be more basal than the last common ancestor between apes and its most closely related living organism. Using the terminology any other way is disingenuous and misleading. Thus, a predecessor to the first primate (depends on how you define things) might be primate-like; but using "ape-like" for a human ancestor is just as deceptive as saying an aye-aye is primate-like while inside of primates.

No, ape-like would have to be non-hominoid Catarrhinid, of which the living form most closely fitting that description would be a gibbon.

So, perhaps that was a bit abstract and focused on hominds. But, consider birds. Saying "birds descended from dinosaurs" is also deceptive. Birds are dinosaurs. We've found non-avian dinosaurs with feathers, long before flight showed up. Sheep and cow are both artiodactyls, saying they "decended from" artiodactyls clearly implies that they are no longer a member of that group. Similar things to this lead to the sloppy use of the word "amphibian".

Amphibian is used in three ways: meaning living amphibiously, in both water and land; meaning being a member of lissamphibia, and this blurry realm of amphibious tetrapods that had not yet broken into the great amniote/lissamphibian split. They are more accurately called "basal tetrapods", or "early amphibious tetrapods" -- but saying "amphibians" is poor word choice.

What this rant serves the purpose of doing is simply to say — watch your language. Watch your terminology. All of us, simply by watching our language, can have an impact and help spread awareness.

Thus end your 2am lecture! Tomorrow: Kepler and my involvment with it.

Update and Shell-less turtles

Posted by tigerhawkvok on November 29, 2008 20:59 in evolution , biology , news , paleontology

Hm, I've not blogged in a bit. Well, I'm working on the graduate school apps with a bit of a mix of physics, astrophysics, paleontology and biomechanics. Some dual applications, some single. We'll see how it plays out.

I've also finally submitted my paper to Proceedings B, and hopefully it will be accepted (or conditionally accepted).

Nah, the real trick is money. The economy sucks, finding a job has been hard, and well, not quite enough money to make rent. Ugh. Well, perhaps I'll blog on science tomorrow at the airport. In particular, Science and Nature have had a few interesting articles as of late, such as one on a new turtle find -- it has a plastron, but no upper shell -- and with teeth! Dubbed Odontochelys, it is placed phylogentically basal to all all extant and extinct testudines. While I find the use of "Ontology recapitulates phylogeny" a bit problematic, its still a very interesting read, and I feel that its sparing use in this context is justified.

Odontochelys

It seems I blogged on science accidentally anyway. Huh. Perhaps not much, but nevertheless.

The full paper can be found here: Nature.com (DOI: 10.1038/456450a , Reisz & Head ).

Update 03/15/09: Link repair

Evolution is NOT chance

Posted by tigerhawkvok on October 08, 2008 11:02 in General , evolution

I think that all those chance-trumpteting, crowing creationsists (aka "fundamentals" and "anti-scienctals") that can't get it through their head that evolution is not chance need to read just two sentences from On the Origin of Species:

I have hitherto sometimes spoken as if the variations — so common and multiform in organic beings under domestication, and in a lesser degree in those in a state of nature — had been due to chance. This, of course, is a wholly incorrect expression [...]*

 

Evolution is not due to chance, folks. It has discrete forces acting on it. The variations arise in certain individuals through chance, but it is not chance that shapes evolution. There is a difference.

*Darwin, Charles. On the Origin of Species (A Facsimile of the First Edition). President and Fellows of Harvard College. 1964. ISBN 0-674-63752-6.  pp131.

Websites & Evolution

Posted by tigerhawkvok on August 02, 2008 18:32 in computers , lhs , evolution

Wow, I didn't think I hadn't updated in a month. I've not even updated LJ much. I suppose I've actually been a bit busy. The macro site is getting along quite nicely. I'm a fair way into it, but certainly not done. Much of my work has been directed at building the collapsing, (soon to be) pop-outable phylogenetic tree and navigation, as well as the live-preveiwing contribution page. With this site, I've gotten a lot more up-to-date in my knowledge of CSS and its failing across browsers, particularly in implementation of psuedo-elements, floats, and CSS3.

Meanwhile, my work for LHS has been coming to a head. I start teaching Adapt or Die next week, which has been intense to gather all this information, make sure I'm up-to-date, and marshal it down into what a 4th or 6th grader can understand. Of course, much comes in the way of actual live critters, and some in the way of games, etc. Here, intrepid reader, I give you a tiny preview: an evolution game that will, over the course of six disasters, give you a feel for how evolution works. Some weird things get put in, some "good" things get taken out, and all in all, you get something that works better than its competition but is by no means perfect. Rob, Alyssa, and I tested this, and it seems that about 3/4 of the population has gone extinct every 3 rounds or so, which can lead to population bottlenecking (sound familiar?) if too small a playgroup is used. I reccommend at least six. Also along the LHS lines, I provide you with a graphical tree of life!

Graphical Tree of Life (click for 32 MB PDF)

Its admittedly weak in places, and doesn't show all kinds of interesting diversity points I feel its most notable in Carnivora, Afrotheria, Metatheria, and Perissodactyla, but I'm a tetrapod man. I know it lacks in Dinosauria, but only so much one can put in with images. Also lacking is inverts (using the paraphyletic definition here), rather obscenely actually. Still, impressive looking.  Catch: most CGI images are screens from BBC's "Walking with" series.  I think this is still fair use, but just a noteworthy caveat.  The other images are either my own or Wiki images from the appropriate articles, with a slew of CC variants.

Now, I will try to update at least once a week, and include an intersting science or technology tidbit each time. So, let's go ahead and start high-rolling. Science has a rather interesting tidbit about snake fangs this week, in which analysis shows that that advanced (Caenophidian) snakes have their various fang morphologies derived from a rear-fanged ancestor. The nifty part? Selective expression of the "sonic hedgehog" gene (shh) relating to the anterior development of the maxilla meant the fangs moved effectivley forward, giving the "front-fanged" appearance of Viperids & Elapids, but these front fangs are actually the rear fangs -- and this single change was utilized twice! Cool stuff.

Now, lets see if I actually follow through with these updates ...

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