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Crowdsourcing Science

Posted by tigerhawkvok on September 10, 2009 20:37 in dinosaurs , research , paleontology , internet

Mike Taylor, Matt Wedel, and a bunch of other folks have gotten together with an ambitious project: to crowdsource science. While this may seem bizzare at first glance, the idea is that there are many, many papers out there, with all sorts of information that can be useful — and in this case, they're looking for measurements on ornithischian limb bones. So, enter the Open Dinosaur Project. For science, for acknowledgements, or for possible co-authorship, just head on over, give it a quick read, and start contributing!

If you want to dive right in, just go straight to the page for contributors.

On a more personal note, this project has re-invigorated me to start looking at the last bits of data for my paper ... it's been sitting idle for too long, it's time for it to get out! It means I need to do some more proofing of it, in addition to filling in the empty bits — if anyone is interested in proofing, let me know.


Tuesday Tetrapod: Ornithorhynchus anatinus

Posted by tigerhawkvok on September 09, 2009 00:34 in tuesday tetrapod

In an attempt to bring some equality to synapsids, and talk about something novel, for today's Tuesday Tetrapod, I bring Ornithorhynchus anatinus, or the platypus.

O. anatinus. Flickr image by kookr.

The platypus is a mammal known as a prototherian, or monotreme. "Prototheria" ("First" or "early" beasts) is in contrast to "Metatheria", or marsupials ("middle beasts") and "Eutheria", or placental mammals ("true beasts"). It is the sole member of its family, ornithorhynchidae, and the other four species of protetherians all belong to tachyglossidae (the echidnas). They have the common synapomorphies of all mammals, with a jaw composed only of the dentary, hair, and the production of milk; however, various other traits commonly associated with mammals are in a different form or absent in prototherians. For example, milk is produced, but it is not excreted from a nipple. Instead, it is excreted directly from glands on the skin. In addition, the live birth that is commonly associated with mammals is only a synapomorphy of the [ metatheria + eutheria ] node, and prototherians, in fact, lay eggs. While extant monotremes lack teeth, their ancestors had tribosphenic molars (though there is debate on common ancestry or independent evolution in the lineage).

Flickr image by ccdoh1.

The platypus in particular is unique in a few other ways. Its bill is electrosensitive, similar to the electrosensitivity of a shark. This works by detecting the electrical potentials generated by the nervous system of animals, in conjunction wit the largely saline solution that the animal is composed of moving with respect to any general ion gradients in the water (though the platypus lives in freshwater). By emitting a low strength E-field from its bill, specialized cells can "expect" a certain field measurement adjacent to it, based on properties of electric fields, and other living organisms distort this field, which then differs by this "expectation" in a characteristic manner. Additionally, the platypus is one of very few venomous mammals. The male platypus possess a spur on its hind feet with a hollow tube for venom delivery.The venom is produced in the crural gland, and the proteins involved are non-necrotic / non-lethal, and instead are designed to produce incapacitating pain and shock in their targets, rather than death.The indirect effects of oedema and shock may be enough to kill smaller animals, however.

Wrongheaded Creationists 1: Transitional fossils

Posted by tigerhawkvok on September 03, 2009 23:53 in evolution , anti-science , creationists

Having blighted the internet and US politics with consistently bad arguments, I decided when I'm so inspired (which is frequently, given how often they make it into the media) I'll post a short blog entry, tackling misconceptions or outright lies by creationists. So, catalyzed by this:

[We will take PZ Myers] down with fine-tuning arguments and universally accepted facts of science like the absence of any transitional fossils in the fossil record. Pwnd.
Source: All-American Gun Show

Allow me to make this abundantly clear.

Pendanticism aside, there is an abundance of transitional fossils in the fossil record demonstrating branching behavior within major lineages, derivation of traits unique to lineages, and of the origination of multiple, major lineages. Denying this is a demonstration of an unwillingness to perform a Google search, deliberate ignorance, or baldfaced lies.

If you just want to read what I written, you can look at:

Crocoduck, as shown by Kent Hovind and Kirk Cameron. Via Freethoughtpedia. NOT a transitional form, despite both animals being archosaurs (crocodiles are crurotarsans rather than mesotarsans, and are no where near the ornithodiran node).

If you want to read some basic Wikipedia articles, you can look at:

A real transitional fossil. Via Wikipedia

If you want something a bit more solid, you can look at the 59983 results at Nature for the search term "Evolution", or the 31953 results from Science. Too hard? Look at the very specific 2008 paper in Nature on the evolution and development of snake fangs (doi:10.1038/nature07178). Finally, and critically, every thing that has ever lived upon this planet is a transitional form to the next generation. There is no, and never has been, a crocoduck. Such things confuse common ancestry with descent, which are markedly different.

Enough by way of transitional fossils and genomic tracking for you? Pwnd indeed.


Broadband Commentary Mark II

Posted by tigerhawkvok on September 02, 2009 15:26 in politics , internet

Remember my recent post on posting commentary to the FCC about broadband policy? Well, it suddenly just became more important. Via Slashdot, we have the following completely predictable in hindsight move by ISPs:

[...] [M]ajor internet service providers in the US are seeking to redefine the term 'Broadband' to mean a much lower speed than in other developed nations. In recent filings with the FCC, Comcast and AT&T both came out in support of a reduced minimum speed. 'AT&T said regulators should keep in mind that not all applications like voice over internet protocol (VoIP) or streaming video, that require faster speeds, are necessarily needed by unserved Americans.' On the other hand, Verizon argued to maintain the status quo, saying that 'It would be disruptive and introduce confusion if the commission were to now create a new and different definition.'

You read that right. The lousy USA ISPs are trying to lower our abysmally low standards even lower. If that happens, you can be assured our poor internet with high price will get poorer. Put it into perspective with Verizon's comment: the best of the lot of them wants to maintain the status quo.

Please, everyone, take 15 minutes and send the FCC your opinions on the state of broadband and what we can do to improve it, and get everyone you know to do it, too. There's always the off chance that enough nerds will say enough interesting things that we might get an improvement! Say anything at all ... the most simple comment along the lines of "not enough competition, poor speeds with respect to the rest of the world, tighten controls and increase the baseline" is enough. Say whatever you're comfortable with (and if you can, throw in something about what would be a good definition for broadband), but say something!

Update: Some baseline information for you:

With the caveats out of the way, what are the results? The median broadband user in the States is getting about 2.3mbps and uploading at 435kbps. That compares pretty unfavorably to some of the industrialized Asian nations, where the median download speed is 63mbps, or Korea, where it's 49mbps. European nations also do well, with Finnish users getting over nine times the bandwidth, and France over seven times. Even going north of the border to Canada would likely to get you a substantial increase in speed, as the median downloader there gets 7.6mbps.
Via Ars Technica, 2008/08/14

This year's analysis paints a slightly rosier picture in some ways, worse in others:

The 2009 speedmatters.org survey finds that the average download speed for the nation was 5.1 megabits per second (mbps) and the average upload speed was 1.1 mbps. These speeds are just slightly faster than the 2008 speedmatters. org results of 4.2 megabits per second (mbps) download and 873 kilobits per second (kbps) upload. In other words, between 2008 and 2009, the average download speed increased by only nine-tenths of a megabit per second (from 4.2 mbps to 5.1 mbps), and the average upload speed barely changed (from 873 kbps to 1.1 mbps). At this rate, it will take the United States 15 years to catch up with current Internet speeds in South Korea. Moreover, the average upload speed from the speedmatters.org survey is far too slow for patient monitoring or to transmit large files such as medical records.

The 2009 speedmatters.org survey also reveals that the U.S. continues to lag far behind other countries. The United States ranks 28th in the world in average Internet connection speeds. In South Korea, the average download speed is 20.4 mbps, or four times faster than the U.S. The U.S. trails Japan at 15.8 mbps, Sweden at 12.8 mbps, the Netherlands at 11.0 mbps, and 24 other countries that have faster broadband than we do.

Moreover, people in other countries have access to much faster networks. Ninety percent of Japanese households have access to fiber-to-the-home networks capable of 100 mbps. According to the Organisation for Economic Cooperation and Development (OECD), the average of advertised speeds offered by broadband providers in Japan was 92.8 mbps and in South Korea was 80.8 mbps download. According to the OECD, the U.S. ranks 19th in the world in average advertised broadband download speed at 9.6 mbps.
Via speedmatters.org

We are poor in terms of provided speed, and even worse in terms of serviced speed. We need reform!

Tuesday Tetrapod: Ambystoma mexicanum

Posted by tigerhawkvok on September 01, 2009 15:24 in tuesday tetrapod

I was going to post another mammal to work on the dearth of synapsids here, but there is (unfortunate) timely news about these guys; so, today's Tuesday Tetrapod is Ambystoma mexicanum, or the Axolotl:

A. mexicanum, wild-type coloration. Flicker photo CC-BY-NC-SA by Flickr user widdowquinn, cropped.

Axolotl are highly paedomorphic (neotenic : retention of juvenile features into adulthood) ambystomatid salamanders, arresting development in their larval stage and thus retaining gills and other structures for living in water. They are adapted for living in isolated lakes with little competition. They are capable of short durations in the air, however, using buccal pump respirations to feed oxygen into their lungs; however, their skin is extremely skin and subject to drying out.

A. mexicanum, second wild-type coloration. Note the gill rakers clearly visible. Flicker photo CC-BY-NC by Flickr user pabloneco.

Unfortunately, A. mexicanum are only native to Lake Xochimilco and Lake Chalco in central Mexico; the former has been heavily impacted by humans, and is no longer a fully-formed lake, and the latter no longer exists, having been drained by the local population to avoid flooding. In addition, introduction of invasive fish has exerted pressure on the primary food source of A. mexicanum, as well as consumed their eggs. These factors have combined on the critically endangered species (as of 2006) to bring its population down to an estimated 700-1200 individuals as very recently surveyed (2009/08/28).

Albino captive specimen. Flicker photo CC-BY-NC-ND by Flickr user Isidr-Cea.

While often found in pet stores, the morphotypes found are often the mutant leucistic or albino variants, rather than the natural black and brown types. They live in vivarium temperatures of 14 - 20 C, with an optimal temperature around 17 C. They are often used in laboratory settings for their abilities to repair almost any wound, including complete limb regeneration. Occassionally, environmental stressors or artificial introduction of iodine / thyroxine will prompt the Axolotl to metamorphose — you can see an image of an adult-form salamander (copyrighted image) at the bottom of this page or at the top of this BBC article (partial metamorphosis).

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

Posted by tigerhawkvok on September 01, 2009 05:06 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.

Too True

Posted by tigerhawkvok on August 31, 2009 16:03 in General , news , paleontology , misc science

Click on the picture to see the whole thing.

Click for whole comic. Via Saturday Morning Breakfast Cereal.

Alas, too true. Also, read today's comic. Also, far too true. That and "feature creep" on papers.

To make this a bit more substantial, how's this for some interesting news: scientists have found microstructures on a fossil feather (40 MY old) that indicate it was iridescent. Nifty!

Is it a weasel? Methinks it is.

Posted by tigerhawkvok on August 31, 2009 00:11 in computers , biology , programming , misc science , internet

Since I've wasted most of today on this (oh feature creep. And an extra "-1".), I thought I'd share. Reading around on Pharyngula, I found myself wanting to make a more customizable, even-less-preprogrammed version of Richard Dawkin's WEASEL program. So, I present you with a Python 3.0+ version of Dawkin's "Methinks it is a weasel" program. It will take any nonzero length starting string, has a maximum generational cap for local maxima, with customizable rates for single-bit errors (like SNPs), duplication errors, number of offspring, weighting for approaching the target sequence, and accepted variability, and whether bad mutations are penalized or not.

Sample output. Click for larger / more lines.

The point of the program, as published in The Blind Watchmaker, is to show that with random mutations over time you can expect to see something like order pop out of a random test string. The version I have below takes the genetic modelling a bit further, starting with any string, regardless of length, and duplication / omission errors will trim down to the right solution. In debug mode, there's an additional completely random selection every 500 generations to help pull the program out of local maxima, but it is not in the primary program.

Click the fold to read the source, or download it here

 (More)

Tuesday Tetrapod: Acinonyx jubatus

Posted by tigerhawkvok on August 27, 2009 22:05 in tuesday tetrapod

Moving eats up time like no other, so here's a late Tuesday Tetrapod, where I'll try to balance my sauropsid bias with another mammal: Acinonyx jubatus, or the cheetah.

A. jubatus, "King Cheetah" morph. From Wikipedia.

The cheetah is fascinating for many reasons; in particular, its highly derived state results in a number of unique adaptations. It has lost much of the skin sheath around the claws, meaning that it's claws are effectivley non-retractable, unlike most cats. This means that the claws are exceptionally good for the purposes of traction, and assist the cheetah in its 100+ kph speeds and sharp turns (which are assisted by the long tail).

Cheetahs are believed to have genetically bottlenecked in the last Ice Age, possibly dropping as low as 100 individuals. This means that cheetahs are so undiverse that they can accept skin grafts from each other with no rejection, and due to inbreeding males have low sperm counts (and the sperm themselves lack motility).

The cheetah can be diagnosed from the leopard by noting the overall more gracile form, and the lack of spots-within-spots (rosettes).

Finally, on a more personal note, for a very long time, cheetahs were actually my favorite extant wild animal, to be later usurped by the Siberian tiger. Nowadays, I'm actually not sure which animal is my favorite!

Broadband Commentary

Posted by tigerhawkvok on August 21, 2009 20:56 in politics , internet

Via ArsTechnica and Blogband, I found my way over to comment on the FCC's request for comment (sound redundant, much?) on broadband speeds:

The best way to define broadband is based on a 24-day mean of a benchmark (say, 100 MiB) file download from the ISP. This 24-day average allows for a new hour to test each day (from 0:00 to 23:00), the file size lowers the relevance of "bursting", and the duration weighs out day-to-day fluctuations. The days could sequence testing HTTP, FTP, VOIP, and BitTorrent traffic, repeating every four days. This would discourage packet manipulation to favor one protocol over another.

Further, I would strongly suggest that the FCC create a definition for both "basic" and "high-speed" broadband, as high-speed is used misleadingly. I would suggest (to spur innovation) that at least [1 Mbps down/768 kbps up] speeds for "basic" (upload speeds have been lacking, probably due to lack of incentive) and at least [5 Mbps down/2 Mbps up] speeds for "high-speed". In 2009, no one should call something broadband with less than a megabit average connection.

I truly feel that these small changes can help make the US competitive in broadband speeds.

If you feel strongly about the broadband situation in this country, I would encourage you to head over to the comment form. If that link doesn't work, go to this page and search for Docket 09-51, select the radio button, and scroll down and select "continue".

Semi-classical Bohr radius calculation

Posted by tigerhawkvok on August 21, 2009 00:07 in physics

I thought I'd share an interested, back-of-the-envelope approximation of the Bohr radius I played with today, that ends up being pretty damn accurate!

The Bohr radius is essentially a classical approximation to the radius of the hydrogen atom. Let's take a semiclassical path there and see what we get. We will assume the following:

  • The total energy is approximately the ionization energy plus the rest energy of the electron.
  • The minimum stable orbit is a single standing wave.
  • The momentum of the electron is entirely described by Einstein's equation E2=p2c2 + m2c4.

We can then say (using 4 significant digits for the fundamental change and mass of the electron; quantities from Wikipedia):

equation1

Where c = 299 792 458 m/s (by definition). This gives us a momentum of ~1.99e-24 Ns. Running this through the deBroglie relation:

equation1

This gives us a wavelength of about 332.6 pm. Assuming you get one complete wavelength in the ground energy level of hydrogen, divide out by 2\pi to get a Bohr radius of 5.29e-11 m.

Now, the actual value is about 53 pm, or 5.29e-11 m. So, basically dead-on! Error in the trailing digits (shows up in the next decimal place) can be attributed to rounding in the values of the electron mass and in Planck's constant. Oddly enough, the fine-structure constant isn't needed here. Not quite sure why (probably this odd semi-classical calculation), but hey, you can now evaluate the Bohr radius quicky!

Update: Kit talks about the divergence of this model from a fully relativistic theory, incorporating the "gamma factor" γ=(1-β2)-1/2.

Cable News and Valley Girls

Posted by tigerhawkvok on August 19, 2009 13:47 in General , news

What the ...

Cable news networks have gone retarted. Just sayin'.

Tuesday Tetrapod: Contia tenuis

Posted by tigerhawkvok on August 18, 2009 22:47 in tuesday tetrapod

For today's Tuesday Tetrapod, I bring another snake: Contia tenuis.

Close up of head


Head, lateral, and ventral sides


Close up of tail

Contia tenuis, or the sharp-tailed snake, as an adaptation of its final tail scale that makes it into a sharp spur. As a defensive mechanism, they coil into a ball with their tail protruding to dissuade predators.

To identify it, note that the pattern of head scalation is unlike the "head shield" pattern that is the namesake of the Lampropeltis genus, with a regular crossbar patterning on the ventral side that is not found in Thamnophis. If worst comes to worst, look for the light yellow/orange/reddish stripe on the dorsolateral side of the animal running down its length,and the black stripe along the side of its head.

Photos courtesy Rachael, and snake courtesy Rachael's cat.

Website Development

Posted by tigerhawkvok on August 16, 2009 00:50 in computers , websites , internet

There's a degree of subtlty in webwork that is missed, but is particularly noticible when you spend a lot of time designing sites, be it for yourself or for clients. I think that I'll break this down into a few miniposts, to share my ideas on the topic, give a bit of threading through a few posts, and, well, to hopefully bring some ideas out. Right now, my plan is to look at:

  • Code validity
  • Aesthetics vs. Usability
  • Simple engines and security
  • Why I hate Javascript and Flash
  • Website modularity
  • Front-end website interfaces

Which brings us to this first post on code validity. Now, that is a bit of an obscure choice to start with. Really, who cares? The number of sites lacking a Doctype declaration is fairly amazing. People still mix display markup with content markup. What's with all this, well, kvetching about web standards?

Let's start with the doctype declaration. For example, this blog uses (for now, anyway, and valid as of this posting) the XHTML 1.1 Transitional doctype:

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

This tells the browser to use this style of interpretation when rendering the markup. In particular, the browser should handle certain not-strictly-OK bits of code, such as <input> tags existing outside of block level elements (that is, elements that occupy a chunk of a webpage instead of being able to exist in-line).

This touches on another aspect of valid code. Different types of elements have different nesting requirements. For example, the tag used to write this paragraph, <p>, is by default a block level element. It occupies a block of a webpage, and cannot have other block-level elements inserted into it, like a second paragraph element, or a <div> element (as a general rule; some elements are special, notably <div> and <table>). A block level element creates a new line when formed.

By contrast, inline elements, such as the anchor tag (<a>, most commonly used for links) are inline elements. They cannot exist outside of block-level elements. This seperation of block and inline level elements simplifies layout design and makes websites render more faithfully across browsers; when this isn't done, the browsers need to make a non-standardized choice about how to seperate these items. Do they form a new line or no? Are the spacings different? Does it implicitly form another block level element until closed? And so on.

The next item is a bit of a change from the old style of coding back in the 90's and early 2000's. It used to be that you could see bits of code like this:

<p><font color='green' type='comic sans ms'>Whee green!</font></p>

Now, you would see one of these:

<p class='greenpara'>Whee green!</p>
<p id='greenpara'>Whee green!</p>
<p style='color:green;font-family:comic sans ms,segoe print,pristina;'>Whee green!</p>

Which would all render

Whee green!

So what is the difference? In the first example, the code's style information was a different element, both block and inline, that would live with the content markup. However, in the latter three, the content is just the paragraph element, and the styling information is referenced by a class identifier (can apply to any number of items with that class), and ID (just one item), or a different style of code, applied to the entire paragraph element. This is known as CSS, or Cascading Style Sheets. This means you can actually have multiple styles for a page, as well demonstrated by the CSS zen garden, which has one page with multiple stylesheets to give it vastly different stytles. Less amazingly snazzy ways of seeing the same thing can be seen in the beta site I had done (wow, has it been a year?) for the UCMP. Over here, you see the full site in all it's CSS glory; over here you see the site with the external CSS sheet stripped out, and only inline elements remaining, and here an alternate color scheme that never got off the ground (and is thus incomplete).

Part of the beauty of CSS was that it allowed stylesheets to be moved externally to other files, and then referenced by <link> or <style> elements. This means the one stylesheet could be used by multiple pages, and be updated seperately and have it reflected across all pages simultaneously. For example, you can see the layout code for this site here.

If you want to check out the validity of your code, you should check out http://validator.w3.org/ — at the time of this writing, the front page (and all the posts on it) have been marked up correctly and return a valid page.

Till the next entry ...

Star Trek - Sunday

Posted by tigerhawkvok on August 12, 2009 02:26 in General , sci-fi

And the wrap-up photoblog from the Trek Con! I'll have some commentary up later this week, I think.

Be sure to check out the original photoblog post over here.

DSCF1961
DSCF2059

Zachary Quinto / Spock [ 2009 Movie ] / Sylar [Heroes]

DSCF2092

William Shatner / James T. Kirk

DSCF2122
DSCF2139

William Shatner and Leonard Nimoy / Spock

DSCF2239_2

Natasha and I before leaving, with Photoshopping to remove the insane amounts of red. Go mixers and curves!

You can read Natasha's impressions of Saturday and her impressions of Sunday — she's definitely more on the ball about posting than I am!

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