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Scientia Pro Publica 32: Biology Overload

Posted by tigerhawkvok on June 07, 2010 03:01 in General , evolution , physics , biology , astronomy , news , anti-science , medicine , paleontology , sci-fi , public science , climate , scientia pro publica

Welcome to Scientia Pro Publica, 32th edition!

Scientia Pro Publica logo

Scientia Pro Publica logo (C) by Flickr user jmarcx via loryresearchgroup. (Hotlinked by my usual policy)

This round, it seems that the name of the game is biology. Submissions really ran the gamut in biology, including some delightfully from-left-field posts. Bryan Perkins having some fun with embryological development, and Amanda Morti shows us why we have actinomycete bacteria to thank for that fresh rain smell (and for throwing off Latinate intuition - anyone else read "actinomycete" and think muscley whale?). Speaking of whales, David "WhySharksMatter" Shiffman does a great bit of ResearchBlogging and reminds us why not all fish (fine, non-sarcopterygian gnathostome) stock are created equal - sandbar sharks (Carcharhinus plumbeus) are closer in population dymanics to bowhead whales and other balaenids than cod.

That wasn't the only bit of ResearchBlogging this time around (Hey! ResearchBlogging! Stop hating my feeds!). Kelsey has a great post about the intraspecific male competition among red-eyed treefrogs. Sure, they amplex for dear life, but what about before that? Turns out that ... they shake their butt (Does that mean that the frog Sir Mix-a-Lot is a lady?). Madhu R-Blogs over at Reconciliation Ecology takes the opportunity to do a great smackdown on a pet peeve of mine — evolution is not a "ladder" or any such silliness. It is blind and targetless. It was a statement from a Stanfurd professor, though, so what can you expect (Go Bears!)? But before we get ranty, Luigi diverts our attention from critterland and the rivalries of my alma mater to teach us about why Kibale's Wild Coffee Project didn't get off the ground, concluding that scientists, once again, just can't do "messaging".

Illustration: Peter Trusler for Wildlife of Gondwana/NOVA (PBS). From Grrlscientist's post.

Thonoir continues to take us down our diversion away from Critterland, showcasing two sets of endangered non-metazoans, and my total ignorance of plant/photosynthizing phylogenies. We don't stray from Critterland for long, though, as John at Kind of Curious details a very interesting ponderous borer. Emily talks about sensationalism, mountain lions, and that Fox, even as they get extirpated from areas densely populated by a certain primate. Which, as Amanda points out, is no good thing, and there are difficulties restoring predators to ecosystems that they have been extirpated from (trust me, a one sentence synposis does not do that entry justice). The great Grrlscientist brings us some aborignal rock art possibly depicting Genyornis newtoni (Dromornithidae, incomplete phylogeny link (Anseriformes)). This is both the oldest paintings in Australia at 40,000 years (predating the earliest European cave paintings) and is of something that can be loosely imagined as an ostrich-sized duck, which simply can't be awesome.

Now, we don't end here. Oh no. That was just organismal biology and evolution. How about a dose of medicine? Michelle Dawson is better than Mary Poppins, because her post about circadian rythyms certainly doesn't need any sugar for you to take it down (and introduces you to an interesting side effect of autism-spectrum disorder). Scientific Chick writes about cell phones improving mental performance in Alzheimered mice. Meanwhile, Wendy at Bioloser gives us the physiological background of shock, and a shocking description of shock in a man nearly severed in half.

The larger constructs of medicine were not neglected, either. Bradley Kreit discusses the fact that we need to accept our intellectual limits, while Luke examines the crazy in large groups, looking at HIV denialism and Ryan looks at child mortality.

Bisected men and child mortality? Lets get a bit more lighthearted. Jessica Drake at Soilduck ponders what makes a scientist a scientist, and Romeo Vitelli tells us how subliminal messaging was an advertising gimmick (how many levels of fake-out is that?). Adam Park redeems some sci-fi stories with various predictions made therein that have come true today. Of course, Asimov gets a mention for the mention of pocket calculators in Foundation, but Asimov also nailed our reliance on them as time went on in The Feeling of Power (psh, arithmetic).

BP, the Gulf, and the utter dismaying farce of the spill have been in the news, and oil makes its showing in Scientia this time around. Scienceguy238 gives us a history leading up to the spill, and Grrlscientist looks at the ethics involved with oiled seabirds. Jeremy at The Voltage Gate writes about how the Saudi coast has recovered, 20 years later, from the 11-million-barrel (1.2 GL, or 1.2e6 m3) spill. A decade afterwards, 1 million cubic meters still persisted. Every spill is different, though, so hopefully ours won't be as bad.

You know you love it.

Finally, we round out with the physical sciences, which didn't get much love this time around. Lab Rat talks about bacteria and climate change, while Matt Wills talks about the more metaphorical breathing Earth, Charles Lyell, and mollusk damage in Greek columns. Finally, Sarah Kavassalis gives a great article on one of my favorite subjects: special relativity, astronomical distances, and the meaning of "now". After all, if a star (super)nova's in the distance, but you don't see (E&M) or feel (gravity) it, has it gone? She even does it without the inevitable jargoning I'd go into!

That does it for this round of Scientia Pro Publica! This was my first blog carnival, so I more than welcome suggestions. Hope you all enjoyed it!

If you want to learn more about this carnival, head over to the carnival's website. Be sure to check out the next round hosted by Andrew over at Southern Fried Science, on June 21st. And remember — this is a blog carnival! Submissions and hosts are wanted! If you're interested in hosting, check out the current schedule on the official schedule thread and drop Grrlscientist a line (or leave a note in the comments). If you find a cool article, submit it! Send a link via this submission form. Thanks again all!

Dinosaurs and Extinct Feather Morphotypes

Posted by tigerhawkvok on May 28, 2010 00:19 in evolution , paleontology

Dinosaurs and feathers. The story has gone from scaly lizards to that of animals strikingly similar to birds. Now, a recent paper in Nature (doi:10.1038/nature08965) further muddies the picture with dinosaurs demonstratedly showing development of feathers as the animal aged.

The paper in question is one describing the find of a Similicaudipteryx in the limestone of the Yixian formation in the Liaoning province in China. It describes how in addition to a marked developmental sequence in the feathers (implying moulting), it also indicates a currently extinct line of feather morphologies and developmental pathways. The authors introduce the term "proximally ribbon-like feathers", best typified by the tail feathers in male Confusciousornithes. These are feathers that are long ribbons until the distal end, where they become pennaceous (like modern feathers).

In Similicaudipteryx, two specimens are compared; a early and late juvenile form (STM4-1 and STM22-6). STM4-1 has pennaceous feathers attached to the hands and rear of the skeleton (tail and rear back vertebrae), but the rest of the feathers are "plumaceous" (think down feathers, like chicks). STM22-6, on the other hand, has had anterior feathers on the head replaced with non-plumaceous varieties and (if it is not a preservation artifact) has gained secondary remiges. Futher, the plumaceous feathers are different from true down, indicating that feather types changed several times during the ontogenetic development of these animals, unlike modern birds.

A nice touch is a passing mention in the paper to feathered-dinosaur-haters; many dissafected with the idea of feathered dinosaurs claim they are remnants of dermal collagen, it is true (and it is brought up) that dermal collagen would lack the melanosomes present in the feathers of fossilized animals.

Fossilized Melanosomes and Extinct Dinosaur Colors

Posted by tigerhawkvok on February 14, 2010 16:24 in dinosaurs , evolution , research , paleontology

ResearchBlogging.org

I may have fallen off the face of the planet, but it doesn't mean science stopped going. So, beginning with a bit of admittedly old news — we've determined the color of a few coelurosaurian theropod dinosaurs' plumage. It's the subject of a few papers that came out in Science and Nature two weeks ago (DOIs 10.1126/science.1186290,10.1038/nature08740, summary: 10.1126/science.327.5965.508). The trick, it turns out, was to use a scanning electron microscope (SEM) to look at the microstucture of the preserved melanosomes in the feathers.

Figure 2, DOI 10.1038/nature08740

a, Optical photograph. b, Strongly aligned, closely spaced, eumelanosomes preserved as solid bodies. c, Mouldic (that is, preserved as moulds) eumelanosomes (at arrow) a short distance above a layer in which the eumelanosomes are preserved as aligned solid bodies. d, Area (at arrow) comprising more widely spaced mouldic phaeomelanosomes surrounded by less distinct, aligned eumelanosomes (top of image). e, Gradational boundary between areas dominated by eumelanosomes (longer arrows) and phaeomelanosomes (shorter arrows), both preserved as solid bodies. Scale bars: a, 50 mm; b—e, 2 µm.

If you can work your way through this paragraph, you can also see why this discovery is not just a novelty, but scientifically interesting (I don't think I can phrase it better):

Integumentary filaments occur both in non-avian theropods that possessed true pennaceous feathers (for example, Caudipteryx) and in those in which the latter are absent, such as Sinosauropteryx, Sinornithosaurus and Beipiaosaurus. The report of superficially similar unbranched filaments in the ornithischian dinosaurs Psittacosaurus and Tianyulong suggests that such structures might be common to all dinosaurs. Many investigators have accepted that these various filamentous to feather-like structures are epidermal in origin and represent feathers; others have disputed this view, arguing, for example, that in the theropod dinosaur Sinosauropteryx they represent degraded dermal collagen fibres, part of the original strengthening materials of the animal's skin. Resolving this fundamental difference in interpretation is important for our understanding of the biology of the taxa in which they occur, but also has wider implications; if epidermal in origin, these structures will inform models of the evolutionary origin of modern feather and the timing of steps in the acquisition of this evolutionary novelty.

Wikified for your convenience


Figure 4, DOI 10.1126/science.1186290

Anchiornis huxleyi, as rendered in Li et al..

Well, it turns out that the preserved microfeatures of the integument on Sinosauropteryx and Sinornithosaurus bear strong resemblance to modern microstructures in feathers known as melanosomes, which are responsible for giving color to feathers. Further, they are located inside the preserved feathers in physical locations analogous to those in living dinosaurs (ie, birds). The Nature paper thus conclusively demonstrates that they are epidermal features of the animals, ie, not degraded bits of skin, collagen, and scales that merely resemble feathers. As a fun fact, it showed that the animals they looked at had black, white, and russet feather colorations, and even color variations along single feathers and colored crests. The Science report suggests that Sinosauropteryx even had banding along its' tail.

Figure 5, DOI 10.1126/science.1186290

Cladogram of feather coloration, from Li et al..

In side-news related to the series of dino discoveries, the discovery of an early alvarezsauroid pretty much once and for all deflated the arguments of Alan Feeduccia. He had essentially resorted to temporal arguments (i.e., Archaeopteryx was older than the oldest found non-avian eumaniraptoran dinosaur) to state that Aves must have had a seperate, basal archosaurian/avesuchian ancestory, not nested within Dinosauria. Goodbye, so-called "temporal paradox". Now I just need to get people to stop saying the K-Pg event wiped out dinosaurs, and get them to insert non-avian in there. Remember, encourage evolutionary/cladistic thinking whenever you can!

Zhang, F., Kearns, S., Orr, P., Benton, M., Zhou, Z., Johnson, D., Xu, X., & Wang, X. (2010). Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds Nature DOI: 10.1038/nature08740


Religion in the Classroom and the Slippery Slope

Posted by tigerhawkvok on February 14, 2010 15:33 in evolution , religion , anti-science , misc science , public science , creationists

Reading an article like the New York Times' recent one on textbooks and religion in the US has the magical ability to just make me so angry. The article itself is mostly neutral, but it brings up Don McLeroy, a dentist in Texas who has remarkable influence over science and history taught to children for the large majority of states. A history-denying activist moron er, "Young Earth Creationist" of the activist stripe, he has said

"Everything that had a beginning we can say had a cause," he tells his class of fourth-graders at Grace Bible Church. "And now science definitely says that the universe had a beginning. Therefore, the universe had to have a cause. And that cause is God."

Citation: Statesman.com

OK, normally, this would just be infuriating as he'd be a nutter on a school board that approves books for a state. But, seeing as Texas is the second largest textbook market in the US, and California is broke, it means this man essentially shapes the education of the rest of the country. To quote the Times,

And James Kracht, a professor at Texas A&M's college of education and a longtime player in the state's textbook process, told me flatly, "Texas governs 46 or 47 states."

As (admittedly) excessively vitriolic PZ Myers and other "strong" "New Atheists" can be, this is the sort of thing that makes me feel their position has merit. Evolution is not under controversy in any way in the scientific or educational community. Filth like McLeroy or David Barton are liars. The "Discovery Institute" are religious shills operating under an agenda to drive science out of the public arena and move to a religious educational system via the "Wedge Document".

Stories like this should inspire activism in freethinkers. Stories like this make it hard to reach a mutually agreeable arrangement in deference to the idea of non-overlapping magisteria (which, incidentally, I find highly problematic besides; a highly flawed concept with arguments similar to those Dawkins makes) — because if you give an inch, fools like Don McLeroy will try to take a mile.

Archosaur Lungs

Posted by tigerhawkvok on January 20, 2010 12:45 in dinosaurs , evolution , biology , herpetology

Just a quick update, before I head to Indiana to visit Purdue and my friend Jessica. I realize I missed yesterday's tetrapod, but I prefer to postpone a week and post a better update rather than a very breif post every week (look forward to sea snakes next week).

In this week's science, there is a paper describing unidirectional airflow in alligator lungs, strongly suggesting that this formerly "avian-style lung" is in fact an archosaurian synapomorphy. That is to say, this paper gets as close as a single paper can get to outright saying that this is a mechanism that helped nonavian dinosaurs get so large. Archosaurs just keep being awesome.

On somewhat related news, I think I'll try to put up a few evolutionary YouTube videos. Rather than a pure bash-on-creationist style, though, it'll be focused on describing particular evolutionary lineages and evidence. We'll see how that works out, though I need to become much more familiar with movie editing software.

Basal theropod, with interesting implications

Posted by tigerhawkvok on December 10, 2009 15:35 in dinosaurs , evolution , paleontology

Now, this is actually an interesting piece. according to LiveScience, a new basal theropod dinosaur, Tawa hallae has been found in lower Triassic New Mexico rocks, dated at ~213 MYA. The paper is due to be published in the December 11th issue of Science, after which I'll post more.

However, LiveScience implies that there is reason to believe that T. hallae was covered in filamentary integumentary structures, adding to the evidence suggesting filamentary integument was at least basal to dinosauria (interesting blog post on that topic, though this find, if LiveScience's implications are correct, would invalidate his point (5).)

To avoid needless speculation, though, I'll avoid talking more about it right now, and instead post a longer entry on it in the next few days when I can look at the actual paper. But I'm looking forward to it!

Darwin Christmas, and Finding Control Groups

Posted by tigerhawkvok on December 06, 2009 19:18 in evolution , biology , misc science

I find this incredibly entertaining:

Darwin Christmas

"Darwin Christmas". Hotlinked since it lives on Imageshack.

Arguably the greatest problem with it is that we're programmed from a young age to think of left-to-right as increasing on a given axis, though obviously this is meant to be read from right-to-left.

In other news, this "weird science" post from Ars Technica comes with this entertaining gem:

This is little more than a press release on some research in progress. Still, even before the results are in, the process of setting up the experiment turned out to be rather informative. The study, you see, is on porn consumption, and it looks like the researchers will be stuck working without anybody to act as a negative control. "We started our research seeking men in their twenties who had never consumed pornography," said Simon Louis Lajeunesse. "We couldn't find any."

Time to stop procrastinating and start properly bolting out those grad school applications.

Wrongheaded Creationists 4: Hitler was an "Evolutionist" (Not)

Posted by tigerhawkvok on November 25, 2009 14:24 in evolution , religion , anti-science , creationists

This comes up so often, it needs a token response. Creationists (mostly) assert that Hitler was an atheist who used evolution to promote extermination of Jews. This is blatantly and verifiably incorrect.

First, so what? Even if he understood evolution and accepted it (he didn't), the fact he liked to drink beer doesn't make all beer-drinkers in favor of eugenics, anti-semetic, and dictatorial.

As to the point itself, here's a rebuttal, courtesy of Hitler himself, yanked from a comment over at Pharyngula:

In Mein Kampf, Hitler asserted the fixity of species, that god made man, that man existed "from the beginning" and did not descend from apes, that man was made in the image of god and was expelled from the garden of Eden, and that Jesus was his inspiration.
His words:

The fox remains always a fox, the goose remains a goose, and the tiger will retain the character of a tiger. - Adolf Hitler, Mein Kampf, vol. i, ch. xi

For it was by the Will of God that men were made of a certain bodily shape, were given their natures and their faculties. - Adolf Hitler, Mein Kampf, vol. ii, ch. x

From where do we get the right to believe, that from the very beginning Man was not what he is today? Looking at Nature tells us, that in the realm of plants and animals changes and developments happen. But nowhere inside a kind shows such a development as the breadth of the jump , as Man must supposedly have made, if he has developed from an ape-like state to what he is today. - Adolf Hitler, Hitler's Tabletalk

Whoever would dare to raise a profane hand against that highest image of God among His creatures would sin against the bountiful Creator of this marvel and would collaborate in the expulsion from Paradise. - Adolf Hitler, Mein Kampf, vol ii, ch. i

My feeling as a Christian points me to my Lord and Savior as a fighter. It points me to the man who once in loneliness, surrounded only by a few followers, recognized these Jews for what they were and summoned men to fight against them. - Adolf Hitler, speech, April 12 1922, published in My New Order

Hitler was a creo.

Yes, Hitler was a strong Christian and unabashed creationist. This does not equate creationists to Hitler, however. They're pretty foolhardy and willingly blinded all on their own accord, with no ties to Hitler's filth necessary.

150 Years

Posted by tigerhawkvok on November 24, 2009 16:22 in evolution , biology

I've been a bit quiet lately, mostly because of work I've been putting into Velociraptor Systems. Last week's skipped Tuesday Tet was especially tragic, as it was half-composed the Wednesday before that!

I'll get that entry, and second one, up later today. However, it's also good to note that today is the 150th anniversary of the publication of Darwin's "On the Origin of Species, by means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life". It is arguably the most significant single text to change how we live, with evolutionary based insights leading to models of heritibility and research into the genome.

I'll link you to Dawkins discussing the subject on CNN's site (note: they either misquoted Dawkins on "over 300,000 million years", or the publication was in error; that number equates to 300 billion years, well older than our universe). But I'll close this entry with a quote:

It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and Dependant on each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost certainly implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

Darwin, Charles. "On the Origin of Species". 1859.

Wrongheaded Creationists 3: Gaps, gaps, gaps

Posted by tigerhawkvok on October 13, 2009 23:56 in evolution , religion , anti-science , creationists

First, due diligence, as this entry in the series is brought to you by Bill O'Reilly:

Oh, Bill. Dare I count the ways you are flawed in your arguments?

  • A gap in scientific data should be explained as either "insufficient evidence" or a scientific conjecture. To quote Dawkins, "It's a most of extraordinary piece of warped logic to say because science can't fill in a particular gap you're going throw in your lot with Christianity." If it should be filled-in with myths, why not the Cthulhu mythos, Invisible Pink Unicorn, Greek Pantheon, Egyptian Pantheon, Norse Pantheon, or druidic theism instead of Christian mythos?
  • You fail Godwin's Law.
  • You realize you spoke more than your interviewee, right?
  • You realize Jesus probably looked more like a middle eastern guy, right?
  • Your theology fails the self-sacrificing pacifist test when you look at religious wars on the behalf of Christianity, and the opulence of the Vatican.
  • Saying there are more X than Y therefore what X believes is true is a fallacy.

I think when I return to SD I might create a powerpoint slideshow to showcase these "alternate viewpoints", and include a few (ie, soup, clay-assisted, RNA-world) scientific hypotheses thrown in for fun. Take it from universe creation to first autoreplicable form.

To drive the point home: gaps in scientific understanding, no matter your level of scientific understanding, should never be replaced with psuedoscience or mythology in its place

Here's a nice YouTube clip that's not quite related, but discusses the spread of misinformation by the Discovery Institute

Evolving AI 2: A Programmatic Brain

Posted by tigerhawkvok on September 24, 2009 18:11 in computers , evolution , programming

OK, I lied. Programming the brain first, even though I wrote it as if I wrote about the body already, it should still mostly make sense.

The core fact to realize about our own conciousness, etc, is the fact that we are not programmed with it. Trying to program self-awareness into a computer simulation has problems because there is no place to start from. Our behaviour is an emergent behaviour, so we need to duplicate this in an simulated fashion.

Given that we've already talked about the modularity of the body plan, how is this body controlled? We assign a virtual neuron cluster to each point of freedom, with each virtual cluster having members equal to the granularity we want to start with. Thus, consider the human elbow. It would be one virtual neuron cluster to control its up-and-down motion (like you're flexing your arms). The number of virtual neurons in this cluster is determined by:

  • 1 per degree of rotation. About 160 for the human elbow.
  • Each virtual neuron can have an arbitrary number of connections within the cluster, but regardless of input signals recieved only outputs one unit of amplitude. We then have 160 control neurons with one "lead" outside the cluster. Control neuron 2 fires two movement neurons, instigating a 2o rotation. Control neuron 139 fires 139 movement neurons, for a 139 degree rotation. Thus, "basic" members in the available movement pool have more connections (more control neuron connections) than more extreme members (ie, movement neuron 160 is only connected to one control neuron)

These virtual neuron clusters are then batched into virtual superclusters, controlling the larger body segment. So, a human shoulder would have one cluster for swinging rotation, one for "flapping" rotation (like jumping jacks). The supercluster has a set of control neurons, broken into a few classes:

 (More)

Evolving AI 1: Evolutionary Trajectory

Posted by tigerhawkvok on September 24, 2009 16:05 in computers , evolution , programming

I was thinking about AI, and I came to the conclusion that, well, computer scientists are doing it wrong. This is a problem with computer scientists trying to do something incredibly improbable, and incredibly difficult, in one giant step.

Instead, I posit, we need to take the route that evolution took, and evolve our way to an artificial intelligence. Much of our behaviour (and after all, we want to get something basically human) is baed on our evolutionary history. We don't think about being happy — we don't go "oh hey, my brain is telling me that for social reasons it's a great idea to smile right now, because I happen to be happy", either. We just do it — that's the essence if instinct, and much of it is vital to the way an AI would need to behave.

Along with my much delayed series on web design, I'm going to write a brief series on how I believe one could evolve their way to AI, but by doing so at a vastly different level than has been done before. This will focus on 4 things:

  • Directed evolutionary paths — how to drive a model organism to intelligent behaviour
  • Modelling parameters and sensory analogs inside a virtual world
  • Controlling behaviour in a virtual environment
  • Population sizes and sexual vs. highest-fitness reproduction
  • CS and engineering implications of this approach

The crux to this whole thing is that, ironically, we'd need to bastardize evolution a shade to pull this off, as we'd play the dubious role of a "guided intelligent designer". Since the model computer world would, necessarily, have less than 5 x 1014 m of surface area, and run what I term "sequence events" at slower than real time, without the vast variation of the Earth's surface, we can't hope to ever run a full simulation of 350 MY or so.

Instead, we would run small sequence events that build on each other, eliciting certain classes of behaviours in medium populations (say, 50 individuals). After their rate of change has stabalized for, say, 1,000 generations, modify the conditions of their environment and pick the top 50% of individuals to expand their behavioral repretoire. Every 100 generations or so, a population snapshot can be made for research, fallback, and archival purposes. Only the top 50% of individuals (of each sex) are always allowed to breed, randomly, with each other, at exactly replacement rate. The only things modified by the programmer (after initial set-up) are the environment, a "fitness bonus" for certain goals, and a "fitness function" that assigns a fitness value to each individual for a given point on the evolutionary trajectory.

I propose an evolutionary trajectory as follows:

 (More)

Wrongheaded Creationists 2: Castrating Darwin?

Posted by tigerhawkvok on September 23, 2009 12:40 in evolution , religion , anti-science , creationists

From your local department of wingnuttery, you get to see the latest attempts of hardline theo-nuts to distort science and push their blindingly incorrect view of evolution on the populace. What do you do when a text is completely and freely available?

Well, you do the only thing you can do. You publish your own version, edited to roughly half-length by a ministry and with a 50-page prelude explaining how evolution is wrong and it's never been proven.

Hang on, didn't I already address this? Well, don't take my word for it, see for yourself:

The Facebook group and the richarddawkins.net page suggest amassing then donating, but the recent info that about half of the content has been killed off, I propose that yes, you amass all those wrteched copies — then go and purchase a cheap first edition and donate it to a library or school.

Utter, shameless propaganda by distributing altered copies of a text. If their argument was convincing, you'd imagine they could leave the text intact!

Phylogenies Everywhere

Posted by tigerhawkvok on September 14, 2009 14:36 in computers , evolution , biology , programming , websites , internet

A surprising amount of this weekend was dedicated to working on phylogenies. I updated non-eusuchian crocodylomorphs, avialae through neoaves to at least extant order; minor updates to sauropoda, and an update on sauropterygia.

The site also finally got a long-needed search engine. It's not the most efficient thing in the world, but doing a binary search is essentially useless. I made it modular, so I may still end up seeing how a sort + binary search with preserved keys turns out, or cut out the cruft (change the amount of the document searched).

I finally also added a dirty implementation of tagging. I used the <tt> (teletype) tag and changed its contents to not display (CSS display:none). Thus, tags for an entry can be hidden in this element, and will be read by the search engine, but not displayed.

I also noticed that it was hard to find some of the sources I cited with just name and year — so I've started adding linkouts, DOIs, or ISBNs too all sources provided, to make it easier in the future.

Kind of looks less in writing than it felt like ... but I'm happy with the way it's going.

Wrongheaded Creationists 1: Transitional fossils

Posted by tigerhawkvok on September 03, 2009 22:53 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.


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