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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

Tuesday Tetrapod: Dermochelys coriacea

Posted by tigerhawkvok on October 07, 2009 12:16 in tuesday tetrapod

Since last week was lacking in the usual Tetrapod, I wanted to do a double-feature yesterday. However, a bug in my phylogenetic page search code (affecting side-cases where you were a certain number of nodes deep with a certain number of closing nodes above you) postponed this post. However, I make it up today, with a makeup post in which we look at Dermochelys coriacea, or the Leatherback Turtle:

Juvenile D. coriacea. Modified photo by Flickr user algaedoc (CC-BY-NC)

D. coriacea is the only extant member of the family demochelidae, a group united by the lack of a hardened keratinous covering within the cryptodires, or turtles that retract their head linearly into their shell. It is worth noting that though this is a synapomorphy for living turtles, basal members of both cryptodira and pleurodira were unable to retract their neck, and better synapomorphies are found in the connective morphology for the adductor muscles. The peculiar shell of Dermochelidae is instead composed of polygonal osteoderms embedded in skin, which covers a carapace 3 - 4 mm thick.

The chelonioids (marine turtles) are the clade of seagoing turtles, which includes Dermochelidae. Dermochelys is the only fully pelagic turtle, and has a metabolic rate higher than most other non-archosaurian sauropsids, allowing it to maintain a body temperature 18 K or more above ambient. Most of this metabolic heat is generated by muscular activity. This is assisted by a network of 'heat exchangers' in its body, keeping warmer blood internal. These features enable the leatherback's wide distribution, including waters as cool as 281 K (8o C).

Females will lay on tropical and subtropical beaches, with clutches of 40-170, averaging 65-80. They nest bi- or tri-annually, navigating via the Earth's electromagnetic field. Their generally pelagic nature is due to the fact that their primary food source is jellyfish, complemented by other soft-bodied marine organisms. They lack both the dentition and jaw strength to consume anything more rigid.

You can easily identify the leatherback by its non-rigid carapace with lengthwise toothed ridges, and a serrated upper jaw. The animal will measure 120 cm - 245 cm. They have a worldwide distribution, from tropical to sub-polar regions. The subspecies along the western coast of the US is known as D. c. schlegelii, or the Pacific Leatherback. Dermochelys is listed as IUCN critically endangered, with population devastation due primarily to trash interfering in their feeding (plastic bags and nets can look like jellyfish), and declines in nesting sites, nesting success, and increases in nesting mortalities and egg harvesting. This has resulted in a nearly 80% global population reduction in as little as one generation.

Tuesday Tetrapod: Gymnogyps californianus

Posted by tigerhawkvok on October 06, 2009 23:36 in tuesday tetrapod

It's Tuesday again — so time for a Tuesday Tetrapod! Today we look at Gymnogyps californianus, or the California Condor:

California Condor

G. californianus. Image by Flickr user Don van Dyke (CC-BY-NC-ND)

G.californianus is a cathartid, or a new-world vulture. Unusually for birds of prey, sexual dimorphism favors males rather than females in condors. They are rated by the IUCN as critically endangered, with such devastation to their habitat and numbers that now captive rearing plays a large role in their current populations. Part of the reason for their declining numbers is attributed to the extinction of north American megafauna, reducing the carrion selection for the birds. In modern populations, lead poisoning from game has led to serious population declines, leading to legislation to ban use of lead bullets in their home ranges.

You can identify the bird by looking for the white underwing linings toward the fore edge of the wing in adults. Young birds are dusky-headeed, and but are twice the size of Cathartes aura, or the Turkey Vulture, and have much broader proportions. You can also look for the tufted feathers around the neck, rather than the smooth feathers characteristic of the other cathartids. They may have a SVL of as much as 138 cm, and a wingspan of 290 cm. Once extirpated in the wild and reduced to two dozen members in the San Diego and Los Angeles zoos, they are slowly being reintroduced into the wild and are about 300 in population.

You can take a look at what you can do to help the condor populations by checking out CACondorConservation.org.

Google Wave and (no) Internet Explorer

Posted by tigerhawkvok on September 30, 2009 16:21 in news , websites , internet

To follow up on my anti-IE6 post, looks like Google's Wave project won't support IE. To quote Ars:

The developers behind the Wave project struggled to make Wave work properly in Microsoft's browsers, but eventually determined that the effort was futile. Internet Explorer's mediocre JavaScript engine and lack of support for emerging standards simply made the browser impossible to accommodate. In order to use Wave, Internet Explorer users will need to install Chrome Frame.

This isn't even just IE6 — this is all versions of Internet Explorer. Hilarious!

Sean Hannity vs. Endangered Fish

Posted by tigerhawkvok on September 30, 2009 14:20 in news , misc science

Apparently, Sean Hannity has it out for Hypomesus transpacificus, or the (endangered) Delta Smelt.

H. transpacificus is an otocephaline teleost, a member of the family Osmeridae. It is actually euryhalinical, and tolerant of a wide range of salinities — so if Stewart is correct on the motivation (salinity), then it is bad news indeed, and the protection needed to be done anyway. The height of the water column is also important to these fish, being pelagic (ie, residing in the middle-area of the water column, away from the surface and from the bottom). However, more importantly, the fish is indeed fairly basic to the food chain, and feeds bass and salmon.

I didn't realize yesterday was Tuesday, so a late Tuesday Tetrapod will be up this afternoon.

Website Development 2: Killing IE 6

Posted by tigerhawkvok on September 28, 2009 15:41 in websites , internet

Believe it or not, I'm finally following up a little on this 1.5 month old post on web development

So, in my standard course of RSS feeds, I ran acrosss Ars Technica's monthly web usage share post. I noticed a nice by-percentage breakdown of IE market share, and realized that Internet Explorer 6 has about 16% market share.

This is a browser that is eight years old, doesn't render transparent PNGs, doesn't render CSS correctly, has missing CSS selectors, and has 139 security vulnerabilities. Oh, for good measure, a number of Javascript commands outright crash it.

There are entire sites devoted to the push to eliminate IE 6:

Even companies, like 37signals, have phased out IE6 support.

Here's a quick thing you can insert into your own pages (right before </body>) for a subtle but effective notice to upgrade, taken from ie6update.com:

<!--[if IE 6]>
<script type="text/javascript">
	/*Load jQuery if not already loaded*/ if(typeof jQuery == 'undefined'){ document.write("<script type=\"text/javascript\"   src=\"http://ajax.googleapis.com/ajax/libs/jquery/1.3.2/jquery.min.js\"></"+"script>"); var __noconflict = true; } 
	var IE6UPDATE_OPTIONS = {
		icons_path: "http://static.ie6update.com/hosted/ie6update/images/"
	}
</script>
<script type="text/javascript" src="http://static.ie6update.com/hosted/ie6update/ie6update.js"></script>
<![endif]-->

It's kind of insane that this browser is still around. Even if you run a small site — enough small sites start popping this up, and you'll get people's attention.

I also have a PHP setup that's more configurable, and if someone wants it, I'll put the code up.

Glenn Beck Vs. Amphibians

Posted by tigerhawkvok on September 24, 2009 22:43 in General , politics , news

Ok — ignoring everything else, if I had had any respect for the train wreck that is Glenn Beck, I'd have lost it after this:

Apparently, throwing frogs into boiling water to make your point is OK. It's possible he didn't actually keep holding onto one ... in which case he's just shamming boiling frogs? Which is also really screwed up. Yeaaaah ....

UPDATE: Nate Silver gives an analysis of Glenn Beck, and what he represents.

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:

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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:

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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!

Tuesday Tetrapod: Cariama cristata

Posted by tigerhawkvok on September 22, 2009 20:33 in tuesday tetrapod

After a brief tour around non-eutherian synapsids, we return to the far more prosperous sauropsids with Cariama cristata, or the red-legged seriema.

c cristata

C. cristata. Modified image by Flickr user kradlum.

c cristata

Seriema face, close up. By Flickr user Toni Barros (CC-BY-NC-SA).

Cariamids are comprised of two species, each belonging to its own genus (the other being Chunga burmeisteri), within the order cariamae. The order shares a common set of characteristics relating to their overall behavior focused on terrestrial predation. In fact, the cariamaen birds include the famous "terror birds" of the Phorusrhacid family. Cariamids maintain the ancestral range of the order, being most prevalent in Argentinian and Brazilian grasslands, and exclusive to South America. They occupy a very similar niche to the Secretarybird in Africa, eating small/medium rodents, insects, and reptiles.

c cristata

Killing a rubber boa. Image by Flickr user Dunleavey family.

In an interesting reversion to primitive traits, Cariama has a recurved and extensible claw on its second toe, convergent on the features found in early avialans and in deinonychosaurs. These claws are often used assistively for feeding.

Unlike Phororhacos and other Phorusrhacids, the wings are not vestigial, and Cariama is capable of flight. It will, however, preferentially run at up to 25 kph before flying, and nests on the ground.


Healthcare and a Public Option

Posted by tigerhawkvok on September 15, 2009 23:16 in politics

A brief comment on healthcare:

A healthcare bill makes no sense without a public option. Whether or not you think there should be a bill is irrelevant to this point. The message that should be out there, on both sides, is that there's no point in debating a bill that does not have a public option, nor is there a point in sponsoring a bill without a public option.

The public option in the US would be fairly different from the way it is in other countries. It would not be mandatory, and indeed, its principle point to exist is to provide a low-level baseline for people of low means (and is thus affordable). If that were the only point of it, yes, it would be a bankrupting bill that would be a colossal tax burden. However, arguably the primary point of a public option, which is often overlooked, is that a public option will serve to compete with private firms, driving down costs via competition. The healthcare system is in a very similar state to our broadband infrastructure — an undercompetitive, and monopolistic mess. This helps everyone — and the individual savings would offset your own tax contribution to a public option to help those who cannot afford a more comprehensive private option. The end result is everyone saves money, and the system is very, very cheap. No options are being removed, only one option being added.

Now, it is perfectly logical and consistent to be against public options in general, but then to be consistent you must be against medicare and medicaid, which is essentially the same system. Ditto for welfare, foodstamps, and unemployment checks. Once you accept that any of these are permissible or even required, then you acknowledge there is some baseline support that a government should provide people in bad times or with low means. Then, to paraphrase a famous quote, we are just haggling over price. While it is possible to support food stamps, unemployment, or welfare without supporting a public healthcare, public healthcare is just a superset of medicare, which is public healthcare for seniors. Thus, if you support medicare, you cannot, consistently and logically, protest against public healthcare. And, for reasons given above, since public healthcare is ill-posed without a public option, you essentially must support a public option if you support medicare.

While there is an argument that the government should provide none of these support programs, and it is internally consistent, it is vital that one recognizes that acknowledging any of these aspects as valid means that you agree in principle, and that you must then define your boundaries, and the logic for those boundaries. Furthermore, that same ideology is almost invariably coupled with a strong capitalism, and thus it almost makes no sense to try to convince people to vote against their own immediate interest (not quite, but as a sweeping, immediate generality it works). Weakening either strong position to any degree accepts either the premise of government intervention on behalf of its people, or on behalf of stimulating competition, both of which the public healthcare option accomplishes.

In 1.5 hours I will lose my health insurance, and will be unable to afford a replacement. I suppose I just hope I don't get sick.

Tuesday Tetrapod: Sarcophilus harrisii

Posted by tigerhawkvok on September 15, 2009 22:58 in tuesday tetrapod

Oddly enough, working on phylogenies made time fly by fast enough that I didn't realize it was already Tuesday — and time for another Tuesday Tetrapod! Let's go for another non-eutherian synapsid. Enter Sarcophilus harrisii:

S. harrisii, by Flickr user ccdoh1 (CC-NC-ND).

Don't let their tiny size fool you. These guys are mean, and their common name is given for a good reason - the Tasmanian Devil. While fairly small (males average ~25 cm and 8 kg), they have attained their moniker for various reasons. When stressed, they release an odor nearly as pungent as a skunk, and their call is said to resemble a very loud and disturbing scream. Their bite pressure is the strongest of any living mammal, running at 35 MPa (the equivalent pressure of 350 m underwater). This prodigous force is used to consume the bones of carrion, which are consumed with fur, meat, and organs. While they largely scavange, Devils are capable of taking down small kangaroos.

Currently, Sarcophilus has been extirpated from mainland Australia, and their closest extant relative is the Numbat. Once relatively stable, a face cancer has infected the population of Devils and has downgraded them to "endangered". The frequent fighting between Devils allow the cancer to be spread by face wounds to different individuals, the disease has nearly a 100% mortality rate, as it interferes with feeding in late stages and leads to starvation. Their low genetic diversity helps facilitate the spread of the transmissble cancer among members. The situation is serious enough that some estimates say they may be extinct within the decade. To read more, check out the official website to save the Devil, as sponsored by the Tasmanian government and the University of Tasmania.

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.

Energy efficiency, cars, and CAFE

Posted by tigerhawkvok on September 11, 2009 18:08 in General , politics , energy

I was thinking today about automobile mileage standards, and like nine in ten Americans, I believe in increasing fuel standards.

Recently, Obama pushed for an increase in standards — large by American standards, but the 2016 goal will be 10 MPG behind Europe and Japan's 2008 standard:

On May 19, 2009 President Barack Obama proposed a new national fuel economy program which adopts uniform federal standards to regulate both fuel economy and greenhouse gas emissions while preserving the legal authorities of DOT, EPA and California. The program covers model year 2012 to model year 2016 and ultimately requires an average fuel economy standard of 35.5 miles per US gallon (6.63 L/100 km; 42.6 mpg-imp) in 2016 (of 39 miles per gallon for cars and 30 mpg for trucks), a jump from the current average for all vehicles of 25 miles per gallon.
Source: Wikipedia.

So, throwing my voice into the veritable shouting match, this is what I'd do to increase the standards in a realistic way:

  1. Increase the 2016 fleet-average goal to 40 MPG.
  2. Based on current CAFE standards, and the 2016 goal standard, fit 2010 — 2015 standards to intermediates (linear)
  3. Beginning in 2017, institute an annual increase of 2 MPG in standards, with this increase to be re-evaluated every ten years, or an automatic re-evaluation if more than 75% of vehicles fail to meet the standard for 5 consecutive years. This will prevent increases from exceeding technological ability.
  4. For every commercial vehicle that falls short of this goal, a state/federal tax of $1000/MPG (rounded up, so 0.1 MPG -> 1 MPG) is imposed on the vehicle up to a faliure of 25%. Further faliures are taxed $2000/MPG, rounded down (0.8 MPG -> 1).

    This heavily penalizes vehicles that are "gas guzzlers". Thus, an 18 MPG car in 2016 fails by more than 25% of 40 MPG (30.00). The first 10 MPG is penalized $10,000, and the next 12 MPG is penalized $24,000, for a total of $34,000 in taxes. In 2016, it is completely unreasonable to have any car whatsoever at 18 MPG, but a rich person (the sort of person that buys a Hummer already) will pay for it in taxes.
  5. Cars that exceed this target gain a $500 tax credit at the dealer per 25% (compounded) they exceed it by.

    So, for example, the 2010 model Prius gets 51 MPG best. This is better than 25%, so gains an immediate, at-the-dealer $500 rebate. The Chevy Volt, however, if it actually gets the 230 MPG rating, would get a [50, 62, 78, 98, 122, 153, 191, < 238] 7*$500 = $3,500 instant rebate at the dealer. These aren't back-breaking to the state or national government rebates, but they'll help a lot in keeping interest up in these hybrids.
  6. These standards are based on the highest EPA rating given to a specific car with a unified standard.

I think measures like this could go a long, long way toward encouraging efficiency in the auto market, and decreasing tailpipe emissions. While many of these will be moved to power and manufacturing plants, better capture and conversion systems, in addition to the overall efficiency at the end of the car and at the plant, will result in net lower energy usage and fewer emissions. As a byproduct? More energy security, too!

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