Missouri Science Standards: Where We Rank

The Fordham Foundation's report on science standards has been released. The report, The State of State Science Standards 2005 examines how well, or poorly, states are doing in creating science standards for education.

Missouri was given a "C". The evaluation for Missouri is available here. The grade seems to be due to inconsistencies in application, but judge for yourself.

In the meantime, Missouri's own underminer of science education, Cynthia Davis, is at it again:

“I think Kansas is doing the right thing,” said Rep. Cynthia Davis, a St. Louis County Republican who last year filed a bill that would have required biology textbooks to include “critical analysis of origins.”

Davis’ bill got a hearing two weeks before the legislative session ended and never advanced out of committee. Davis, who plans to file similar legislation for the 2006 session, hopes next year will be different.

“I think its opportunity to be successful is greater every year because people are becoming more informed and taking time to read and understand,” she said.

*snip*

“You look at Galileo who was criticized as being a heretic because he thought the earth revolved around the sun instead of the other way around,” she said. “There are doctors who were ostracized because they washed their hands in between patients. Today we know that sometimes you’ve got to change with the times.”

Um, Cynthia, dear, would that be evolution?

Of course Missouri is different from Kansas:

Perhaps the most obvious reason anti-evolution forces have had a harder time in Missouri is that its state board of education is appointed by the governor. The eight members serve eight-year terms, with one member’s term expiring every year.

Missouri’s education board sets broad education standards. But it is up to local school boards to set policies on textbooks and what is taught in the classroom, officials with the Department of Elementary and Secondary Education said.

Missouri lawmakers, though at times sympathetic to intelligent design arguments, have been reluctant to mandate what is taught in the classroom.

“If you start in one area and start mandating what’s in textbooks on the state level, then where do you stop?” asked Senate Majority Leader Charlie Shields, a St. Joseph Republican.

The bad news:

Though Shields said he believed the theory of evolution “is in question,” he prefers to leave such issues to local school boards. That also has been the approach favored by Gov. Matt Blunt, who earlier this year indicated he would at least consider intelligent design proposals.

“I believe evolution is a theory, and there are other acceptable theories to explain the creation of Earth and the creation of man,” Blunt said. “I generally believe such decisions are best left to school districts.”

Of course, giving Blunt's low popularity that may be a blessing in disguise as people might not go for it because he wants it.

There is hope:

Dudley, though, said intelligent design proponents are trying to inject faith into science. A self-described conservative Southern Baptist, Dudley said she believes in God as a creator — but a creator who uses the process of evolution.

“There’s what I believe as a Christian,” she said, “and then there’s what I can teach in my classroom.”

Is it any wonder we get a "C"?

And speaking of Kansas Red State Rabble is reporting the Professor Mirecki has resigned as chair of the Religious Studies Dept. at KU.

Olduvai George

I've not really covered this since PZ Meyers and Carl Zimmer, among others, have mentioned it on their blogs. However, I feel flattered that an artist of quality of Carl Buell would link to me so I have to return the favor. I have added Olduvai George to my blogroll and would encourage you all to do the same. Also, visit his site, you will be richly rewarded.

Welcome to the blogosphere Carl!

Finally, Something Good Comes from Dembski

Namely, a link to this, which is hysterical!
What makes it even funnier is the thought of an ID proponent linking to a guy making fun of creationists and using that as evidence of a culture war?? Anybody see the irony?

Professor Mirecki Beaten

I first stumbled across this at Pharyngula. There is also a story at Red State Rabble who links to this story.

Apparently Professor Mirecki - the Kansas professor who was going to teach a religios studies class debunking ID - was assaulted earlier today. I guess since lost in the world of science, lost in Dover, and are losing in the court of public opinion they have resorted to other methods of supressing free speech. As Isaac Asimov was fond of saying 'Violence is the last refuge of the incompetent"

Pass the news on...

I'm Sorry, I Can't Resist...

I have, as you may have noticed, been following the 40,000 year old footprint story with keen interest. I realize, however, that we are ignoring the methodology that could settle the question for us. Yup, Intelligent Design. ID advocates are always trying to claim archaeology is all about detecting design and argue that archaeology could benefit from ID. Well, here is their chance to prove it! Dembski can run the thing through his design filter and tell us if they are footprints! Be a great coup. Perhaps someone with access can leave a comment at his site letting him know he's missing a wonderful oportunity. Giggle! Snicker!

I Fibbed

Apparently, I have a little more time to write a short post. I emailed the author of the press release about the way the British team's dating methods. His response was that C-14 was the main source of the British team's dates. He mentioned he wasn't familiar with with the other methods used so he asked Dr. Renne about them ans was told they were not as accurate as Ar/Ar dating.

Having said that, I am inclined to agree with alun and Abnormal Interests. I recently received the Nature article, from my good blog buddy Aydin at Snail's Tales, so as soon as I have had a chance to read it I will probably have more to say. Personally, I would like to see more proof that they are, in fact, footprints. Until then dating is irrelevant. Although, I will say that when this deabate is finally resolved, one way or the other, it will make a very instuctive example of how science operates.

Strange Behavior

By Blogger that is. I can log in and write posts but can't get to my site to respond to comments - of which there are several I would like to respond to. In the meantime, Mrs. afarensis needs the computer so you probably won't here anything from me till tomorrow.

Outrageous: Rape Victim Made To Pay

Check out the story here.
Totally apalling. This judge needs to be removed from the bench! You can also go here:

The Washington County District Attorney's Office declined to prosecute the case against the men. Robert Hermann, the county's district attorney, said prosecutors reviewed all the information and statements but didn't think they could prove a rape allegation.
Ted Naemura, the assistant city attorney who prosecuted the case, said the woman's false accusations were serious enough to lead to charges. The young men faced prison sentences of at least 7 years and a lifetime labeled as sex offenders. In addition, police spent considerable resources investigating the accusations.

So basically, a girl gets raped, the DA can't come up with enough evidence to prove it so he prosecutes the victim. Remind me never to move to Beaverton!

A Cure for Gassy Cows?

No, really! Scientist in the UK (those daffy Brits) are working on decreasing methane emissions from cows:

Cows belching and breaking wind cause methane pollution, but British scientists say they have developed a diet to make pastures smell like roses — almost.

“In some experiments we get a 70 percent decrease (in methane emissions), which is quite staggering,” biochemist John Wallace told Reuters in a telephone interview.

At least they didn't take the New Zealand approach:

In New Zealand the government in 2003 proposed a flatulence tax, with methane emitted by farm animals responsible for more than half the country’s greenhouse gases. The plan was ultimately withdrawn after widespread protests.

40,000 Year Old Footprints: Revisited

Something is bothering me about this story. Consider this quote (from the press release:

Renne determined the new date using the argon/argon dating technique, which reliably dates rock as young as 2,000 years or as old as 4 billion years. The British-led researchers, however, relied mainly on carbon-14 dates of overlying sediments. Carbon-14 cannot reliably date materials older than about 50,000 years.

This is incorrect. This is a list of the dating methods used by Dr. Gonzalez's team:

1)Accelerator Mass Spectrometer radiocarbon dating (AMS) was carried out on mollusc shells and organic balls at the Oxford Radiocarbon Accelerator Unit (ORAU) by Drs Tom Higham and Chris Bronk Ramsey of Oxford University.
2)Electron Spin Resonance (ESR) on a mammoth molar found in the Barranca Caulapan (Valsequillo Basin), was carried out by Professor Rainer Grün, Australian National University.
3)Optically Stimulated Luminescence Dating (OSL) on sediments and the Xalnene Ash was carried out by Dr Jean-Luc Schwenninger from Oxford University
4)Argon-Argon dating on the Xalnene Ash and overlying lava was carried out by Dr Simon Kelley, Open University.
5)Uranium series dating on animal bones from the Valsequillo Gravels was carried out by Dr Alistair Pike, Bristol University.



above is a schematic of the stratigraphy with locations were they took the samples and what type of method was used. For those who don't like drawings:

The results derived from different dating methods indicate that the Valsequillo gravels from the Barranca Caulapan area range in age from the Late Pleistocene, around 40,000 years ago, to the early Holocene, around 9,000 years ago. It is important to note that the Barranca Caulapan sands and gravels analysed were taken from strata geologically younger than the Xalnene ash layer in which the footprints were preserved.

The mammoth molar was dated at approximately 27,000 years old using ESR; while an organic ball in the gravels was dated at 25,000 years old using C14. These materials were transported and incorporated into the fluvial sequence of the Barranca Caulapan.

However, the mollusc shells are in situ in the deposits and were dated between 27,000 and 39,000 years old using C14.

Attempts were made to date the Xalnene ash using Argon-Argon dating but the amount of potassium present in the ash was too low for a reliable age determination.

More successful was the Optically Stimulated Luminescence (OSL) method to date quartz crystals found in baked lake sediments incorporated into the ash (as xenoliths) and secured an age of around 40,000 years. The sample was taken from the working quarry, 200m south from where the footprints were found.

I'm in the process of tracking down the Nature article to see what it says, but certainly this press release mischaracterizes the work of Dr. Gonzalez and his team. I'm wondering if a correction needs to be issued on this, but I'm not sure if one can actually issue a correction on a press release. I'm debating emailing the contact on the press release, anybody have any advice on the subject?

Platynereis dumerlii, Acropora millepora and the Human Genome: Part Three

There are two issues. One is that a large number of genes in Drosophilia melanogaster and Caenorhabditis elegans are highly modified. Another is that, as mentioned in previous posts, D. Melanogaster and C. elegans may be more closely related to each other than to vertebrates. The two combined suggest that comparisons based only on these organisms could be misleading. What about using a different outgroup, such as the Cnidaria? The Cnidaria are regarded as a sister group to the Bilateria (that is, those organisms displaying bilateral symmetry). Results of several such comparisons are interesting. For example, the paper linked to above focused on Acropra millepora - a type of coral considered to be a basal metazoan - and discovered striking asymmetries in the frequency of gene loss across the Bilateria. More specifically, the study noted that extensive gene loss had occured in Drosophilia and Caenorhabditis while vertebrates seemed to conserve genes. In other words, vertebrates in general, and humans in particular, share more similarities with Acopora than flies and nematodes do. How is this possible? The divergence times between theses groups extend quite a ways back and one would expect humans to share few sequences in common with Acropora. According to the study:

Although a close relationship between coral and human sequences is superficially surprising given that the cnidarian and bilaterian lineages are thought to have diverged in deep Precambrian time [22], this is largely a consequence of the relative pace of change in the model invertebrates. The greater divergence in D. melanogaster and C. elegans sequences is unlikely to reflect uniform rates of change over long time periods; rather, rapid genome change is likely to have occurred recently (and probably independently) in these organisms and be associated with intense selection for small genome size, rapid developmental rates, and the highly specialized lifestyles of the fly and worm. Although D. melanogaster had the previously reported fastest rate of sequence change, the genes of C. elegans are evolving even faster [23 and 24], and genome rearrangements are occurring approximately four times faster in the worm than in the fly [24]. Typically long branch lengths in phylogenetic analyses (see Figure 2) support the idea that many D. melanogaster sequences are highly derived relative to their coral and human counterparts. This is also true of many C. elegans sequences [23 and 25]. (the numbers are to references in the original article - afarensis)

A similar study involving Platynereis dumerlii comes to much the same conclusion. PZ Meyers has a explanation of this bit of research.
This result, that humans are evolutionarily slow has been portrayed as a bit of a surprise, but is something that has been in the works for awhile. For example, as early as 1992 it was known that insulin genes in humans and apes evolved at a slower rate than in monkeys. The phenomena, called the "Hominid-rate-slowdown hypothesis". was first suggested by Goodman in a 1961 paper entitled "The Role of Immunochemical Differences in the Phyletic Development of Human Behavior" (published in Human Biology) and led to papers being published on the subject up to the present (here and here for example). Which, of course, indicates evolutionary biologists need to pay more attention to anthropologists!
The larger point to these posts is that scientific research raises more questions than it answers and leads us down new, unexpected, paths. I started this series looking at the relationship between nematodes, flies and humans and followed a path to recent rapid genome chang in flies and the hominid slowdown hypothesis. HAd we gone back in time rather than forward we would have ended up talking about the origin of methanogenesis and phototrophy or or the rise of multicellular life.

The FBI and CIA: Protecting You from Terrorism

Worried about terrorism? Don't worry the FBI is on the job:

FBI officials mishandled a Florida terror investigation, falsified documents to try to cover mistakes and retaliated against an agent who complained about the problems, The New York Times reported in its Sunday edition.

Citing a draft report of an investigation by the Justice Department's inspector general's office, a copy of which was obtained by the newspaper, the Times said that in one instance correction fluid was used to alter dates on three FBI forms to conceal an apparent violation of federal wiretap law.

*snip*

The FBI was considering initiating an undercover operation and asked an agent with expertise in the area to take part.

But the agent, Mike German, soon told FBI officials the Orlando agent handling the case had "so seriously mishandled" the investigation that a prime opportunity to expose a terrorist financing plot had been wasted.

The report however concluded that "there was no viable terrorism case."

*snip*

The report also said that after German began making his complaints about the case, the head of the FBI undercover unit, Jorge Martinez, froze him out of teaching assignments in undercover training and told one agent that he would "never work another undercover case."

Ain't the PATRIOT Act wonderful?

The CIA is doing a great job as well:

Coats informed the German minister that the CIA had wrongfully imprisoned one of its citizens, Khaled Masri, for five months, and would soon release him, the sources said. There was also a request: that the German government not disclose what it had been told even if Masri went public.

*snip*

The Masri case, with new details gleaned from interviews with current and former intelligence and diplomatic officials, offers a rare study of how pressure on the CIA to apprehend al Qaeda members after the Sept. 11, 2001, attacks has led in some instances to detention based on thin or speculative evidence. The case also shows how complicated it can be to correct errors in a system built and operated in secret.

Detaining people based on thin or non-existent evidence...almost impossible to correct errors...anybody getting warm fuzzies over our governments ability to catch the bad guys?

The CIA, working with other intelligence agencies, has captured an estimated 3,000 people, including several key leaders of al Qaeda, in its campaign to dismantle terrorist networks. It is impossible to know, however, how many mistakes the CIA and its foreign partners have made.

You should really read the rest of this article, it's scary as hell.

Casey Luskin: Working in the Quote Mines

Casey Luskin discusses chromosomal fusion. I'll be doing a post on this later, but in the meantime I can't resist pointing this out:

One way around the problem in (1) is to find a mate that also had an identical chromosomal fusion event. But Valentine and Erwin imply that such events would be highly unlikely:
"[T]he chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event."

(Erwin, D..H., and Valentine, J.W. "'Hopeful monsters,' transposons, and the Metazoan radiation", Proc. Natl. Acad. Sci USA, 81:5482-5483, Sept 1984)

From the article:

Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile; the chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event.

Hysterical! Luskin is talking about chromosomal fusion and claims Erwin and Valentine say it's unlikely, but Erwin and Valentine are talking about mutations of structural and regulatory genes - not necessarily the same thing! Even more interesting is the gist of the article itself. Erwin and Valentine's article is actually concerned with the origin of morphological novelties - specifically whether "...microevolutionary substitutions involving structural genes..." can be considered a plausible mechanism for morhphological novelties. They say no. Then they suggest an alternative based on horizontal trnasmission of genes via viruses:

Mutations associated with viruses that preferentially insert at specific loci are hardly random; furthermore, a population infected by such a virus would possess numbers of individuals with frequently identical mutations.

A little later in the same article:

Viral transmission of genetic material may also involve the horizontal transmission of new genes or gene variants, enabling them to spread through a population in much less time than fixation requires.

Both of which totally undermine the point of Luskin's quote. Even more interesting is their application of the idea of horizontal and vertical transmission of genes to the Cambrian radiation - but I'll leave that to the reader.

Transitions: The Genetics Page

Two more parts of Evolgen's series on "Detecting Natural Selection" are up at Transitions: The Genetics Page. Check them out and don't forget to visit Evolgen

Archaeopteryx and the Raptors

National Geographic News and New Scientist are announcing the publication of a new archaeopteryx fossil - pictured below.


Actually, it's not so much new as previously unavailable:

Nine previously known specimens of archaeopteryx have led palaeontologists to conclude that birds probably evolved from small meat-eating dinosaurs, and are closely related to the dromeosaurs, a group that includes the velociraptor. Yet precisely how archaeopteryx is related to the raptors has remained unclear – key pieces of these previous specimens are missing.

But the newly revealed fossil appears to fill in many of the gaps. The specimen comes from the private collection of a worker at the Solnhofen limestone quarries in Germany, where the first archaeopteryx fossil was discovered. It has remained unknown to science until its owner's death, when the new owner made it available to scientists at the Wyoming Dinosaur Center in the US.

The interesting thing about the fossil is that, unlike previos specimens, this one has feet.


What makes this interesting is that:

Archaeopteryx, the fossil shows, had a hyperextendible second toe. Until now, the feature was thought to belong only to the species' close relatives, the deinonychosaurs.

*snip*

Contrary to all previous reconstructions of Archaeopteryx, the hind toe of the new specimen is not completely reversed to form a "perching" foot as it is in modern birds.

The researchers believe that the fully reversed hind toe in other Archaeopteryx fossils shifted during preservation and never existed in the live animal.

In the new fossil, the foot looks more like that of the four-toed foot of Velociraptor and its other nonwinged theropod relatives. The specimen clearly lacks a reversed toe.

Because Archaeopteryx lacked this stabilizing toe, it almost certainly did not habitually perch in trees.

*snip*

The shape and articulation of other bones of the new specimen also help tie Archaeopteryx to the theropods.

The bones of its hind legs, for example, have played an important role in the dispute about bird ancestry. The new Archaeopteryx specimen shows a clearly visible hind leg bone structure that is identical to that of theropod dinosaurs.
Archaeopteryx, therefore, is closely related to the theropods. This in turn means that theropod dinosaurs are the ancestors of the modern birds that followed Archaeopteryx.

The find, according to Mayr, "not only provides further evidence for the theropod ancestry of birds, but it blurs the distinction between basal [the earliest] birds and basal deinonychosaurs," their fearsome-clawed ancestors.

"I do think that the question of a theropod ancestry of birds can now be considered settled once and forever," Mayr said.

There is a dissenting view however:

Mayr told New Scientist that there are no unique traits shared by archaeopteryx and other early bird-like fossils that are not present in dinosaurs. This would either mean that archaeopteryx cannot be classed within the same evolutionary group as birds or that this group needs to be redefined.

But Peter Makovicky of the Field Museum of Natural History in Chicago, US, says those results are shaky because Mayr's group considered only three bird-like creatures; archaeopteryx, confuciusornis and a primitive bird called Rahonavis, that lived much later.

In October 2005, Makovicky carried out a separate study that links Rahonavis directly to the dromeosaurs and suggests this species may have evolved flight separately from archaeopteryx and other birds. Makovicky told New Scientist he found no change in the shape of his evolutionary tree when he added the new traits found for archaeopteryx.

Mayr's study will be published in tomorrow's edition of Science... (sigh)

Dear Kitty has a post on the subject as well (and I'm sure The Hairy Museum of Natural History will be doing a post on it!)

40,000 Year Old Mexican Footprints: Update

Abnormal Interests has an update on the story. He also has an interesting take on Dembski's comment about the intelligent designer. Check them out!

Added Later: Proponnents of the 40,000 year old date have responed here:

It is clear that the dates reported by Renne’s group need to be replicated and independently confirmed. This is important because we applied the Ar-Ar method as well and had no good results, and concluded that they were not reliable. Also, it is not clear from where exactly they took their samples and which fraction was dated. We took our samples directly from the footprint horizons.

Even if we are wrong and the Xalnene ash is indeed 1.3 million years old, as suggested by Renne’s et al, that is not automatically a reason to disregard interpretation of the features reported as “footprints”, simple because they are not in agreement with the established models for the settlement of the Americas.

This highlights the desperate need of further dating with different methods on the deposits in the Valsequillo Basin to make sure they make sense and to be able to establish a reliable chronology, considering the palaeontological and archaeological evidence included in them. This is exactly what we are doing at the moment with a grant from NERC (Natural Environment Research Council), during the next three years.

What we have ahead is a new era in the scientific research of the archaeological evidence found in the Valsequillo Basin and that is what Science is all about.

Our own dating efforts up to now and arguments explaining why we interpret the trace fossils preserved on the ash as human footprints will appear in the January issue of the Quaternary Science Reviews.

Interactive 3-D Mouse Brains

You will find them here. You do have to register. Cool Stuff!

Platynereis dumerlii, Acropora millepora and the Human Genome: Part Two

Let's approach this from another direction we can look at nematodes and compare their genome with flies and humans. So researchers compared more than 100 nuclear protein alignments. The original study used the 18S rRNA. In nematodes this has particularly long branches, indicating an increased rate of sequence change. What this means is that, basically, nematodes have an increased rate of nucleotide substitution which creates a longer branch phlogenetically - in essence high rates of sequence change give the appearance of greater age and are pushed further down on the phylogentic tree (called long branch attraction).



Which is where they are placed in the coelomata hypothesis. Supporters of the alternative view argues that this is because of long branch attraction. The writers of the papers linked to above reasoned that if nematodes cluster at the base of the phylogeny because of long branch attraction then the best place to find support for the alternative, Ecdysoza, hypothesis is in slowly evolving proteins. Their results actually supported the Coelomata hypothesis - that is that humans are more closely related to flies than nematodes. They suggest that the linkage of nematodes with flies is an artifact of of analysing only one gene.
But there is another wrinkle, which I will discuss tomorrow.

My International Readers

There is a post over at Pharyngula comparing international readership on liberal vs. conservative blogs . Here are my stats. I'm happy to note that 44% of my visitors came from overseas.



56 56.57% United States United States
7 7.07% United Kingdom United Kingdom
6 6.06% Denmark Denmark
6 6.06% Canada Canada
4 4.04% Ireland Ireland
4 4.04% Australia Australia
4 4.04% Netherlands Netherlands
4 4.04% Czech Republic Czech Republic
2 2.02% Taiwan Taiwan
2 2.02% India India
1 1.01% Sweden Sweden
1 1.01% Switzerland Switzerland
1 1.01% Puerto Rico Puerto Rico
1 1.01% Germany Germany

You Know You Have Been Reading Too Much Biology When...

You know you have been reading too much biology when everytime you get an idea for a post you discoverPZ Meyers has already written a post on the same topic! I started on mine yesterday, got lazy and decided to turn it into a two parter - that's what I get for procrastination! The sad thing is, I have been reading a lot of anthropology lately (I'm currently reading L.S.B. Leakey's "By the Evidence")but for some reason I keep posting on biological topics. As soon as I get over being befuddled by it, I'll finish that post becuase I'm actually going somewhere slightly different with it. In the meantime I think I'll try to forget about biology by immersing myself in Walker and Leakey's "The Nariokotome Homo Erectus Skeleton" I'd like to see a post on that over at Pharyngula!