VOX RE-DUX

Everyone's favorite libertarian character (and evolutionary skeptic) Vox Dei is up to his old rhetorical tricks in a recent post, wherein he reviews an article at PhysicsBlog which is turn is based on a paper by Mark Pagel and his colleagues at the University of Reading which was published earlier this month in Nature.

Now, the original paper in question uses phylogenetic trees to compare different models for how speciation occurs, and concludes that : "....it is the natural selection element that has even less reliable scientific evidence to support it than speciation or the concept of evolution itself."

I find this latest offering from Vox to be delightfully 19th century. Vox, you are gloriously, spectacularly wrong in multiple ways on this post. Though, in your favor, you are taking reportage in an on-line 'physics' source at face value, reportage that does a clumsy and misleading job of conceptualizing another discipline.

The big problem here is in the opening paragraph: the Red Queen hypothesis proposed by Leigh Van Valen is not strictly speaking a hypothesis about how speciation occurs, but rather about the way evolutionary arms races shape evolution. Van Valen predicted that speciation should in fact be relatively constant, and that either stasis or anagenesis should be more common than cladogenesis. It is true that Darwin (not necessarily Van Valen) tended to think entirely in terms of gradual change, changes that (in his words) would be 'insensible'. As it turns out, Darwin was wrong on both points. That hardly counts as evidence that natural selection does not occur, or that the former can not lead to new species.

Now, Pagel and company have apparently applied this 'Red Queen hypothesis' rather broadly as a term for a model of speciation, but when I read the description of the model provided in the article, it doesn't sound like a description of Leigh Van Valen's 'evolutionary arms race' promoting stasis and anagenesis over cladogenesis. It sounds like a description of phyletic gradualism, which in its strictest form is not consistent with modern evolutionary theory. So, from my point of view, the article Vox cites has Pagel et al. are said to be making claims against a theoretical model, but one which is something of a 'Straw Man'.

In fairness to Pagel et al, I don't think the reportage is very good at the site Vox cites. Here's another discussion of the same paper. Would you be surprised to learn that they directly cite Pagel, and that Pagel comes to a slightly different conclusion than was previously reported? It turns out that Pagel's group actually endorses the Red Queen hypothesis of constant speciation rates, but proposes a novel reinterpretation of the data uncoupling the former from phyletic gradualism.

Anyway, rapid anagenesis within an isolated lineage can occur as a result of natural selection. As it so happens, just this evening I saw the latest episode of NOVA .


It featured a very straightforward demonstration of natural selection acting on a population of pocket mice, wherein a rare mutation conferring protective coloration in a lava field gradually becomes more widely distributed, as in the case of the peppered moth. You can watch OR download a video about the evolution of pocket mice from HHMI, here:


What makes this example particularly robust is that scientists who studied the pocket mouse populations in nature were able to determine precisely which coding genes (exons) were switched 'on' and 'off' by mutations affecting the action of regulatory genes (introns) to make the change, and how the different lineages flourished in response to different environmental pressures. In other words...natural selection!

The program ('What Darwin Never Knew') takes many of its clearest examples straight from Sean Carroll's book 'The Making of the Fittest'. I might add that the particular set of molecular 'switches' studied in pocket mice appear to be conserved across many taxa, and are typically employed in setting external coloration and pattern. A general discussion of genetic switches can be found in this interactive page from NOVA.

Want more? Check out this interactive series of pages, where you can look for start and stop codons, molecular switches, ancestral and hitchhiking segments of DNA, and other details as you 'Explore a Stretch of Code'. This is a bit older (2001-02) but still very 21st century.

Now, why do I refer joshingly to Vox's post as '19th century'? Because Vox is actually espousing a viewpoint similar to that of Darwin's contemporaries, who were persuaded by the Origin's presentation of evidence for 'descent with modification', but had serious reservations about Darwin's proposed mechanism, natural selection. Today, the situation is notably reversed amongst most creationists, who typically admit natural selection occurs and that evolution of a sort occurs within a lineage (anagenesis), but deny the large-scale 'macroevolutionary' pattern of cladogenesis and the descent from a common ancestor which is implied.

I've posted something similar in the comments section on Vox's blog and emailed him, so it would not be surprising to see the two of us go back and forth on this.

THE PRAIRIE HOME CURMUDGEON

I apologize in advance for being a bit contentious in the holiday season.

But this ridiculous piece by the 'humorist' Garrison Keillor so plainly toys with anti-Semitism that it cries out to be taken seriously. Summary for those not interested in reading the whole thing: Keillor wants non-Christians (such as Unitarians and Jews) to not appropriate anything like the traditional Christmas vibe of his own upbringing, reaching a peak of invective with this rant:

Unitarians listen to the Inner Voice and so they have no creed that they all stand up and recite in unison, and that's their perfect right, but it is wrong, wrong, wrong to rewrite "Silent Night." If you don't believe Jesus was God, OK, go write your own damn "Silent Night" and leave ours alone. This is spiritual piracy and cultural elitism and we Christians have stood for it long enough. And all those lousy holiday songs by Jewish guys that trash up the malls every year, Rudolph and the chestnuts and the rest of that dreck. Did one of our guys write "Grab your loafers, come along if you wanna, and we'll blow that shofar for Rosh Hashanah"? No, we didn't.

Ick.

Speaking as a Christian myself, I would like to know how anything Unitarians or others might do with Christmas tradition invalidates my own experience? Or, for that matter, how innocuous popular songs written by Jews or non-Jews makes the Incarnation less, well, incarnate. "Spiritual piracy?" Please. Real Christians know that God is always with them, and who wrote the tune shouldn't be that important.

I bet Mr. Keillor has enthusiastically sung 'Hark the Herald Angels Sing" many times without troubling himself over Felix Mendelssohn's family history. Should the Eastern mysticism cultivated by Gustav Holst cause us to excise 'In the Bleak Midwinter" from the hymnal? Do the Unitarians need to get permission from Mr. Keillor's approved theologian for adapting a song written in the 19th century for their needs, as part of worship? For crying out loud!

It seems to me that Mr. Keillor has learned the wrong lesson. The success of others does not make us failures, and there is something deeply unsettling about Mr. Keillor's willingness to take a cheap shot at non-Christians involved in holiday entertainment. The day that some enterprising Hollywood secular type has the stones to make an historically accurate film about Martin Luther, he might (as a Lutheran) have cause to cry 'foul'. The fact that some great Americans like Johnny Marks (Bronze Star in WWII) or Irving 'God Bless America' Berlin happen to have made a living penning holiday-themed songs with a wide appeal doesn't hurt me.

Why it bothers Mr. Keillor is a mystery to me.

HOLIDAY WISHES

In which two Evil Empires are united in cloying cuteness for all eternity:

Courtesy of my Comic Con buddy, James!

In all seriousness, in case you haven't heard, there is a merger afoot. Some shareholders have balked and launched legal missiles. Others no doubt are just waiting for their opportunity to vote it up or down . . . on New Year's Eve.

Perhaps we are nearing the dawn of a new era!

BULLARD TRIUMPHANT

On Friday, a 54-year quest ended for the Knights.

No, they didn't find the Holy Grail. But the Bullard High School football team did succeed in nailing down the Division I valley championship in football. And that is a very good thing not just for our school, but as some folk recognize, for Fresno Unified in general:

Athletes are generally above-average students, a fact that goes against the image of 'jocks' that many of us carry in our personal stereotype folder.

I've known some athletes who were not good students, and we have all heard or seen instances in which the rules are sometimes bent for the popular, the pretty and the precociously talented. But that doesn't actually describe most high school athletes, who are not necessarily more popular, pretty or pampered. Typically, in order to play, they have to perform---not just on the playing field, but in the classroom.

Athletes must adhere to a demanding schedule of practice, travel and competition in addition to all the other obligations of students. In general, it takes awhile for most students to be able to find the necessary balance to do that and maintain a decent GPA. A thletes who shine as freshmen are typically above-average in the life skills department out of necessity.

Anyway, I am proud to be associated with the team, its hard-working coaching staff, and the school. I hope that it will lead to our school once again attracting more players away from the border with Clovis and Central Unified, and inspire us to success not only on the field, or in the classroom, but in life. A kid who achieves the balance necessary to be a true student-athlete has done something you can't assess with a Scantron, but which is arguably more important for their future than a lot of the content in the state standards.

IN WHICH MY STATUS IS RESOLVED

Hmph. I guess I'm not an academic.

Another brilliant offering from Jorge Chan's strip Ph.D.

WHEREFORE EARTH SCIENCE?

I work for Fresno Unified (FUSD). In the past ten years, I have taught all four of the main sequence standards (Biology, Chemistry, Earth Science and Physics) in California, standards that have been in place without modification since they were adopted in October of 1998. You can get a list of all the science standards, by grade level, in this PDF file.

Now, as you might imagine, in order to satisfy the Biology standards, you have a course based on those standards, most typically called 'Biology'. And so I have taught courses called Biology, Chemistry, Earth Science and Physics, and I have taught them all at least twice. I would guess that I might be the only such teacher in Fresno County, and one of the few in the state, who can say that. What can I say? Jack of all trades, master of none, I suppose.

Anyway, I have an unusual familiarity with the standards. But I have never taught an Honors or an AP course, and so the question of which of my students might qualify for the University of California is not exactly my first priority. But circumstances of late have led me to think about this. The UC requires two years of laboratory science, but strongly recommends a third year. And so, in its wisdom, Fresno Unified mandates a third year of science of some sort in order to graduate.

This year I've been lumbered with teaching a course, however, that is not directly tied to the standards, an elective called 'Environmental Science' that will allow juniors and seniors who don't want to tackle Physics or Chemistry a way of earning a third year of science from FUSD, which requires one year of some sort of science beyond the two years mandated by the UC. Well, I have to ask: what is the point of that? Read this carefully: the UC only accepts Biology, Chemistry, Physics and their AP and Honors permutations as 'laboratory science.' That's right, the UC doesn't accept the other main standards-based course (Earth Science) at all! That is because (frankly) it is an inferior course. There are no prerequisites for Earth Science, whereas Biology kids must have passed or currently taking Algebra I (which is, in case you don't know, the number #1 grade-killer in high school).

So, poorly-prepared freshmen are put into Earth Science instead of Biology when the system works right, see...and the UC people know this, so they won't accept it as a laboratory science course. This means that, in order to get that recommended (if not required) third year of laboratory science, a kid who takes Earth Science as a freshman will have to take three additional science courses to qualify for the UC. Somewhere along the way, this led to a whole bunch of juniors opting out of standards-based courses entirely, because they often don't pass Biology the first time they take it. They haven't had much success in science, and they hear how hard Chemistry and Physics are supposed to be, and they punt.

Well, when a kid makes this choice as a junior, they are choosing not to be eligible for the University of California. So, under this circumstance, why treat them as if they still need to take a third year of science? It's not going to give them an advantage in applying to a CSU or a community college. What's the point?

If the point is to make sure they get that third year of science, then I say 'epic fail.' That's just so much 'eat your spinach because I said so' to me. Electives should be enrichment for those who want to take additional coursework in a given area, not a remedial program for people who struggled with past science coursework. Most of the students in my Environmental Science class would benefit more academically from some kind of performing arts elective, frankly.

If the point is to raise the overall science literacy of the population, then again I have questions. The emphasis on rote learning and factoids in order to finesse the standards-based tests works against real science literacy, which involves internalizing the process, practice and critical thinking skills used in science. That's a lot more important more than (say) knowing how many stars are in the Milky Way Galaxy (an actual standard in Earth Science). And, since all the electives we offer are in the life sciences, a student can actually graduate from high school without any general science knowledge in things like electricity, magnetism, changes of state, machines...in other words, exactly the kind of science literacy that people in trades and everyday life are likely to find most useful.

So why is this happening? Well, the short hand answer is standards mania. See, kids in an elective science course still have to take a standards-based test. They get three years of standards-based science, even if it's in a course (like Earth Science, or the elective I teach) that is not considered up-to-snuff by the UC.

That's why all our electives seem to be in the life sciences, because the Biology test is supposed to be 'easier' than the Chemistry or the Physics. Ecology? Environmental Science? Physiology? Zoology? All our juniors in these courses still take a science test, so (the thinking goes) let's make sure it's the Biology CST. Never mind that Biology is actually the biggest challenge to teach due to the combined depth and breadth of the standards, and that you can't actually cover all these standards well in a course that has a narrowed 'elective' focus. In fact, one of the biggest complaints Bio instructors make to one another is how difficult it is for them to cover all the standards in Bio. Ironically, from the teacher's point of view, it is quite a bit easier to cover all the material mandated by the state in the Physics and Chemistry classes! If that sounds hard to believe, remember, I've taught all these courses at least twice, and I know what I'm talking about here.

So what to do here? Under the circumstances, I think we need to rethink our sequence at Bullard. Most of these kids are not going to go to the UC, but all of them are going to be tested in science their first three years of high school. Science typically forms a small part of the API score (about six percent), but under the present system nearly half of the students are going to have no real physical science. Sorry, but if Earth Science doesn't count as a real science for the UC, how can we argue that kids who take it are getting a quality science course?

So, as the saying goes, catch-22. How to best serve the average students? If we send poorly-prepared freshmen into Bio, they tend to fail, fall behind and hate science. If we put them in Earth Science, they are getting a year of science credit with the district but they are essentially a year behind qualifying for the UC, and their chances of taking an AP science course are also significantly diminished. When we turn a third-year elective into a remedial class, we essentially tell that population that science is spinach. Oh, and while I'm on a roll here, my gut tells me that assessing the juniors with a test that's intended to go with a different course is a bad idea, no matter how we slice it. If kids need to take a standards-based test, they need to be in a standards-based course.

What we need is a course that will give freshmen credit with the UC for laboratory science, but which will nurture their curiosity and give them a chance to catch up academically. I don't know if that is really possible, because the UC and the CST's are ultimately not all that well-aligned. None of this would matter were it not for the fact that California (like most states) is so addicted to federal education dollars that they must comply with NCLB.

EUGENIE SCOTT VIDEO, PARTS 1-?

Here's the opening segment. I'm going to have to split the second segment into two parts in order to get them on YouTube, so that may have to wait until tomorrow:

GENIE!

WOW.....

So, like, we had a really big crowd for Dr. Scott's talk on Wednesday evening:



As it turned out, I was sort of drafted at the last minute to tape Dr. Scott's talk (with her permission!) since I had brought my little Flip video recorder. All praise to the Generator Of Diversity, Madhu was able to loan me a tripod, or else I really wouldn't have been able to enjoy the talk. I couldn't video the whole deal with the Flip's limited hard drive, but Madhu also recorded the audio, which we hope to podcast.



Who knows? We may be able to combine the audio, what video I have and the Power Point and make a pretty slick little deal. But, seriously, while I love my Flip, the resolution is pretty low and I am starting to wonder what it's going to take for me or some other local science geek to invest in a better video setup for these kinds of events. I'd like to come up with some one-size-fits-all technology that would connect to any presenter's laptop, automatically stream the images of their Power Point, and record their audio to hard disk. Any thoughts, gentle reader?

Here's a brief (and probably incomplete) outline of Dr. Scott's talk:

1) Introductory remarks, the image of 'monkey to man', through presentation of the evidence for descent with modification (Darwin's original phrase), which is to say, evolution from a common ancestor

2) Exploration of the nature of science, drawing on an idea of the physicist James Trefil:



(click on the picture to read the introductory chapter of Dr. Scott's book 'Evolution and Creationism' )


3) The 'Pillars of Creationism'

4) The Creation-Evolution Continuum

5) A brief discussion of the role played by NCSE in defending the teaching of evolution.

Anyway, in a few days I'll start releasing segments of the talk here as YouTube thingies.

I'M THANKFUL FOR . . .

Eugenie Scott, who will be appearing in Fresno on Dec. 2nd (Wednesday), and who does such an important job really well.

Bringing Dr. Scott is a nice way to finish out the 2009 bicentennial of Darwin's birth and the 150th anniversary of the publication of the Origin of Species, and bringing Dr. Scott to Fresno is a bit of a coup for my colleagues at CSU Fresno. The Consortium for Evolutionary Studies ("Darwin's Bulldogs") at CSU Fresno is presenting to special lecture along with the Tri-Beta Biology Honors Club, the Noyce Scholars Program, the Natural Sciences Student Club, and Associated Students.



I will be at this event, with bells on!

FOR WHAT PURPOSE, THANKSGIVING?

I get a variety of views in my mailbox. Here, for example, are the thoughts of that great bear of burden, Newt Gingrich. Short version: let's remember that the purpose of Thanksgiving is to give thanks to God. Well...duh. But Newt goes a bit farther, and seems to miss the fact that going farther creates an obvious conflict. Right after acknowledging that not all Americans are Christians, he seems to blithely assume that even the non-Christians believe in something not just like 'God', but the God of Washington and Lincoln. Hard to believe the guy was a college professor.

Then, there is Jorge Chan's take from Ph.D. (Piled Higher and Deeper):

There's also the bracing honesty of Charles Barkley, who favorably compares Thanksgiving to the greed of Christmas in an extended rant about the need to lose weight. One gets the impression the 'Round Mound of Rebound' would tell the prof in Ph.D to take a long walk off a short pier:






Finally, check out PZ's subtly-conflicted view: Time off with the family and friends, he's OK with it. Praying to an imaginary being, not so much. But...what if the whole point of the holiday, as (ugh) Newt Gingrich says, is to give thanks to some imaginary being or another? Ack! Must reclaim holiday time in name of non-belief! Like I said, conflicted!

SOME SMALL COMFORT: MILLER'S ON THE CASE

You can watch CNN's coverage of the Ray Comfort-modified Origin giveaway going on this week on a video right here, featuring NCSE member Ken Miller doing what he does best, which is to say defending the science of evolution from the ignorami:


One of these days, maybe Kirk Cameron will actually experience some intellectual 'Growing Pains', but right now he's nothing more or less than the poster boy for faith-based ignorance:



Watch the opener of this video on Kirk and Ray's 'Way of the Master' YouTube channel. Kirk makes the following claims:

"Our kids can no longer pray in public."

"They (kids) can no longer freely open a Bible in school."

"The 10 Commandments are no longer allowed to be displayed in public places."

"The Gideons are no longer allowed to give away Bibles in schools."

All of these are false or misleading statements! Let's take the first two out for a test spin:

"Our kids can no longer pray in public."

"They (kids) can no longer freely open a Bible in school."

What? Kids can certainly pray in public, even in public schools. How could you keep them from doing it? They have more freedom to exercise their religious beliefs than either teachers or administrators do, in fact...which is the way it should be, given that the latter (including myself) are de facto agents of government. The state has no legal mandate to prevent students from praying silently in class, or reading their Bibles, or writing essays that touch on their beliefs, or publicly discussing their beliefs in an appropriate manner.

At the same time, the state must not endorse any particular student's exercise of their religious freedom, or allow anyone (teachers, administrators or students) to hijack the legitimate purpose of education to serve a sectarian agenda. Many Christians have a hard time understanding this, but if you give instructional time or extracurricular time on campus to present a student's beliefs without a clearly-stated and legitimate secular purpose, you are effectively privileging that student's beliefs in an educational setting. Not only does this risk alienating or offending others, not to mention the triggering of legal action, it also places a burden on that student which, in most cases, they would not seek on their own, and do not want.

How about this one:

"The 10 Commandments are no longer allowed to be displayed in public places."

Nuts. SOTUS has never issued a blanket ruling to that effect. Some government displays of the 10 Commandments have been ruled to have a legitimate purpose, and others have not. You can read about that here.

And, finally:


"The Gideons are no longer allowed to give away Bibles in schools."

This is deeply misleading, to the point of being disingenuous. It is true that giveaways during instructional time have been subject to legal challenges, as that practice constitutes a de facto endorsement of sectarian religion by agents of government. But the Circuit Court of Appeals in the most publicized of these cases (Lonney Roark v. South Iron R-1 School District) ruled that while said district could not give Bibles away during instructional time, that there would be nothing unconstitutional about preventing 'any printed material' approved the District Superintendent to be distributed to students on campus outside classroom time.

And, indeed, on my campus (and pretty much every high school campus in Fresno County), Campus Youth for Christ and Fellowship of Christian Athletes routinely hold meetings at lunch or after school, often giving away printed materials or showing faith-themed media on-campus. This is routine. If the Gideons wished to give away Bibles to students outside of class in Fresno County, they could certainly do so.

So, Kirk's claims are wildly inaccurate, sorry. As a Christian, as a parent, he can be expected to know a little something about this, so he's without excuse. The best we can say about this is that Kirk may not be deliberately lying, that he may be simply repeating 'facts' drummed into him by his fellow evangelicals.

But if I can't trust the statements of a Christian parent about the freedom of religious expression kids enjoy in the public schools---something he can be reasonably expected to know something about---why should I, or anyone trust anything he says about a scientific theory? The guy earned a high school diploma between takes on a sitcom. How much can he know about learning laboratory science in a public school setting, much less what should or shouldn't be taught? I'm sorry, but being pretty and personable (as aging child stars tend to be) does not qualify you to speak on science education.

MEDIA 'MINI-BLITZ'

OK, out of the blue yesterday around 5:00 I received a phone call from Gail Marshall, who produces radio programming at KYNO (1300-AM).

It was an offer to appear TODAY on the Bill McEwen Show around noon. Bill, a long-time Fresno Bee reporter and columnist, has a well-deserved reputation as straight-talking observer of the Fresno scene and (at times) a biting critic of what isn't necessarily right about it. Both I and my student collaborator Brianna Christoffersen will be Bill's guests at KYNO's posh digs. Cool!

Prior to appearing on the program, Central Valley Cafe Scientifique will have produced a press release for general distribution to the media talking up their organizing committee member's good fortune in winning a contest from a national magazine.

This will be a good opportunity to say some good things about my student, my school site and various ways the community can support science education. I will be talking up Cafe Scientifique, 'Darwin's Bulldogs' and the impending December visit of NCSE's Eugenie Scott, a coup for CSU Fresno's College of Math and Sciences. Funny how opportunities arise to 'spread the word' when you put yourself out there . . .

WOW!

BUT, if you don't catch the program live, there will be a podcast posted on this page. Thanks to everyone for supporting science in the Central Valley!

A MAJOR AWARD!

In 1983, Bob Clark (previously best known for a series of low-budget exploitation films) made the film for which he will doubtless be remembered long after offerings like 'Deathdream' or 'Children Shouldn't Play With Dead Things' go by the wayside. That film was 'A Christmas Story', an instant holiday classic based on the humorous memoirs of Jean Shepherd, about growing up in northwest Indiana.


The story revolves around the scheming of the 9-year-old protagonist, Ralphie Parker, to obtain the most fabulous of Christmas presents: "an official Red Ryder carbine-action 200-shot range model air rifle with a compass in the stock, and this thing which tells time."

A major sub-plot though, is another obsession, that of Ralphie's father, with entering newspaper contests to win "a Major Award". Mr. Parker (referred to in the film simply as 'the old man') eventually wins a risque lamp in the shape of woman's leg. The mother objects to its prominent display in the living room window, and eventually the 'Major Award' is ('accidentally?')destroyed and 'the old man' humiliated. Pride goeth before a fall of a lamp!

Well, I am tickled to say that I have also won a 'Major Award' whose cash value is virtually nil, but like 'the old man', its symbolic value is high: Discover magazine sponsored a contest, many moons back, as to who could make a video that explains evolution in two minutes or less. The contest was judged by PZ Myers of Pharyngula fame, and you can listen to his explanation of why he chose my entry here.




You can also view my 'Major Award'-winning video here!




Having seen the other four runners-up, I have to say that I lucked out a bit. The other four films are pretty good, and they did a far better job of presenting some of the details of evolutionary theory than my offering. Interestingly enough, Discover magazine had sponsored a similar contest in the past on string theory, and my initial attempts to make a video was much more like these past entries and the four runner-ups in this year's contest. I had begun work assembling stills and making animations along with some kind of narration to present the important concepts: variation, heritability, the struggle for existence, differential reproductive survival, etc. As you can tell by that thumbnail sketch of my first idea, my original scheme was rich in content and vocabulary.

But I ran into a problem. I knew that I could just squeeze in everything if I wanted to present a 'just the facts' approach, but that it would lack a certain warmth and accessibility. On the other hand, if I added some user-friendly asides for the audience, I seemed to always end up either talking at a breakneck pace or being 6-8 seconds too long. Since it was a cardinal rule of the affair that it be no more than 2 minutes, and since I was determined to produce something that stood out, I began to rethink my approach. Finally, it occurred to me that since I am an amateur musician with some talent and a lot of recording equipment, perhaps the best thing to do would be to take advantage of a skill set that most of the other entrymakers probably didn't possess. I wrote an original song, the (self-referential) lyrics of which are below:

THE EVOLUTION SONG

So you say there's a time limit,

you must explain in just two minutes,

Why there are so many different things alive?

But I can summarize: in just FIVE seconds:

Mutation, translation,

expression, occassioned

genetic variation,

population selection!

We're all members of populations,

We carry patterns of information,

We try to pass them on to the next generation,

New combinations: genetic variation!

The population's tend to thrive,

until they shoot past the food supply,

no surprise, it's a struggle to survive,

We can now ask why---some live and some die!

Mutation, translation,
expression, occassioned
genetic variation,
population selection!

EVOLUTION (changes occur)

EVOLUTION (it'll change the world)

EVOLUTION (the changes go on and on and on...!)

On and on and on and on and on and on and on!

If you've an advantageous gene,

and pass it on to your offspring,

They'll have the same advantage, too!

And they in turn, have more success

at reproducing, we witness

the fitness that's produced

when Nature gets to choose:

let's give Darwin his due!

Over time, the population

if left in isolation,

is free to go its own way, too!

Speciation! Something new,

and all the beauty and diversity

of the natural world!

EVOLUTION (changes occur)
EVOLUTION (it'll change the world)
EVOLUTION (the changes go on and on and on...!)
On and on and on and on and on and on and on!

Music and Lyrics copyright (c) 2009 by Scott Hatfield

A FEW DISCLAIMERS:

While I conceived the song, created some of the animations and storyboarded the narrative, I had help in realizing the video. My former student, Brianna Christophersen, was a senior in the spring of 2009 and working at our school's Mac lab in a video production class. She shot the video of me lip-synching the tune and edited the whole thing together using Final Cut Pro and some other tools. I couldn't have done this without her, and I am happy that she now has a 'Major Award'-winning production to go in her student portfolio.


Also, I should point out that by submitting my video along with my song I agreed to give Discover magazine the right to post the material. The video itself is not my property, and for the purposes of the contest I agreed to grant Discover magazine the rights to present this content. I am reproducing the lyrics to make my amateur efforts more accessible. Since Discover magazine is providing this content free on-line, I think it is 'OK' to post the lyrics here as long as there is no attempt to repackage the content without the permission of Discover magazine.
For my next trick where teaching evolution is concerned, I'll be taking courses while visiting the Galapagos Islands in the summer of 2010. I plan on taking a video camera with me and documenting all my thoughts and impressions while there, then turning that content into an online web site that can be used for science education. More free content, I guess, but that will help me write off the expenses of the trip for professional purposes.

CAFE SCIENTIFIQUE NEWS

Central Valley Cafe Scientifique is now meeting at Piazza Del Pane, near the intersection of Palm and Herndon, on the first Monday of each month in session:


Our new guidelines for attendees is that we encourage them to have dinner before the presentation, so that more attendees can fit into the patio area without the crowding of a full-course meal with plates, silverware, etc. We received very strong positive vibes from the nearly 80-odd folk who attended last month's gathering, and support for having dinner earlier and facilitating more room for the actual presentation.

Our next presentation, this Monday evening (Nov. 2nd), should be a hoot:



Here's the flyer for next month's speaker (click to enlarge, it's a fairly big image) . . .


Well, what can I say? It's science, open to the public and free! We encourage you to get a beverage or even a full meal, and most people do, but that is completely optional. Why not check it out, with or without appetite, and support science and science education?

NEIL SHUBIN ON 'YOUR INNER FISH'

PZ Myers has been live-blogging a conference at the University of Chicago that I would dearly love to attend myself, as it has a host of luminaries on the subject of evolution: historians, philosophers, and even scientists!

One particular talk described by PZ, by Neil Shubin, seems remarkably similar in outline to an address that Shubin gave in California a while back, which aired on UCTV this month. The whole thing can be viewed below. It's a hoot, enjoy!

MUSIC: A LEG TO STAND ON

Beauty and cruelty, and somewhere in between, humor of the gallows variety. That probably doesn't sound too ennobling, but it's how I often see the world. It is filled with beauty, but also cruelty, and we might as well laugh when we can. As the saying goes, no one is getting out of here alive.

So, at my church, the present choir director is a charming older lady who has worked more years than I have memories as a singer, choir director and voice coach. She has probably forgotten more about how to train singers than I have ever known, and while she is not particularly spry, she is surprisingly firm with her singers, and gets remarkable results in terms of balance and intensity with the older (and not particularly skilled) singers at my church. I doubt very much that I could achieve what she is achieving, and certainly I couldn't in her circumstance.

You see, she's old and has many ailments, the oddest being a left arm that has been so damaged by past illness that it is essentially a lump of flesh. And she's reached a decision that it has become more of a nuisance than it's worth, prone to infection, painful edema and a weight that must be carried. So, for purely practical reasons, she's getting rid of it. She's having it amputated. To commemorate the affair, she has been circulating a dummy arm and asking her friends and family to write notes on it, as if it were a cast, to transform the surgery from mutilation to liberation:

The many notes on it are homey and filled with corny attempts at humor. But there is no doubt that she is truly looking forward to it, even though she is already rather old and reduced in strength. The risk of surgery in her case is not negligible, but she wants to proceed. And by the time I am finished writing this, she will no doubt be out of surgery, trimmed of the impediment of her arm. I wish her the best.

Meanwhile, my former father-in-law, a musician of no small reputation, took a fall over the weekend. Yesterday, it became clear that he sustained some sort of head injury and he was admitted to his local HMO, where a concussion was in fact diagnosed. Given that he is on the rat poison Warfarin (relabeled coumadin as a blood thinner), he has been placed in ICU for observation while other means of reducing the effects of hypertension are put in place. Hopefully his stay will be brief.

Finally, I attended an Academy presentation last evening by our new President, Nancy Key, who is also the owner of Key Writing Concepts and a collaborator with the rest of us in Cafe Scientifique. Nancy's presentation started with a discussion of the possible selective value of musical ability within human populations, then segued to a discussion of her great pasttime, which is participating in a taiko drum troup. Her fellow taiko players then gave a colorful and raucous demonstration of some taiko pieces. It was exciting, and inspiring, and the drums they used were all the handiwork of one of the group members, who has fashioned them out of modified wine barrels:

Given all the turmoil some in my circle have experienced the last few days, the energy and joy radiated by this group was a real blessing. As Nancy speculated in her paper prior to playing for us, music is soothing because it allows to express and work out emotions that might otherwise be left neglected.

CATCHING UP

Well, I look at the blog and I see basically just one post for September and only one since that time, which was essentially a repost of a little trash-talking over at the baseball blog.

I've been quiet of late, for a lot of reasons:

First, and of greatest importance, I've been busy moving. We bought a new house, renovated it, then moved in the 95 percent of our possessions that have been in storage for a year. It's a nice house, but not as big as our previous residence in terms of storage, and so I've been having quiet a time with it. It's still not where I'm happy with it, as my studio gear is still largely unpacked and we are doing without a bedroom set after dolefully coming to grips with the fact that our former bedroom set was just too much for our bedroom (we sold it).

Also making me busy: the beginning of a new school year, and an additional prep for a course I've never taught previously, 'Environmental Science.' It's a third-year science course for the juniors and seniors who need a third year of science to graduate from Fresno Unified, but who don't want to essay either Physics or Chemistry. It's also different in that there is a public policy dimension to the course. The textbook is by a Ph.D who is also a lawyer, and there is an emphasis on how to communicate science to the public and policymakers. This is a bit different from what I'm used to. It would be nice to report that my 11th and 12th graders have the necessary literacy and math skills to make integrating this stuff a snap. Alas . . .

Also, I've been trying to resolve some technology problems at my school site. Administration giveth (new laptops for the classroom-yes!), but they also taketh away (not supporting teacher grade scales in the district grading program this year--boo!), and in some cases their best intentions haven't been realized. I am making an effort to not knuckle under to the pressure to conform. Hopefully the 'powers that be' in the district's technology wing will see the tender light of reason.

Another reason is that I'm soured on controversy at the moment, what with trying to get reestablished at work and at home. It's pretty clear from some stuff that's happened in the last two months that I have some creationists who have been trolling my blog trying to find some dirt on me. 'Anonymous' complaints and the like to my employer, baseless and unwarranted, petty harassment. Ordinarily that would just stoke my fire, but I'm just not in the mood right now. Maybe in a few months. One thing's for certain, when it comes time to teach Evolution I'll be in full bore. Cafe Scientifique is up and running again, too. Oh, and for you IDevotees out there, be advised that Eugenie Scott will be coming to Fresno and I fully intend to publicize it to the hilt.

So that's a lot of stuff, but I am starting to catch my second wind. In general, my Biology kids seem more engaged and higher-achieving than in the past, a lot of good things are happening at my school site and the house is starting to shape up. I'm getting a little bit more energy to do things, including this blog. So I hope my readers will still check in on me now and again...SH

There has been some discussion on this blog about the merits of a certain Royals pitcher. Would he really, as some suggest, have done better pitching for an AL East team than for the weak-hitting lineup fielded in Kansas City? Or would he, as others have claimed, had more wins but an inflated ERA?


To shed some light on this discussion, consider the stat known as 'adjusted ERA', or (more commonly) ERA+. Here's an explanation of the stat. Essentially, a major-league pitcher who pitches what their ballpark and league scoring environment predicts is given a score of '100'.


It turns out that since major-league baseball moved the pitching rubber to its present distance from home plate (60' 6") back in 1893, there have been 33 seasons in which a pitcher has achieved a score of '200' or higher, which would mean that they were one hundred percent better than their own league that yaer, or (gulp) more.

Five of those seasons belong to Pedro Martinez, four to Walter Johnson, three to Roger Clemens, two each to Christy Mathewson and Greg Maddux. Dutch Leonard, Bob Gibson, Addie Joss, Grover Cleveland Alexander, Lefty Grove, Cy Young, among others, one each. Essentially a list of Hall of Famers, with an occasional one-year outlier (Kevin Brown, Dolph Luque) who were stars in their day.


Oh, and one Zack Greinke, with the 29th-best season since 1893 and a score of 203. Here's his competition in the best-pitcher-in-baseball bragging rights, identifying all the big-league hurlers who had at least 25 starts and a sub-3.00 ERA in 2009 . . .

Chris Carpenter 185

Felix Hernandez 174

Tim Lincecum 173

Jair Jurrjens 160

Roy Halladay 157

Clayton Kershaw 147

Javier Vasquez 145

Jon Lester 139

Adam Wainwright 135

C.C. Sabathia 133

Justin Verlander 132

Josh Johnson 129

Matt Cain 124



As you may also know, ZG led the AL in least HR per 9 IP (0.4). But he pitched so many innings he gave up 11 dongs. Interestingly enough, all but two were solo shots. Here's the tale of the tape:

gordham beckham (solo shot)
carlos quentin (solo shot)
alex rios (solo shot)
andy marte (solo shot)
willy aybar (solo shot)
adam jones (1 on)
marlon byrd (solo shot)
a.j. pierzynski (solo shot)
mark reynolds (1 on)
lyle overbay (solo shot)
adam lind (solo shot)

I may as well bring on the really obnoxious comment now. He's going to get better, this Grienke guy. Justin Verlander will not lead the AL in strikeouts next year, nor will Roy Halladay lead in innings pitched, I reckon. He's only 25 years old, and he has less than a thousand innings in the big leagues. The odds are good that he'll be the dominant guy in the league for the next 4-5 years, Royals or no Royals. Kthnxbai.

THE SOCIALIST AGENDA

No, really. Here it is:

Prepared Remarks of President Barack Obama
Back to School Event

Arlington, Virginia
September 8, 2009

The President: Hello everyone – how’s everybody doing today? I’m here with students at Wakefield High School in Arlington, Virginia. And we’ve got students tuning in from all across America, kindergarten through twelfth grade. I’m glad you all could join us today.

I know that for many of you, today is the first day of school. And for those of you in kindergarten, or starting middle or high school, it’s your first day in a new school, so it’s understandable if you’re a little nervous. I imagine there are some seniors out there who are feeling pretty good right now, with just one more year to go. And no matter what grade you’re in, some of you are probably wishing it were still summer, and you could’ve stayed in bed just a little longer this morning.

I know that feeling. When I was young, my family lived in Indonesia for a few years, and my mother didn’t have the money to send me where all the American kids went to school. So she decided to teach me extra lessons herself, Monday through Friday – at 4:30 in the morning.

Now I wasn’t too happy about getting up that early. A lot of times, I’d fall asleep right there at the kitchen table. But whenever I’d complain, my mother would just give me one of those looks and say, "This is no picnic for me either, buster."

So I know some of you are still adjusting to being back at school. But I’m here today because I have something important to discuss with you. I’m here because I want to talk with you about your education and what’s expected of all of you in this new school year.

Now I’ve given a lot of speeches about education. And I’ve talked a lot about responsibility.

I’ve talked about your teachers’ responsibility for inspiring you, and pushing you to learn.

I’ve talked about your parents’ responsibility for making sure you stay on track, and get your homework done, and don’t spend every waking hour in front of the TV or with that Xbox.

I’ve talked a lot about your government’s responsibility for setting high standards, supporting teachers and principals, and turning around schools that aren’t working where students aren’t getting the opportunities they deserve.

But at the end of the day, we can have the most dedicated teachers, the most supportive parents, and the best schools in the world – and none of it will matter unless all of you fulfill your responsibilities. Unless you show up to those schools; pay attention to those teachers; listen to your parents, grandparents and other adults; and put in the hard work it takes to succeed.

And that’s what I want to focus on today: the responsibility each of you has for your education. I want to start with the responsibility you have to yourself.
Every single one of you has something you’re good at. Every single one of you has something to offer. And you have a responsibility to yourself to discover what that is. That’s the opportunity an education can provide.

Maybe you could be a good writer – maybe even good enough to write a book or articles in a newspaper – but you might not know it until you write a paper for your English class. Maybe you could be an innovator or an inventor – maybe even good enough to come up with the next iPhone or a new medicine or vaccine – but you might not know it until you do a project for your science class. Maybe you could be a mayor or a Senator or a Supreme Court Justice, but you might not know that until you join student government or the debate team.

And no matter what you want to do with your life – I guarantee that you’ll need an education to do it. You want to be a doctor, or a teacher, or a police officer? You want to be a nurse or an architect, a lawyer or a member of our military? You’re going to need a good education for every single one of those careers. You can’t drop out of school and just drop into a good job. You’ve got to work for it and train for it and learn for it.

And this isn’t just important for your own life and your own future. What you make of your education will decide nothing less than the future of this country. What you’re learning in school today will determine whether we as a nation can meet our greatest challenges in the future.

You’ll need the knowledge and problem-solving skills you learn in science and math to cure diseases like cancer and AIDS, and to develop new energy technologies and protect our environment. You’ll need the insights and critical thinking skills you gain in history and social studies to fight poverty and homelessness, crime and discrimination, and make our nation more fair and more free. You’ll need the creativity and ingenuity you develop in all your classes to build new companies that will create new jobs and boost our economy.

We need every single one of you to develop your talents, skills and intellect so you can help solve our most difficult problems. If you don’t do that – if you quit on school – you’re not just quitting on yourself, you’re quitting on your country.
Now I know it’s not always easy to do well in school. I know a lot of you have challenges in your lives right now that can make it hard to focus on your schoolwork.
I get it. I know what that’s like. My father left my family when I was two years old, and I was raised by a single mother who struggled at times to pay the bills and wasn’t always able to give us things the other kids had. There were times when I missed having a father in my life. There were times when I was lonely and felt like I didn’t fit in.

So I wasn’t always as focused as I should have been. I did some things I’m not proud of, and got in more trouble than I should have. And my life could have easily taken a turn for the worse.

But I was fortunate. I got a lot of second chances and had the opportunity to go to college, and law school, and follow my dreams. My wife, our First Lady Michelle Obama, has a similar story. Neither of her parents had gone to college, and they didn’t have much. But they worked hard, and she worked hard, so that she could go to the best schools in this country.

Some of you might not have those advantages. Maybe you don’t have adults in your life who give you the support that you need. Maybe someone in your family has lost their job, and there’s not enough money to go around. Maybe you live in a neighborhood where you don’t feel safe, or have friends who are pressuring you to do things you know aren’t right.

But at the end of the day, the circumstances of your life – what you look like, where you come from, how much money you have, what you’ve got going on at home – that’s no excuse for neglecting your homework or having a bad attitude. That’s no excuse for talking back to your teacher, or cutting class, or dropping out of school. That’s no excuse for not trying.

Where you are right now doesn’t have to determine where you’ll end up. No one’s written your destiny for you. Here in America, you write your own destiny. You make your own future.

That’s what young people like you are doing every day, all across America.
Young people like Jazmin Perez, from Roma, Texas. Jazmin didn’t speak English when she first started school. Hardly anyone in her hometown went to college, and neither of her parents had gone either. But she worked hard, earned good grades, got a scholarship to Brown University, and is now in graduate school, studying public health, on her way to being Dr. Jazmin Perez.

I’m thinking about Andoni Schultz, from Los Altos, California, who’s fought brain cancer since he was three. He’s endured all sorts of treatments and surgeries, one of which affected his memory, so it took him much longer – hundreds of extra hours – to do his schoolwork. But he never fell behind, and he’s headed to college this fall.

And then there’s Shantell Steve, from my hometown of Chicago, Illinois. Even when bouncing from foster home to foster home in the toughest neighborhoods, she managed to get a job at a local health center; start a program to keep young people out of gangs; and she’s on track to graduate high school with honors and go on to college.

Jazmin, Andoni and Shantell aren’t any different from any of you. They faced challenges in their lives just like you do. But they refused to give up. They chose to take responsibility for their education and set goals for themselves. And I expect all of you to do the same.

That’s why today, I’m calling on each of you to set your own goals for your education – and to do everything you can to meet them. Your goal can be something as simple as doing all your homework, paying attention in class, or spending time each day reading a book. Maybe you’ll decide to get involved in an extracurricular activity, or volunteer in your community. Maybe you’ll decide to stand up for kids who are being teased or bullied because of who they are or how they look, because you believe, like I do, that all kids deserve a safe environment to study and learn. Maybe you’ll decide to take better care of yourself so you can be more ready to learn. And along those lines, I hope you’ll all wash your hands a lot, and stay home from school when you don’t feel well, so we can keep people from getting the flu this fall and winter.

Whatever you resolve to do, I want you to commit to it. I want you to really work at it. I know that sometimes, you get the sense from TV that you can be rich and successful without any hard work -- that your ticket to success is through rapping or basketball or being a reality TV star, when chances are, you’re not going to be any of those things.

But the truth is, being successful is hard. You won’t love every subject you study. You won’t click with every teacher. Not every homework assignment will seem completely relevant to your life right this minute. And you won’t necessarily succeed at everything the first time you try.

That’s OK. Some of the most successful people in the world are the ones who’ve had the most failures. JK Rowling’s first Harry Potter book was rejected twelve times before it was finally published. Michael Jordan was cut from his high school basketball team, and he lost hundreds of games and missed thousands of shots during his career. But he once said, "I have failed over and over and over again in my life. And that is why I succeed."

These people succeeded because they understand that you can’t let your failures define you – you have to let them teach you. You have to let them show you what to do differently next time. If you get in trouble, that doesn’t mean you’re a troublemaker, it means you need to try harder to behave. If you get a bad grade, that doesn’t mean you’re stupid, it just means you need to spend more time studying.

No one’s born being good at things, you become good at things through hard work. You’re not a varsity athlete the first time you play a new sport. You don’t hit every note the first time you sing a song. You’ve got to practice. It’s the same with your schoolwork. You might have to do a math problem a few times before you get it right, or read something a few times before you understand it, or do a few drafts of a paper before it’s good enough to hand in.

Don’t be afraid to ask questions. Don’t be afraid to ask for help when you need it. I do that every day. Asking for help isn’t a sign of weakness, it’s a sign of strength. It shows you have the courage to admit when you don’t know something, and to learn something new. So find an adult you trust – a parent, grandparent or teacher; a coach or counselor – and ask them to help you stay on track to meet your goals.

And even when you’re struggling, even when you’re discouraged, and you feel like other people have given up on you – don’t ever give up on yourself. Because when you give up on yourself, you give up on your country.

The story of America isn’t about people who quit when things got tough. It’s about people who kept going, who tried harder, who loved their country too much to do anything less than their best.

It’s the story of students who sat where you sit 250 years ago, and went on to wage a revolution and found this nation. Students who sat where you sit 75 years ago who overcame a Depression and won a world war; who fought for civil rights and put a man on the moon. Students who sat where you sit 20 years ago who founded Google, Twitter and Facebook and changed the way we communicate with each other.

So today, I want to ask you, what’s your contribution going to be? What problems are you going to solve? What discoveries will you make? What will a president who comes here in twenty or fifty or one hundred years say about what all of you did for this country?

Your families, your teachers, and I are doing everything we can to make sure you have the education you need to answer these questions. I’m working hard to fix up your classrooms and get you the books, equipment and computers you need to learn. But you’ve got to do your part too. So I expect you to get serious this year. I expect you to put your best effort into everything you do. I expect great things from each of you. So don’t let us down – don’t let your family or your country or yourself down. Make us all proud. I know you can do it.
Thank you, God bless you, and God bless America.

Well, there you have it. The President's personality cult in full swing. Damn Commie prevert, trying to talk kids into doing homework, staying in school and making a difference.

WORK IN PROGRESS (HOUSE)

Well, over the three-day weekend I worked a tad. I took part of Sunday afternoon off to attend the 'Heretic's Barbecue' sponsored by CVASS. They had a nice turnout. I got my money's worth in the food department, I donated a couple of copies of an 'old earth creationist' book to an auction to raise funds for CVASS and got to 'walk on water' when they put together a demo of a non-Newtonian fluid (corn starch suspended in water). This is a classic demo:



But all good things must come to an end. My genius wife had the walls painted various colors, our tile guy laid tile every day and I spent time laying paver stones, stripping old paint from baseboards and installing various items (toilet paper holders and the like). I am bushed. More photos and descriptions to come. If all goes well, we should carpet on Thursday and move in on Saturday. Our year of Purgatory is nearly behind us.

NO PRIVILEGED BELIEFS

This is a screen shot, with individual's names redacted, of an email I received yesterday from the school district. Of particular emphasis is this directive: "If teachers decide to use the live broadcast as an educational opportunity, and they have students that do not wish to participate, please make provisions for those students."

The only provision that should be made for such students, frankly, is that they should be allowed to earn a failing grade on any assessment directly linked to this event. If you start allowing students in a social science class to 'opt out' of an activity based upon their political beliefs, you can pretty much kiss any discussion of current events goodbye....and this is pretty much embedded in the California State Standards for Social Sciences:

Pg. 47, Grades 9-12, Historical and Social Sciences Analysis Skills

1) Students compare the present with the past, evaluating the consequences of past events and decisions and determining the lessons that were learned

4)Students relate current events to the physical and human characteristics of places and regions

I tell you this much: I will never go along quietly with some directive that tells me allow students in a science class to 'opt out' of any assignment based upon the State Standards that they think troublesome to their personal beliefs. That effectively privileges ignorance. They do not have a right to dictate which State Standards are taught, or which should be used in determination of their grade. If they want to change what is taught, they need to participate in the process like the rest of us.

Fresno Unified knows darn well that legal recourse exists should instructors abuse the 'bully pulpit' of the classroom, and they have a vested interest in discouraging bad instructional practice. But the mere presentation of a current event, even one with partisan overtones, does not in itself rise to the level of endorsement of any particular viewpoint by the instructor, much less the district's employer. And, even if it was perceived as such by other partisans, that would not necessarily run it afoul of the Establishment Clause, which is concerned with the free exercise of religion, rather than political points of view.