An Exciting Weekend!!!!

Looking for things to do this weekend (and you do)?

Why do you need something to do, you ask? It's Valentine's Day weekend you point out. You plan on lots of dancing and romancing with your significant other, you say. So why do you need something to do?

Two reasons: 1. To prevent chafing, it's not a bad thing to take a break. 2. To embrace some science.

On Saturday:
we have the annual homeschool (creation) science fair taking place at Northwestern University in Roseville. The fair is in the Maranatha Hall lobby.

From 36 head north on Snelling Ave.

Judging is from 10:00 - 12:30, so the kids will be there then. I love talking science with kids, so I plan to be there around 11:00. Afterwards I plan on having lunch at Grumpy's (marked with a star). Even if you don't go to the fair, feel free to join me afterwards. I'll be at Grumpy's, in the bar area, sometime between 12 and 12:30. If you go to the fair because I brought it your attention, you must play nice with the kids.

On Sunday:
we have Dr. Sehoya Cotner speaking at the Southdale Library at 2:00. Her talk is "Are we still evolving?" Of course the answer is yes, but there is much interesting information and fun associated with these talks. Afterwards there may be a lunch, although I'm not sure I'll be going. I may have to brew up some beer instead.

The pin denotes Southdale Library - Duh

If you go to the talk because I brought it to your attention, feel free to be an ass. (Not responsible if Dr. Cotner kicks your ass though.)

Highly Conserved Is Relative

When discussing some aspect of biology, we often want to know how common is the gene, pathway, structure, interaction, or other phenomenon we are interested in. This can be important in two distinct manners: 1. if we find our gene, pathway, etc. is maintained in many different types of organisms, this suggests that our gene, pathway, etc. likely plays an important or fundamental role in some level of biology; 2. if we find our gene, pathway, etc. is not found in different types of organisms, this suggests our gene, pathway, etc. likely can tell us something about the unique biology of what we are studying.

To discuss this phenomenon of commonality, we say that something is conserved (or not). Of course saying a gene, pathway, etc is conserved doesn't tell us much by itself, because we need to know the level of conservation. Is the gene, pathway, etc. conserved among sister species? within a class? a phyla? a kingdom? The answer to this question tells us a lot about whether we are looking at a fundamental process or at the level of specificity of the process. In the seminars and papers I read, I generally see a short-hand approach to discuss conservation where the speaker or author uses a superlative or adverb to suggest the level of conservation.

For example, I recently heard a talk where the presenter stated that a protein was 'highly conserved, being found in both mammalian systems and yeast.' That sounds pretty impressive. But I immediately thought of eukaryotic phylogeny (mammals and yeast are both eukaryotes), and this figure I borrowed from Lab Rat a former FoS blogger who blogs at Scientific American. This is a figure my Eukaryotic Microbiology students see every week in class (the bacteria and archaea are not included in this figure).

I want to draw your attention to the Opisthokonts over at ~4:00. This is the supergroup of eukaryotes containing the metazoa (animals) and fungi. If we blow up this area of the figure, the last common ancestor of animals and fungi is indicated by the red arrow. (FYI humans, including you, are indicated by the green arrow.)

Now look at the first picture and think about all the eukaryotic diversity absent from the Opisthokont group! Is something found in both mammals and yeast highly conserved? I suppose so, since that last common ancestor lived ~1 billion years ago. But mostly I suppose not, because the vast amount of eukaryotic diversity lacks it.

A tangential point, but it's probably worth pointing out that the eukaryotic kingdoms we mostly hear about: animals, fungi, and plants represent little of eukaryotic diversity. Animals and fungi are contained within the Opisthokonts and plants are contained within the embryophytes at ~1:00. Everything else on this wheel represent non-animal, non-fungal, non-plant eukaryotes.

Bill Nye Won the Debate and Why I Think It Matters.

Not actually Ken Ham

There are 2 rules most people know:

1. Never get involved in a land war in Asia.
2. Never go in against a Sicilian when death is on the line.

I would like to promote a third that is less commonly known:

3. Never debate a creationist*
*unless you're Bill Nye, the science guy.

First, I will up front state that I was not a proponent of Bill Nye agreeing to debate Ken Ham at the Creation Museum on a topic related to evolution and creationism. In fact, if another debate were planned, I am still against Bill Nye participating. I saw and foresee nothing good coming from said debates.

Second, I was wrong.

Super-genius

I am not in favor of a debate between evolution and creationism for a variety of reasons:

• There is no basis for comparing these two topics other than a lot of people have issue with one topic or the other. Evolution is so strongly supported and affirmed by the evidence, a debate equating evolution with creationism is akin to a debate on gravity and consciousness-dependent falling. 
• Many of the points creationists use were debunked years ago. It has been explained over and over, and yet they keep using the same points. It's almost as if they are being willfully ignorant or outright lying. I saw a talk last semester that used the same discredited talking points Ham did. 
• Debates are not about truth or getting at the truth, but are exercises in oration. Who has the best oratory skills does not equate with who is correct or not correct.

This particular debate was worse because it took place at Ken Ham's Creation Museum. Furthermore, the tickets were siphoned towards a creationist-friendly audience. So not only was the environment completely lopsided in pro-creationist favor, but the Creation Museum made money on the endeavor through ticket sales and the soon-to-be-available DVD. Even if Nye were to win (doubtful given the audience), the mission of Ken Ham would be supported.

One thing I did not consider was the internet. The debate was streamed live for free and is currently still available for viewing. Importantly and surprisingly, the debate was watched live by at least a half million viewers! So while Nye clearly lost the debate in the forum it was held, he won in a landslide via the intertubes. As to my first premise that Nye lost in the forum it was held, the evidence comes via Matt Stopera of Buzzfeed who took these  pictures among others of event attendees:

It is, they aren't, because it is. (How can both a sprinter and a faucet run?)

It does not. (Look up on a sunny day if you don't understand why.)

Garbleblarglegable, non-sequitor

However, in the intertubes Nye kicked ass or maybe a better way to put it is Ham presented his own ass to Nye on a silver platter. Why do I say Nye won? Well actually Christian Today says Nye won or at least the readers of Christian Today think so. The fact that >500,000 people saw the debate streaming live tells me Nye won. First, these were not carefully screened creationist-friendly viewers such as those found at the Creation Museum. Second, Nye had all the evidence and Ham had….. Third, Nye was fortunate enough to have Ham keep opening his mouth.

Nye in his opening remarks noted that billions of believers accept evolutionary theory (in general terms). This is a powerful point to make because Ham likes to link evolution to atheism as much as possible (disregarding the facts that most Christians accept much of evolution and the physics and that much of evolutionary theory and physics was developed by believers).

The question the debate centered on was "Is creation a viable model of origins in today's modern, scientific era?" Nye essentially addressed this question throughout the presentation; Ham noted the question and then proceeded onto the standard talking points. This was obvious to any viewer.

But perhaps the kiss-of-death occurred during the question and answers. When asked 'what would change your mind?' Ham responded with essentially 'nothing would change my mind' and Nye responded with 'evidence' and then listed some things that evidence could look like.

Why I think this is important is that in a more accessible format, Ham showed the Christian community in this country how 'stone cold fuck nuts (thanks Mr. Black)' he and his followers are. When the state legislature in South Dakota is trying to bankrupt a community by preventing K-12 administrators from preventing science teachers from teaching creationism, we need Christians to realize how dangerous these peoples are.

So I was wrong, at least in the larger context. I think the debate was a win for science and Bill Nye and for that I thank Mr. Nye.

Poor US Education Meme Infects the Minnesota Daily

It's bad enough reading the standard misinformation regarding K-12 education in the popular press, but now it has infected our student paper too. The editorial compares the curricula of Germany with that of South Korea as educational systems that could be modeled to improve US education. But the question, the answer to which is assumed in this editorial, is, is the US education system doing poorly?

Dunces unite

Based on the popular press, you'd think US education is in complete disarray. This idea is supported by tests that compare the US to many other countries.

For example, Pearson ranks the US as 17th overall in cognitive skills and educational attainment (Finland, South Korea, Hong Kong, Japan, and Singapore rank 1-5). The US is between Belgium and Hungary and for the record Germany comes in at a devastating 15th. These rankings spanned 2006 - 2010.

Furthermore, the Programme for International Student Assessment (PISA) 2012 rankings have US 15 year olds at 17th in reading, 23rd in math, and 21st in science out of the 34 Organisation for Economic Co-operation and Development (OECD) countries. (The US ranked 36th in math of all countries/areas tested.) 

Highlander ranks higher than
US in math and kicking ass

These rankings are problematic for several reasons.

Zero Sum Games: For the US to move up in its rankings other countries must go down. As the Highlander says 'There can be only one.' Is the US education system likely to be that much stronger than education system of the United Kingdom? Germany? Japan? Canada? France? Belgium? I'm not suggesting we should not try to attain the greatest achievement possible, but don't you think these other countries want to have student success? Even if we thought of it first (we didn't), other countries would likely have noticed and followed suit.

Apples and Oranges: The US is not a monolith of education. If anything we're a monolith of stupidity. We have a decentralized education system. Each state can do what it wants, thus states like Tennessee and Louisiana, which overtly teach biblical creationism, may do poorly on science exams. Using the US as a single entity for comparison sake does reveal major shortcomings in our educational system. But it's basically worthless, unless your goal is to eliminate public education and replace it with a mechanism to move more taxpayer money into corporate hands.

From Slate

 If we look at states individually, something different emerges.

On the PISA exam, the US math average was 481, placing us at 36th of OECD. The average for the OECD countries was 494, putting the US well below average. But if we look at individual states we find that average in Massachusetts was 514, Connecticut was 506, and Florida was 467. Two states doing well above the OECD average and one state 4 points below Croatia, a country recently established from the ruins of Yugoslavia.

Similar results are seen in the science averages. US average: 497; OECD average 501; Massachusetts average 527; Connecticut average 521, and Florida average 485.

Any guesses on reading literacy? US average: 498; OECD average 496; Massachusetts average 527; Connecticut average 521, and Florida average 492.

Do you see a trend there? It looks like some states, Massachusetts, do extremely well helping promote a strong US score. Yet other states, I'm looking at you Florida, fuck it up for everyone. You'ld think the talking heads would be asking 'what's working in top performing states like MA, NH, MN, etc?' or even 'what's not working in bottom performing states like FL, MS, AL, etc?'

I bet people in Massachusetts really want to overhaul their successful education system in order to try out a new one that might improve Florida's scores.

We spend so much time disparaging teachers that many rankings done in the US use teacher tenure, teacher seniority, and charter school availability as major criteria in their evaluations of state education. Regardless of student outcomes! If a state has teacher tenure and great student achievement, should that state be dinged? For example, the American Legislative Exchange Council (not affiliated with Congress) came out with their rankings: Massachusetts received a C; Florida a B.

I suggest you go back on look at the PISA scores and then let that digest a minute. If you think the PISA test is a Muslim plot, you could also look at the USA USA USA National Assessment of Educational Progress NAEP rankings: MA, with MN and NH, first in 4th grade math; Fl 30th. MA first in 8th grade math; FL 37th. MA, first in 4th grade reading; FL 13th. MA first in 8th grade reading; FL 33rd. (Was that a complete sweep?) Yet the ALEC says FL is a clear letter grade better than MA. WTF?!?! (ALEC cares little about education and more about policy that ends public education: Vermont and Rhode Island received D+'s yet were 2nd and 6th in the country on the NAEP tests respectively; Utah B- and South Carolina C were 41st and 50th on the NAEP test respectively.)

For the record, MA and other top performing states do well across economic spectra. These results are not simply due to socio-economic differences. However, poverty clearly has a profound effect on education achievement. 

Coming full circle, it's not a zero sum game here either. For FL to improve its ranking other states have to lose positions. The point is that using the US as an education collective to compare against actual education collectives is ridiculous.

Regardless, I am tired of hearing about the travesty of the US education system, when in fact many states are doing great, but are dragged down in national surveys by poor performing states (I'm looking at you deep south). We should look at the data coming from these assessments and tests and determine what is valid (are students in Singapore better prepared for the test due to timing of the curricula? do all students go to school and are they all tested in China?). We should also celebrate our accomplishments, YAY Massachusetts, and recognize our problems, I'm looking at you Florida, I'm also looking at Minnesota which is doing great on these tests but still has a huge achievement gap.

So thanks Minnesota Daily for getting me to write this. For the record, we don't need to look to South Korea or even Germany to fix our education system. First, we have to realize the US education system does not exist, so it can not be broken and need to be fixed. Second, we only have to look at our neighboring states to see what works and what doesn't. Third, if there are applicable educational innovations developed overseas or even up North, I'm all in favor of trying them. But realize much of our system works well and let's not fuck it all up because of Florida.

What I read (2013)

(Grade A-F, no E's) Title-Author Additional thoughts

A- Abaddon's Gate by James S.A. Corey. A great read. Completes the series and answers those questions that can be answered while throwing up their hands at the answers that could not legitimately be answered. Sometimes we just don't know.

A- Batman: A Death in the Family by Jim Starlin et al. I forgot about this story line. It looks like The Joker might kill Robin and fans were asked to vote: Live or Die. The epilogue to this story is also included, which is really just another story.  

B+ Calibans's War by James S.A. Corey. The sequel to Leviathan Wakes. Not as a good as the original but it moves the story forward.

B Hogfather by Terry Pratchett. Sometimes you just need a laugh and DEATH AS SANTA CLAUS IS HUMOROUS.

A Leviathan Wakes by James S.A. Corey. Not normally a fan of epic science fiction, but this was a realistic space opera. While dealing with a monstrous not understood space 'organism' sent billions of years ago, the story is really about people and human interactions. It's also a mystery.

C The Third Kingdom by Terry Goodkind. We begin to fall into the trap of having read this story before.

B+ The Omen Machine by Terry Goodkind. I enjoyed the Sword of Truth series (some books more than others). This continues the tale by introducing a new threat to the hard won peace. Not as robust as some of the earlier stories, but there's enough new to be interesting.

C+ Happy Hour in Hell by Tad Williams. I really like this plot. Angels and devils acting at an almost human level dealing with souls. Here the angelic protagonist descends into hell, somewhat following Dante's layers to save his demonic girlfriend.

A Microcosm by Carl Zimmer. A great introduction to microbiology and the importance of this subject through the lens of a single (albeit important) bacterium.

F Shadow and Claw by Gene Wolfe. There were some interesting ideas in this story, but ultimately they did not coalesce into a compelling or even a good story.

C The Penultimate Truth by Philip K. Dick. A good short novel that reawakens the importance of science fiction in discussing the human condition. Stories like this can address concepts that are too loaded with political baggages to discuss in realistic terms.

A- World War Z by Max Brooks. Fun fun fun read. Reminded me in part of Bram Stoker's Dracula in how the story telling is done. Not sure how this was adapted into a movie, but I am sure I will only be seeing it on cable.

A Maus Vol I by Art Spiegelman. Everyone should read this book. Along with The Watchmen (I know these stories should not really go together) Maus reminded me of the value of the Graphic Novel as a literary medium. 

C Witch Wraith by Terry Brooks. A decent enough story, but I think I read this trilogy before albeit with different titles.

A Colonel Roosevelt by Edmund Morris. A compelling read on the post-presidential years of Teddy Roosevelt. I look forward to reading 'The Bully Pulpit', which appears to cast the relationship between Roosevelt and Taft in a more collegial light.

B Ocean at the End of the Lane by Neil Gaiman. A nice story, not much else to say.

B+ Species: A History of the Idea by John S. Wilkins. Want to know how the species concept came to be and the historical baggage associated with it? Read this book. I wish more time had been devoted to modern ideas regarding the species concept, but there are many places to get this information.

A- Full Dark, No Stars by Stephen King. A great collection of extremely dark short stories. Unlike many of King's stories, these explore the darkness of humanity. There are no supernatural or fantastical threads, with the exception of the devil as a plot device in one story (the story is about jealousy and greed). 

C Lord Valentine's Castle by Robert Silverberg. A good premise and story. This tale takes place on a gigantic planet with billions of people. Everything is big, the mountains, the seas, the length civilizations have existed, etc. The problem is that the story does not convey this sense of size. We only know about it because Silverberg tells us directly, otherwise it is lost in the storytelling.

B+ Paleofantasy by Marlene Zuk. A great book that debunks pseudoscience, explains evolution, and describes the human condition in an easily digested book.

A- Wards of Faerie by Terry Brooks. I like Terry Brooks a lot, but many of his stories read as rehashes of previous stories. This one sets the table for a new adventure within the Shannara mythology, but ultimately (next book) becomes a rehash. 

D Deadhouse Gates by Steven Erikson. My own damn fault. The sequel to Gardens of the Moon, which other reviews suggested was much better than the original. It wasn't. It suffers from the same loss of thread and too many characters doing too many things without enough development to follow. At 800+ pages I expected better. 

A Why Evolution Is True by Jerry Coyne. An extremely good book on evolution. A brilliant focus on islands vs the mainlands (an approach used by Darwin) to explain some of the vast evidence for evolution. The only critique I have is the heavy investment on sexually reproducing animals, but this is a problem throughout biological works. 

C- Gardens of the Moon by Steven Erikson. There is just too much going on and not enough story to be able to keep things straight. The plot seems interesting, but it often gets lost. Definitely in need of a good editor.

B+ Good Omens by Neil Gaiman and Terry Pratchett. A devil working with an angel, enough said. Plus the book was kind of along the same lines.

C+ The Night Circus by Erin Morgenstern. Not my usual fair, but my book buddy from Grumpy's has introduced me to some good books (The Passage), so I took her advice. Basically a love story, but with enough mystery and fantasy to make a worthwhile read. 

A The Red Knight by Miles Cameron. A great read! Numerous characters and plot lines that do not necessarily converge. Unlike other books I read this year, the multiple plots were not distracting and difficult to keep track. I look forward to reading the second book in this series, which came out a few days ago.

B The Endless Knot by Stephen Lawhead. Completing the trilogy. Overall an interesting story line, but everything works out too well for the protagonists, even if the associated people and communities are devastated.

A Memory of Light by Robert Jordan and Brandon Sanderson. w00t!!1!1!1leventy1!! The series is over! I enjoyed the first few books, and then the series lagged greatly and the writing suffered. Brandon Sanderson brought the writing back to it's roots and I am glad he put Jordan's ideas into words for these last few books.

B+ The Wind through the Keyhole by Stephen King. A story within a story within yet another story type of story. A new Dark Tower story that has little to do with the actual story narrative but does establish more of the mythology of Mid-World.

A The Ancestor's Tale by Richard Dawkins. A reread. My favorite Dawkins book, much better than the excellent The Selfish Gene. As with many biologists, Dawkins only considers species from the standpoint of sexually reproducing plants and animals (in the book) and I have some issues with his thoughts on race. However, this is a must read for anyone even remotely interested in biology.

B The Silver Hand by Stephen Lawhead. A pretty easy read and an interesting plot. 

Damn! 32 books this year, not counting another graphic novel and a couple books I started but haven't finished yet. This is the first year that none of the books I read were books I read to my son. He is a voracious reader himself, but unlike his dad enjoys rereading books over and over. He completed the Eragon series and in currently on the last Hunger Games book. Again most books (25/32) were fiction I read to relax, including 2 by Terry Pratchett (I'm counting Good Omens co-written with Neil Gaiman). Of the remaining 7, 5 were about biology in nature and 2 were history (I'm counting Maus here, although both Maus and Colonel Roosevelt could be considered biographical). Need to complete some of the philosophy I started, although the Species book is philosophy, and read a classic or two, Dicken's Bleak House was a Christmas gift to myself.

Merry Holidays and Happy Christmas

While we are in the closing days of the annual (war on) Christmas season, I wanted to address a meme that floats around yearly. It showed up in my Facebook feed a bunch of times and is a meme spread by FAUX news for the last few weeks.

This clever sounding sound-bite makes a clear point: Christmas is the only holiday we are allowed to care about. Not Hanukkah, not Kwanza, not the solstice, definitely not the new year, nor the oxford comma. I expect some people promoting this meme are generally well-meaning and not the douches they seem to be. So with some limited holiday spirit in mind, I want to take a minute to let you know what 'It's not happy holidays, it's Merry Christmas!' means and doesn't mean to me.

What it means: It means you fail to recognize your Christian privilege. You assume that since Jesus is important to you, he should be important to them too. You assume that since in your tradition you choose to have the winter solstice represent the birth of Jesus that everyone else should too. No matter what someone else's religious, non-religious, cultural, tribal, or other background is, they must enjoy this time of year as you deem fit.

What it doesn't mean: It doesn't mean that you are expressing goodwill or joy or happiness or any other positive feeling to others (Christian or otherwise). You are making a political statement. Your 'Merry Christmas' is not actually a message of hope that I am merry on the 25th of December. It's a demand that I prostrate myself to your overbearing and extremely limited interpretation of Christianity. 

What it means: It means that the first amendment means little to you except a protection of your religious beliefs. When states make laws demanding that stores are closed on Christmas (interfering with the free market), it has to be (and has been) justified from a secular standpoint. Of course everyone knows these kind of laws are only established to benefit Christianity, the justification promoted uses a reach around approach to avoid this obvious position.

What it doesn't mean: It doesn't mean that all people in this country are equal under the law. Or maybe I should say that all people are equal under the law, but some animals are more equal than others (thank you public education).

What it means: It means that when a stranger tells me Merry Christmas, I now have to wonder if they actually are expressing well-wishes and happiness or being douchebags like the people who post pictures like the above on Facebook. For that, I want to wish you a:

(I wasn't going to write this post, but then I came across the Grumpy Cat picture, which made me laugh so hard, my 11 year old wanted to know what was so funny. After that I had to write this post. So thanks and Happy Holidays to all the Grumpy Cats in the world (and a Merry Christmas to everyone).)

My Favorite Time of the Year

From here

One of the courses I teach culminates with blog posts written by the students. This is the third year I have used this assignment and is one assignment the students actually enjoy doing (at least based on student feedback from previous years). Students will be submitting their final essays on some aspect of research on eukaryotic microbes in the next few days and you will be able to find them here. Until the new ones are posted, you can see some essays written previously.

FYI: The assignment is to write an essay of 1000 - 1500 words for a lay audience of science enthusiasts that incorporates at least primary research papers on a eukaryotic microbe. (Microbe being defined in the course as an organism that exists primarily as a single celled organism, thus excluding microscopic multicellular animals.) Students were allowed to write in any voice and use any style of writing.

If you read through an essay, please leave a comment for the student.