Angry by Choice

Santorum Is an Ass, a RANT (You Were Warned).

2012-01-31T21:12:00.001-06:00

So here is Santorum going after colleges and universities last week:

The question is 'Why?' Has America reached this point, where we cheer the demagogy of higher education. Fuck, we don't need no engineers, scientists, doctors, historians. Them bastards just think they know shit we don't know.

62% of college students who enter steeped in faith, leave without it. Hmm, so college educated students think something different than when they were 7 and going to Sunday school. How can Santorum actually say colleges indoctrinate adults and not be hit upside the head by an exploding irony meter? I guess where he comes from all those weeks of Sunday school that 4-10 year olds go to isn't indoctrination, but those courses 18-21 year olds choose to take are. Of course we have our ACLU dog whistle. You know, I never hear the right wing talk about those cases where the ACLU defends the rights of Christian students. (Of course it's not about defending rights, it's about Christian hegemony).

62% of college students who enter steeped in faith, leave without it. What does that say about your faith Rick?

What's Santorum's solution? Stop funding higher education. Yeah, fuck em. They just think they know shit and stuff.

This isn't just a bat-shit crazy fucknut Santorum, Gingrich said much the same:

'Take back power from the minority elite.' Not trying to blow any racist dog-whistles there are you.

So we have the right-wing bringing out ELITIST as a derogatory term, yet again. I'm not sure they actually put it away, but it is front and center again especially when it comes to Obama (you know the guy raised by a single mom without a trust fund or rich parents to pave the way, although she was educated so obviously elitist). Of course when republicans are talking about the elites, they are talking about the college educated. They are not talking about the multi-millionaires, like Romney. They are not talking about those with the keys to power, like Boehner or Gingrich. They are not talking about the aristocracy, just the serfs who were fortunate enough to have the ability to think above their station. They are talking about those people who have studied hard, probably taken a bunch of student loans they are still paying back, and learned something most people may not know or understand very well. This seems to piss the aristocracy off, so they call us elites to fire up the rest of the serfs to hate those serfs were able to leave serfdom behind. Yet somehow the aristocracy avoids being called on their position of eliteness. By the way, I don't have any reservations using aristocracy, look at who are leaders are. Bush, Bush Jr, Jeb. Mitt and George. Teddy and Franklin. Power is concentrated in the few, and they want it to stay that way. Education can be a great equalizer and most of the entrenched elites aren't fans.

This is the problem with readily available education. If you are smart enough (and butt-ass lucky if you happen to come from an impoverished background), you can enter into the halls of these educated elites. Those college professors and instructors do not care who your daddy was and what kind of car you drive (hell, my 'new' car was 10 years old when I bought it). You can become the leaders of tomorrow in whatever field you chose, but since your parents weren't already part of this elite group, the aristocracy does not approve.

It almost warrants a high school analogy. Republicans are talking about those geeks and nerds that could help you with your homework in high school. You know back when the geeks and nerds knew their place. See the jocks had the world on a stick then, they could be good at football or basketball and people cheered, the town supported them, everyone wanted to be their friend. Of course the nerds and geeks had their spelling bees and science fairs and maybe we could appreciate the star tennis player or track star occasionally, but those didn't really count to the world at large. The true elites have always liked their position and really don't want any of you non-elites fucking with their chi.

2012-01-24T20:22:00.000-06:00

My Star Wars name is Tol Rukbat
A slave master from Exodo II (my students may say Im from Maine)

Get your own Star Wars names from The Star Wars Name Generator!

H/T Mike

Origin of Species Book Club: Historical Sketch & Introduction

2012-01-19T23:32:00.012-06:00

Alright apologies to those waiting for updates on OoS, but real life is a fuck-all-the-time-and-not-in-a-good-way (fattaniagw). Anyway, here are some of my thoughts on the Historical Sketch and Introduction. Please add any thoughts you have including disagreements in the comments and we can continue a discussion there.

Historical Sketch: This is really damn important for all of us involved in the culture war. I think by-and-large people think the concept of evolution started with Charles Darwin. But this is not true. First of all, we have to realize the problem Darwin was trying to address and that is clearly laid out in the title of his book Origin of Species. Where do species come from? That is the question he was dealing with. As I look in my fairly simple backyard, I can see grass, a white pine, lilac bush, gray squirrels, rabbits, juncoes, and a cardinal. (Often there are blue jays, roses, daffodils, chickadees, chipmunks, etc). Where did these different organisms come from? how did they come about? why do they stay as discrete entities and we don't see chipbits or cardinadees or even squirrelpines? Basically, Darwin is asking that age old question, what the fuck is going on?

This is the current problem, because when we think about it from the grandiose perspective of 'what the fuck is going on?' we step on the toes of religion. This was not Darwin's purpose or goal, but it is a ramification of the fact that Darwin is even asking this question. What's important is to realize that Darwin was not the only one asking these questions. In fact, these questions have been asked since humans gained the ability to ask questions. Although Darwin mentions Aristotle in his historical perspective, he really focuses on scientists writing in the 100 years prior to Origin of Species. The point he makes over and over is that many of the observations that he will use throughout the Origin were made by earlier scientists. Basically 34 previous scientists had established the facts that variation exists within a species and that species indeed change over time. The question that had not been adequately addressed was why had species changed. Essentially no viable mechanism had been proposed that explained all the data available. Admittedly Lamarck made an impressive stab at this problem but it didn't make sense in many cases nor was it supported by available data. At this point in time, the Christian idea of creation as defined by Genesis chapter 1 (not chapter 2) held sway. Although it had been clearly incorrect for several hundred years, an explanatory hypothesis had not yet been put forward.

Favorite passage (emphasis mine and I appreciate the recent musings of Cornelius Hunter for making this so amusing.):

This address was delivered after the papers by Mr. Wallace and myself on the Origin of Species, presently to be referred to, had been read before the Linnean Society. When the first edition of this work was published, I was so completely deceived, as were many others, by such expressions as “the continuous operation of creative power,” that I included Professor Owen with other palæontologists as being firmly convinced of the immutability of species; but it appears (‘Anat. of Vertebrates,’ vol. iii. p. 796) that this was on my part a preposterous error. In the last edition of this work I inferred, and the inference still seems to me perfectly just, from a passage beginning with the words “no doubt the type-form,” &c. (Ibid., vol. i. p. xxxv.), that Professor Owen admitted that natural selection may have done something in the formation of a new species; but this it appears (Ibid., vol. iii. p. 798) is inaccurate and without evidence. I also gave some extracts from a correspondence between Professor Owen and the Editor of the ‘London Review,’ from which it appeared manifest to the Editor as well as to myself, that Professor Owen claimed to have promulgated the theory of natural selection before I had done so; and I expressed my surprise and satisfaction at this announcement; but as far as it is possible to understand certain recently published passages (Ibid., vol. iii. p. 798) I have either partially or wholly again fallen into error. It is consolatory to me that others find Professor Owen’s controversial writings as difficult to understand and to reconcile with each other, as I do. As far as the mere enunciation of the principle of natural selection is concerned, it is quite immaterial whether or not Professor Owen preceded me, for both of us, as shown is this historical sketch, were long ago preceded by Dr. Wells and Mr. Matthews.

Introduction: This is basically what we now call an abstract for a scientific paper. Although at 5.5 pages for a 600+ page book seems sedate. Here, Darwin starts with his voyage on the Beagle and lays out the basic question being addressed and how he is going to go about answering it. I am not going to pick out a favorite passage here, because the entire thing is an eloquent and clear description of the wonderful things to come.

OK, book club readers, please toss in a response even if it's 'ditto' (better not be though, Im not Rush fucking Limbaugh). The pressure of knowing others are involved will help keep this book near the top of my personal to do list.

Next up: Chapter 1: Variation Under Domestication (Let's shoot for the end of the month, I have a grant due soon.)

Save the Date: Lying to Children in the Name of God Poster Session

2012-01-19T20:31:00.000-06:00

TCCSA science

In a month (February 18-19), the annual Home School Science Fair is taking place at the Har Mar Mall in Roseville. I will of course be attending this year and will report to those of you who cannot make it.

Remember these students will be primed to go, they are told to:
1. Know your material.
2. Be confident.
3. Communicate well.
4. Be thorough.
5. Pray your exhibit will witness to non-Christian visitors.

So you know there should be some quality science taking place.

Just to be clear, the Home School Science Fair is brought to you by the Twin Cities Creation Science Association TCCSA (emphasis mine). The TCCSA science fair motto:
Unlike Some Science Fair Sites
We Are For Real!
Unlike Many Secular Educators
We Teach The Scientific Method! (emphasis theirs)

Creation thinking impedes understanding

2012-01-19T01:43:00.019-06:00

I have become aware of something during my recent blogument with a ~~wall~~ creationist. Actually it was a comment left on defense of the creationist's position that really nailed down an idea I had floundering in the back of my mind. But I think a little background is necessary for those who haven't been reading some of my recent posts. The issue started over bad use of probability and ended up coming back repeatedly to the origin of life.

I pointed out that biologists do not propose that cells simply poofed into existence from a bunch of precursors. This was in response to creationists, who suggest that biologists think this, and then laugh at the ridiculousness of such a proposition. A creationist, who chose to rear his delicate sensibilities, then accused me of being a doody head for suggesting that creationists make such accusations. He then accused biologists of thinking that cells just poofed into existence. (Rinse and repeat.)

I realize that the creationist doesn't understand biology, although he thinks he does. This leaves him having to insist that biologists must accept the fact that cells poofed into existence fully formed if they accept evolution, because that's the way he conceptualizes what's going on. Based on his limited (extremely limited, I might add) imagination, the only thing he can come up with is POOF, therefore that must be the only possible solution to the problem. This is the 'if the only tool you have is a hammer, all problems look like a nail' fallacy.

So this is kind of where things were percolating and then I saw this comment:

I think you've entirely missed CH's point: Per "evolutionary" dogma---which doesn't allow any "teleology"---the ONLY way that a cell (=life) can come about is from "scratch", else something would be "swimming around in that warm little pond before evolution got going."
It's your point of view that forces the issue; not the non-Darwinian perspective.

Again, this person has an understanding (a profoundly incorrect one I should add) of what is going and decides that this is 'the only way' things could possibly happen. You know because nature never figured out really cool surprising ways of doing things.

Drakea pretending to be a female wasp in order to get pollinated by a male
wasp that is just trying to get laid.

So, now we have two potentially independent people who have the same misconception that the first cells poofed into existence. Want to see an independent representation of this kind of 'thinking'? Here's a Bananaman example. Bananaman argues that evolution can not be true because the first female elephant to evolve would need to mate with a male elephant that has not yet evolved. Again the underlying assumption is that the first female elephant evolved by poofing into existence, and of course Bananaman let's us know this is absurd. (Although Bananaman is perfectly fine positing a magic megalomaniac poofed elephants into existence.) These utterances led me to wonder where this misconception comes from. I think it's because people intellectually require that things have a beginning and an end. But why do we have this intellectual bias?

Babies are not born with an understanding of object permanence, the idea that when a toy or person can no longer be sensed it no longer exists. Hence peek-a-boo can be fun or terrifying depending on the newborn. An understanding of object permanence develops within a couple of months, although peek-a-boo can still be a fun game, mostly because infants enjoy watching their parents make fools of themselves. So maybe object permanence is hardwired into our brains and that explains the need to have things poof into and out of existence.

Mountain

However, I think there is another reason, at least in the US, and that is Christianity. Well not Christianity so much, but the Bible and Genesis in particular. Even if your children are not attending church regularly, they live in a Christian culture, which they cannot readily escape. Children are indoctrinated at a very young age that the Earth, Sun, Moon didn't exist and then...God poofed them into existence. One minute, no celestial bodies; next minute, they're all there. We indoctrinate infants that animals, plants, people didn't exist and then...God poofed them into existence. One minute, no giraffes; next minute, giraffes. It won't be for another ten or so years before we start teaching them that things came from earlier things, which may have been much different. I think the problem is that early in childhood we plant the seeds of an intellectual framework that becomes so deeply intrenched in our psyche that it is easy to be unaware of it as adults. Except the real world doesn't work that way. Consider the mountain. Has that mountain always been there? Did it just poof into existence? Some think the answer to both questions is 'Yes,' but the answers are of course no.

One way a mountain can form, or at least a mountain range, is when two tectonic plates slam into each other. As the plates collide, they can push each other up or one plate can be pushed up over the top of the of the other. This is an incredibly slow process, by human standards of time.

When we look at a mountain, we are looking at a snapshot in time. So when did that mountain begin? When the plates first meet, there is no mountain. As the plates are colliding or moving past each other, the land is rising, but still there is no mountain, although some hills are probably formed. Part of the problem with the question 'when did that mountain begin?' is an issue of language and the imprecise nature of words. What is the definition of a mountain? How much higher does it have to be in relation to the surrounding land to be a mountain? 500 feet? 1000 feet? Everest is ~29,000 feet. How steep does it have to be? If the elevation changed 1 inch every half mile, it would be a long, ~174,000 miles, but relatively easy walk to the top of Everest (not factoring in the reduction in oxygen here). For our purposes, let's simply say that a mountain is a land mass that rises 500 feet above the surrounding area with a minimum slope of at least 15°. When that land mass was 499 feet, it was not a mountain. When it was 499.5 feet, it was not a mountain. When it was 499.75 feet, it was not a mountain. When it was 499.999 feet, it was not a mountain. But when it gained that extra 0.001 feet (~1/100th of an inch), it instantaneously became a mountain. So I guess it did just poof into existence.

Ford Model T

Even in the artificial world things don't poof into existence. Cars are a given in this day and age. A couple of hundred years ago there were no cars. When did the first car poof into existence? Again there is the issue of language. We make ultimately arbitrary decisions on what defines a car, does it have to have four wheels? Does it have to run on gasoline? Let's say yes to both of these questions. Is the Model T the first car? No, there were earlier versions of cars. There were wind-powered cars developed hundreds of years earlier. The engines in early gas powered cars were derived from earlier engines invented for different purposes. If we take any of these early cars and say that this is the first car, ergo cars poofed into existence at this point, then someone can readily show us something earlier and legitimately argue that this is the technology that is derived into the 'first' car, ergo cars did not poof into existence.

What about life? Some argue that life begins at conception. While the genetic contingent that represents you did not come together until your parents got busy, that does not mean you poofed into existence. Did your life begin when that sperm borrowed it's way into the egg? or was it when the calcium flux occurred that prevented other sperm from borrowing their way in? or was it when the sperm nucleus fused with the egg nucleus? Were the sperm and egg not life and if not, when did they die? If the fertilized egg represents life poofing into existence, does that mean identical twins are each a half life or did life poof into existence independent of fertilization? Don't even bother to ask about asexual organisms. Maybe you think these ideas are ivory tower philosophical musings, but remember a fair number of political elections are based on these musings (usually by people that don't bother musing too much).

The point I am trying to make here is that at least some creationist thinking about evolution is locked into the creation framework. God poofs things into existence. Therefore, evolution poofs things into existence. But evolution is not simply a rebranding of the Christian God concept. No more than understanding electro-magnetism is a rebranding of the Zeus concept. They are not equivalent. This makes it nigh impossible to discuss evolution with determined creationists. They are intellectually wired in a way that makes common ground an undiscovered country.

The creationist mindset impedes understanding things in historical terms. When the human decision is made for when God did his poofing, that's it. There can be nothing earlier. That mountain was always there, cars were invented de novo, and life began at conception. It's quite sad actually when you think about all the things we understand in this universe and how this knowledge is not available to the creationist.

What I read (2011)

2012-01-07T09:20:00.001-06:00

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

B+ The Girl with the Dragon Tattoo by Stieg Larsson Reasonably good story which I flew through in a couple of days. Mostly enjoyed the cultural differences reading a book written by a Swede and taking place in Sweden and translated into English.

D- Science and Religion edited by Gary B. Fergren The subject of a blog post, but really a book containing mostly apologetics with a bonus chapter on Intelligent Design.

A Watchmen by Alan Moore & David Gibbons Just a great story.

B- The Lightning Thief by Rick Riordin Interesting retelling of Greek Mythology in a modern age. Definitely for kids, but I prefer the classics.

B The Measure of the Magic by Terry Brooks Enjoyed it, but the ending wrapped up a little too quickly and neatly.

B A Dance with Dragons by George R. R. Martin Good storytelling, but the plot needs to start moving forward.

C Harriet Spies Again by Louise Fitzhugh Meh

B A Feast for Crows by George R. R. Martin A reread in preparation for A Dance with Dragons

A Parasite Rex by Carl Zimmer Only Zimmer could get you to commiserate with life threatening parasites.

B The Escapement by KJ Parker

C Harriet the Spy by Louise Fitzhugh A read this as a kid and read it to my kid. I remembered it a lot differently.

A The Rise of Theodore Roosevelt by Edmund Morris Excellent book. Did you republicns were not always insane?

B+ The Passage by Justin Cronin Good story, especially the first half. Recommended reading by a server at a pub I frequent.

D The Lost Symbol by Dan Brown Kind of liked it the first time I read it when it was called The DaVinci Code.

B Lord Brocktree by Brian Jacques

A The Physics of Superheroes by James Kakalios All around good time reading. Makes a number of important points about science and society along the way.

B The Towers of Midnight by Robert Jordan and Brandon Sanderson This story has to end soon. Although the books have gotten better.

C+ The Gathering Storm by Robert Jordan and Brandon Sanderson

C Knife of Dreams by Robert Jordan I read the first 7,8,9? books about 10 years ago and got sick of them. Started strong and then nothing happened to drive the story forward for about 5 books so Knife of Dreams sat on the shelf until this year.

A- The Greatest Show on Earth by Richard Dawkins Great book on evolution (Not quite as good as The Ancestor's Tale). Some new ways of thinking about evolutionary concepts for me.

C Evil for Evil by K. J. Parker

A The Hobbit by J.R.R. Tolkein Great book I read to my son, who of course loved it.

A Why I Am Not a Christian and Other Essays on Religion and Related Subjects by Bertrand Russell Wow! and people say the New Atheists are mean and horrible. I guess they don't like Russell much either.

A Jesus, Interrupted by Bart D. Ehrman Great description of the New Testament and issues therein.
B- Harry Potter and the Goblet of Fire by J.K. Rowling The beginning of what I like to call the whiny years in the Harry Potter universe.

B Shadowheart by Tad Williams I've always thought Tad Williams was a good story teller, same applies here.

26 books this year (again). Only 6 were books I read to my son this year. Of the remaining 20: 13 were fiction for fun (holy crap no Terry Pratchett this year, must rectify that in 2012), 1 was biography/US history, 3 were philosophy/religion, and 3 were science (2 were biology).

Once more into the dark...recesses of a creationist

2012-01-05T21:30:00.005-06:00

I hate to send traffic to a creationist but so it goes.

I wrote, what I thought, was a thoughtful response to a question I was asked regarding math and evolution and creationists. This, not surprisingly, raised the hackles of a creationist who wrote a series of obsfucated posts in response.

In my original post, I pointed out one creationist argument against the theory of evolution misuses probability. The argument goes like this: using these assumptions, the odds of life originating is infinitesimally small therefore god and Jesus and homosexuals can not visit each other in the hospital. Of course the creationist does not ever say 'using these assumptions'. Instead the creationist uses definitive sounding statements that allow them to move unquestionably to calculating odds. Creationists often use the number of atoms in the universe as the biggest big number and then show the odds (calculated incorrectly) against evolution happening being greater than that biggest big number. Ergo god-->Jesus--> no gay hospital visits. One point of my post was to show that it is trivial to get an infinitesimally small odds number using common examples, like flipping a coin or playing the lottery. However, I note, quite clearly IMHO, that the assumptions creationists use in these situations are bullshit. From this one post (that had more in it than this), creationist Cornelius Hunter wrote his series.

Post #1 Cornelius tries a different example. Instead of dealing with the fact that creationist assumptions are pure fiction, Cornelius takes a different tact. Poker and scrabble. See the odds of three players each getting an amazing poker hand at the same time is a really small number therefore evolution can not be true or the odds of pulling out scrabble tiles in order that spell out CONSTANTINOPLE is a really small number therefore evolution can not be true. So if flipping a coin or the lottery are not sufficient evidence, then poker and scrabble will be? Poker and scrabble did not even exist 10,000 years ago, therefore the world can not be that old (if I understand Cornelius' way of thinking). The problem isn't getting small numbers. That's easy, I brought up two ways and now we have two more. The problem is the assumptions creationists make, they are not reality.

Post #2 Cornelius doubles down on the stupid. Cornelius spends most of his post rewriting the story of Darwin and Kelvin and the age of the Earth that I wrote. Ultimately he arrives at this conclusion:

In any case, geology soon extended the age of the earth into the billions of years, and evolution’s requirement for long time periods, so it seemed, was fulfilled.

So Cornelius is accepts that the Earth 4.5 billion years old. Except he doesn't or he does I get confused. You tell me, here's what he writes next (emphasis mine).

It is now known, however, that evolution has nowhere near the eons of time it requires. Indeed, the time windows available are even less than those allowed by William Thomson, which themselves were unacceptable to the evolutionists. This falsification of evolution’s expectation does not derive from the age of the earth, but rather from the fossil record. We now know that, even with billions of years of earth history, the major events in the fossil record take place in time windows that are no longer than a few tens of millions of years or even less.

William Thomson (Lord Kelvin) had the age of the Earth at 20-40 million years, not 4.5 billion. So how old do you think the world is Cornelius?

Cornelius says nothing here but make grandiose statements with no backing. So the major evolutionary events occurred in tens of millions of year. What is a major evolution event and how long do you think it will take? Presumably he is talking about the Cambrian explosion. I ask you, how long should it have taken and based on what to you make these calculations? A lot of diversification can happen rapidly. After most dinosaurs died out (65 million years ago), mammalian diversification exploded over 10 million years or so. Flowering plants had a massive diversification over about 40 million years. Changing body types is quite trivial, here's what selection (albeit man-made aka artificial) did in a couple of hundred years without knowing much about what we were doing.

Dogs

Convergent evolution

Given the opening of new niches due to the extinction of most dinosaurs, nature can have a grand old time selecting for variants better suited to aboreal life, marine life, underground life, open plain life, etc. Want another example, compare marsupials in Australia to mammals in North America. Species occupying similar niches evolved similar characteristics. Selection is a powerful process providing the raw material (genetic diversity) is available. You want a major event in evolution, screw small changes in body plan. Go with something really major like the first eukaryotic cells! Bacterial-like cells first show up about 3.8 billion years, it took almost 2 billion years before the first eukaryotes showed up! That must have been a major fucking hurdle. It was another billion years before complex multicellular life is observed (major event?). From the time simple animals are observed it's only 400 million years to get all the animal diversity we see today. All the hard stuff was already done in the first 3 billion years of life. So while the Cambrian explosion is impressive in its macroscopic visual appeal, it probably represents little from the standpoint of major evolutionary events. (I am using 'major' as in difficult).

His penultimate paragraph (the last is simply playground "Im telling mommy' rhetoric) contains some gems (emphasis mine):

But of course this is all wrong. If evolution is true we must believe it performs its uncanny miracles much faster than 4.5 billion years. The creation of life, the origin of fantastically complex cells, the creation of biology’s myriad designs, new species arising, and yes giraffes could not have evolved over billions of years. They could not have evolved even over hundreds of millions of years. It all must have happened much faster, in what are sometimes referred to as evolution’s “Big Bangs” where evolution leaves the equilibrium and for some reason becomes punctuated.

It all happened much faster?!?! What the hell does that mean? Doesn't Cornelius realize billions (X,000,000,000) is larger that hundreds of millions (X00,000,000)? Oh look, Cornelius uses words he heard before like 'punctuated' and 'equilibrium'. It's almost like he knows something about biology. Here's an interesting point, Cornelius often makes the case that evolutionists say there are no problems or issues in evolution and then pulls punctuated equilibrium out of his ~~ass~~ hat. Here's an issue that is not resolved in evolutionary biology. Regardless I posted this still unaddressed comment in response to this post.

"You state that 4.5 billion years isn't long enough. How long is? How to you come to that conclusion? What is the evidence to support your conclusion.
Here's evidence from scientists, not creationists, molecular genetics, using established mutation rates, comes up with ~3.5 billion years for the last common ancestor. Earliest fossils are ~3.5 billion years bacteria. Seems to fit within the 4.5 billion year time frame.

Your evidence is what? Nah Ah, ergo Jesus?"

Post #3 Cornelius makes up bullshit scenario to show evolution wrong. Remember at the beginning of this post I mentioned assumptions creationists use but never define as assumptions? They tend to be along these lines: one day there were a bunch of chemicals in a pool of ichor, lightening hit said pool, and WHAMMO a fully formed cell containing all the information and proteins needed to survive was formed. I stated repeatedly that no scientists worth their salt thinks this is what happened. What is Cornelius' response (which includes a quote from me in blue)?

So chemicals did not come together to form the first cell?

I don’t want to get into a discussion about the origin of life in this post,
Because the absurdity of the creation myth would rapidly become apparent. It would be a tremendous miracle—the spontaneous formation of the first cell, and all life thereafter.

See that comma at the end of my quote? Want to know the whole sentence was? Let me simply put up Cornelius' response again with my sentence intact.

So chemicals did not come together to form the first cell?

I don’t want to get into a discussion about the origin of life in this post, but I do want to stress that I have never seen the absurd idea that cells just poofed into existence fully formed from scratch except by creationists.
Because the absurdity of the creation myth would rapidly become apparent. It would be a tremendous miracle—the spontaneous formation of the first cell, and all life thereafter.

It is Cornelius who has an absurd (I wonder what made him use that word absurdity) creation myth. You know a talking snakes that has legs, genetic bottleneck of two (really one) people, women being the downfall of all mankind, all that fun stuff. He is stuck on the idea that scientists think a cell just poofed into existence, regardless of what we say, he refuses to accept it and keeps harping the same lie over and over.

Want to ask me how the first cell showed up? Well, I don't know. I've read a few things about some ideas and work that is being done to address these ideas, but frankly I don't know. But do you know what? That doesn't mean Cornelius gets to make up any old shit he wants and say that's what happened. Here's a big difference between Cornelius' world-view and mine. My world-view allows us to ask questions and test those ideas to gain a greater understanding, I could know a lot more about the current thinking on the origin of life if I spent time reading up on it. Would I be able to tell you exactly what happened? No, but I could tell you what the people thinking the hardest about it are finding out. We don't know everything, if we did we would stop. Cornelius' world-view is that the Bible (as he interprets it) is correct and the universe must fit into that tiny little corpuscle of his imagination. He is intellectual stagnation. What has he offered to explain the diversity of life on the planet? What evidence does he have to back up those ideas? Mostly, he seems to spend his time making glib inaccurate posts that misrepresent evolutionary thought. I'm sure that appeals to his readers, but it kind of pisses me off that he lies (commandment IX). (In his defense he doesn't use swear words like those I've used in this post including bullshit, ~~ass~~, shit, and fuckwad, oh wait I didn't use that word I just thought it....crap....double crap. Someone get Cornelius a couch to faint on.)

I know it's not an echidna

Origin of Species Book Club

2012-01-03T18:09:00.000-06:00

OK, hopefully everybody has a copy or access to a copy of Charles Darwin's Origin of Species. Although it is not in the book, I am reading the 6th edition based on the fact it has Chapter VII Miscellaneous Objections to the Theory of Natural Selection. Those of you reading earlier versions will not have this chapter. Alright, this week I'm reading 'An Historical Sketch' and 'Introduction' and will get a post up Sunday. I look forward to your thoughts and comments regarding these readings when the post is up.

Creationists Respond and Spanked

2011-12-24T11:34:00.001-06:00

I put up a post the other day in response to a question I was asked. It must have been one of my better ones because it has raised some creationist hackles. Of course there are significant issues with comprehension, which doesn't surprise me based on their understanding of basic biology.

First to come at me is Cornelius Hunter who seems to get the vapors when adults use bad words like dumbass, which he writes as dumb***. I mean really? See, in this make believe world writing things like 'fuck' is bad, but writing things lke 'f@ck' is acceptable. The meaning is not important, its the order of the letters that imparts some magical power, like CONSTANTINOPLE.

Cornelius starts by using the example of a poker game where each person has an amazingly strong hand. He then states that everyone know the hand was rigged. This is another example of an inappropriate 'what are the odds?' scenario I addressed in my previous post. I'll let him speak for himself.

For instance, evolutionists claim that all the evidence supports evolution. Amazingly, they say there is no contradictory evidence, no scientific problems to deal with.
When I first heard this argument I was astonished. But when you are certain you are right, then any and all arguments must support evolution.

What is this contradictory evidence? Does poker constitute evidence? Show me where a scientist has said there are no scientific problems to deal with.

'But when you are certain you are right, then any and all arguments must support evolution.' is laughable coming from a creationist. Pot, Kettle?

You can see an example of this claim here where an evolution professor calls some mathematicians dumb***** (while issuing several other profanities) and assures his readers that he is “unaware of any general concerns with the theory of evolution that is not steeped in religion.” One reason the professor makes this monumental scientific blunder is a fundamental yet typical misunderstanding of our second principle above.

I stand by that claim. We do not understand everything, unlike you apparently. This is why we still do research and continue to ask questions. How much do selection and drift contribute to the evolutionary process? How do genome duplications promote speciation? But these are not general concerns with the theory. Instead of handwaving on your fainting couch about my f*cking word choices, tell us a general concern with the theory of evolution that is not steeped in religion?

While it was obvious to most of us that the poker game was rigged, evolutionists make another one of their losing arguments to get around the problem.

Is that your concern, the theory of evolution does not fit with your cute analogy? Well unfortunately your analogy sucks (I hope sucks is ok on his delicate sensibilities). Cornelius quoted my points using the lottery to show how trivial it is to get big probability numbers for his readers, he then did the sweet little trick of using that against me.

There you have it. The creationist is wrong again. All of biology isn’t improbable any more than winning a million jackpots. All outcomes are equiprobable so a royal flush, CONSTANTINOPLE, and yes evolution, are not at all unlikely.

Of course, he left off this little part of my post that is kind of relevant.

The assumptions used to make the calculations regarding evolution in the first place are suspect (wrong is a better word, fraudulent is the best word because those making these arguments have had it explained to them before). For example, the assumption in these types of calculations is that there were a bunch of chemicals and then WHAM these chemicals came together to form the first cell. First, no scientist worth her salt has ever made such a claim, although a lot of creationists have. I don’t want to get into a discussion about the origin of life in this post, but I do want to stress that I have never seen the absurd idea that cells just poofed into existence fully formed from scratch except by creationists. Irony alert: creationists think life zapped into being en masse by god, but ridicule biologists for thinking cells zapped into being en masse by evolution (even though biologists don’t think that).

I pointed out that scientists don't think life is like the lottery system (or his poker analogy). However, he ignores that and continues to suggest scientists do think that and then uses that to tear down evolution. That's called a Straw Man fallacy. The person who continually does it is an *sshole, I mean asshole. (I'll point out profanity is not in the commandments, but lying is.)

Second, to come at me is the Discovery Institute. It makes me a little sad that the traffic coming to AbC from the DI, the flagship of the creationist movement, is less than from Cornelius. The sadness is that I may send a couple of page views their way.

Anyway, the DI post is nothing but a rant that seems to be written be someone who will may be institutionalized soon.

An anonymous professor at the University of Minnesota writes a blog that came to our attention because he tries to knock down not an actual argument for intelligent design but the most simplistic parody, provided to him not by any actual ID advocate but by an unnamed female friend whom he quotes:

It's pseudonymous, not anonymous and why does that status of my friend's identity matter? Also, if you read the post (or at least didn't lie about it), then you know I was not knocking down an argument for ID. I was answering a question asked by an 'unnamed' friend. Oh wait, it's right there in that sentence you wrote. So you're upset I responded to a thoughtful question someone asked me?

Replying under the title "Evolution: Time Is on Our Side," the professor-blogger not only doesn't write under his own name but is cagey about what department he teaches in -- though he says he has "a background in Biochemistry and Molecular and Cellular Biology." The blog itself is called, promisingly, "Angry by Choice."

How is it cagey? It says right in the about section available in the top right corner of every page of my blog "Oh, the opinions expressed here are my personal viewpoints and not those of my employer, family, or dog." Yes, my blog name is promisingly named Angry by Choice, like yours is promisingly named 'Evolution News and Views'. Unlike my blog, which actually has attitude that I choose to use as my voice (hence the name), your blog is a creationist mouth piece. I love the suspicious style used by this anonymous writer on a website that does not allow commenting.

Then there's a paragraph that tells their readers I made fun of them (I didn't mention the DI at all, though I did mention creationists), suggests they have rebuttals to my points, and then hits us with none of those rebuttals.

Maybe Dr. Angry is ticked off because he couldn't cut it at the U. of M.'s elite Morris campus, where our buddy PZ Myers teaches. Even PZ seems more familiar with the Darwin-doubting arguments he derides than this fellow does, and surely everyone knows that if you want to refute an idea convincingly you need to go to a sophisticated presentation of it and argue against that. To make things really easy for Angry, we suggest that he do a word search here at ENV for the phrase "probabilistic resources."

Really? I love the insult me, the entire UMN-Morris campus, and Professor Myers at the same time. You guys are precious. Regardless, let me grant that their 'probabilistic resources' are correct (they aren't, this is simply for the sake of argument). Go to the post in question and read the first part. Initially there was a mathematical argument to think the Theory of Evolution as proposed by Darwin was not correct. However, that mathematical argument was subsequently shown to be based on incorrect assumptions. The ID movement argues that their math nullifies all evidence that supports the Theory of Evolution, from fossils to genomics to observations of populations over time. Isn't it possible that maybe, just maybe, their assumptions are wrong (they are).

Finally, DI ends with this.

But we're not holding our breath. This is how these folks always respond to probabilistic arguments against Darwinism (or materialistic origin of life scenarios). They implicitly treat the prior probability of alternatives such as ID as being vanishingly close to zero. Therefore, something like Darwinian evolution must be true, since we're here. So whatever the improbability, the actual proves the possible, and there's only one possibility worth considering.
Which just goes to show that no argument is sufficient to persuade the committed materialist. It doesn't follow that there aren't good arguments available for the open minded.

See, they suggest I do something (and presumably every scientist that understands evolution) and then come back at them. They then assume I won't and conclude that no one ever will. I understand that position. They have made the same arguments for decades, been responded to numerous times, and ignored those responses. It makes sense they assume everyone else acts the same way.

Although in this case they are right. I don't have the time or the emotional energy to read their crap now, although Behe's Darwin's Black Box is on my shelf of books to read. I suggest they or their readers look a the ruling on the Kitzmiller vs. Dover trial on teaching Intelligent Design.

Evolution: Time is on Our Side

2011-12-21T19:16:00.001-06:00

A friend of mine asked me the following ‘I just learned that mathematicians assert (not necessarily in an argument to support God) that there hasn't been enough time for the theory of evolution to be viable. I'm making an assumption you have been aware of this given your profession and scientific mind and I'm curious of your take on this.’

My initial response was along the lines of ‘I don’t have time for a substantive response at the moment but the short answer is that some mathematicians are dumbasses.’

This represents my more substantive response because I know she is interested in an actual answer. A problem comes from the nature of the question itself. I do not know the context with which these statements of mathematicians came up. Was the discussion with an actual mathematician or is this some second hand remark made by a stealth-creationist. (Although the conversation may not have been directly related to a god concept, I am unaware of any general concerns with the theory of evolution that is not steeped in religion.) What was the conversation that led up to this point? I do not know the answers to these questions, but I have a couple of educated guesses what the context was, but if I am far from the mark my friend can let me know and I’ll add another post if needed.

So my two thoughts on how a conversation related the issue of mathematics and time for evolution can be grouped into the following categories: 1. Historically Inspiring; 2. Tedious Probabilities.

Historically Inspiring (please be this one).

The theory of evolution is a dramatically different beast from that first outlined by Charles Darwin in the 1859 publication Origin of Species. (This is not a drawback of science, it’s a feature. Science progresses.) When Origin of Species was written, geologists had calculated the age of the Earth as 20 - 400 million years old. By geologists, I refer to Lord Kelvin of absolute zero fame. My friend may remember Lord Kelvin from Mr. Daigle’s chemistry class as the person who calculated absolute zero as -273°C or 0°K (the K stands for Kelvin). Anyway, Lord Kelvin calculated how long it would take the Earth to cool to its current temperature if it started as a molten ball and came up with a range of 20 - 400 million years in 1864, 5 years after Darwin published.

Kelvin ultimately settled on a more narrow range of 20 - 40 million years. Regardless, Kelvin believed this was too short for evolution to explain the diversity of life on Earth. You know what, Charles Darwin concurred. Darwin knew that his theory requires that the Earth to be extremely old. In the first edition of Origin of Species, Darwin argued that the time necessary for erosion to form the Weald in England is at least 300 million years (But we would also need to factor in the time to deposit all the material to be eroded among other things, which brings us to an age of billions of years). However, based on Kelvin’s calculations, Darwin removed these arguments from later editions of Origin of Speices and referred to the problem (or Kelvin) as an ‘odious spectre’ in letters. To be clear here, both scientists had data to back up their claims, but Darwin was quite cautious in his claims.

Smarter than me, but
still totally wrong

The interesting point is that Kelvin was flat out wrong. Based on what was known at the time, Kelvin’s approach was defensible. However, this was before we knew about radioactivity. The Earth did cool, but it is not simply a loss of heat issue, as assumed by Kelvin. Radioactive decay generates heat, and there is a lot of radioactive decay within the planet. Kelvin thought the Earth’s core was solid and that all heat transfer was by conduction (wrong on both counts).

By making a number of assumptions, which were defensible at the time, Lord Kelvin mathematically derived an age of the Earth that undercut the Theory of Evolution as well as most of geology. However, data was already in existence that suggested the Earth was much older than the age calculated by Kelvin. As more knowledge was gained, it became clear that Kelvin’s assumptions were invalid and thus his calculation wrong. Turns out the Earth is ~4.5 billion years old, which is plenty of time for geological formations to arise and giraffes to evolve. Interestingly, molecular geneticists have calculated that the last common ancestor of life lived ~3.6 billion years ago, which is not long (relatively speaking) after the planet formed. Supportive evidence for these dates comes from the earliest fossils, which are ~3.4 billion year old bacteria.

(Point of reference, Kelvin, a faithful Christian, calculated that only a moron can believe the Earth is a few thousand years old.)

Tedious Probabilities (probably this one)

Another common way to try and use math to disprove the theory of evolution is to misuse probability. The idea is to come up with a probability statement and then use that to show there is not enough time in the age of the universe for life to have occurred. If the odds against an event happening are so huge, it is impossible for the event to have occurred within the time frame the universe has existed. There are two problems with these approaches. First, it is trivial to come up with probabilities that sound impossible for events to occur even those for those events that have already happened. Second, those making the probability statements make assumptions that have nothing to do with biology or reality for that matter.

Making big numbers to impress those not used to big numbers.

Let’s start with a simple probability idea and work our way up. If we get a penny and flip it, the chance of it coming up heads is ½ or 50% (the other possibility being tails of course). The odds of getting heads twice in a row is ¼ (½ x ½) or 25%. Similarly the odds of flipping a coin and having it come up heads and then tails is also ¼. We can take this a little further, the chance of flipping a coin 10 times and having it come up heads each time is 1/1024. 1/1024 is the same as 0.0009765 or 9.77x10^-4 or ~1x10^-3_. It’s about 1 time in a 1000. The important thing here is that the odds of getting any specific combination of heads and tails in 10 flips is about 1 in a 1000. However, if you flip a coin 10 times, you will get a specific combination. I just flipped a nickel 10 times and got T(ails), T, H(eads), T, H, T, H, H, T, H. Was the chance of that happening 1 in a 1000? Well, it was before I flipped the nickel the first time, but now that it has happened the chance that it happened is 100% or 1/1.

When making these kind of arguments, the person picks a really big number to be awe inspiring, like the number of atoms in the entire universe. The number of atoms in the entire universe is ~1x10⁸¹, which is a 1 followed by 81 zeros. Everyone knows the universe is really fucking big (what’s bigger?) and atoms are really fucking small, so it makes intuitive sense that the number of atoms in the universe is probably the biggest big number of them all. So, if you can come up with a probability that is greater than the number of atoms in the universe, it must be impossible right?

Remember when we flipped the coin 10 times above? The odds were ~1/1000 (a 1 followed by 3 zeros) that any specific sequence would come up. Well if we flip that coin 270 times, the odds of it coming up heads every time, or any other specific sequence, is 1/1.9x10⁸¹. If I flip that coin every 15 seconds, it will take me just over an hour to get enough flips to get a sequence of heads and tails. If we calculate the odds of getting that sequence ahead of time, we get a number greater than the number of atoms in the universe! Using the creationist logic, then it was impossible to get the sequence of 270 Heads or Tails we just got.

Catnip for dumbasses

Maybe a more current analogy is in order. Powerball! The odds of a specific set of Powerball numbers coming up is 1/1.9x10⁸ (1 time in 190,000,000 tries. Face it, while someone will win occasionally, you won’t). The odds that the last 3 drawings would give rise to the numbers 13,28,49,51,59, 33; 2,24,46,52,56, 19; 4,19,33,41,59, 9 is 1 in 6.86x10²⁴. However, these numbers were in fact drawn. On Dec 9^th the odds were 1 in 6.86x10²⁴ now they are 1 in 1 or 100%. The difficulty with thinking about these types of calculations is that we forget that although any specific event may by improbable, a specific event will happen.

Just to get a number bigger than the number of atoms in the universe, the biggest big number, let’s go back 12 Powerball drawings, which would be drawings that occurred over roughly the last month (11/9/2011 - 12/17/2011). The odds of all the specific numbers being drawn were ~1/2.21x10⁹⁹ which is more than the number of atoms in the universe by 1,000,000,000,000,000,000 times (10⁹⁹ - 10⁸¹). Ergo, those numbers could not possibly have been drawn! But these odds were only true before the Nov. 9^th drawing. Again, the odds today are 100%, because this event already happened. It’s pretty easy generating really big numbers to sound impressive, but just because someone has a big number doesn’t mean he knows how to use it right.

Which leads us directly to the second problem here, the assumptions.

The assumptions used to make the calculations regarding evolution in the first place are suspect (wrong is a better word, fraudulent is the best word because those making these arguments have had it explained to them before). For example, the assumption in these types of calculations is that there were a bunch of chemicals and then ...

...these chemicals came together to form the first cell. First, no scientist worth her salt has ever made such a claim, although a lot of creationists have. I don’t want to get into a discussion about the origin of life in this post, but I do want to stress that I have never seen the absurd idea that cells just poofed into existence fully formed from scratch except by creationists. Irony alert: creationists think life zapped into being en masse by god, but ridicule biologists for thinking cells zapped into being en masse by evolution (even though biologists don’t think that).

The ‘calculations’ I have seen use assumptions like the following. Let’s assume that a cell needs 100 different proteins to survive and a protein is on average 100 amino acids long. (This is great because then the creationist can then honestly state that these are conservative estimates. As far as we know a cell needs more than 100 types of protein to live and proteins average length is more like 300 amino acids. This serves to make the result of the creationists argument that much more impressive.) With these (wrong) assumptions, what are the odds that the 20 kinds of amino acids will randomly come together to form all these proteins simultaneously to allow for a viable cell.

Using these assumptions, which have nothing to do with reality, the following ‘calculations are made. The chance of a single protein randomly assembling is 1/1x20¹⁰⁰ the denominator, as you know, is a number bigger than the total number of atoms in the universe. Add in the factor that you need this to happen 100 times (for each protein). It ain’t never gonna happen! CHECKMATE biologists, the theory of evolution is impossible.

Of course, no biologist thinks or suggests that the above happens. But why let reality interfere with your delusions.

To summarize:

There was a legitimate concern about the age of the Earth and whether there was enough time available for evolution to explain the diversity of life (and geology to explain the geological formations around us). This concern was resolved soon after by physicists and geologists.

Probability is poorly understood and can be used quite effectively to convince people of erroneous ideas. This provides a chance to reinforce the importance of critical thinking and skepticism.

It is easy to demonstrate something cannot be true if you are comfortable being a liar. First, misrepresent the position you are arguing against. Second, make up a bunch of bullshit premises you state represent the position in question. Third, show why the position is wrong because the bullshit premises are bullshit.

If that does not address you question, please let me know.

Regardless, if it wasn't clear enough, here is what the Rolling Stones have to say on the matter.

Origin of Species Book Club

2011-12-13T18:57:00.001-06:00

Ok, back on the 150th anniversary of the publication The Origin of Species by Charles Darwin, I wanted to read The Origin of Species and blog about it at the same time. Too many distractions came up, so I didn't finish the adventure, but it is time to revisit it. So, if you want to join me, we'll start the first of the new year. If you do not own this book yet, the bonus is that you can put it on your wishlist. Im reading the version depicted to the right. Although I previously read about a third of it, Im starting fresh from page 1 and will try to do a chapter a week.

So who will join me? Already read it? maybe this is the time to read it again. I'ld start now, but I need to finish the mind numbing 'Science and Religion' book shown under the what (apologetics garbage) I'm reading list first.

I'ld like to have a healthy discussion about the various chapters and we can see where this goes. Again if you haven't read it, now is your chance to read it with others, without having to put on pants and go out!

Student Blog Posts: Read 'em and Comment

2011-12-03T10:18:00.000-06:00

There is a new blog Traveling Small with a Nucleus I want to draw your attention to. It is on the writings of students from my Eukaryotic Microbiology course. Go and read them, enjoy them, and comment if a spirit moves you to do so.

Misplaced Gratitude: God 1 Teammates 0

2011-12-03T10:05:00.001-06:00

Probably all of you know Tim Tebow, the starting quarterback for the Denver Broncos, is a man of great faith and conviction. If you don't know, he'll probably be stopping by your house soon to let you know. Now I'm sure Tebow is a great guy (Actually, I don't have a fucking clue, he could eat puppies for breakfast for all I know.), but he is also a tremendous boor.

Jesus' QB

Look I know it's Christmas season and all and some of the faithful need to make sure Jesus is brought up at every opportunity, but Tebow does this non-stop 24/7. Many, most, football players are believers and many of them pray before and/or after games, point to the sky after a good play (presumably to god, but maybe to honor a deceased relative or friend), etc. But for some reason Tebow is different and gets tons of media attention about it. The difference is that he is totally in your face about it. This is the guy that had bible verses in his eye black in college and starred in the anti-woman superbowl commercial.

Well Jake 'the snake' Plummer, former Arizona Cardinal and Denver Bronco QB, was interviewed recently and when asked about Tebow made mostly positive supportive comments, but also noted:

“Tebow, regardless of whether I wish he’d just shut up after a and go hug his teammates, I think he’s a winner and I respect that about him,” Plummer said. “I think that when he accepts the fact that we know that he loves Jesus Christ then I think I’ll like him a little better. I don’t hate him because of that, I just would rather not have to hear that every single time he takes a good snap or makes a good handoff.” Read more here.

Of course when someone is questioned about their faith or the proclamation of their faith, much pearl clutching must ensue. Most of it is pointless, but Tebow was asked about this in an ESPN interview and I find his response compelling.

"If you're married, and you have a wife, and you really love your wife, is it good enough to only say to your wife 'I love her' the day you get married? Or should you tell her every single day when you wake up and every opportunity?
"And that's how I feel about my relationship with Jesus Christ is that it is the most important thing in my life. So any time I get an opportunity to tell him that I love him or given an opportunity to shout him out on national TV, I'm gonna take that opportunity. And so I look at it as a relationship that I have with him that I want to give him the honor and glory anytime I have the opportunity. And then right after I give him the honor and glory, I always try to give my teammates the honor and glory.
"And that's how it works because Christ comes first in my life, and then my family, and then my teammates. I respect Jake's opinion, and I really appreciate his compliment of calling me a winner. But I feel like anytime I get the opportunity to give the Lord some praise, he is due for it."

First, Tebow as a never married virgin is probably not the person to be using spouse analogies. Not surprisingly, his analogy blows. It is a failure in extremes. Is it really a choice between telling your significant other "I love you" on your wedding day (sorry homosexual community, you're not allowed to say it at all I guess) or at every opportunity? Every opportunity? Really? When do you talk about your day or thank them for some kindness or ask to pass the salt? I realize that probably is not what he meant, but it is what he implied. Do you know what I call someone who talks incessantly about their significant other? A tremendous fucking boor!

Go to a friend's house for a nice meal. Afterwards, talk about how your spouse is such a tremendous cook and how the meal you just ate makes you think about being home to eat your spouse's meal. Comment on how well kept your spouse helps keep your house and how your spouse's job is really awesome and how great your spouse is at their job. My spouse is smart and personable and a joy to talk too....How long before you are politely, or not so politely, asked to leave and go back to your fucking spouse.

The thing that irritates me most is how over-the-top Tebow is with thanking god for every fucking little thing. Maybe you should thank your receivers for practicing so hard and putting their bodies on the line to catch some of those ducks you throw (nope god put the ball in their hands). Maybe you should thank your, albeit not that dominant, offensive line for blocking the 300 lb defensive linemen trying to put you on your ass. (nope god makes the linebackers trip). Maybe you should thank the opposing team defenses for laying down in the fourth quarter (nope god takes away their spirit). If the other team starts praying more, will they win? Can we simply count up the number of 'Hail Marys' said and choose a winner and not waste the 3 hours playing the game? It is misplaced thankfulness.

Why not thank those who work hard? Don't thank the surgeon who replaced your child's heart, thank Jesus. When the TV camera is in your face, don't thank the firefighter for going into your burning hose to save your dog, thank god.

Does your faith give you a sense of purpose and place? Great, good for you. But don't let that interfere with gratitude and appreciation for actual real people doing actual real things. Why not thank the real people first (Doesn't god already know you love him? If so, what if he was watching the other game, would he still not know?)

Why Students Cheat

2011-11-27T12:13:00.138-06:00

As a member of an academic integrity committee at my university I have learned a lot of things. Some of these things I wish I hadn't. Maybe the better way to put it is Im glad I learned these things, but wish the problems did not exist to have to learn about them.

Over the last year, we have had many discussions about cheating at the collegiate level. These discussions have been driven by a number of distinct, though related, factors. Regardless, work by Donald McCabe was recently brought to my attention. Now I have not followed the literature on scholastic dishonesty, although I am starting to become more familiar with the 'genre'. First, I was not actually aware there was a body of literature, because I thought the problem was too small. Yes, students cheat. Students cheated when I was a college student and students cheat now. But I do not cheat, therefore I assumed most others do not cheat.

Donald McCabe

A 2010 report of >40,000 high school students suggests that 60% cheated on an exam and 80% of students copy homework. Interestingly, it didn't matter if you were male or female, planning to go to college or not, played varsity sports or not, were a student leader or not, or attended a public or religious school, the only group that showed significantly reduced numbers were those (few) students attending a private non-religious school. While this study was for high school students, not college students, I think the habits/patterns students come to college with are important. A vast majority of students copy homework. I cannot say Im surprised about this one. I remember high school and how many assignments seemed like simple busywork with no real point. I expect much copying occurs on those irrelevant practice problems you didn't have time to do because of band practice or you had a basketball game. I think the issue is that once copying is common place or feels acceptable, what effect does that have after high school? Does the ability to decide that homework assignments are not worthwhile help establish a sense that the student decides which assignments matter? Does copying someone else's assignment make it is easier to rationalize copy-pasting assignments? I was surprised by the level of cheating an tests, 60%! Again, it mattered little if the student was college bound or not (59% or 68% respectively), in honor's or not (56% or 62% respectively), or active in the CharacterCounts! program or not (62% or 58% respectively). (CharacterCounts! is the organization that conducted the study.) This data contradicts my own bias that it is the struggling or apathetic students that cheat. Apparently no such difference exists. So what does this mean about the standards and ethics of the students entering our colleges or directly entering the workforce?

So there is a problem in our colleges. Cheating is endemic and occurs institutional wide. Of course we should probably figure out ways to deal with it, but it is probably important to try and understand why students cheat in order to prevent or at least reduce the incidence of cheating most effectively. Luckily McCabe has already done the hard work for us in the form of confidential surveys. Students themselves tell us why they cheat and I think there are some important things to think about.

First, it's the students themselves. (I'm doing this one first because it fit into my bias that there is something wrong with those who cheat. The nice thing about this mindset is that the solution to deal with cheating is simply punitive.)

1. 'Students cheat because the class is too hard.' Well boo-fucking-hoo. Welcome to the real world. You don't have to go to college, you don't have to take the class. Maybe if my required class is too hard for you, maybe you should find another major because maybe, just maybe, you are not cut out for the field.

2. 'Students cheat because they don't like the class.' Since you do not have a vested interest in the material, all rules of ethics and appropriate conduct are moot. Now that is a value system I think society will be happy to know is coming.

3. 'Students are paying a ton of money to take the class.' Ah the old entitlement argument. Yes, you are paying a ton. In fact I would argue that you are paying too much. But even though money is changing hands, you are not a customer, therefore the concept 'the customer is always right' does not apply. Your payment allows you the chance to strive to get those grades and that degree. Diplomas are not handed out once your check clears. It was a lot cheaper to go to school when I went and I was able to get by with a part-time job and some modest loans. College students often are working 30+ hours a week while taking full credit loads. I point out to my students that university policy states that a 3 credit class should equate to an average of 9 hours of work/week for a student to get a C grade (ergo more hours to get a better grade, in general). So if you are taking a 15 credit load, that equates to 45 hours a week to obtain a C. If a student sleeps 7 hours a night (not enough), devotes 50 hours a week to studies (in order to get a couple Bs), works 30 hours a week, spends 2 hours a day commuting to school, work, and home, then that student has ~2 hours a day (every day) to eat, shop for necessities, breathing, wash the car, etc. It is virtually impossible to take a full credit load and work even 30 hours a week and expect to do well.

4. 'Students cheat because the professional world teaches them it's ok.' Pretty much true isn't it? How many people went to prison or even lost their jobs following the financial collapse? We had to deregulate the banking industry and look what they did with that newfound power. Of course, the financial crisis has nothing to do with corporate greed, it is all the fault of the poor who bought houses they couldn't afford. Look at our political leaders, how many obvious unethical acts happen in Washington and are actually punished? Charlie Rangel anyone? Newt Gingrich anyone? One's still in office and the other is the current frontrunner for the republican ticket for president of the US. So really, at even the highest levels, we are teaching students that cheating for personal gain can be acceptable and that the ends do indeed justify the means.

5. 'Students cheat because all the other students cheat.' I have some sympathy for this one. It really is a fairness issue. If you know that your colleagues are cheating and getting good or even better grades than you, then what can you do? You could bring it to the instructor's attention, we are not as omniscient as we want you to believe we are. Still the 'if everyone jumped off a bridge, would you?' adage comes to mind. (Full disclosure, my friends and I used to jump off a bridge into the Saccarappa River in high school.)

(Actually, we jumped off the wall to the left of the electrical tower on the left of the video.)

Second, what about the faculty, do they play a role in student cheating? Obviously, the faculty are not actively helping students cheat, but are they indirectly contributing? What do faculty do or don't do that may make cheating acceptable.

1. 'Faculty would report cheating but there are no rewards.' The old, I would do something about it, but what's in it for me? Really? This strikes me as another sense of entitlement response. If there is nothing directly in it for me, why should I do it? How about dealing with issues of fairness the students brought up a minute ago? If you know students are cheating and doing little about it, then you contribute to the mindset outlined above. I expect that most colleges/universities have policies dealing with issues of cheating. For example, all cases of cheating at my university must be reported to the appropriate office. (The instructor has complete control over the action to be taken regarding the incident, but the information needs to be provided to the central office.)

2. 'Faculty would report cheating but it's too much work.' Another for the 'boo-fucking-hoo' file. I guess students who have many things pulling on their time are not allowed to pick and choose what to do ethically, but faculty who have teaching, research, families, and other things pulling on their time can freely pick and choose what aspects of their jobs to do ethically.

3. 'Faculty would report cheating but it's an administration job.' No it's not. This seems more a glorified version of #2. How is it a job for administration? Your class, you have to report it to get it into administrations hands in the first place. Have you at least done that? Didn't think so.

4. 'Faculty would report cheating but the administration puts up too many roadblocks.' Well, now I can commiserate. It is a pain to deal with a student who has cheated. I am not talking about the paperwork and process, just the mental energy required. We are disappointed in the student and ourselves, we realize the ramifications reporting could have on the student (yes, it's their own damn fault, but it still sucks). Of course some roadblocks are real and some are imaginary. Speaking of my own experiences and my institution the direct roadblocks were mostly imaginary. Yes there is paperwork to fill out, but it is not too onerous. Basically, what happened, what did you do, and did you tell the student. It is important though, because students have rights. Once the report is filed (remember it's your job to do it) the student is notified and can appeal the instructor's sanction. The appeal is heard by a student-faculty board and the sanction is almost uniformly upheld. However, instructors can and do make mistakes, so this is an important committee to have in place. I would point out that generally the instructor does not even have to attend the appeal session. (I point these latter issues out to offset concerns that it's a lot of extra work for instructors and that students can use this system to readily get out of the repercussions.) Now that I've established that there are few direct roadblocks, there are indirect roadblocks. We used to have a student group that discussed cheating, including plagiarism, and why it's an important issue to new students. This group was disbanded in large part because the administration thought it sent the wrong message, 'we have a cheating problem'. (I expect to hear that the administration will also disband the police department to avoid concerns over a 'crime problem'.) This attitude sends the message to faculty that the administration takes a 'see no cheating, hear no cheating, speak no cheating' mentality and that of course leads to faculty not seeing and hearing cheating, and certainly not reporting it.

5. 'Faculty would report cheating but I'll get hurt in the student evaluations.' This is not so much a case for me, but I know of situations where this is an issue. It is well documented that student evaluations, both good and bad, have little value. Evaluations and earned grade is tightly correlated. However, if renewal of your contract is in part based on student evaluations, you don't want to fail a student over plagiarism. At least one school, removes the evaluations of students sanctioned for academic dishonesty, which can help offset that problem (although the student's friends might still nail you in the evaluations).

6. 'Faculty would report cheating but we don't want to hurt the student's future.' This one did not come from McCabe's studies, but I've heard it numerous times. See it apparently not the student's fault they cheated, it's the instructor's for reporting it. That's a great approach especially when we are shipping these graduates off to run businesses, become doctors, lawyers, etc. Part of this probably stems from the fact that many instructors do not know what happens to reports of cheating at our institution. Basically, reporting serves two functions, to ensure students know their rights (again faculty make mistakes) and to have a history. When a student in my senior level course cheats, it probably isn't the first time. However, from my perspective it is the first time. If I report it and there is a history of previous cheating, the university can now step in and potentially suspend or expel the student.

Third, what about the institutional role? Does the institution play any role in establishing conditions that tacitly promote or actively reduce cheating? (Short answer: Yes.)

1. 'The institution contributes to student cheating by promoting faculty adherence to policy.' As noted above, most, if not all, colleges/universities have policies related to academic dishonesty in some form. However, having a policy does no good if there is little to no adherence to it. Having a policy is good, but colleges/universities have a huge number of policies that can be inundating to the faculty. Some ways to get around this is to organize the policies into easily identifiable units (Teaching policies). Since everything has moved online, there needs to be a simple way for faculty to be able to find and access it. If I've spent ten minutes searching for the policy on cheating and have come up empty, I'm probably done looking. Sending timely and appropriate reminders to faculty regarding policies is helpful. Send the links to policies related to teaching a couple weeks before each semester starts, send the links to policies related to research whenever a research grant is funded, etc. If faculty are aware of the policies, they are more likely to be responsive to them. If the administration makes it clear that these policies are important (by making it easy to find and identify them for example), it encourages faculty adherence.

2. 'The institution has an honor code and stresses its importance.' This appears to be one of the most critical factors in reducing student cheating. Schools with a strong honor code have less endemic cheating than those without one or that have one but do not support it. It's important not only to have an honor code, but to have student involvement with maintaining the code. If there is student buy in at the get go, there is student support. Students are more likely to report cheating by colleagues when it is viewed as an honor code violation. For this to happen, the administration needs to be actively involved. If the administration is actively involved and the students are actively involved, then the faculty will have to be onboard as well.

These latter two points I thin can be filed under the idea of community establishment. If students are part of a community (even if it is a large university), then they have a vested interest in its and their reputation. Things like honor codes and student involvement serve to establish a sense of community.

Here's an NPR interview with Dr. McCabe from 2010 on cheating. I also encourage you to look at the associated story and check out the comments to see many of the above issues described.

We Have a Winner

2011-11-22T17:40:00.002-06:00

My favorite 'philosophy of science' blog Evolving Thoughts had a contest last month. Well it was more of a raffle than a contest. Regardless, the prize was a signed copy of Dr. Wilkins book Species: A History of an Idea. (Since the prize still exists, should the previous sentence be in the present tense?) The results of the raffle are in.....and I'm a winner! Well, I'm a winner anyway, but I also will be the recipient of the aforementioned scholarly work.

So is the point of this post just to gloat?
No. The point of this post is not just to gloat, although that certainly is one of the points.
It's also to introduce to the Evolving Thoughts, which has a plethora of outstanding posts on biology, philosophy, and assorted topics. If you have some time to invest, I highly recommend some of the beefier posts found under the 'Ideas' tab.
It's also to share my excitement on having a text on the species concept. Right now the best book I have dealing, at least partially, with the topic is Ernst Mayr's The Growth of Biological Thought. I think the species concept has too much historical baggage and am not convinced that it is particularly useful in modern biology.

Paramecium, nice to meet you

2011-11-20T10:23:00.001-06:00

How many of you recall one of the first cool science related thing you experienced? I bet if you think about it, even if you no longer give a rat's ass about science, you can come up with something from childhood. Maybe seeing puppies or kittens being born, watching a frog or butterfly develop from a tadpole or caterpillar respectively, seeing light split into diverse colors through a prism.

Malamute puppies

Prism

Chrysalis

I can think of two things that got me hooked on the wonder and awesomeness of biology. One was 'discovering' my brother's microscope. It's a single eyepiece light microscope. I still have the beast and it still works, although it needs a new bulb. Once this device was discovered, it opened a whole new world to me: pondscum. That was when I was first introduced to a beautiful little beast. I didn't know its name or even what the hell I was looking at. What I did know is that it was love at first sight. Now I admit our relationship faltered when I met colecovision and was ruined when I realized the opposite sex was more than just a cootie factory. However, it ignited a longing that burned deep within me, forever influencing my...well let's not get overly dramatic.

The shear awesomeness that comes from seeing these little beasts swimming around in the pond behind your house with your own eyes, well eye since it was a monocular scope is inspiring. Here's a video using a much better scope than I had, which I hope can give you an inkling into that sense of wonder that arose in a child.

There are many aspects of Paramecium biology worthy of discussion: separation of 'somatic' and 'germ line' nuclei, the trichocyst, digestive progression, whole genome duplications, macronuclear development, RNA editing, endosymbiosis, etc. We will touch on a few of these in the next few weeks.

In God You Trust

2011-11-04T20:08:00.000-06:00

I cannot tell you how happy it makes me that the House of Representatives took it upon themselves to reaffirm the national motto of 'In God We Trust', Thanks douchebags, all 396 of you including my own representative Betty McCollum. Thanks for telling me that despite being born and raised in the United States of white heterosexual christian parents who themselves were born here of whit heterosexual christian parents who were also born here, I am not part of this country. I am not a member. In God We Trust. Thanks for promoting the hegemony and giving power to the tyranny of the majority.

As an atheist I do not trust in god. So that means I am not part of the 'We'. Since this is the national motto (for the last 55 years anyway, for the first 180 years we didn't have a motto about god), I guess I don't rate as part of the nation.

So to better ingratiate myself with the ~~borg~~ religious collective I will do the following,

I will:
trust in god to prevent hurricanes if more people pray more.

trust in god to prevent floods in a floodplain if more people pray more.

trust in god to stop the volcano from erupting once we throw a virgin girl in.

trust in god to protect my property, though not my neighbor's who believes differently.

trust in god that my football team will win if more people pray.

trust in god that the douchebag at work's basketball team will not win if more people pray.
trust in god to cure my treatable illness without modern medical interventions.

trust in god to look out for my family when I die.

trust in god to destroy the muslims.
trust in god to destroy the christians.

trust in god to destroy the buddhists.

trust in god to destroy the pagans.

trust in god to be better than all the other gods.

trust in god to make me superior to other races, sexes, nationalities, ethnicities, generations, and other people I don't particularly like.

trust in god to become corporeal in bread, me eat him, and it not be cannibalism.

trust in god that I will go to heaven because I am baptized.

trust in god that babies go to heaven even if not baptized.

trust in god that heathens go to hell regardless of age.

trust in god that undifferentiated cells are people.

trust in god that undifferentiated cells are not people.

trust in god to burn all the gays and lesbians in hell (unless there's the potential for a hot 3-way).

trust in god to allow gays and lesbians to minister and preach god's word.
trust in god that marriage is forever.
trust in god that divorce is ok too.
trust in god that gays destroy marriage.
trust in god that its ok to keep slaves.
trust in god that keeping slaves is an abomination.
trust in god that I get to rule my wife.
trust in god that I also get a bunch of virgin to screw when Im dead.

trust in god that he has actually had sex with a virgin and knows why this would be a good thing.

trust in god that there are unforgivable sins.

trust in god that all sins can be forgiven.

trust in god that only 144,000 people go to heaven and Im one of them.

trust in god that I am blessed, but the 12 year old starving African who is victim of countless rapes is not.

trust in god that by happenstance of my birth I get a free ride to heaven.

trust in god that voting on mottoes is a useful job of congress.

You know what? God as an idea seems capricious and arbitrary. Maybe it's not so bad being an outsider.

Loraxian Superheroes: Voting No were Rep. Jerrold Nadler (D-NY), Rep. Gary Ackerman (D-NY), Rep. Justin Amash (R-Mich) (You totally kick ass Mr. Amash!!!), Rep. Judy Chu (D-CA), Rep. Emanuel Cleaver (D-MO), Rep. Mike Honda (D-CA), Rep. Hank Johnson (D-GA), Rep. Bobby Scott (D-VA), and Rep. Pete Stark (D-CA).

Loraxian Heroes: Voting present were Rep. Keith Ellison (D-MN) and Rep. Melvin Watt (D-NC).

The Daily Show
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Its Official: Fungi Kick Mammalian Butt

2011-10-26T21:06:00.000-06:00

Bats with WNS

Since 2006 certain species of hibernating bats have been dying off in dramatic fashion by what has been called White Nose Syndrome (WNS). It is named as such because of some fungal growth around the nose of many affected bats. In 2008, Blehert and colleagues identified the fungus as Geomyces destructans and showed in early 2009 that the fungus was widespread throughout affected populations. In previous posts on these issues, I raised concerns because there was no data demonstrating causation. In fact, while noting that G. destructans could indeed be the etiologic agent of WHS, I also noted that it could be an indirect effect of some underlying problem. For example, the bat immune system could be impaired by a biological or chemical agent that allows G. destructans to infect and ultimately kill the bats (akin to HIV in people).

Well Lorch et al report in Nature that G. destructans is directly causing WNS in bats. Lorch et al essentially test the third of Koch's postulates, which are:

1. The microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms.
2. The microorganism must be isolated from a diseased organism and grown in pure culture.3. The cultured microorganism should cause disease when introduced into a healthy organism.
4. The microorganism must be reisolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent.

Now even Koch realized his postulates are not universal laws. For example, asymptomatic carriers kind of screw over postulate #1 and non-culturable organisms make #2 an impossibility. However, when fulfilled even partially, these postulates provide powerful information in the etiology of disease.

In the case of G. destructans, postulate #2 was fulfilled previously. In the study by Lorch et al, postulate #3 is shown to be true. If you grow G. destructans in culture and then expose healthy (but susceptible) bats to the fungus, they get l00% infection (Treated in table below), but similarly treated, but without the fungus, control animals should absolutely no development of WNS. More than 95% of infected bats succumbed to WNS within 3 months on infection! (Although it sucks for the bats, this provides definitive evidence that the fungus is the causative agent of WNS!!!1111!

Nature Table 1 (partial)

Furthermore, the authors found the fungi in lesions on the wings where most of the disease damage is thought to occur (despite the 'nose' being part of the name). This helps fulfill postulate #4.

This work is important because it affixes a firm target on the culprit. We can rule out other biological or chemical agents causing susceptibility to WNS. This also helps deal with postulate #1. Postulate #1 has been a complete dick in the case of WNS. This is due to the fact that G. destructans is found associated with European bats that are healthy. What Lorch et al's work tells us is that the situation is more complex than initially realized (but the truth of the matter is that life is always more complex). Maybe European bat species have immune mechanisms that prevent WNS. Maybe the G. destructans strain in the US is more pathogenic than the European isolates. Regardless, these are testable hypotheses. We can also definitively add mammals to the animals fungi feed on. Happy Halloween!

Lorch, J., Meteyer, C., Behr, M., Boyles, J., Cryan, P., Hicks, A., Ballmann, A., Coleman, J., Redell, D., Reeder, D., & Blehert, D. (2011). Experimental infection of bats with Geomyces destructans causes white-nose syndrome Nature DOI: 10.1038/nature10590

Amy Dickinson: Dumbass

2011-10-10T18:29:00.000-06:00

Amy Dickinson: First ever awardee!! Grats Amy!

This week in the Star Tribune advice column (it's next to the crossword so I often read it), Amy Dickinson responds to a young adult grappling with their non-belief. The concerned 16 year old no longer wants to attend services and is worried that when the subject is broached, their mother would enroll them in some kind of religious counseling. Admittedly, this is a tough one and these kinds of discussion can tear families apart. However, it is my experience that it is the religious person that tears the family apart, not the non-believer. The religious authoritarian mother or father can not abide the non-believer/gay/evolution supporting/democratic/sexually active child and throws them out or worse. Now these specific parents may be completely ok with their child having different beliefs, but there are reasons why this 16 year old may be concerned.

So what is Amy's 'advice'?

You could show how mature you are by seeking the advice of your clergy on your own before discussing this with your folks.
This is a familiar issue, and a compassionate pastor may actually encourage your parents to give you more space.

Yep, if you do not believe a certain religious dogma, then you should seek the advice of the sellers of the dogma. If you want to stop smoking cigarettes, don't consult a doctor, go see a Philip-Marlboro representative. If you are concerned you are gay, don't talk to a counselor with expertise in sexuality, go see Marcus Bachmann's faith-based reorientation counselors.

Did it occur to Amy that the clergy member has a vested interest in retaining this soul for Allah, Jesus, Zeus, whomever? Yes, a compassionate pastor may be helpful, but is it worth the risk to the 16 year old to take this chance? What if you are wrong Amy? It is worth noting the 16 year old is concerned about being entered in religious counseling. Doesn't that suggest the parents may not belong to the most empathetic sect on the planet? Why send the young adult to the clergy and not a humanist? It seems Amy's advice serves to cater to the parents' potential needs and not the 16 year old's.

Critical Thinking: Can It Be Taught?

2011-09-30T21:09:00.001-06:00

Rodin's The Thinker

This represents that last and a long time coming post on 'critical thinking' that derived for a number of reasons. I previously discussed 'what is critical thinking?' and 'is critical thinking worth teaching?' In those posts I suggested that critical thinking is a skill set that allows one to establish the veracity of an idea, data-set, etc. and to develop logically cohesive ideas, hypotheses, etc. and Yes, it is worth teaching. In this post, I want to hit on the questions 'Is it possible to teach critical thinking?' and 'If so, how does one teach critical thinking?'

The first question is easily answered 'yes'. The second question is generally avoided usually with some muttering and lack of eye contact. Teaching is hard. Teaching a skill is harder. One thing that makes teaching 'critical thinking' to college seniors difficult for me is that these students have done relatively little of it. Period. On those few occasions when they were doing it, it happened almost by chance, there was no instruction into the process. How many essays have students written? lab reports? compare-contrast assignments? These are all easily 'critical thinking' activities. However, if the critical thinking aspects are not taught in a useful context, it makes little sense and does not stick.

I recall being taught the philosophy behind different types of writing styles. I also remember being taught some extremely basic philosophy of science. But these activities were done in high school, without any context! In college, when it came time to write lab reports, the focus was on the formatting, the style. Does the report have an abstract? Are the results in the past tense. When I had to write a report on Russian Foreign Policy in Afghanistan compared to US foreign policy in Vietnam the focus was on the formatting. Is there a clear comparison or contrast statement? Were the references formatted correctly? We have a disconnect in our teaching. We teach things piecemeal. I learned about compare-contrast essays in English, there was no connection to these types of assignments in history or math. I am not suggesting changing entire curricula, but once students start going to different teachers for different subjects, there needs to be some overlap in the instruction. Math is important to science, science is important to history, history is important to health, health is important to art, art is important to english. What we currently teach is that once you leave class A, you enter a completely different silo called class B. After several years of this kind of training, we can not teach logic in 10th grade english and expect it to carry over to chemistry.

So how does that relate to 'critical thinking'? Well the answer goes back to my definition of 'critical thinking' as a skill set that allows one to establish the veracity of an idea, data-set, etc. and to develop logically cohesive ideas, hypotheses, etc. The point is that we, as teachers/parents/adults can teach 'critical thinking' in all of our classes, during our day-to- day interactions, and even in the car. It's actually quite easy in principle, you need to ask questions. The hard part is asking the 'right' questions. In my primary teaching assignment, I have incorporated some socratic teaching methods. I ask questions, get responses, ask more questions, get more responses, and we move forward together. It can be as simple as asking how do the authors (of this paper) know that? or how would you test this hypothesis? Students will frequently and spontaneously engage in mini-debates when discussing some issue. To teach 'critical thinking' is to teach students to ask questions. When we teach high school students about various logical fallacies in sophomore English class, other teachers need to use some of those fallacies in their history, music, and physics classes. All teachers should be asking their students to think, to come up with their own ideas, to follow a thought process to its end regardless of whether you know the end is futile.

I remember one of my high school english teachers. She was not the most pleasant teacher in the school and ultimately became the assistant principal (if that provides any insights into her personality). It was the first year we had summer readings and many of the books became some of my favorites: Exodus, 1984, and Anthem to name a few (others sucked like Fountainhead, I never did finish that one). When we were discussing 1984, Ms. Teacher, who I don't think cared for my casual approach to school much, asked me what happened at the end of the book. My guess is she assumed I hadn't read it (a la Fountainhead), and she could use this as a way to take me down a peg. I told her Winston gets killed by the state. She told me I was wrong, big brother only killed him metaphorically. The person he was was dead, but the human was still a living breathing entity. I disagreed and she asked me to back up my opinion. So I went to the passage near the end about the bullet entering his head and argued that the passage made no sense as a metaphor. I also noted that earlier in the book, Winston notes another character that big brother had 'enlightened' who was soon to be killed because that was what happened. Big brother tortures you into believing in big brother, releases you for others to see, and then kills you when it no longer matters. She still said I was wrong, but she backed the fuck off after that. As much as I thought said teacher was basically a troll (in the pre-interent sense), I appreciated the fact that she challenged us, or at least me. She is the only teacher I asked to sign my high school yearbook.

So how does one teach critical thinking? I don't know, but I know what I do. I ask questions. I'll take just about any response and go with it. Even a piss poor response that is fatally flawed because of confusion over transcription versus translation can be a teaching tool. You know who I do think teaches 'critical thinking' by demonstrating it?

Jon Stewart.

Watch The Daily Show for a week. Virtually all of the first two segments every night is an exercise in critical thinking. Stewart and team take something said by a politician or seven or some big issue and asks questions about it. The questions are tacit, but they are there.

For example, one of the most poignant segments ever deals with the taxes and poverty.

The Daily Show With Jon Stewart

Mon - Thurs 11p / 10c

World of Class Warfare - The Poor's Free Ride Is Over

www.thedailyshow.com

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The questions that were tacitly asked and addressed are plentiful.

As another example we could ask some critical thinking questions about the uproar over Chaz Bono on the all important show Dancing with the Stars (really? stars?). Thankfully, we don't have to, Lewis Black already did (plus he hit on apple juice too).

The Daily Show With Jon Stewart

Mon - Thurs 11p / 10c

Back in Black - Threats to America's Children

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Daily Show Full Episodes

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I think this is one of the main reasons The Daily Show has done so well over the years, they ask the questions we do not take the time to ask or do not know how to ask. And since not everyone gets Comedy Central, we need to take the time to ensure we truly do teach critical thinking skills to as many people as possible.

Plus, we already have too many damn sheeple.

DADT repealed:God to Smite Us in 3, 2, 1...

2011-09-20T18:10:00.000-06:00

Its official, DADT is repealed. Being psychic, I predict that within 5 minutes of the next natural or man-made disaster some religious leader douchebag will say said disaster is due to Big Sky Daddy being all pissy about it.

The More Things Change

2011-09-05T05:40:00.003-06:00

I have my disappointments and concerns about the Obama administration, but it seems the republicans haven't changed much in 80 years.

(AbC also just passed 50,000 page views. Some sites get more than that in a day, but it's still a milestone of some sort. UPDATE: I just realized that these numbers are since moving to FoS, not from the inception of AbC.)

Some Suggestions for Studying

2011-08-28T14:06:00.001-06:00

Since a new semester is about to begin I think a post on how to study would be apropos. So here is an advice column for students looking for some techniques to improve their study habits. I am not an expert in learning, but I am an expert in being a college student with no fucking idea how to study and had to figure it out over the course of a year or two. I was one of those students who didnt have to do much to maintain an A/B average in high school. Although I was exposed to study skills and habits while in high school, none of it stuck because I really didn't need to study to do reasonably well. So here is what I learned that worked for me. If you have your own successful techniques, please feel free to add them in the comments.

Learning is an active process, it requires energy. It may not be as physically taxing as a 45 minute work out, but then again you my not be doing it right. What I discovered is that I learn when I do things, when I engage the material, when Im an active participant. If its a couple of days before the big exam and you're wondering to yourself 'What's the best way I can study? I know Ill take some time to play online and get some tips.' Well, if this is you, you're fucked or at least I don't have anything for you. Come back after your upcoming exam, my advice might help you for the next exam. Right now, you are in cram mode, so you better start cramming not wasting your time reading blogs. I will admit that cramming works, to a degree. Cramming is a short term solution, getting enough material under you belt to survive or even succeed at the exam. But it's a long-term problem. Are you really in college to survive exams and classes? That was really high school wasn't it? Cramming is problematic because the material is never actually learned, it may come up again on the final, it will likely be important next semester or the semester after that in your more advanced classes. Learning and cramming both take energy, but the former is far less stressful and provides both short-term and long-term gains.

Step 1. Find an environment to study in. Ultimately this became at my desk in the bedroom of my apartment. I also kept my stereo close to police notification level. I learned quickly that I could ignore the music, but sounds from the street, from the kitchen/dining/living room area, or from anywhere outside my room were distracting. To this day, when Im working on grants or papers and do not want to be disturbed, I close my office door and crank up some music. Although I am a chaotic person by nature, my desk was neat and organized. I needed a place to work comfortably and that was it. My textbooks and notebooks were stacked in/on some milk crates I used for shelves. (These of course were the store bought kind of 'milk crates' not the easily available sturdy and inexpensive milk crates available behind 7/11s, like the one across the street of my apartment. Although if they were the illicit version, which they weren't, they would have been returned when I moved to go to graduate school.)

$0.69 for 3 in 1989

Step 2. Get a bunch of notebooks. I used spiral bound notebooks available for next to nothing at drug stores. Of course these notebooks will have absurd cover designs or pictures you would never in a million years gravitate towards (see picture of my Molecular Biology notebook). That's not the point. The point is what's inside the notebook, and that will be gold. I mixed up the designs on the notebooks I bought so I could easily identify which one I wanted. The alternative is to be flipping through them wondering if this is the black notebook Im looking for. Get one notebook for every class you take (except maybe for the golf/tennis/etc classes). Any class that has a lecture has its own notebook. No cheating by getting a three-subject notebook. Also, get a couple of additional notebooks.

These things are evidence of evil

Since you're at the drug store all ready, get some pens and pencils. I love pens, but despise cheap ass ball point pens. You'll be using these a lot, so get pens/pencils you are comfortable with. Make sure you get a variety of colors. I survived with black, blue, and red, but there is a veritable palate of colored inks now. Get what you love or at least can tolerate. I prefer mechanical pencils, but if you get classic ones, you better kick in for a decent pencil sharpener or two. Also grab some highlighters also in assorted colors.

Step 3. Do the readings strategically. Chapter 3 is covered Wednesday? Read it through by Tuesday night. That isn't very strategic is it? The strategy is to skim read the text. Get a sense of what's in there and what will be the likely topics and points for the upcoming lecture. You don't need to be more than familiar with the material. (In the case of labs, this is not true. You must be intimately aware of the material, because you will be using that information in the lab. Hell, there may even be a quiz on the lab manual!)

Step 4. Go to class. Although you probably couldn't pass a quiz on the readings material, the vocabulary is familiar. Now you already know a bit about the upcoming lecture. Gather up your pens and pencils and one of the extra notebooks. Leave your textbooks at home, along with the highlighters, and other notebooks. You don't need much.

Get to class on time and get a good seat. In large classes, I recommend a seat near to the front and in the middle where the professor can actually see you. Why? Psychology that's why. Take two students doing equally well, one student the professor recognizes, even if there is no name associated with the face, and one student the professor has barely, if ever, seen. If both come to discuss an issue regarding an examination or writing assignment, which one will have at least a sub-conscious advantage?

Open your notebook to page 1 get out a couple of writing implements and get ready. If the professor has handouts or, god forbid, print outs of the slides, then definitely pick them up, but DONT use them during the lecture (with rare exception). Your job is to take a shit ton of notes. Don't worry about neatness and perfection, just get the stuff written down. Write down the points on the slides, the drawings, incorporate what the professor is saying. The very act of writing things down is helping you learn the material. 'But we have the slide print outs, so why write stuff down?' you ask. In my more youthful days I would have responded with 'Because we didn't have the material presented to us, so stop being so fucking needy.' But in my dotage I think an example is better. What is another name for a television? Did 'idiot box' spring to mind? There's a reason for that. Some people watch tons of TV, these are not inherently the most educated people in the world. My mother loved to watch soap operas during the 70s, hours of soap operas. She was not an expert in social interactions because of this nor was she an expert story teller, she just watched a lot of soap operas. This is one of the biggest impediments to learning, fucking handouts. Remember I said learning was an active process. Lectures are not television. You should be doing something not just watching. The problem with handouts is that it facilitates the TV watching mentality. There are reasons to hand out the notes, which is why you are collecting them, but wait until later to use them. For now, take a shit ton of notes. Do not be tempted to put notes in the margin of the print outs, you bought the cheap ass notebook, so use it. (Plus you'll want a pristine copy of those hand outs for later.) So, you were in class sitting in a strategic location, you took a shit ton of notes, now what? Go to your next class and repeat using the same notebook.

Notes on chromosomal
melting temps.

Step 5. THE MOST IMPORTANT STEP: The next day. So you went to all your classes, even the ones you think are boring, and you took a bunch of notes, even on things you think you know already. Now what? Hang out with friends, watch TV, play some Xbox, then go to bed and the next day go to all your other classes. At some point on this second day, you need to carve out some studying time. When depends on your schedule. I did this in the mid-late-afternoon, because I was generally done with classes then. Go to your studying environment, get out your notes from yesterday, one of the fresh notebooks that will be specific for a specific class, any handouts, and your textbook. Now you will rewrite your notes in a more organized and legible manner. As you rewrite, you will refer to the text for additional points, and in your class-specific notebook you can either incorporate the textbook material or simple refer to the page numbers/figure numbers. Either redraw or cut out the handout figures you need and add them to your notebook. This could take as long as the original lecture, but probably won't. Regardless, you are now learning some serious material. The act of rewriting helps embed the information into your memory, by organizing the material in a manner that works for you (which is probably like it was presented) you are thinking about the material in total not simply one fact after another. You are also reading the text in a more in depth way, which is easier because you already skimmed it and went to the lecture. Do this for those boring easy classes too. It helps maintain good study habits and instead of simply learning the material, you'll own it. Another benefit is that if you do this, you will know before the next lecture what material you may not understand. This gives you a ton of time to meet with your colleagues, TAs, professor to get things straight.

Step 6. When you finish going through the crappy notes, rip out the page(s) and throw them away. You don't need them anymore because they are rewritten and you'll feel good about the progress you made.

I won't guarantee these steps will improve your grade, but I do guarantee that they will improve your understanding and knowledge of the material.

Additional thoughts:

A. Write in your textbooks, at least highlight important information. I used different colored highlighters for different purposes. Red was for definitions, blue was for what I thought were key concepts, red was for things referring to my class notebook. Will writing in your textbook reduce its value when you resell it? Well hopefully you will not resell it. Having that chemistry textbook could come in handy when you need to revisit something you forgot in your molecular biology class. If you absolutely do not want the book, why buy it in the first place? Probably you could borrow one from a colleague or use the library.

B. Scheduling. You need to prepare ahead of time when things are getting done. If you don't, you will almost certainly get behind or not have enough time. If you want to go to that party or game, you may need to start rewriting your notes earlier than normal to make sure you have enough time to finish before going out. Also, there will be several big assignments due for other classes throughout the semester, you'll need to be prepared for catching up on those notes you couldn't rewrite the day after class. (Don't get more than a class or two behind or you'll defeat the purpose of rewriting.)

C. Turn off your phone. You can survive an hour or two without reading all those awesome texts and facebook postings coming in. A 30 second distraction actually amounts to much longer, because it takes time to get back to where you were before you were distracted. Every time you break focus, you are back to a more superficial level of learning and it takes some time to get back to that deeper level.

D. When it's test time, you'll find it much easier to study. The material is already there in your mind because you've been through it at least twice already. You may have to pull an occasional all-nighter, but it will be different than the cramming you did previously.

Notes for a recently submitted grant
from a relevant paper.

E. For the record, I still use these techniques to prepare grants and papers (see photo). I do a lot of background reading and have notebooks dedicated to taking notes on the papers, complete with different colored pens. This allows me to make connections and think about the material in a much deeper way than I would be able to otherwise. Same for seminars I attend, I bring a notebook.

With those words of advice,
Good luck and have a great semester!

Precision: why we should not submit

2011-08-24T21:30:00.004-06:00

An On Scientific Writing post.

One aspect of scientific communication that is essential in both oral and written modes is precision. Scientific writing should be precise. Of course, we know have to define what it means to be precise and maybe the best way to do that is to use some examples. As you read each sentence below picture the image the sentence conveys to you.

1. "An animal went into a building," is a fairly vague sentence.
2. "A cat went into the brick building," is a lot more specific.
3. "A Siberian tiger went into the brick hospital," is more specific still.
4. "A sick Siberian tiger went into the brick animal hospital on 4th St," is the most specific example to date.

Now I expect you imagined something completely different with the different sentences, particularly sentences #3 and #4.

One of the points I want to emphasize is that words have meaning. Depending on the word choices we make, we can communicate effectively or we can communicate in a much less efficiently. This is precision. In the case of science writing I prefer the 'distinguished from every other' definition of precise. You want to be clear when you write and one of the ways you do that is to use the most concrete and direct words possible, a sick Siberian tiger vs an animal, a building vs. the brick animal hospital on 4th St.

One problem in trying to be precise is the invention of fucking pronouns. Pronouns breed imprecision. In your science writing the mantra should be 'pronouns are used with extreme prejudice.'

The car was parked on the street, it was blue. What was? The car? The street? Fucking pronoun.

Another problem in trying to be precise is that the meaning of a word is somewhat fluid, words exist in cultural contexts, and the definition of a given word can evolve. Our language conspires against us. Now we could take the relativistic approach, throw up our hands, and give up. I prefer to take the bit by the teeth, get my hands dirty, and actually try to communicate. (This latter approach is generally worthwhile if you happen to live amongst other humans.) The point is that we have to be vigilant and thoughtful by the time we have completed our writing (the emphasis on the finished product is intended because, if we worry about 'perfect' word choices while we are drafting, then we will never get out of the starting gate).

Jack and I went to the gay parade yesterday. Meant something slightly different in 1911 than it does in 2011.

which brings us to 'submissive'. When you read the following, what does 'submissive' mean?

"Tax law? I hate taxes," she [Michele Bachmann] continued. "Why should I go into something like that? But the lord says, be submissive. Wives, you are to be submissive to your husbands.'" CBSNEWS.

In the universe Michele Bachmann inhabits, submissive = respect. In my universe, submissive means something a little different. Things like relinquishing power to another, compliance, to be subservient to, cowed come to mind. Respect? not so much.

In my quest to obtain the Bachmann quote, I stumbled across a site that provided the following opinion regarding Bachmann's ~~submissiveness~~ respect.

According to Karen Seat, a religious studies professor at the University of Arizona, some conservative evangelicals argue that women’s deference is itself empowering, because it’s what God intends, and because it is the fullest expression of womanhood. In this world of opposites, submission is strength and inequity is proof of equality. It’s quite possible that a President Bachmann would primarily define herself not as the first female president of the United States, but as a wife and mother. And she would not see that as anything less than progress.

But of course we have always been at war with Eurasia.

On scientific writing

2011-08-20T07:01:00.002-06:00

In science, communication, both oral and written, is a critical skill. I know the stereotypical scientist is some extremely awkward asocial geek or nerd (at least when they aren't maniacally evil). Of course this is not true¹. Although an argument can be made that scientists are not necessarily good at communicating with the general public, to be a successful scientist you need to be able to discuss your work and the work of others and to write papers/grants/etc effectively. Unfortunately scientific communication is skill that is often developed on the fly.

¹OK, Ill admit physicists really are awkward.

I argue that we should be teaching scientific writing early, at the undergraduate level. But unfortunately for undergraduate students, at least in the life sciences, a few stock lab reports, the occasional 10-20 page essay, and maybe a research project thesis represents their 4 year scientific writing experience. More problematic however is that there often little instruction given to the writing apart from the different sections that you need to include (abstract, introduction, etc.). As instructors, we rely on the English department, at best, or high schools, at worst, to teach students how to write. This generally leads to failure. The failure is not due to poor instruction by the English department, but due to the fact that the mission of the English department is not to teach scientific communication. The College of Biological Sciences (CBS) wants to rectify this issue by promoting student writing at the undergraduate level and providing some cohesion in writing instruction throughout the college.

CBS tries to get faculty cohesion in writing instruction.

To date I have been involved in a number of meetings (we're good at that) with colleagues to define the goals for CBS student writing. In part, we developed a list of the characteristics of science writing, realizing that a review paper and lab report have some different characteristics. Over the last two years, I have been introducing more writing and writing instruction into my fall semester course and I am continuing that trend this year. So with a few years of experience plus a small number of 'student writing' focused meetings under my belt, I will be posting (yet another probably never finishing) series regarding science writing.

This was supposed to be the first post in that series, but my introduction got so long the point was going to be buried. So I decided to make this an introductory post, another will follow shortly.