Field of Science

Damn Dirty Apes

You take some time from blogging about all the cool science going on, railing about the culture war, and generally typing to hear myself think, and the spambots start to flood the comments.

So, I have introduced some measures to help reduce the bots. Grant goes out this week along with another paper, then hopefully will have some time to get some blogging in...

Blogging the Origin

Alright a couple of points before we even get started. Before the actual book is a historical perspective and introduction written by Darwin. Take home message, ideas and thoughts about the origin of species had a long and noble life before Darwin. The decades leading up to 1859 had a fair number of ideas related to species the environment and diversity. (Actually it is harder to believe this wouldn't have been the case, many people had many animals and plants and exposure to many more animals and plants. You just can't miss the diversity out there, the effect of the environments on organisms, and the intrinsic problem with trying to organizing life into understandable units.)

The introduction is essentially an extended abstract of the book. Darwin briefly explains the point of each chapter so you know what's coming.

OK, once I complete chapter 1 Ill be back with a few notes on thoughts from said chapter "Variation Under Domestication"

Response from a non-football fan aka debate attendee

While I was not able to attend the seminal debate between PZ Myers and Jerry Bergman addressing the question "Should intelligent design be taught in the schools?" several of my colleagues did. (Big shoutout to my peeps.) One attendee had a particularly eloquent synopsis for me that they kindly said I could post. I have included a few comments, in black, and only edited for anonymity.

... you didn't miss much. PZ did clean up the floor with Bergman. But I have to be honest - Bergman was so disorganized and so off topic the whole time I almost felt sorry for him. He came across as someone dangerously close to having a treatable mental illness. He squandered most of his opening 20 minutes blithering on about his own upbringing (although he conveniently failed to describe his sham PhD). In one sentence (and he did this *multiple* times) he would go from the irreducible complexity of quarks (I kid you not (thank you Sarah Palin for ruining this phrase)) to the multiple functions of the human appendix to the horrors of Nazi Germany. There was just no following the guy. And oh - the delusions of persecution (another sign of psychiatric pathology). There are apparently scores of ID-loving biologists in fine universities across the country who are afraid to "come out of the closet" for fear of losing their jobs. In spite of this, they have published about 1000 (Bergman's number) papers in the scientific literature on ID. Of course, there was not a single citation offered, nor an explanation as to how one gets published from in the closet. Pseudonyms? (Clearly, I gravitate to those of a more sarcastic nature)Bergman himself has been ostracized from the Jehovah's Witnesses (he was one for years) and the atheists (he was one for years), and now all his Nobel laureate friends won't write back to him now that he's an ID'er. That last one sounded like a pretty bad delusion of grandeur to me. And - it was all on Powerpoint slides. He never actaully answered the question, which was Should ID Be Taught in Schools? He did go on and on about his own groundbreaking work in the development of MRI and other imaging technologies and his cutting-edge research on mutations in cancer cells. Oh - and he was among the first to prove that so-called junk DNA isn't junk after all. Hard to believe that a CV like that can't get you a better job than at a community college in Ohio .....In any event, he (Jerry Bergman) freely admitted (multiple times) that ID has no actual stated theory, mechanistic explanations for how things work, empirical data to go on, or predictive power. But, since evolution is only (his words) "From the goo to you, by way of the zoo" then ID must be right. How *do* you debate someone that far off the rails?

PZ was spot on, and used what I thought were several interesting tacks besides science. For instance, he pointed out the ethical responsibility teachers have when they agree to work within a curriculum and framed it in a very compelling argument.
(This is a great point until you realize how tenuous the hold of science is in these issues. If the curriculum is changed to a creationist one, then teachers would also have a legal, note I didnt say ethical, responsibility to work within this curriculum. Cheri Yecke almost derailed the last Minnesota science standards, not to mention Kansas, Texas, Florida, etc.) He also talked about how new ideas in science get vetted, starting at the highest levels, and how ID has attempted to do an end-run around the whole process.

Sadly, but not surprisingly, there were plenty of bible-clutching home-schooled teenagers there drinking the koolaid with their parents/teachers. One teenages had the ignorance to trot out the "But it's *only* a theory" whine when the Q&A started. PZ answered it beautifully, without condescension.
(Clearly a missed opportunity)

(and probably the most important point my friend made was....)On the whole, I doubt a single mind in the audience was opened or enlightened, much less changed (and herein lies our greatest hurtle). One debater was prepared and focused, and the other would probably benefit from medication.

Many thanks for giving me a run down of the "debate" and allowing to post these comments. And I truly am sorry and wish I had been there to see PZ toss his notes over his shoulder when he realized they would be superfluous.

More fun the football


"Should Intelligent Design Be Taught In The Schools?"

Monday, November 16, 2009
7:30pm - 9:30pm
St Paul Student Center
2017 Buford Ave S
University of Minnesota
St. Paul Campus

I mean come on, Baltimore is going to crush Cleveland...although ID will likely make the Browns look good.

Real Americans Wanted

Thanks Michelle Bachmann. Thank you for being the poster child of uncivil discourse. Thank you for leading the masses into a vitriolic hate-laced frenzy that will inevitably lead to more people getting hurt. Now I freely admit Representative Bachmann is not the only one using this approach to effect policy, but she always seems to be smack in the middle of it.

Socialist, Fascist, Death panels, elitist, DemocRAT, the list goes on....but now we have "real Freedom loving Americans." This is to compare with those Americans that are less real and hate freedom.

Let's back up a minute and think about human nature. What is it that allows people who love their parents, their children, their neighbors to do horrible despicable things to other people? How does someone torture, murder, maim one person but go home to hug their spouse and tuck in their children only to spend the night worrying over a sick pet? You know what, let's be completely honest for a minute. Instead of torture, murder, and maim, let's you actual events that happen. People mutilate each other, sever hands, breasts, tongues, gouge out eyes. Rape, gang rape, sodomize others. Will kill one member of a family in front of another, will burn human beings alive.

I guess we can assume that people who commit such acts are really inhuman. But frankly I think you're kidding yourself and are abjectly horrified to look in the mirror. African fighters that mutilate children and innocent men and women are different, they aren't like us. We say that as we embrace Jack Bauer obtaining that vital information in any way possible. We say that as we allow Dick Cheney to walk free and happily laud his role in legalizing torture. You know because when we do it, its different.

Regardless of your politics, I think there is one important psychological trait that allows church going family members to be evil (and that's really what we're talking about). That trait is making the human being you are torturing, about to murder, raped no longer a human being in your mind. Once you have separated a person from the circle of humanity, it becomes possible to justify anything as morally legit.

Every year at this time I set a bunch of traps to eliminate the field mice that move in when the weather changes. Im not a fan of killing cute mammals, I rescue moles from the window wells in the summer and release them in the woods. But I separate these field mice from the circle of cute mammals but throwing in a destructive pest criteria. This allows me to easily set the traps and dispose of them. It allows me to euthanize those mice that were caught but not killed without regret (except that they werent immediately killed and suffered in the short term). It allows me to set glue traps, when the spring traps continually fail. I think it less quick and more stressful on the mice, but they need to go and I can't keep fattening them up on peanut butter. That's how I sleep at night killing field mice. You might be thinking, "come on, its just a freaking mouse, grow a pair!" I agree, its just a mouse. Now how do you think our neighbors that dragged a black man to his death, beat the homosexual to death, murdered women and children in Vietnam sleep at night? I think, except in cases of sociopathy, its much the same way. All you need to do is separate the person that you are torturing from the circle of humanity. Once they become the "other" anything goes.

And you know what? The faces of the republican party are excellent at establishing the "other." Michelle Bachmann knows a rat when she sees one. Ann Coulter logically deals with contra-arguments. But you know what, these people the Limbaughs Hannitys and Becks of the world tell us about, they aren't real, they definitely don't love freedom, and they are most certainly the "other." And since they are the "other" you may freely hate them. Despise them. Loathe them. And when one of you decides to torture murder maim and/or rape one of them, remember its ok. Because the "other" really isn't one of us anyway. But don't take my word for it. Im not even real.

Origin of Species - a bookclub

Happy 150th anniversary of the publication of On the Origin of Species by Charles Darwin. I started this book several years ago but quickly got bogged down with other things. I thought I would (re)read it and try to toss out a few post on my thoughts as I go. Maybe a post a chapter, we''ll see. I thought about getting Bananaman's version of the book but I wasn't sure what I would do with all the vomit.

Anyway, I recommend you all pick up a copy from the library, dust off the copy on your shelf, or even shell out a few bucks to a bookstore and read it with me. (although to be completely honest Im not going to burn through it so you'll probably finish it before me)

No Longer Proud

WTF Maine?!?!

Do you not remember this?
Have you not heard about hospitals refusing to allow same sex partners or their children to visit patients as they are dying?

Well good for you Maine.
You have protected the institution of marriage!

Remind me from what?
Is your divorce rate magically going down now to pre-May 2009 levels?
Less domestic abuse occurring?
Adultery, which never occurred before last May will now stop?

Or maybe your just keeping the good word of your god?
Banning marriage is one thing, but it shouldn't stop the divine retribution you might be concerned about.
So I expect the death penalty is back on the table?
Off to ban lobster fishing next I expect?

Any rationale reason why equality is a bad thing? I know many people (men) have the "eww" factor when they think of gay men kissing, so what many people (men) have an "eww" factor when they think of menstruation. Maybe reproductively mature women should lose their rights too.

Until I get a rationale reason to explain these results, Ill go on the assumption that Maine is populated with a majority of ignorant bigots. And despite the fact that I have a few dear friends and relatives in Maine, Im still sending a big FUCK YOU back home.

Amateur bioterrorism, now available at McDonald's

The Department of Homeland Security defines bioterrorism as "A biological terrorist attack would be the deliberate release of anthrax, smallpox, ebola, a plague, or another highly fatal organism in a large, unsuspecting civilian environment that would be conducive to the rapid spread of the organism."

Then I am made aware of this Craigslist posting:

11/1: Chicken Pox Party (Spokane)
Date: 2009-08-29, 12:29AM PDT
Reply to: [Errors when replying to ads?]

I am trying to put together a chicken pox party and am looking for someone to donate their chickenpox to the event.
I was thinking of having it at McDonald or some place with toys to play on.
if you know anyone who would like to contribute or would like more information on a time and place let me know.

Location: Spokane
it's NOT ok to contact this poster with services or other commercial interests
PostingID: 1348079907

I realize that there are many people that do not understand infectious diseases, public health, or science but this goes beyond the pale. I can even understand why parents may not worry so much about chicken pox. Many parents remember having chicken pox as a kid or knowing people that had it and it not being a big deal. Of course that overlooks the entire world of shingle's, but nevertheless I can understand it.

However, how whacked do you have to be to plan to have an infectious disease party in a public place!?!? I realize these parents care about their kids. Of course the parents that beat their kids out behind the tool shed also care for their kids. But in so many ways these parents are wrong, factually wrong. What is the risk associated with the chicken pox vaccine (and there is one)? What is the risk associated with chicken pox, including relapses later in life as well as costs to society by infecting others? I expect these parents have an idea about the former question (even if its overblown with fake autism linkage) and have no idea about the latter question except anecdotes and personal beliefs. (By beliefs I do not mean religion, but the belief that chicken pox is perfectly fine based on insight.)

Regardless, this parent and others like this one, is going beyond the pale. Its not sufficient to have an infectious disease party. Nope, you need to make sure its done in a public place where other kids, parents, teens, adults who think you are batshit crazy have no protective recourse. A fucking McDonalds?!?! Lets spread the virus all over the toys?!?! What the hell is wrong with you?

Couple of things to consider batshit crazy parent. What if there are other kids there who are in some way immunocompromised. You know maybe recovering from leukemia or other disease? I know, its not your kid. What about adults that never had chicken pox as a child and catching it could be fatal? I know, they're not your friends. What about the elderly? I know, not your parents.

Here's a thought, what if there is a small outbreak of chicken pox that is tracked to a specific McDonald's? Think that will help with business? I know, that's not your problem. That's what I despise about these people, they want all the freedom in the world but aren't actually willing to be a part of the society that helps maintain all those freedoms.

I realize terrorism requires some political or social coercion, but damnit how are these people not bioterrorists?

H/T Aetiology

Proud to be a Mainer

This is a bit dated, being from last Spring, but nonetheless it makes me proud to be from the state of Maine.

Reminds me of my greatgrandfather who lived in Guilford and also fought in WWII.

H/T Colloquoy via Greg Laden

Why we need healthcare reform

Not much brings out the hate like the healthcare debate in the US. The first thing we need to establish is whether we actually need healthcare reform or everything is hunky dory. As a first step I recommend the following.

An Archival repost

Francis Collins has just taken over as the head of the NIH. There has been much (rightfully so) discussion of his evangelical christian thoughts in regards to science and what has come from his work. However, as weak as Collins' philosophical arguments are here, I want to touch an a horrifying trend I see coming down from on high (in other words from the director of NIH).

As recently noted at WEIT there seems to be the idea that "Big Science" is better than figuring shit-out-science. One of Collins big credentials was administering the NHGRI, which is a plus, no doubt. But science is more than generating data, even copious amounts of data sufficient to choke a rodent. As I noted in the WEIT comments, any primate (or well trained mammal) can generate copious data points. It is true scientists that figure out what these data points mean, if they mean anything. Thus, I leave you with a repost, while I get back to my day job of trying (desperately) to keep people gainfully employed.

How related are you to a......?

You must check this out! Have fun with comparing your favorite Latin named organisms.

Time Tree

Plus, you can learn some cool things....

Like, Baker's yeast (Saccharomyces cerevisiae) and the oral thrush culprit (Candida albicans) diverged ~ 500 MYa
or that Baker's yeast (Saccharomyces cerevisiae) and people (Homo sapiens) diverged ~1300 MYa
or that Baker's yeast (Saccharomyces cerevisiae) and another yeast (Schizosaccharomyces pombe) (pombe is Swahili for beer :)) diverged ~900 MYa

So there's almost as much diversity between beer brewing organisms as there is between these organisms and people.

Mmmmm, beer

Rules of the game-Argumentation

Why do I like to argue? Ostensibly its because I like to win, but in reality I am interested in the truth or at least the closest approximation to "truth" we can get. If indeed the goal is to reveal truth, then there are rules we need to follow. (Actually this is in-and-of itself a supposition that could be argued. However, I am going to assume that if there are no rules, then truth cannot rationally be identified. This is like the underlying argument of a creationist, if god can just bring everything into being using no rational or understandable rules, then evolution must do the same thing: Thus, we hear the "never seen a dog evolve into a cat" and the "the odds of randomly getting a specific 100 amino acid protein is too great" arguments. These arguments are based on creationist understanding of how god did it, which was ruleless.)

As a primer to understanding argumentation, and to allow me to expand my own education into logic and philosophy I refer you to Dr. Wilkins excellent site Evolving Thoughts and his recent post on "A Code of Conduct for Effective Rational Discussion," and the references therein.

Obama's First Semester Grades

Obama completed 100 days in office and while 100 is a nice round number it doesnt have much significance as a time frame. A semester represents ~110 days depending on the year, state, school, etc. In a semester, there is the understanding that a significant body of material can be mastered (albeit, in my experience the material is often flushed down the toilet after the final).

Now President Obama is taking a full credit load. Using the issues posted on his website we have 22 courses! So lets grade each course and see how he's doing:

Civil Rights I Incomplete

Defense I Incomplete

Disabilities I Incomplete

Economy C Well we gave a lot of money to the ultrarich people, and gave a lot of nice words to everyone else. Its early so I won't be cynical yet, but call me skeptical. Credit card reform is in full swing and the auto industries have been dealt with fairly strongly. Also Obama has identified "science" as a major economic resource and begun to re-fund it.

Education B Not much has been done definitively but he has really pushed forward ideas for strong education and training as well as continuing education. He has noted the costs of education and he made some strides to begin addressing finances.

Energy & Environment B Words only to date, but he is generally putting great people in positions to give good advice.

Ethics D He has said some great things and then completely about-faced in practice. The idea of preventing lobbyists from working in the administration is reasonable but has been contradicted numerous times (Daschle for one). However, I do think the policy that prevents people in the administration from becoming a lobbyist for a significant time period (18 months iirc) after leaving is more important. Its too early to see if this will be enforced, but the backpeddling on the hiring lobbyist does not instill confidence. (Also, I would suggest that it is probably next to impossible in some instances to get top notched experts that are free from all lobbying, but I didn't make the ethics statement, Obama did.) Finally, this grade reflects the fact that Bush was as unethical as it gets and Obama basically rode that wagon, therefore expectations for Obama are high. 

Family C I waffled on a D. Obama is keeping the faith-based stealing of tax dollars started under the previous administration. Since some of the organizations getting this money are not big on "Family" unless they get to define all aspects of said family, I think this is detrimental. However, he has spoken specifically to parents to be involved in their children's lives and is setting an example with his own children by at least making some time for them.

Fiscal Responsibility D Basically allowed the unscrupulous to abuse the gullible (pretty much the GOP platform, that and no sex). So while the gullible are being forced to learn some responsibility (and rightly so), the unscrupulous are learning that its AOK to screw people over.

Foreign Policy I Meh, too early to tell. On the right path to regaining some respect in the world, but this will take some time. Let's see how the first major conflicts are dealt with (Iran or North Korea being likely sites of political conflict).

Health Care B Still all talk, but getting his ducks in row. Daschle was not a big plus here.

Homeland Security I Too early to tell, has reversed course on many promises regarding full disclosure, but has kept some. Much to Cheney's disappointment, no US cities in flames since the election.

Immigration I Not much happening on the front as far as I can tell.

Poverty B Tentative grade, giving big kudos towards tackling the credit card industry.

Rural I Not sure if Obama wants to urbanize rural areas or bring rurality(?) to urban centers.

Seniors & Social Security I Nothing to mention at the moment.
Service B Talks well about service and education (as a way to contribute to society). Michelle Bachmann is not a fan......of either.

Taxes I Basically not much to talk about yet.

Technology B Putting money into science, which directly leads to new technology. That's all good.

Urban Policy I See "Rural" above

Veterans Not much happening, but seems to see veterans a people not grist that fell out of the grindmill before they could fulfill their destiny as righteous matyrs to the lord American heroes.

Women  C Is putting many outstanding women in key positions in his administration. Always room for improvement.

Additional Issues I ???

So, giving a 1.0 for a D, 2.0 for a C, 3.0 for a B, and a 4.0 for an A and not counting incompletes I give the administration a grade pint average of 2.36 for the first semester, a good solid C approaching C+ range. I am not a fan of grade inflation so a C to me is considered a good starting spot. Also, this is not "average" in the sense that this is what an average citizen can accomplish, this is average from what we should expect from the president of the US. 

This is not bad, its average 

NETs: protection from pathogens or men

Alright a colleague of mine gave a talk a few weeks ago in an extremely informal format (yes booze was involved). Anyway these talks tend to be over-the-top excellent, not because of the content, but because they tend to be thought provoking. These are talks that have not been sterilized by the rigorous standards usually associated with polished talks. They often represent ideas without much data to back them up, pilot studies, etc. For this scientist, these are a blast!

Anyway, the talk was only peripherally associated with this post, in fact there were a couple of specific pictures shown and statements made that, in conjunction with some facts I am aware of, led me to the following thoughts. (BTW bitches, this is how science works at its best!)

First, you need to know about neutrophils. In short, neutrophils are one of the asskicking cells of the immune system (this is the system that has allowed you to live long enough to read this). When you are infected (and you are currrently infected with a bunch of things), your cells recruit neutrophils and other immunologic cells to the sites of infection to basically go ape-shit on the infectious particle's ass. Neutrophils are the kamikaze fighters of your immune system. While I am in fact being metaphorical here, in many ways the kamikaze analogy holds up well. When combatting infectious agents, such as bacteria or fungi, neutrophils act like suicide bombers secreting enzymes that are destructive or make destructive toxic chemicals that kill the infecting particle and the neutrophil (for the record the primary component of pus, the gunk you squeeze out of your forehead when combatting zits) is basically the carcasses of dead neutrophils that gave up their lives to the cause).

Now the self-sacrifice of neutrophils has long been known. However, it has recently been demonstrated that these dead neutrophils have an additional function. The DNA from these dead neutrophils is released into the environment and makes up a meshwork of DNA and enzymes that act essentially as nets to trap infectious microbes and kill them with the associated enzymes. These structures are aptly termed NETs (neutrophil extracellular traps) and are reviewed here (subscription required).

Now I realize all of this neutrophil biology is really cool, but what is the point?

Neutrophils, and other cells, can be extruded across epithelial cell layers into the lumenal environment of various tissues. In the vaginal cavity, neutrophils are extruded across the vaginal squamous epithelia where they can interact and kill resident bacteria. Now the vaginal cavity is home normally to bacteria, namely the Lactobaccili. However, these normal, commensal, bacteria do not cause neutrophils to do this. This property is left to non-resident microbes, in other words pathogens. When pathogenic bacteria and fungi colonize the vaginal track, neutrophils extrude through the epithelial cell layer, enter the vaginal cavity and attack the microbes, dying in the process, building NETs and continuing to kill microbes. The link between the microbe and the neutrophil is actually the epithelial cells. Epithelial cells sense the presence of pathogenic microbes and send signals to the neutrophils, essentially telling them to "CHARGE!" (More on this story in another post)

Now what's interesting is that sex also causes the same effect. Neutrophil extrusion. The question is why. My short answer would have been epithelial damage that occurs during the physical process of sex. Even the best sex causes some damage to the vaginal mucosa. However, that short answer would have been wrong, or at least incomplete. It turns out that if you simply add seminal fluid to vaginal epithelial cells, the epithelial cells respond to recruit the neutrophils. So vaginal epithelial cells respond to seminal fluid in about the same way that they respond to Neisseria gonorrhoeae bacterium. Which brings us to the painful fact, that for all you men out there, your significant others bodies still view you as a bad thing.

Now this linkage of neutrophil extrusion with sex makes a lot of sense. When you engage in sex, you are always taking a risk. No matter how much your partner swears fidelity, there's always a chance they are lying. So potentially your mate may be bringing something to the table you weren't planning on. Further, the female is at greatest risk here because of the physical trauma associated with the act and the fact most of the of the relevant secretions are within her body. So having a potent immunological cell dive into the frenzy to deal with these potential problems is a good, albeit untested AFAIK, idea.

Now I got to thinking, which is not necessarily a good thing, that while an immune response to the seminal fluid is a good idea to protect the female could there be other factors in play here? For example, maybe there is a selective advantage to males by having promoting an immunologic response in the female reproductive track. For example, once sex is over, the female may seek out other mates, if you are the first male, then maybe the elicited immunologic response kills off competing sperm. This would certainly increase your chance of being the lucky genome donor. Maybe females are most likely to breed with the "optimal" mate first and then, in social species like primates, breed with less optimal mates for political reasons (food sharing for instance). This would increase the chance that your genes are mixed with those the genes of the optimal mate and not the slack jawed yokel monkey who just happened to find black gold, texas tea in them there hills.

Again AFAIK these ideas have not been tested, but I think they are interesting and potentially thought provoking. This is a reason I love science, its fun to play arm chair theoretician.

G&G on the Radio

Check it out, a discussion in science education that couldn't be more timely.

Lynn Fellman will be quizzing anthropologists Genie Scott of the National Center for Science Education and Greg Laden of the University of Minnesota on the subject of creationist attempts to weaken science education in K-12 education.  Dr. Scott testified before the Texas State Board of Education as the board was considering how to rewrite the scientce standards.  Texas is critical because of the number of pupils.  Textbook publishers write their books to fit with the Texas standards, and if evolution is weakened at the whim of Texas creationists, it affects education in the rest of the states.  Dr. Laden has been watching development of the Math and Science Standards for Minnesota and will provide some updates.

Greg and Genie will also be discussing the various approaches to religion in promoting and protecting science education.  The NCSE is careful to assure religious leaders that science, properly done, is not necessarily dangerous to their faith (unless strict creationism is a cornerstone of their faith.) Many atheist scientists think that this is a dangerous approach because it dilutes science's naturalistic methodology.  They will discuss what the best approach may be, whether it is "New Atheism" or "Friendly Atheism."  

Atheists Talk is produced by Minnesota Atheists.  Stephanie Zvan is the host, and Mike Haubrich is the director.

- Tune in or kittens may be smitten

Update on Science Education in Minnesota

It is with great pride and belated exhaustion that I present to you:

Science Standards w00t!!!11!!

On a related but tangential note, tomorrow at 9:00AM on AM 950 "Atheist Talk" is having Blogger Greg Laden (I think he may do other stuff too) and Genie Scott (the NCSE executive director) on to discuss Science Education. I believe this is simply coincidental but you know what lunatics people say about interesting coincidences.

Ray Comfort. Feeble? Physically no, mentally apparently

Its time for another addition of "WTF! Ray Comfort has more money than you!" It's only shocking when you realize the mindnumbing vacuousness of Bananaman's intellectual acumen OR It's only shocking when you realize how fucking stupid this guy is.

Back once again to dissect a cute little blog post called The Atheist Starter Kit which begins

If you are a beginner atheist, there's a belief system you should embrace and a language you should learn, or you will find yourself in trouble. Here are ten suggestions for the novice:

FYI "novice" in Bananaman's world means mindless fucking idiot. This is contrasted by "experts" which are totally mindless fucking idiots. Since we already dealt with #3, lets hit....

8. Deal with the threat of eternal punishment by saying that you don't believe in the existence of Hell. Then convince yourself that because you don't believe in something, it therefore doesn't exist. Don't follow that logic onto a railway line and an oncoming train.

Ok there are actually a couple of different points here that are not logically connected. But Bananaman has never been one (as far as I can tell) to let logic screw up an argument. Lets take them one by one.

First: "Deal with the threat of eternal punishment" Wow, good reason to choose a god to worship. The old fear of hell. Yep nothing says true devotion and love like abject horror. Like all those wives who get beaten routinely by their husbands, they love in a way all those unbeaten wives couldn't possibly love their husbands. When your child says he or she loves you, backhand them across the face to help teach them true love or better yet hold them over a well and say your fingers are slipping and its all their fault. That apparently is Bananaman's reason for worshiping his demented fuck of a god. Threat of eternal punishment. Sounds to me in the next rewrite of the old bible, the apostle Paul's name should be changed to Paulie, and John, Johnie, maybe throw in a Luigi or Vinnie, then Don God can call on some true muscle for conversions.

Dear true believers, if at any point you actually use this argument in conversations with potential converts think about this. If indeed fear was the reason you choose to bow down, don't you think an omnipotent god would realize you aren't serious simply scared shitless? Well I was horrified at first, but now I have true love....Yeah yeah, and your daddy only broke your arm because you spilled the milk. Now that you're trying so much harder and being so good, you clearly love your daddy and he you.Bananaman's idea of god, of course the little thing on top is either the holy spirit or Bananaman himself, I get confused.

Second: "convince yourself that because you don't believe in something, it therefore doesn't exist" So many ways to deal with this, brain about to explode. Let's go route Orwell....So by saying not believing in something, therefore it does not exist, you mean like fossils? Biogeography? Biochemical data? DNA sequencing? Laws of physics? Plate tectonics? Nah that's too easy. Let's go route Luther....So by saying not believing in something, therefore it does not exist, you mean like the mythologies of Islamics? Wiccans? Norse? Greeks? Apaches? I get so confused, why is your myth better than all these others? What truly and tangibly separates them? I know your god threatens eternal suffering (w00t him), but so do most of the others, its kind of a way to guarantee control of the masses and for those human beings at the top of a given religion to maintain power.

How about if you believe in something, you provide evidence that it exists. Oh and burnt toast with Norman Rockwell styled pictures of Jesus don't count. (kind of dropped the ball from the old talking burning bush days). You don't believe the Nigerian Prince has $175,000,000 and will give a portion of it to you, just send along your bank account information? Well your lack of belief doesn't mean it doesn't exist, so send along your information post haste....otherwise you'll suffer eternally BWAH HAHAHAHA.

Third: "Don't follow that logic onto a railway line and an oncoming train." Non-sequitur much Bananaman? Ok, you believe you have one chance at life and that's it. Yep, better kill yourself. How about, you think your message is so important to get people right with the fear and horror about crossing your god, why don't you step in front of the train Bananaman? Surely old goddie will spare you to do the good work and maybe will do it with enough flair to actually provide some evidence of his existence. Worse comes to worse, he sleeps in, but you'll still be trucking straight to box seats to watch the rest of us burning it up for eternity (why do so many fundamentalists seem to get a spiritual stiffy when they think of non-believers suffering eternally?)

Bananaman logic
1. If you don't believe in hell
2. Then convince yourself it doesn't exist (this is a totally redundant and could be said to logically come from 1, kind of)
3. Kill yourself (this logically....wait, what now? Did someone forget his banana meds?)

This made me LOL in RL so I had to share it!
Happy belated bunny day

H/T Pharyngula

Science Standards and Global Warming

The final draft of the Minnesota K-12 Science Standards is not yet finalized. However, some concern has been raised as highlighted by this MinnPost article. In short the concern is that there is not enough overt emphasis on global warming and/or global systems. (BTW Im sick of this trendy new "systems" terminology that is apparently epidemic in the sciences now. No one does genetics, you have to do genome systems research to be cool.)

Dr. Rudnick is clearly on top of the global warming issue and wants its importance to society highlighted in the science standards. While a noble goal, is that really the purpose of the standards? We want to have scientifically literate citizens. We want citizens to be able to think critically and rationally, science provides tools to do that. Do we want global warming experts? As noted in an update for the article, there are various points throughout the standards including the earth sciences, physical science, and life sciences. It seems Dr. Rudnick will not be happy unless there is a dedicated section of the standards dedicated specifically to global warming. The standards are not curriculum, although the standards to help establish curriculum. If a school district wants to encompass a set of standards and benchmarks into a module devoted to global systems, it can. However, it is not required to.

I understand the importance of understanding and training people to deal with the effects of global warming. However, I think Dr. Rudnick takes it too far. He says the "standards are fundamentally flawed" and that the Dept. of Education "immediately suspend the current process" (emphasis mine). Nice sense of self-importance there. In the comments section, Dr. Rudnick provides a copy of the letter he sent to the Dept. of Education Commissioner Seagren. I, for one, appreciate his candor and passion. However, as I read Dr. Rudnick's letter I got the sense that he is not so much interested in the scientific education of Minnesota students (I know this is a gross overstatement) but in preparing a legion of scientists to combat global warming. Im not sure, but is it ethical to "draft" our K-12 students into global system sciences without a referendum or something similar? There are standards devoted to species extinction, environmental change, water cycles, greenhouse gases, or at least the important concepts behind these issues, isn't this enough? Are these standards only applicable to global warming and if not, should we make it seem like they are?

I do not mean to imply or diminish the critical importance climate change will certainly have on the next few generations. However, that does not mean I support an approach to essentially force a generation of students interested in science into a global warming-curricula. When Sputnik flew overhead did schools across the nation dump physics and chemistry to focus on rocketry and jet propulsion? When Russia obtained nuclear technology, did we have mandated nuclear physics curricula? Just saying...

While I disagree with Dr. Rudnick's inherent accusation that the science standard committee fundamentally failed and I disagree with the over-the-top rhetoric used in his letter. I will commend him for taking a pro-science stand and being passionate about K-12 science education.

Remember the Alamo, unless it contradicts Christian orthodoxy

Really you must go here and read about what's going on in Texas.

Im particularly concerned/pissed off about what is happening in Hicksville Texas, because Texas buys their K-12 textbooks as a state not as a local school district (like every other state). So Texas has a huge effect on the textbooks that are written and essentially control textbook publication for the entire country. Thanks Douchebags for taking your education duties so fucking seriously.

Ray Comfort. Clever? Maybe, but horses protest

In case you are new to this whole science-religion clash going on, by and large behind the scene, in this country, you may not have heard of Ray Comfort. He is slightly infamous for a particular argument he made in 2001 regarding bananas, which has culminated with him earning the title bananaman.

Lorax's Points of contention:
1. The banana numbnuts has is not a wild god-manufactured item. It is an artifically selected beast derived from something akin to this:

2. Based on Bananaman's rationale, it seems like the banana is specially designed for another purpose, although the non-slip feature could be problematic.

3. Yep, the pomegranate. What the hell was bananaman's god thinking when he pulled the pomegranate out of his omniscient ass?

Now the reason I bring bananaman up is that he "writes" books. I use the quotes, because I use write loosely. Its better than a roomful of monkey's with keyboards, but I think that's mostly because of all the bananas. Bananaman writes books and has a blog. Much of his points are based on clever (again I use that loosely) arguments, you know like the banana one above. Anyway Bananaman wrote a cute little blog post called The Atheist Starter Kit. Its 10 important things all atheists need to know before getting started. (By the way, I won't link to bananaman's blog directly, but anyone that can break away from the awe inspiringness of a banana can find it with no problems). I am still under the gun with real life writing, but I thought I could keep my foot in the blogosphere by hitting on these 10 things in a series of posts.

So without further delay and in no particular order

If you are a beginner atheist, there's a belief system you should embrace and a language you should learn, or you will find yourself in trouble. Here are ten suggestions for the novice:

Suggestion 3. When you hear that you have everything to gain and nothing to lose (the pleasures of Heaven, and the endurance of Hell) by obeying the Gospel, say "That's just the old 'Pascal wager.'"

Well in fact it is Pascal's wager/gambit. Since you have everything to gain and nothing to lose you should just go with the god exists hypothesis. Despite the blatant absurdity with this approach, I wonder how bananaman feels about the fact that Pascal thought there was no evidence to support the god hypothesis and thus no rationale to believe it either. However, if you think its a win-win deal, you should hedge your bets.

Is it a win-win? As stated you have nothing to lose, nope nothing, not 10% of your income, not time, not energy. If you go Bananaman's way you don't have to give up ignorance or a sense of foreboding and confusion about the world around you. Just go back into your cave being afraid of the thunder and don't walk too far or you may fall off the edge of the world. Hmm, that doesn't sound too win-win to me.

Also, dont use Bananaman's response "That's just the old 'Pascal wager,'" go with "You're Right, Damn, why didn't I think of that! All Hail Mohammed! I mean Odin! I mean Yahweh! I mean Shiva! I mean.....oh crap. Bananaman, do you simply wager on all the gods? Because they all tend to be jealous insecure little pricks." Indeed theologians in other religions have made similar appeals.

Finally, if you are simply hedging your bets and paying lip service to Shiva, wouldn't Shiva kind of figure out you were full of shit? I mean this is a god we're talking about right? Of course I have failed to consider the hypothesis that when people refer to omniscient gods, they really only refer to omniscient in regards to your sexual habits otherwise they are kind of clueless. Dawkins has actually suggested a counter-gambit that if there is a god(s), maybe it would reward a striving for learning and knowledge. It may reward those who try to understand the universe or the moral and good people. Maybe those into blind ignorant faith or live lives of asocial superiority and hatred of their fellows are going to piss god off royally.

Update: States that have problems with science

Mississippi has a sticker campaign. Current status is "dead in committee"

Missouri Academic Freedom Bill
Oklahoma Academic Freedom Bill, (+2 based on Richard Dawkins coming to town, see Oklahoma house resolution 1014 and 1015)
Alabama Academic Freedom Bill
Iowa Academic Freedom Bill
New Mexico Academic Freedom Bill
Florida No longer Imminent Academic Freedom Bill

Texas Science Standards and Creationism

NCSE has much up-to-date information on current legislation as well as a plethora of additional resources.

Stimulus money for NIH

$200,000,000!!! Isn't that awesome?

Well it is better than a poke in the eye with a sharp stick, but how good is it? First, the grants are for 2 years with a $1,000,000 maximum, so expect that the vast majority of submitted grants to be for $1,000,000. That would allow for the funding of 200 new grants, w00t!

But realize, there are 50 states in the union, so that works out to 4 grants/state. or
NIH has defined 15 challenge topics for the funding, so that works out to 13 grants/challenge area. or
NIH has defined 207 specific challenge topics for the funding, so that works out to <1 grant/specific challenge area!

Again that was < (LESS THAN) 1!

I would have preferred many fewer challenge areas, say 100 or less, and more resources devoted to developing these areas. Its better having 4 individual labs taking different approaches towards a problem, than 1. One concern is that only the biggest most popular labs will get the money, and not the best science.

I realize this money is not for science per say but for job creation. However, I am not sure how successful this use of funds will be in that regard. If I get a grant funded, I will hire someone, although most lab heads will likely be retaining people they would otherwise let go because of the difficulties in getting and maintaining long-term grant support. But in two years without a continuing influx a money, those people hired will all be fired. Maybe the point is a short-term solution with the hope of an improving economy that will solve the longer-term problems. However, two years is an extremely short period of time and I wonder how much real improvement we will see.

Ah well, better get writing...

Science versus Religion: can't we just get along?

Science and religion are often seen at odds. Currently in the US, the political party that cloaks itself in the most religious terms is also the most anti-science. Compared to the general population, scientists are more likely to be atheists. For example see this letter to Nature 10 years ago (subscription required). In the table, below, it is apparent that a belief in a personal god dropped dramatically over the last century among scientists.

So, are these two approaches to understand ourselves at odds or is this simply a matter of perspective? Well, first we have to realize that we are dealing with words (science, religion) that mean different things to different people. So before we answer this question let's define our terms.
Science: a natural philosophical approach to understanding the universe and all that is in it. The underlying supposition of science is that the universe can be understood without appeal to supernatural mechanisms. (The way in which science is done is well well well beyond the scope of a single blog, much less a blog post!)

Religion: a belief system that encompasses faith as an approach to understand the universe. The underlying supposition of religion is that the universe can be understood by revelation. (Revelation contains personal revelation, revelation from a church leader, and revelation from religious texts.)

Alright, we have some terms (admittedly both are superficial, but they serve to basically hit the main points). Are these compatible? Well, the short answer is no. Actually the longer answer is no as well, just with additional points. Now I am not saying that one cannot be a scientist and religious. I would never say that, and if I did I would be proven wrong immediately and emphatically. However, I do think that the only way someone can be completely rational (and no, I am not completely rational, Im only 1/4 Vulcan) is to NOT be religious. I need to stress that I am not making value judgments with these statements. One can be a great human being and do great things for society and be a deeply religious person. However, and I need to stress this, the converse is true as well: One can be a great human being and do great things for society and be an atheist. (Those who think this is completely wrong can now take a flying leap along with your psychotic lackeys like Sarah Palin.)

So, I have stated for the record that being religious or an atheist does not necessarily have anything to do with a person's role in society, why then do I think there is a problem between science and religion. Well, the problem comes from the fact that religion requires revelation and this is anathema to science. Just because Darwin wrote it doesn't make it true, the fact the we can observe it, make predictions and find that these predictions are correct, etc makes it true. Maybe it would help to think of it this way, if Darwin never wrote On The Origin Of The Species or even never existed, evolutionary theory would exist today pretty much as it is. If the Bible had not been written, there would be no Baptists today. This is the difference, the "truth" established by science can be determined independently by anyone (exceptions apply), but the "truth" established by religion does not exist without someone saying it does. this is why there are moral people in the before the presence of and in the absence of Christianity. Not killing other humans in your society can be considered a natural morality not a religious mandate.

Now I realize the human brain is outstanding in its ability to compartmentalize conflict, so rational people can easily go to church on Sunday and hang with their homies givin' it up to god and what not. That doesn't mean religion and science are compatible simply that people are odd odd creatures. Since we are so good at compartmentalization, does it matter that science and religion are not compatible?

ABSO-FUCKING-LUTELY!!! See here, here, and here for a few reasons why. This is a problem inherent with religion because it requires this appeal to revelation. If Pope Louis the π/2 said it, David Koresh said it, Sir Loin of Beoff said it, then it must be true. Of course it may not be true, now its up to the individual to decide where faith ends and reality begins and that my friends is the problem. When push comes to shove it is in fact a fight between faith and reality! Reality! Not some philosophical approach to knowledge, REALITY!

Why was it wrong for the Manson family to kill Sharon Tate? The killers had faith, no different than any other believer.
Why is it wrong for fuck-head islamic fundamentalist to behead prsioners? The fuck-heads had faith, no different than any other believer.
Think we are any different? If you support or supported the wars in the mid-east, tell me that you never justified them in part based on the differences in religion between them and us.

Why is it wrong to teach creationism in schools?, Why is it wrong to teach that the earth is 6000 years old?, Why is it wrong to teach the earth is flat? All of these questions are equally supported by faith and completely overturned by REALITY.

No, religion is not the cause of all of our problems, but it is an intellectual maelstrom that allows and justifies the causes of many of our problems.

-Edward J. Larson and Larry Witham, Nature 394, 313(23 July 1998), "Leading scientists still reject God," doi:10.1038/28478.
-Leonardo da Vinci’s "Vitruvian Man"
-Michelangelo's "La Creazione"

Something for the end of February

While I wish to be posting more frequently, trying to finish a few papers and work on grant proposals is taking up most of my work and free time. I am not a fan of posting random links on my blog, but a little music now and then can be refreshing.

Gerry Niewood (saxophonist, playing flute in the video) and Coleman Mellett (guitarist), two band members with Chuck Mangione, died in the flight 3407 crash outside Buffalo Feb. 13, 2009.

A Panel Discussion and a bonus comparison of science fairs

Well after having a pretty damn good time at the Minnesota Atheists panel discussion on evolution, creationism, and the classroom, I decided to stop into the creationist (attempt at-)science fair. BTW I am that freaking stupid.

First, the panel was outstanding, although the moderation could have been improved somewhat in my opinion. I learned a few things I wish I hadn't. Randy Moore told us that 25% of all Minnesota public school students have been taught creationism, this includes students taking AP biology in case you wanted to use that as a hopeful crutch (I did when I first heard the statistic). Think about that everyone, 1/4 of all students are being subjected to illegal instruction.

(BTW, to any of the hard working public school teachers for my son, if you teach creationism in a science class in anything other than a historical context I will be your worst fucking nightmare. Also, to any hard working public school science teachers in the area, if you need some help or a guest speaker for some reason, Im happy to help.)

Secondly, I was disheartened to hear questions from the audience that showed a profound misunderstanding of evolution. Along the lines of "as the most complex organisms on the planet...." "since western civilization is so evolutionarily advanced" type of questions. I appreciated Dr. Phillips response to a "destroy the planet" type question, we can kill ourselves and a great many other higher eukaryotes, but the planet will be just fine without us and life will go on pretty much as it always had.

Third, kudos to Dr. Cotner and her response to the question "Can't we just tell students to say what we want on the tests, get their passing grade, and move on?" Her response, paraphrasing, BULLSHIT! You explain the data, the facts, the real world that everyone can see and study, but nope this tool is going to go on believing some mythological bullshit that is really no different than the mythological bullshit the ancient Egyptians were believing, and we're supposed to be happy with that?

Personally, I dont need a student to rehash shit I already know to stroke my mental ego, my ego is just fine. I want them to understand (not simply memorize and regurgitate) the world around them. Also, I find that question tantamount to saying, ok students if you disagree with me, go ahead and lie to get your grade. As an active practicing scientist, nothing could more define anathema than advocated lying.

Fourth, and finally "free will." The question that basically derailed the discussion, mostly because time was up but also because the questioner was trying to set up yet another false dichotomy. I realize some people will never be happy unless someone tells them that they are better than something. So for all you self-esteem emo-kid wannabes, you are better than something out there for some as yet undefined reason. Feel better?

Alright, I left this talk, which despite my criticisms above was a lot of fun. I got to see some colleagues I havent seen in too long and also got to meet Randy Moore and Mike Haubrich (of Minnesota blogging fame).

I decided to stop into the Creationist Fair on the way home and I dont have much to say. In fact, I really only want to contrast it with the K-8 science fair I was a judge at early in the week. A more complete assessment can be found at Pharyngula. However, one of the commenters (Kimberly #34) noted that the age appropriate breakdown should go something like: K-1st: Collections with labeling to explain relationships; 2nd Demonstration with explanations of what is happening; 3rd use a model and explain the advantages and disadvantages of the model; 4th Experiment/demostration; 5th Experiment or invention.

I would say that of the K-8 public school exhibits most were in the demonstration/model-explanation vein. Whereas the creationist fair was mostly in the experiment/demonstration vein. Of course I dont have numbers to say how many of each grade level I am comparing so this is just my overall feel. However, the presentations actually being judged at the K-8 fair were outstanding! The students did a great job addressing a scientific question (not all questions are scientific, which is something the creationist fair organizers could have learned.) In fact the presentations were so good of three judges, all of us had different orders for 1, 2, 3 and all of our 1, 2, 3, scores were tightly grouped. Anyway my take home point was that the creationist fair was nowhere near as blatantly non-scientific as last year and was more like any other science fair. However, the failing came with what was considered an acceptable question. The remedy for this requires some parental/organizer involvement Of course, since any parent can teach their children anything there tends to be little to no expertise (unlike public school teachers that require licensures). Thus, I can see why failure to adequately teach scientific methodology would be more lacking in the homeschool environment than the public school environment.

My Darwin Day Contribution or On a Mechanism of Speciation

How do new species originate? This is a question I am not going to ultimately answer here, but I am interested in this issue and have had some thoughts about it. Now the first issue that needs to be dealt with is "what is a species?" Since many people have been fighting with that question for centuries without coming up with a clear precise definition that applies to all organisms, I am not about to answer it here. So, I will limit our concept of species to sexually reproducing organisms. This allows us to define a species as a group of organisms that can interbreed and give rise to fertile offspring. This allows us to separate horses and donkeys into separate species, since mules are viable but not fertile.
OK, so we have defined a species. Now what? Well in general terms there are four ways speciation can occur: allopatric, parapatric, peripatric, and sympatric speciation. The first three of these modes of speciation involve the spatial separation of two populations of a species in various ways. Once separate, the two populations then evolve independently ultimately becoming distinct species. Its the last mode of speciation, sympatric, I am interested in here.

In sympatric speciation the two populations are not separate but occupy the same niche. There are several models describing how sympatric speciation can occur, including sexual selection models and polyploidization. However, I want to discuss a third model which is based on an initial genetic isolation. The paper that really got me thinking about it was one we discussed in my course from PLoS Genetics. Well this paper and the fact that I have never been happy with the primacy of allopatric speciation (a post for another time).

First it is helpful to think about the ultimate output of the genetic material (aka genes), which is proteins. In many, if not most, cases, proteins do not act as individual molecules, doing their job, and moving on. In fact, most proteins act in complexes with other proteins. What this means is that the proteins must physically interact with each other, and if they don't, the process they are involved in fails. Second, there is a lot of variation out there in the world. Most of this variation is neutral, neither good nor bad, it just is. (Bad variation generally disappears quickly; good variation generally is fixed quickly.) These are our assumptions both of which are well documented, read some textbooks/journal articles for support of my first assumption (proteins act in complexes); go to the mall and people watch for support of my second assumption (variation is out there).

OK, lets take a hypothetical example. In the species of blue-butted gnus, two proteins (A and B) interact to make the blue pigment in said gnus butts. In the first couple of blue-butted gnus we studied, we saw that the gnus had alleles A1 and B1 of these proteins and of course their butts were blue. However, we looked at several other gnus and identified alleles A2 and B2 of these proteins. Upon closer examination, we find lots of A1B1 gnus and a few A1B2 and A2B1 gnus, but no A2B2 gnus. That seems odd, so as junior scientist-heroes, we grab an A1B2 animal and mate it to an A2B1 animal and find out that low and behold we can get an A2B2 animal!!!11!1 But HOLY SHIT, it has a green butt! Did we just make a new species of green-butted gnus? Sadly, we find that gnus, regardless of butt color only want to mate with blue-butted gnus with blue butts. So, no gnus will mate with a green-butted gnu, which as you know is not good news for the green-butted gnu. Now the A2 and B2 alleles do not matter at all, except when combined together, so this has the effect that gnus with the A2 or B2 alleles tend to become isolated, the A2 gnus tend to be at the left hand side of the field over by the swamp, whereas the B2 gnus are found more often at the other side of the field near the woods. What we've done is begun to genetically isolate populations. So although all blue-butted gnus can mate, green-butted gnus are immediately removed from the population. Of course random drift can lead to the complete loss of either A2 or B2, which would end this discussion. However, additional random mutations can and will occur and genetic drift now has a mechanism that can further genetically isolate these gnus into distinct, but spatially overlapping populations. Give me another 40,000 years and a glass of wine and Ill give you two species of gnus: the swampland blue-butted gnu and the woodland blue-butted gnu.

That was hypothetical example (my wife says "lame" is a better word than hypothetical), the paper is a real life example. Saccharomyces cerevisiae (beer/bakers yeast) has been isolated from many sources over the last hundred years and studied in detail. S. cerevisiae is great because it is stable as a haploid or diploid and comes in two mating types and you can mate them in the lab no problem (which is why S. cerevisiae is THE eukaryotic genetic system. One thing that was noted early in studies with S. cerevisiae is that some strains do not mate to give rise to viable progeny. So, strains A and B do not mate well. However, strain C can mate with either A or B just fine. So what gives? Well, the read the paper, but the short story is that there are alleles of genes encoding proteins in an essential complex. When these alleles are in the right combinations the proteins are incompatible and make a defective complex, which equals death, or at least a lack of life.

I think that this model, genetic isolation, may be a common mechanism of separating populations, which can lead to speciation. So why are the other three mechanisms so widely taught (particularly allopatric speciation)? Well its simple to observe and study: find an island and see how the species are similar/different from the mainland. Its also conceptually a little easier, a big giant mountain range comes up splitting a species into two distinct populations, they can and will vary independently. But just because something is easier to observe, doesnt mean its the most important just the most studied (take natural selection vs genetic drift).

Happy Darwin Day everyone!!!

(Incompatibilities involving yeast mismatch repair genes: a role for genetic modifiers and implications for disease penetrance and variation in genomic mutation rates. Demogines A, Wong A, Aquadro C, Alani E. PLoS Genet. 2008 Jun 20;4(6):e1000103.)

Come celebrate Darwin's Birthday

LIFE: A Journey Through Time
North American Premiere /Darwin Day Opening Event
Thursday, February 12, 2009, 7 to 9 p.m.
Bell Museum Auditorium
$10/ free to museum members and University students

Celebrate the 200th anniversary of Charles Darwin's birthday with a special preview of LIFE: A Journey Through Time. The event will feature top University biologists using Lanting's photographs as a springboard to deliver a rapid-fire presentations relating their research on evolution to the images. From the big bang to the human genome, hear the newest theories on how life evolved and enjoy the North American premiere of one the world's most celebrated photography exhibits. Think speed-dating - Darwin-style!

Speakers include:
Mark Borrello <---- Teaches on the history of evolution, and is an anti-creationist superhero
Sehoya Cotner <---- Teaches about Sex and evolution, dont tell the Georgia state legislature
Mark Decker <---- Teaches, Writes, Teaches, Skydives, oh and strives to improve Teaching (Plus he doesn't snarf your scotch when you are off teaching.)
Greg Laden <---- Not sure about this guy, does something or other someplace
Keith Olive <---- A physicist! Clearly, a late addition to make the biologists feel inadequate...or maybe I'm transferring.

BTW its a birthday party. There will be cake!

Bats: are belfries their only option?

Small mammals are dying and we don't know why! Does it matter? I've posted why it does and what we know previously. Well it looks like white-nose syndrome is spreading from a couple of caves in NY 2 years ago to 6 states already this year....this is not a good thing.

Mexican free-tailed bats © Lynn McBride (JPG)

One thing that stills concerns me is that researchers are trying to find ways to combat the Geomyces fungus, which is infecting the bats and is the white in white-nose. This is good, however I still have not seen definitive cause-effect data that suggests that fungus is the problem and not a symptom. I hope research is still being done to determine why bats are coming down with these fungal infections.

1. This is an emerging pathogen that has developed virulence properties. While these fungi do not grow at human body temperature, Im not a cheerleader of emerging mammalian infectious agents.

2. Environmental toxins are screwing up the bats immune system or physiology.

3. A virus is acting similarly to the environmental toxin example (analogous to HIV in people).

4. Others I have yet completed the thought on.

How to make a virus

There was a pretty good seminar I saw on the subject of virology, which is not my area of expertise nor necessarily of interest. However, the presentation and work done was explained well and was done in an engaging way, such that even though this is an area I am not particularly concerned with, I enjoyed immensely.

(Aside: These leads to a particular rant I have. I see that many lab heads avoid departmental seminars unless said seminar is directly related to their particular field. I understand this mindset, because we are all extremely busy, we have many seminars, meetings, and duties beyond research and teaching that vie for our time. However, this mindset is being passed down to the post-docs and, more importantly, the students in these labs. Over the course of several years of this, the end result is a batch of students with little breadth beyond their specific research area, students who are unaware of technical or intellectual advances in other fields that may in fact aid their research, and students who may not have the skills to succeed on their own. /Aside)

The specific seminar I attended was on Hantavirus. Like all organisms, even pseudo-organisms like viruses, there are interesting biological problems and questions associated with them. One thing of interest with the Hantavirus, and other viruses of the Bunyaviridae family, is that it has a segmented genome. This is similar to us, our genome is comprised of 23 individual chromosomes (2 copies of each). Thus, our genome is segmented. This can be contrasted to many, but not all, bacterial species, which have their genomes comprised on a singular circular chromosome. So, the Hantavirus genome is comprised of 3 segments. If you click on the picture, which is from the CDC, you can actually see some of the strands in the viruses that are the RNA segments that comprise the genome. In answer to your question, yes RNA! These viruses maintain their genome as RNA, not DNA. So the discovery of the virus, seeing it inside of cells, analysis of its genomic structure is all basic biology that was worked out over the last few decades.

So what is the profoundly interesting thing here? Well, its a question I do not know the answer to, nor am I sure anyone does in this particular case. However, it does represent an interesting biological problem. A bit more background, when a virus infects a cell, the genome regardless of RNA or DNA is uncoated, in other words freed from the protein shell it travels around in. This allows the virus to replicate, make messages, and make all the proteins necessary to make more viruses. Now once all these new viral genomes are made, they have to be packaged into new shells before leaving the host cell. (Free nucleic acid in the environment usually gets eaten.) For a virus with a single bit of RNA or DNA that gets packaged, you can simply have a protein that grabs one end of the genome and nucleates shell formation or you simply make a bazillion protein shells along with a bazillion genomes and simply play the odds: some shells will be empty but many will not be.

However, our organism of interest, Hantavirus, has a segmented genome. The virus requires all 3 pieces of its genome to be in a shell to have a productive virus. Our previous 2 approaches no longer work so well. In the first approach we need 3 proteins, one for each genomic segment. We could use the same protein 3 times, but how can you ensure all three segments are in each shell and not simply segment 1 and its associated protein 3 times. We could have 3 different proteins, 1 for each segment. The problem here is that Hantavirus only encodes for 3 different proteins total: the shell protein, the RNA polymerase, and an RNA binding protein that does several different things. So we don't appear to have the information necessary to take this approach.

The second approach tends to fail as well. If we make a bazillion shells and a bazillion of each segment. If there is an 80% chance a given segment randomly ends up in a shell then we have a 0.8 x 0.8 x 0.8 = 51% chance of a shell getting all 3 segments, so 0.5 bazillion. That doesnt sound so bad, but I did just make up the 80% number, what if its 50%? then ~12.5% of the shells will have all 3 segments. Is that enough to maintain a viable infection? I don't know, but its knowable and interesting to think about. This issue is more complicated, because we have assumed that once a given segment gets in, the same segment won't get in again. If we abandon this assumption, then our 80% chance of a given segment to get in isn't 51% but 11% (.8 x (.8 x 2/3) x (.8 x 1/3)) We could help our scenario out by making the shells large enough to hold more than 3 segments worth of material. If a shell can hold 5 segments worth of material, then we dramatically increase our chance of getting all 3 segments in.

So what does Hantavirus do? Well based on the seminar, that is still a question that needs answering. Maybe one of the above approaches is right or maybe the 3 segments are not truly separate but tethered together with 1 or more of their proteins or host proteins that the virus coopts for its own devices or maybe its something else even more interesting! Regardless, this is why biology and science in general is cool. We have an obvious problem an organism (Im using the term loosely) needs to solve, how does it do it? By the way, his isn't simply fun for the sake of fun, in the case of Hantavirus, if we know how packages its genome maybe we can develop ways to stop it and effectively combat Hantavirus it or similar viruses.