Thursday, May 31, 2007

Good Virus, Bad Creationist

Man Mark over at Good Math, Bad Math got an advanced copy of Behes latest, 'The Edge of Evolution.' (Foiled by D-list blogging again-- Deniers didnt send me an advanced copy of Blondies 'Science Outsold'. I even asked!)

Now, Behe has always aggravated me, as I first became aware of his existence when I was taking introductory immunology... and I found I could refute his 'arguments' regarding the immune systems. "That dude isnt right" I said to myself at the time.

Ive tried to ignore him as best as I could since then. Honestly, I thought it was a little funny that he went after the bacteriologists with the damn flagellum and the immunologists with "Immune system cant evolve blah blah", but I never thought he be silly enough to go after something I research. I mean Im sure he reads my blog daily and knows hed be snarkified by a chick half his age if he tried to touch stuff I do.

GM/BM-- Anyway, the new book is based on what comes down to a mathematical argument - a mathematical argument that I've specifically refuted on this blog numerous times. I'm not mentioning that because I expect Behe to read GM/BM and consider it as a serious source for his research...

Okay, so I cant claim 'D-list blogger help help Im being repressed' this time. I guess Behe doesnt read much of anything, if Marks summary of his latest book is accurate.

The basic argument in this chapter is the good old "fitness landscape" argument. And Behe makes the classic mistakes. His entire argument really comes down to the following points:

  1. Evolution can be modeled in terms of a static, unchanging fitness landscape.
  2. The fitness landscape is a smooth, surface made up of hills and valleys, where a local minimum or maximum in any dimension is a local minimum or maximum in all dimensions.
  3. The fitness function mapping from a genome to a point of the fitness landscape is monotonically increasing.
  4. The fitness function is smoothly continuous, with infinitessimally small changes (single-point base chanages) mapping to infinitessimally small changes in position on the fitness landscape.
Ouch. I dont talk about my research directly a whole lot here (except for pretty pictures, of course), but like I put in my blurb, I study the evolution of HIV within patients and within populations. Fitness and fitness landscapes are vital to my research. And if Mark has summarized Behes claims properly-- Im kinda peeved *fumes*

No one can have a basic, basic, basic understanding of 'fitness landscapes' and come out thinking those four points are valid. Just watch, Ill explain fitness landscapes to you all right now in the context of HIV, and you will get it! You, even those of you with zero biological training, will be able to refute Professional Creationist Michael Behe! Yay!

Okay, check it out-- think of a graph. On the Y-axis, think of something that contributes to natural selection. For HIV, a good one is T-Cell escape. On the X axis, every point is a potential HIV sequence. EVERY possible HIV sequence. X-axis is real long, but lets pretend it looks like this: The HIV genome sequences that are 'better' at staying under the radar of T-cells have higher Y-axis values (peaks), and the ones that cant escape very well have lower values (valley).

This is a two dimensional graph. Its not really two dimensions. You see, for every contribution to natural selection, you add another dimension. Add a Z-axis to that graph-- escape gp120 antibodies. Add a W-axis-- escape gp41 antibodies. Add how fast Env can get the virus into the infected cell, host nutrition, resistance to Drug 1, resistance to Drug 2, resistance to TRIM5a, resistance to APOBEC, etc etc etc etc etc. Physicists get excited when they find another dimension... but they aint got nothin on HIV fitness landscapes. I dont think you could even quantify how many dimensions there are to that simple 2D graph from above.

So Sequence 1 might be GREAT at escaping T-cells... But it might be awful at controlling TRIM5a. Sequence 2 might be incredibly efficient at infecting cells, but isnt resistant to Norvir. So HIV explores all these possibilities and creates a quasispecies-- instead of points on a graph, like above, when you combine all the possible fitness axes, you get a cloud of maximally fit viruses. NOT optimally fit! Maximally fit, for the given parameters!

This is what you find when you take a blood sample from an infected patient and sequence all the HIV viruses you find-- Most viruses have a very similar sequence, but different enough that you get a cloud, not a single point of identical viruses. Let me amuse you and draw a picture in paint:
But this picture is just a snapshot. One week later, the patient might try a new drug-- the quasispecies will shift. One week later, the patient might transmit a virus to her partner-- quasispecies is presented with an entirely new landscape.

  1. Fitness landscapes are never static. At least I cant think of a scenario where that would happen. Ever. Someone give an example if you can think of one.
  2. A peak in one dimension can be a valley in another dimension. This is clearly demonstrated in HIV, where drug resistant viruses obviously have a fitness cost. When you take the patient off the drug, drug resistant HIV is rapidly overtaken by wild-type viruses.
  3. What is it with Creationists and things always getting 'better'. Right now Im trying to determine if fitness increases/decreases/randomly changes over time in long-term drug naiive HIV patients. For all I know, HIV viruses are decreasing in fitness over time, but increasing in transmissibility. Things dont always go in one direction!
  4. Dumb, dumb, dumb. One/Two/Three base-pair changes in HIV can tank a sequence from the top of a peak in one dimension (replicative capacity) to the bottom of that dimension, and pop you to the top of the quasispecies in another dimension (drug resistance). One mutation doesnt equal a little better, another mutation equals a little better, another mutation, etc etc etc.
There ya go folks. I promised you all could understand this, so if you dont, please leave your questions in the comments!

Wednesday, May 30, 2007

Origins of Life: Slightly Less Mysterious

The best 'Fundies Say the Darnedest Things' EVER, in which a Creationist almost discovers the Sun:

"One of the most basic laws in the universe is the Second Law of Thermodynamics. This states that as time goes by, entropy in an environment will increase. Evolution argues differently against a law that is accepted EVERYWHERE BY EVERYONE. Evolution says that we started out simple, and over time became more complex. That just isn't possible: UNLESS there is a giant outside source of energy supplying the Earth with huge amounts of energy. If there were such a source, scientists would certainly know about it. [emphasis added]"
But the Sun isnt the only energy source available to life on this planet! Dont forget the 'fire' below our feet, and the science that can happen where that energy is released-- Like at hydrothermal vents on the bottom of the ocean!

Thermal vents' place in abiogenesis didnt totally make sense to me before. I was thinking of their potential contribution as like, a natural PCR machine. When DNA is close to a thermal vent, the high temperature causes the double-stranded DNA to 'melt' into single-stranded DNA. As the ssDNA rises via convection through the thermal column, DNA replication machinery can get in to replicate the ssDNA into dsDNA. Floats down, gets close to the thermal vent again, and the process happens again! Lots and lots of copies! Neato!

Well, um, yeah that 'makes sense'... but it leaves more questions than it answers. Where the hell did the first DNA strand come from? Whered all the replication machinery come from? Whats keeping everything contained? Huh??

Leave it to the folks at NAS to turn a kinda weird idea up on its head and twist it into a viable hypothesis. They go back further than DNA. Further than the RNA World. They go back and try to explain the development of the RNA World itself!

Extreme accumulation of nucleotides in simulated hydrothermal pore systems


hehe So in other words, forget everything I just typed about thermal vents and DNA!

Just picture a hydrothermal vent: a chimney through the earth. But this chimney is composed of a maze of iron-sulfide compartments instead of bricks (is, not maybe, these still exist today). When combined with the energy from the hydrothermal vent, this maze acts like a sieve, first collecting mononucleotides. The nucleotides utilize the abiotic catalysts in the iron-sulfide rock (FeS and NiS) to generate strings of nucleotides: RNA (in their experiments, Baaske easily get strands ~100 bp long this way). As the strands are pushed further away from the thermal vent by convection, the temperature lowers enough that the strands are able to ligate to one another and recombine, exploring the sequence space (all possible base-pair combinations) even further.

This essentially allows hydrothermal vents to turn into little RNA factories! Every possible impossible RNA sequence can be tested. Invented, lost to degradation, and invented again! Impossible events happening all the time! Ribozymes, polymers, replicases, tons of stuff! Abiotically!

Alas, always remember your assumptions! What are these folks needing to assume? The presence of mononucleotides. Drat! The answer to life, the universe, and everything still remains elusive. But as the PNAS commenter so aptly put it:
"...the transition from a solution of small organic molecules to a population of RNAs, now appears much less mysterious than before."
Edit 5/31/o7-- Head over to VWXYNot? for more tricks RNA can play!

Tuesday, May 29, 2007

One More Creationist Cookie: Top Misconceptions about Intelligent Design

You know that feeling you get after a string of friends birthdays, or the winter holidays, when youve just eaten so much cake and cookies and drank so much booze, the only thing that sounds appetizing is a nice salad with a glass of water? Youve just had so much junk food, you cant stomach it anymore?

Thats kinda how Im feeling after this weekends Creationism Museum Carnival. It is going to take me weeks to get through all those posts! And though Im really excited about reading everyone contributions... I dont know if I can take any more Creationists. I want some real food-- some real science. Ive got some sweet science posts lined up (hint-- find out what these words have in common: marsupials, retrotransposons, immune system, sharks, YAY!!!).

But theres just one more cookie at the bottom of the Creationist jar this week, and I gotta eat it.

I mean I CANT let it go to waste!!! Its got chocolate in it, I cant give it to Arnie! Sure its kinda old, its kinda stale... BUT ITS A COOKIE!

A cookie provided to us, once again, from my Intelligently Sequenced doppelgangers. Paul is so relieved that someone has consolidated several of the usual arguments against Intelligent Design Creationism and clears the air for us.

Well thank goodness! Im excited to read this article too! I mean we cant get Dembski or Behe to define any of their terms or even tell us what the hell 'Intelligent Design' means, maybe finally we can get some answers! Yay!

Top Misconceptions About Intelligent Design

Now, I know you all are a clever bunch, so Im only typing this for the people who dont want to give these tards a site hit. Okay, follow me here-- Number One misconception about ID:

It's Creationism in Sheep's Clothing
Okay, now, what is the name of the site that is hosting this article? New Creationism.

Now dont laugh, readers! They dont have irony meters on Mars, they dont know what theyre saying is funny. So look at this as an outreach opportunity! Drag one of your broken irony meters out of the basement, let some 12 year old aspiring engineer tinker it back into working condition, and donate it to these poor souls! Common everyone!

In all fairness, the author is right in his defense of Number One:
...hypothetically there could be atheists that buy into ID.
Yes, theoretically there are atheists who are clueless enough to 'buy into ID'. Thats the perfect choice of words, my dear.

Number Two is also wonderfully hysterical, if you read Carl Zimmers blog, The Loom:
An Expectation of Optimal Design
This is the Casey Luskin defense of IDC-- The Pinto Argument. Of course this is a funny joke, but 'An Expectation of Optimal Design' is a problem supported by Creationists! Ive seen it from the Young Earthers and from ID Creationists over and over and over and over and OVER! Every base pair is sacred!
... But when Design is suboptimal, its because of sin/the Will of the Designer/etc.
...... But Evilution is unfalsifiable.

I lost all hope of getting any details about ID Creationism at Number Three:
3. Intelligent Design is guilty of the God of the Gaps

...So what makes the framework of Intelligent Design any different from other attempts to ascribe authorship of objects and events to supernatural influence?

Intelligent Design Theory builds upon the foundation of advances in scientific knowledge, not the absence of it. Specifically, Intelligent Design Theory leans upon the science of information theory, astrophysics, chemistry, and biology...
Specifically. Specifically. You know, I dont suppose any ID Creationists have any examples of, you know, specifically, how ID Creationism 'leans upon', say information theory? No? Too specific? Well, okay...



Aaaand Number Four-- the 'Play for Confusion' to get people to think theyre ID Creationists when theyre not:
4. The Strong Dichotomy with Evolutionary Theory
...In fact, theistic (or directed) evolution is arguably a form or expression of Intelligent Design...
Noooooo. Not really. You see, Theistic Evolution is a philosophical position. IDC is a methodological position. Theistic Evolutionists say they believe their deity designs through evolution. IDC say they have proof of Design, therefore they have 'proof' of a Designer. Theistic Evolutionists are not Intelligent Design Creationists.


Okay, seriously, I gotta go take some antacid, loosen the belt a notch, and get some real science in my system. If only insulin cured Creationist Overload too!

Monday, May 28, 2007

YECs are racist too?

So I was looking at some sneak-peek pictures of the Creation 'Museum', and Ive got just one question, not related to science/biology/evolution.

Would someone please explain to me why the human characters in the Creationism 'Museum' are white?

How Skeptics do Diets

Okay okay, Ive been hard on the Biblotarians for how they do diets and their fitness advice.

Are skeptics any better? The current issue of SKEPTIC magazine has an article on diet and another on a supplement. How do they stack up to my amateur fitness-buff standards?

First is a short piece from The SkepDoc, Harriet Hall, M.D., "Dont Let Them Hoodia-Wink You"
Its short, sweet, and to the point. After writing a brief intro to the history of Hoodia and what people in the U.S. think it can do (suppress hunger, if you believe the diet pill commercials), Dr. Hall asks the question all skeptics are thinking: "What is the evidence?"

The answer: "At this point its strictly anecdotal." And what is the line that recites in my head every time I hear an anecdote used as 'proof'? A million anecdotes arent worth one, randomized, double-blind, controlled experiment.

Dr. Hall then points out what the experiments have shown:

"Products that have been tested have contained between 0.1 and 0.01% of the active ingredient claimed. One testing company estimates that half of the Hoodia products they test contain no Hoodia at all."
Well that wouldnt be so bad if the efficacious dose of P57 (the 'active' ingredient in Hoodia) was really small... but there have been no double-blind studies... soooo... Yeah, dont waste your $$$.

The next article is "The Gospel of Food: The Myth of the Doctrine of Naught", by Barry Glassner.
Now I will state up front that this article is about eating for general health. I dont just eat for general health, and I wouldnt recommend his conclusions for anyone hoping to run a marathon or get ripped. Hes writing for a majority of people wondering "What the hell am I supposed to eat???"

Glassner hits at the root of the problem of dietary guidelines and the research theyre founded upon, and believe it or not, its Hoodias problem! No double-blind studies!
"You cant give one person a T-bone and another tofu and have them believe they are eating the same thing. The closest that nutrition researchers come to randomized trials are experiments in which they assign people to eat particular foods rather than give them free choice."
There are more problems with this. Most studies on diet and disease are retrospective studies. Jimmy ate red meat every day, and he had a heart attack. Johnny never ate red meat, and hes fine. Okay, thats a correlation, but is that a causation? Nope.

Glassner, to my delight, also highlights more problems with 'diet' that I will preach over and over and over to anyone asking me what I eat, thinking that they can eat the same thing and have my physique:
"... He (Ronald Krauss) and other researchers have documented that individuals react very differently to low-fat or reduced-salt diets, for example, depending upon their genetic predispositions. One persons LDL or plood pressure plunges, while someone elses remains neraly unchanged."
Odds are, you cant eat what I eat to look like I look. If I ate what 'diet and fitness' magazines said I 'should' eat, I would die of starvation within a month (I eat a LOT). You have to experiment with your diet to see how you respond! It sucks! It took me years of keeping nutrition journals to figure out what I should eat, and what I need to keep in moderation (or stay the hell away from).

But remember, I have very specific fitness goals. Whats an Average Joe who just wants to avoid heart problems and cancer supposed to eat? This is the best advice ever from Marcia Angell (former editor of New England Journal of Medicine):
"Within limits they should eat the way they want to eat. What are the limits? I think they should eat in moderation, and I think they should eat as varied a diet as possible because thats good insurance. You dont put all of your eggs in one basket, or in this case, your health in one egg. You try to cover the waterfront because youre operating from a position of extraordinary ignorance, so your best bet is to eat a varied diet."
Eat a steak, if you want it! I dont want it, I think theyre gross, but eat a damn steak! But dont just eat steak! Eat a damn apple every once in a while! Maybe some eggs! How about a glass of milk? Gaining weight? Dont eat so much steak, but you can still eat the steak! YAAAAY!

You could make a whole new sub-magazine: SKEPTIC Diet, Fitness, and Supplement

But these articles are a good start-- give them a read!

Sunday, May 27, 2007

The Creation Museum

Ive been looking forward to this since PZ first mentioned it a week or so ago.

Like PZ mentions, what does it say about todays 'journalists' when a bunch of amateur bloggers can provide a better critique of Creationism and Ken Hams Magic Museum than the supposed professionals?

So here, hopefully, is a go-to post for people who want to know whats up with Young Earth Creationism and why scientists are so upset about the Creation Museum.

The Creation Museum Carnival

Fast link to my contribution

Saturday, May 26, 2007

ID vs ERVs-- Part Thirteen: Lets Cut to the Chase

Ive been putting off finishing the Sternberg paper because, well, I havent been feeling so hot lately, and Mr. Black Holes post-modern crap-fest doenst help with the nausea so much. I mean seriously, look at how he tries to 'disprove' transposable elements impact on 'macroevolution' (note: hes pulling all of this out of his ass. None of this is actually scientific, hes not talking above you, its po-mo.)

Consider now a developmental "selector gene" locus with an organization similar to that of the β-globin locus. Our not-so-hypothetical locus is a functional composition of various cis-acting (I, R, M, E, S, and P) and protein-coding sequences (G). So our developmental locus can be formally defined as: Locus = (I, R, M, E, S, and P) Now there must exist a morphogenetic rule, f, that maps from "genome space" (the set of genotypes) to "phenotype space" (set of morphologies) the information contained in the locus, with the phenotype being designated here as Φ. Alternative ways of expressing this relation are:

f: (I, R, M, E, S, P, G)--> Φ or
f((I, R, M, E, S, P, G)) = Φ

Let Locus now be subjected to the insertion of a TE unit (Locus-TE). This means that the following mutational event has occurred:

(I, R, M, E, S, P, G)--TE-->(I, R, M, TE, E, S, P, G)

For the TE to have a phenotypic effect, one of two things appears to be necessary. Either the set of morphogenetic rules F interpret Locus-TE in a way such that a different point in phenotype space is accessed, say Φ' instead of Φ, or F cannot interpret Locus-TE, and an entirely different phentotype is attained by default. What is crucial to note now is that the TE insertion can only act as the material cause of the phenotype shift, whereas F is the set of efficient causes generating an effect (phenotype shift), the effect itself being constrained by the structure of phenotype space, with the latter entailing formal (causes) rules of morphology. In other words, TEs can only affect how morphogenetic rules interpret genomic data; these sequences cannot, of themselves, "write" new morphogenetic rules or restructure phenotype space. Genomic turnover due to TEs and other REs can provide new data/information for the system of Fs to interpret and use, but the important causal basis of differences in body plans resides in the formal rules that structure phenotype space.


Look, this is the exact same argument as we got from the know-nothing YEC author at AiG. The whole premise of Mr. Black Holes paper is that mobile elements are integral, so mobile elements utilized by an organism are evidence of Design, but mobile elements cant 'write new morphogenetic rules or restructure phenotype space', so Evilution is false. Again, heads ID wins, tails Evilution loses.

But remember, folks, its Evilution thats unfalsifiable.

Mr. Black Hole insists that his hypothesis is falsifiable. You see, if we can just make/find an organism without any mobile elements in it, then we've proved him wrong!
One potential falsification of the integral function framework would be the construction of an artificial eukaryotic genome that lacked any form of REs and that, nonetheless, maintained all normal genomic/epigenetic functions. For example, ablating all REs from a complete set of Takifugu chromosomes, placing this diploid nuclear complement in an anucleated Takifugu zygote, and then observing normal Takifugu ontogeny would effectively negate any global functional roles of REs.
This is not a falsifiable statement. Asking for an organism without mobile elements is like asking for an organism not made of DNA-- Not because it is essential for all forms of life, but because thats how life evolved on this planet, our only source of 'life' samples at this point.
The very beginning-- the very root/net/swamp base of the Tree of Life is a mess of mobile elements and pirate DNA, thus the prediction from evolution would be that there are no organisms on this planet free of them.
Additionally, the puffer-fish has been evolving with its mobile elements for >millions of years. Why would you think you could just pop stuff out of their (or any modern) genome and everything would be hunky dory??
Oh, well I guess we always have the option of building an organism from scratch.

Ugh. Lets finish this crap.
Given all that we know of REs, the selfish DNA narrative may explain aspects of the origin of these sequences, but it certainly fails to capture the diverse roles of these elements in chromosomes and during ontogenesis.
The 'retroviruses' that created our HERVs are all dead. There are no infectious counter-parts. So ERVs are the ultimate selfish DNA-- they are retroviruses that have found a way to 'survive' where their counterparts have failed. The insertions were co-opted as needed with no original intent, which perfectly explains the diverse roles of mobile elements.

Not only that, but the selfish DNA narrative appears to be refractory to any type of falsification. Inferred evolutionary effects of REs also appear to be just-so stories.

As unpalatable as this may be for most readers, it would seem that the selfish DNA narrative and allied frameworks must join the other "icons" of neo-Darwinian evolutionary theory that, despite their variance with empirical evidence, nevertheless persist in the literature.
Oh 'icons of evolution.' How cute.

LOL Creationists

Yesterday the Hoofnagle brothers put forth a challenge: LOL Creationists.

Im totally late, but I hope my entry is worth it. I tried real hard.

Heres part 2 from from Denialism.


Thursday, May 24, 2007

Guess the Activism Group: Clitoraid

One of the many horrific 'customs' that still exists on this planet is female genital mutilation. An activism group has set up a non-profit organization hysterically called: Clitoraid

It is a crime against humanity that today, in this so called enlightened 21st century, women in under-developed countries are subjected by force to participate in the sex trades, are denied common freedoms as we know and enjoy in the west, and in certain cultures, are slaves to barbaric practices such as clitoral mutilation in the name of religion and, moreover, male dominance.


According to a barbaric tradition that still persists in some parts of the world, female children are forced to undergo an excruciatingly painful procedure through which the clitoris is excised. The act is typically carried out without anesthesia and is often performed by female relatives, themselves earlier victims of the practice.
An estimated 135 million women worldwide are victims of this detestable tradition. Until now, with the damage done, little could be done to help them achieve the sexual pleasure known to the rest of humanity.
Damn right. You know, this is one of those things that we can universally agree on, I think. This is like child hunger and making sure everyone has safe water to drink. This should be a universally condemned issue... but its still going on. But Clitoraid is trying to do something. Theyre trying to help. as many women as possible to regain their sense of pleasure and founded Clitoraid, a private non-profit organization with the aim to sponsor those women who want to have their clitoris rebuilt.

“Adopt a Clitoris” program was designed not to help just a few women, but to finance the construction of a unique, sanitary and specialized medical unit in which women of all nationalities and religions could have their clitoral sensation “rebuilt.”

We can all help. we can support our sisters, and Adopt a Clitoris!
Sweet! This is a fantastic idea! I mean, cant you picture the people who started this? Quirky, fun, feminists, who arent just mad-- theyre mad and doing something about it! My kind of people!

You can imagine my surprise (since you will be too) when I found out who started this charity. The Raelians.

Well knock me over with a feather.

Wonder how much proselytizing goes along with this? No matter the answer, I cant honestly say I wouldnt rather have the Raelian Missionaries around than the Christians. I dont know what to think about this. Like I said, genital mutilation should be a universal "NO!"... so why dont we have a world, secular organization like Clitoraid? Or do we, and I just dont know about it?

Wednesday, May 23, 2007

Carl Linnaeus & a Liberal Arts Education

Today is Carl Linnaeuss birthday. You may not recognize the name, but I know you know one of his contributions to science: Kingdom, Phylum, Class, Order, Family, Genus, Species.

Well, thats certainly helpful, but why am I writing a post about Linnaeus? He wasnt really into microbiology.

I have a personal connection with Linnaeus :) When I was an undergraduate, one of my projects was designing a horologium florae. Flowers usually open at the same time every day (of course, depending on latitude/rain/clouds/etc). For example, at my universitys latitude, the blue pimpernel opens at 9 am, and the moss rose opens at 10 am, and the passion flower opens at ll am, and so on. Linnaeus noticed this, and thought it would be a neat idea to make a 'clock' out of flowers. He just wrote about this idea, he never followed through on it.

But I did! Sure I was a hard-core pre-med, not really into real biology at the time, but I went to a liberal arts school, goddammit! I was gonna plant me a garden for the campus! Oh, but not just any clock garden, folks-- A SUPER clock garden! A clock garden superimposed on a sundial!

One of the physics professors designed that for the garden-- And I found flowers that could fit into each time slot to plant in the open areas. Its harder than it sounds! The opening times of flowers isnt something normally found in gardening books or websites, so I had to do a ton of research and 'experiment' with different flowers. Very, very different from what I do today-- but sooooo much fun! Man cannot live on viruses alone :)

For more information on this garden and for pretty pictures, click here!

Tuesday, May 22, 2007

"Oh my god! Thats a lot of pus!"

So the bacteria were jealous of all the attention viruses were getting in my personal life.

"Youre supposed to be a microbiologist!" they said. "Dont you listen to a word those Creationists say? You should teach all sides of an issue. If you talk about viruses you have to talk about bacteria!"

"But I dont have any bacterial infections? I mean, theres our commensal bacteria and such, I could write about that. But I only gave EBV the air-time because it was giving me so much trouble," I replied, a little confused.

And then the bacteria just started laughing.

I didnt understand why, at the time, but now I get it. You guys know what I have now? DRUG RESISTANT STAPH. AAARG! Can I please be healthy for 24 hours? 24 hours, thats all Im asking.


I went back to the doc this morning because some of my rash spots werent going away, and they itched really bad. One of them was, well, huge. And painful. So my doc chopped it open to drain it (lots of lidocaine, didnt feel a thing).

"Oh my god! Thats a lot of pus!" she yelped. Immediately trying to regain professional composure and to keep me from freaking out, she added "Dont look."

Well me being me, I looked. Sooo gross you guys, so gross. "Ugh, what is it?"

Doc, "Probably Staph. Probably drug resistant Staph. A lot of people carry it on their skin with no problems, but with your rash..."

Ugh I totally got Staph across the skin boarder when I was scratching that damn rash! ARRRRG! So Im on a lot of antibiotics right now. And vicodin.

**faint sound of teeny tiny bacteria laughing**

Oh Ill get the last laugh, you bastards.

Monday, May 21, 2007

ID vs ERVs-- Part Twelve: What are the YECs saying?

In honor of PZs (hopefully one time) Creationism Museum Blog Carnival, I might as well extend the ID vs ERV series to include what the Young Earth Creationists are saying about ERVs.

What is THE go-to resource for Young Earth Creationism 'science'? Why, AiG, of course! Lets go see what they have to say about ERVs. If you click around on a few, and youre familiar with the 'ID vs ERV' series, Im sure you will be shocked, shocked, dear readers, to notice that Intelligent Design Creationist and Young Earth Creationist claims about ERVs are absolutely identical.

IDC: "ERVs are good and part of the Designers Plan. Not junk like those stupid Evilutionists think!"

YEC: "ERVs are good and part of Gods Plan. Not junk like those stupid Evilutionists think!"
Im sure many of you regular readers can play this game and find AiGs errors on your own at this point, but since this is a Carnival post, Im going to go through several of them for the new readers :)

Lets start with 'Human endogenous retroviruses (HERVs)—evolutionary “junk” or God’s tools?'
Once the retrovirus enters a host cell, its RNA genome is made into DNA (through an enzyme the retrovirus carries) and the DNA is integrated into the host genome—becoming a type of endogenous retrovirus, meaning that it is now a part of the genome in that cell.
No. No. No. Exogenous retroviruses dont become endogenous when they insert themselves in the genome of some of your cells during an infection. Retroviruses become endogenous when they infect a germ-line cell and are 'transmitted' vertically, thereby having its genome in every last one of the cells of the offspring. Someone getting infected with HIV is not an example of an endogenous retrovirus.

Unlike HIV, these “ancient” retroviruses purportedly integrated themselves into the genome long ago and have since accumulated mutations that have rendered them unable to produce infectious, exogenous viruses.
No, not 'purportedly.' They were. This isnt religion, where you cant know The Truth(TM) unless you open your heart to any number of deities. Its science. Dont believe a claim? Look it up yourself. For instance:

Differences in HERV-K LTR insertions in orthologous loci of humans and great apes.

The classification of the long terminal repeats (LTRs) of the human endogenous retrovirus HERV-K (HML-2) family was refined according to diagnostic differences between the LTR sequences. The mutation rate was estimated to be approximately equal for LTRs belonging to different families and branches of human endogenous retroviruses (HERVs). An average mutation rate value was calculated based on differences between LTRs of the same HERV and was found to be 0.13% per million years (Myr). Using this value, the ages of different LTR groups belonging to the LTR HML-2 subfamily were found to vary from 3 to 50Myr. Orthologous potential LTR-containing loci from different primate species were PCR amplified using primers corresponding to the genomic sequences flanking LTR integration sites. This allowed us to calculate the phylogenetic times of LTR integrations in primate lineages in the course of the evolution and to demonstrate that they are in good agreement with the LTR ages calculated from the mutation rates. Human-specific integrations for some very young LTRs were demonstrated. The possibility of LTRs and HERVs involvement in the evolution of primates is discussed.
YAY! PubMed works just like Google. Put in some search terms, look up anything you read that you dont believe! Cant access the article? Go to your local public library or university library and they will help you out!

Heres a nice example of how Creationist 'science' writers have no idea what theyre writing about, they only know the talking points, thus they dont know when theyve contradicted themselves. This example is particularly funny because the author is attempting to make a joke at the expense of Evilutionists, but the author is the one that looks like an idiot:
...Contrary to being “junk” DNA, HERVs are thought to play at least three major roles...
...It was recently reported that an endogenous retrovirus in sheep was necessary for maintaining pregnancy, as it was important in the formation of the placenta...
...This means that retroviruses jumping in and out of the genome caused changes that were selected for, supposedly resulting in microbes becoming microbiologists. This type of evolution requires a gain of information that is not accomplished by retroviruses jumping around in the genome.
Did you catch that? Mammals gained the function to generate a placenta with an ERV so Creationism is true... but ERVs cant allow a gain of function so Evilution is false. Heads they win, tails we lose.
ERVs are a beautiful example of Evolution in Action.

The location of integration sites of transposable elements are used to determine evolutionary relationships: “A specific retroviral integration site shared by two species is indicative of a common ancestor because the likelihood of independent integrations at exactly the same locus (insertional homoplasy) is negligible.”1 Their presupposition of common ancestry is supporting their interpretation of the evidence for common ancestry. Could it also be indicative of a common designer?
This is THE Creationist Claim for ERVs. "ERVs dont mean common descent! They mean Common Design!"
No. Its not just the ERVs or their insertion sites. Its also how theyve mutated or been co-opted over the course of time.

It is possible that certain sites are predisposed to the insertion of retroviruses.
Certain areas are predisposed to the insertion of retroviruses. Some retroviruses like to be inserted near actively transcribed genes. Some like to insert near silent genes. Some like to be near regulatory genes. This isnt 'possible', we know this. However, the actual insertion, which base pairs are on the left and right of the insertion, that is random.
Additionally, if two retroviruses happened to insert themselves in the same location, we would be able to tell the insertions apart. The retroviruses themselves would be different (retroviruses love them some mutations!), and they would have mutated differently over a few million years.

Biblical creationists do not think that HERVs are “junk” DNA, but much work needs to be done to gain a greater understanding of the role of HERVs in the past and present. The difference is our starting point—the Word of God versus the word of man.
Thats a dishonest statement. Young Earth Creationists dont do laboratory research. 'More work needs to be done?' YECs dont do any work at all, especially with ERVs. If you know of one, send him/her my way.

Sunday, May 20, 2007

I want to start a new meme: Active Atheism

Im going to try to cut back on ripping on theists, and instead move towards positive atheism. Being negative is a wonderful vent for me, but it ends up leaving me more depressed. Thus Id like to introduce a new meme.***

A few descriptions of me Ive heard:

None of those accurately describe me. 'Militant' describes my conviction, but it gives an inaccurate impression of why I do what I do. So why do I do what I do? Why do I speak out against the behavior of Fundies of all Flavors?

Because the one thing I cannot do is sit on my hands while bad things are happening. Thats what originally drew me to the medical profession, and what ultimately drew me to HIV and cancer research. When everything goes wrong, I dont cry, I dont pray to Jesus, I dont play blame games, I dont run to Mommy to make things better (Okay, Im lying with that one. When Im really sick, I want Mom.)-- I do something. Maybe a nice side effect of growing up nontheistic ;) Want to get something done, you do it yourself!

So my new descriptor, whether you all want to use it or not, is Active Atheism. It means when Fundies intimidate homosexuals, Im going to be there to defend the rights of homosexuals. It means when Fundies attack, Im going to offer to help their victim any way I can. It means when Fundies start stalking science like the reanimated undead, Im strapping on a chainsaw.

hehehe Edited to add because I got excited about The Simpsons:
It also means that Im going to take preemptive action against potential Fundy behaviors, such as science outreach, women empowerment and encouragement, and just putting it out there that Im an atheist so other, closeted nontheists know they have someone to talk to. And supporting my fellow nontheists and their pro-reason projects any way I can.

I dont expect all atheists to be Active Atheists, not everyone has the interest or are in a position where it is 'safe' to be active. But I expect to be able to go to all other Active Atheists for help when I need to get things done.

*that someone else has probably thought of before
**that probably wont catch on, ie Brights

Saturday, May 19, 2007

A Christian who might *get it*

Like many of you, I have 'atheism' as a keyword for my GoogleNews. Today, this article popped up.

It is at this point that T.S. Eliot’s Notes towards a Definition of Culture is more important than ever. He forecast that the indiscriminate unification or harmonizing of a culture would achieve naught but its own debasement. In our time, when cultural diversity (to use Francis Fukuyama’s astute formulation) is little more than an "ornament to liberal pluralism", supplying the otherwise dull veneer of Western culture with a certain culinary and aesthetic flair, the multiculturalist refusal to, as Hirsi Ali puts it, "classify cultural phenomena as 'better' or 'worse' but only neutral or disparate" actually reinforces the barbaric treatment of women within Islamic communities. What is called for is not intellectual tolerance and mutually-degrading respect, but rather division.

We should be thanking these anti-theists for picking a fight that we should have started long ago. The only question now is, as Christians, will we have the courage to oppose our common foe — what Barth rightly termed "religion as unbelief" — or will we retreat to the safe-ground of religious obsolescence?

He might *get it*. Maybe. He might just be viewing this as 'Atheists are allies against the Muslims!' instead of the usual 'Muslims are allies against the atheists!' line. But Im not sure if he understands the implications of *getting it* even if he does understand our position. Active Atheism isnt just about stopping 'the barbaric treatment of women within Islamic communities.' It means we arent going to let Christians get away with 'the barbaric treatment of women' either. It means we arent going to let Christians get away with 'the barbaric treatment of homosexuals'. It means we arent going to let Christians get away with 'the barbaric treatment of science.' And so on. He would definitely be put into a position where he would be working against 'fellow Christians.'

If Mr. Stevens acknowledges and accepts this conclusion, then I would happily accept him as an ally.

Horowitz sure does like the sound of his own voice.

This was just going to be a fluff post on a MADTV skit I saw this morning (it was a repeat, so it was old news). As I was Googling in an attempt to find a clip to post, I found I was already beaten to the punch by Skeptico! Well, go there to read that post-- its hysterical-- but as I was searching YouTube, LOOK WHO I FOUND AGAIN!

Part 2
Part 3
Part 4


A four part radio interview with my good friend Leonard Horowitz!! And gosh golly wouldnt you know it, but comments and ratings are disabled! Im so shocked! Im sure you readers will be shocked to notice, as well, that the YouTube description urges people to visit a website called Educate "Oh," you readers might say, unimpressed, "That is nice. Educating yourself is a good thing. Horowitzs crap was probably posted by a skeptic."

HAHAHAHA! NOOOOOO readers! Dont forget to translate 'educate yourself' into woo-speak! What are some of the things you can 'educate yourself' on over at Educate Yourself?

  • Colloidal Silver
  • Chemtrails
  • Sylphs
  • Forbidden Cures
  • Ozone
  • Immunity Boosting
  • Nutrition
  • Mind-Body Connection
  • Bioelectrification
  • Vaccine Dangers
  • Mind Control
  • Dowsing
  • 'Peak Oil'
  • Project Blue Beam
  • British Israel & The End Times
  • Cloak & Dagger Board
  • Metal Free Dentistry
  • Global Warming
  • Depleted Uranium
  • Healing Thought Forms
  • Monoatomic Gold
Niiice! Go on, check it out! Wallow in the woo for a bit, then go take a shower. You know you want to know what a 'sylph' is :P

Speaking of radio interviews, I cant help but notice that Dr. Dentist doesnt have our interview on his webpage. I mean, I have it up, and Im just a blogger. Why wouldnt he add our debate to his media CV? I just dont understand why he wouldnt add it. Im so confused. Maybe he just forgot. That must be it.


Eh Ive only listened to bits and pieces of this interview, I might give it thurough listen later. But I havent even gotten around to eating Horowitzs peer reviewed paper yet! So much woo, so little time!

Friday, May 18, 2007

I got my first Technorati Favorite-ed!

I still dont totally understand all the features of Technorati-- I really just use it to see if anybody is linking to me (it took me 3 months to realize my 'pings' werent registering).

But I got favorite-ed by somebody today! So I shall plug her blogs! Especially cause they look like good reads :)

Women in Science

Biology in Science Fiction

The Road Less Traveled

Around Yucaipa


Hitchens. I like this guy!

Big thanks to PZ for posting these, as 'Hannity and Colmes' isnt on my normal viewing schedule :P

Warning-- I laughed so hard at Hitchens last jab I almost puked:

Did you catch that?

"If they gave Falwell an enema they could have buried him in a matchbox!"


As far at the 'H & C' premise-- that we should 'respect Falwells family'... Fuck that shit. If his family was actively working against Falwells Ministry of Hate, then they would most certainly have my condolences. For the life they had, for the burden they have to bear just because of who their father is, their future lives wasted cleaning up Falwells mess instead of following their dreams, and Id give them a grim hug as they breathed a sigh of relief that he can do no more harm.

But thats not the deal.

As far as I understand, Falwells family has inherited his business. They plan on carrying on exactly how Falwell would have wanted. His family has no doubt benefited from the millions he has conned from the stupid masses that follow him. They probably never went wanting at Christmas or birthdays, or were denied trips to Disney World and Hawaii, while Falwells sheep emptied their pockets in his trough. His sons probably enjoyed a place of privilage all through their education just because of who their father was, while their homosexual classmates lives were made miserable by Falwell. They cant have ever shed a tear for the Hell on Earth that they helped create, or they would be trying to fix it.

Falwell is an ass. His family is a bunch of little assholes. Im glad Falwells dead, and I wish he took his poor little family with him.

Edited 7:15 pm to add-- In a perfect world, Falwell rules.

Atheists on the news in Oklahoma

Well! I guess us atheists are turning into a guaranteed ratings boost for TV stations! The local NBC news had a segment last night on 'Atheists in Oklahoma... Living In The Shadows'. DUN DUN DUNNNNN!!!!

Atheist segment starts at ~ 7 minutes. Or watch the whole thing and laugh at Oklahoma news. Oh, and the link doesnt work in FireFox. Why? Because this is Oklahoma. If the link doesnt work, its the Thursday 05-17-07 10 pm newscast at KFOR.

Its not too bad. Of course they give the last word to some nauseating Biblo-pusher. "Think with me... about how preposterous it is to believe that everything happened from nothing!" he says, baffled.


I think Christians are from Mars. That wasnt English. I mean, it was English words, but when you put them together the way he did, they make zero sense. The cherry on top would have been if the next sentence he said included the words "evidences" or "fellowshipping".

And you know, since they ended the atheist segment with a True Believer, that must mean all the True Believer segments will have atheists getting the last words now, right? Right? Brows the KFOR archives. Youll see lots of fun videos on Hell and exorcisms and ghosts and stupid shit, so Im sure theyll be ending all those segments with rational thoughts, since they ended the segment on rationalists with a loony?LOL. Riiiiiiight.

Thursday, May 17, 2007

My UD Prediction: Herpes Viruses Proof of Design!

No, not in the way youre probably thinking ("Punish dem damn fornikaters for screwin 'for dey get hitched!").

If their train of thought (I know, 'thought', lol) with transposable elements follows for viruses, then this paper is just more evidence for Intelligent Design!

Pop Culture Summary
Actual Article

See, all us Materialists Evilutionists think that viruses are just de-evolved organisms. Theyre the ultimate selfish genes (I havent gotten to this part of the Sternberg paper yet, but ID Creationists dont believe in selfish genes, either). So we never bother researching whether viruses might have A Purpose. Therefore, any time a researcher (no doubt a closet ID supporter) publishes a paper where a virus has a positive effect, that research supports Design.

Researchers at WashU discovered that if they infected mice with mice herpes viruses, then exposed them to the bad-guy bacteria that cause encephalitis, meningitis and The Plague, after the acute infection the mice were resistant to the bacterial infections. They found that having a latent herpes virus sitting around somehow activated a lot of macrophages-- not just the ones latently infected with the herpes virus. And they werent just 'activated'. They were on little macrophage rampages, looking for bacteria to eat.

In contrast to macrophages explanted from mock-infected mice, macrophages from latently infected mice were bactericidal, killing L. monocytogenes rapidly after uptake.
This paper couldnt have come at a better time, considering my recent Epstein Barr Virus fun (EBV is a kind of herpes virus, so is chicken pox, and the oral and genital herpes we all know and love). Unfortunately not all mouse herpes viruses they tried provided the protective effect. HSV-1 might give us humans some protection against bad-guy bacteria, and EBV might not. We dont know yet.

And, this research is on mice, not humans. Heres the usual animal model disclaimer-- animals are priceless models for testing drugs and studying infections and molecular pathways, but you always have to take animal research with a grain of salt when you use them as descriptors for how things work in humans. See Oracs DCA posts for more on how research in animals and petri dishes can lead to hysteria in humans.

So here I must use my default phrase for when someone finds something neat, but not so practical yet: "This research provides some interesting avenues for future investigations!" YAY! I see RO1s in these researchers futures :P

Oh, the authors also address the fact that herpes has been with humans since we split from reptiles, thus this putative protective effect might be a co-evolved thing. We've had about 100 million years to co-evolve, according to the article. That silly common descent thing you dont need to understand to be a physician. I guess the Creationists will just have to ignore that little fact.

The only outright strange thing I saw in this article was the quote from a Dr. Bernard Roizman at the end of the pop culture article. I know Dr. Roizman is a Big Guy in the herpes world, but I assumed he had been shamed out of being quoted in pop culture articles after he stole a patent from one of his post-docs and fired her in the hopes shed never find out. Maybe Im out of date on those goings on.
But its not just that-- its his quote:
" my mind the only good virus is a dead one or one that has been silenced for life."
HUH?? Um, you all know Im being sarcastic with "UD says herpes is evidence for Design", but this is exactly the kind of loose, stupid commenting that feeds their quote mines! Ohhh look at that Evilutionist saying all viruses are bad and all junk DNA is useless! "Viruses help control Red Tides, therefore Creationism is true!" "Viruses might give us Plague resistance, therefore Creationism is true!" That comment is just stupid, and I hope Dr. Roizman didnt really mean it.

Wednesday, May 16, 2007

Hitchens. Do I like this guy?

I dont *get* Christopher Hitchens.

I dont know whether I like him or not.

Maybe its because I dont trust him not to say stupid things. I mean, Dawkins can go on '700 Club' if he gets invited-- I know hes not going to say anything that will make me wince. But Hitchens... eeeeh?

But I think I might have to get his book, God is Not Great, if only as a kudos for this:

And then I did a quick Google to see some of the Churchies reviews of his book, and theyre even dumber than the 'reviews' Dawkins got! Here are a couple off the top:

Leora Tanenbaum - Huffington Post
If I were sitting in the pews listening to Christopher Hitchens delivering a sermon on his new book, a denunciation of religion, I would roll my eyes, perhaps doze off, maybe even walk out. This is what believers in houses of worship do when confronted with overblown, out-of-touch, and insulting words from the pulpit.

Father Raymond J. De Souza - National Post
At a certain point in reading God is not Great, Christopher Hitchens' broadside against religion as a false, immoral, man-made construction, I half-expected Hitchens to write that if God were real and omnipotent, and consequently Hitchens so wrong, then God should have arranged things so as to prevent him from writing his book. But the book exists! So God couldn't stop it. And why couldn't he stop it? The simplest answer is that he does not exist!

Dennis Covington - Paste
But as learned and well-researched as it is, God is Not Great merely offers a fleeting critique of what we think of as organized religion. At its center lies a broader attack against those who, religious or not, believe in the life of the spirit as well as the life of the flesh. In short, Hitchens has written a hymn of praise to scientific materialism and, sad to note, a clumsy apology for its own many crimes.
What then of the National Socialist scientists who conducted experiments on Jewish children in Hitler’s death camps? Clearly psychopaths and brutes, they did not claim “a heavenly warrant” for the cruelty they inflicted. Should they, too, have been “understood” since they were not committing their crimes in the name of God, but in the name of science?
hehehe! Zombie Hitler? Zombie Hitler?? I HAVE TO READ THIS BOOK!

Tuesday, May 15, 2007

Little Doogies Whoop Creationist Booties

You all remember Mr. Professor of Neurosurgery? Engor-something-or-another? Ah, seems like yesterday he was bitching and boasting about how little he understood evolution!

Well the contest that put Mr. Professor of Neurosurgery in the lime-light finally has some winners!

  1. Gregory Simonian, 10th Grade
  2. Merve Fejzula, 12th Grade
  3. Shobha Topgi, 11th Grade
  4. Linda Zhou, 9th Grade

The winner said the essays would be uploaded soon... but ARG!!! I wanna read their essays now! You know theyre adorable!! It would also help restore my faith in humanity a bit.

Edit 5-16-07: Shoot! Forgot to link back to Orac!

Monday, May 14, 2007

ID vs ERVs-- Part Eleven: DaveScots Rude Interruption

Dang it. I was really hoping to get through Sternbergs space-time-continuum ripping paper before I got to any other ID vs ERV garbage, but I cant do it. There is just too much poo to wade through in Mr. Black Holes paper, and to be timely, I should respond to DaveScots recent comments on UD (only give them a hit if you have to).

Dave starts out with a simple, but basically correct description of retroviruses and how they can become endogenous retroviruses. Sure he says 'translate' instead of 'transcribe', and he over simplifies what can happen to ERVs over the course of time (usual Creationist lack of creativity), but eh, not so bad.

Then I think he starts to pull crap out of his ass. Right about... here:

It should be noted that human designers use domesticated RVs as delivery vehicles to insert foreign genes into genomes to create so-called GM (genetically modified) organisms like tomatoes with longer shelf lives and whatnot. Theoretically this can be used to distribute vaccines for various diseases. A GM banana for instance could carry genes that cause it to manufacture a vaccine for malaria. Eat a GM banana and you’re immunized against malaria.
Yeah.... no. Plants dont really 'do' retroviruses. They like RNA viruses more, cause they can modify plasmodesmata and slither through to new cells. You dont make GMO plants with retroviral vectors. You make them either by using a gene gun, or the agrobacterium method.

Yeah... that kinda puts a kabosh on the rest of his post, even if you ignore the logical problems with DSs case for design.
More significant to the case for intelligent design is that this is a mechanism a designer could use to modify genomes - introduce a virus into the population which inserts genes that cause the spawning of a new species.
Nope. Unless youre playing the Old Creationist Game: Nothing is important except for animals cause they got named by Adam and were on the Ark. Because retroviruses are basically an 'animal' virus. I think theyve found 'retroviral like' viruses in plants, but retroviruses arent a source of novel genes in non-animal organisms. Try to give an E. coli a retrovirus. Shell look at you like youre on crack.

So if anyone asks about possible mechanisms a hypothetical designer could use to intervene and direct evolution that’s a good answer. Human designers are already doing it so it’s a proven mechanism.
No, you just made up an ad hoc explanation for a scientific phenomena that directly contradicts your Creation myth in order to align your views with reality so your head doesnt explode. You also did it by not understanding what you were talking about-- using retroviral vectors to transform cells is only possible in animals. Youve still got to explain the evolution of a few billion other organisms, who have pseudogenes and other genetic artifacts that act just like ERVs.

Morever a highly infectious retrovirus inserting genes that cause modification and speciation could convert entire populations into a new species in just one or several generations and at the same time cause the original species to become extinct virtually overnight.
*looks around* What the hell are you talking about, Davie? How about you give an example of a retrovirus doing this? Maybe some experimental data? No? To much for the Creationist to actually, you know, do something? Easier to just pull crap out of your ass? Okay then.

That fits wonderfully with the indisputable testimony of the fossil record which paints a picture of abrupt speciation, millions of years of little if any change in the new species, followed by an abrupt extinction. A mechanism for causing saltation of new species is thus shown.
YAAAAAAY! +10 to Crappenpuff for managing to mangle punctuated equilibrium out of the blue!

If common design instead of common ancestry the designer is evidently using existing species in situ as the template for new species. If that’s the case there’s effectively no difference whatsoever between common design and common ancestry.
In which Davie almost realizes he needs a negative control. Almost.


Im not reading the 'comments'. I heard Sally-baby left a stinker, and Im sure some beautiful evilution straw-men and arguments from personal incredulity were erected, but Im still not feeling so well. I cant imagine Creationist Crap will improve my health.

But if you guys happen to click over to read the UD article and find a juicy Creationist Claim-- please feel free to squash it over here *devilish grin* That will cheer me up!

Saturday, May 12, 2007

Bushs approval rating must be really low...

Moms Jewish. Dad is Catholic. I have Baptist cousins. Mormon cousins. Episcopalian cousins. Lutheran cousins... I got everybody.

You know Bushs approval rating is low when my mom got an anti-Bush e-mail from the Southern Baptist cousins. Theyre really Southern Baptist-- no dancing, no playing cards, the works. Heres what she sent my mom:

A 70-year-old Texas Rancher got his hand caught in a gate while working cattle. He wrapped the hand in his bandana and drove his pickup to the doctor. While suturing the laceration, the doctor asked the old man about George W. Bush being in the White House.

The old Texan said, "Well, ya know, Bush is a 'Post Turtle.'"

Not knowing what the old man meant, the doctor asked what a Post Turtle was.

The old man looked at him and drawled, "When you're driving down a country road and you come across a fence post with a turtle balanced on top, that's a Post Turtle."

The old man saw a puzzled look on the doctor's face, so he continued to explain:

"You know he didn't get there by himself, he doesn't belong there, he can't get anything done while he's up there, and you just want to help the poor dumb bastard get down."

The Mystery at ERVs Lymph Nodes: The Plot Thickens!

My next doctors appointment isnt until Monday, so Im venting about this illness here until then. WARNING: Super gross pics! Not for the squeamish! Ill hide them in links rather than direct posting.

I found out yesterday that this adventure was me getting mono. The fast test gave me a negative result, but my other tests combined with the 'slow' EBV test turned up a definitive 'yes' to EBV (dont tell the HIV Deniers-- theyll start saying EBV doesnt exist if they hear about my test results).
Well, okay, that sucks. I missed getting it in high school when wave after wave of it hit my basketball team/soccer team/etc... Makes sense I would get it NOW. Ugh. So doc put me on some prednisone to help with my lymph node and tonsil swelling. I was feeling a lot better.

Until yesterday.

Yesterday was my last dose of prednisone. Thought nothing of it, until I went to the restroom at ~9:30 am. I had a few teeny tiny red spots on my tummy. 'Weird...' I thought, and went about my day. Couple hours later, went to the bathroom. More spots. Climbed up to my chest and arm pits. As the day went on, I got spots on my arms, neck, back, face... So I called the doctor.

Doc: Well, we have your tests back-- its definately mono.
Me: Thats nice! So, Im covered in spots.
Me: Yeah, little pink spots-- like someone flicked red watercolor on me.
Doc:... Do they itch?
Me: Nope!
Doc:... Well, sometimes a rash comes with mono, but I would have thought you would have had it earlier.
Me: Lots of spots.
Doc: Come in on Monday.

So I wake up this morning, to this:
Arm (where they drew blood for my tests)

My whole face is swollen-- lips, tongue, and those spots are actually raised on my face. Everywhere else theyre flat. Im hoping that this is my immune system bouncing back from being immunosuppressed under the prednisone, and that these spots are a good thing. And not, like, the measles.


God bless the Google Machine. It knows everything-- all you have to do is have the right question! Okay, so before we knew it was mono, the doc gave me some Augmentin. We had no idea what the hell was wrong with me. "If you dont feel better in 48 hours, take these" she said. I was not better. So I took one dose last Thursday. One. Later in the day I had another doc appointment, and doc told me she had a big hunch it was mono, despite my negative monospot, and to stop taking the amp. Why?

Rashes. Since the sore throat and fever seen with mono often leads to a mistaken diagnosis of strep throat, children and teens with mono may be given antibiotics, and some are given ampicillin or related drugs.

The vast majority of adolescents and adults with mono who receive ampicillin-like drugs develop a red raised rash over a good portion of the body. Other antibiotics, such as penicillin, also can cause rashes with mono but not as predictably as ampicillin. The rashes may be itchy, but they are not serious and will go away in a few days without any specific treatment. Rashes are not seen as commonly in young children, even when they are given ampicillin-like drugs. (link)
One dose of amp a week ago, and I look like a red alligator.

I think the Mystery at ERVs Lymph Nodes has been solved!

Friday, May 11, 2007

The Power of Faith

So ABC finally aired their bit on the Smalkowski Affair. Sure it was only ~5 minutes of a 2 hour show on "Lets all credulously accept complete and utter bullshit! Magic hugs! Magic tears! Maaagic YAAAY!!!"... But it was actually kinda good.

They gave the evil Good Christian(TM) fuckers who attacked this family about 2 second of air-time to say "Um, we didnt do anything wrong" and the rest of the segment was very sympathetic coverage of the shit Nichole had to deal with.

Nicole said that once she told peers at school that she was an atheist, her relationship with the other kids changed. "You know they would call me devil worshipper. I'd walk down the halls, people would laugh at me. They would look at me really weird and stare me down."

Then, according to Nicole, the teachers also began harassing her, one going as far as to say, "This is a Christian country, and if you don't like it, get out."

Diane Summerford is a substitute teacher at the high school Nicole attends and is married to one of the town's religious leaders, Pastor Truman Summerford. She said there was no discrimination against Nicole. "I have never seen anything in the school where the kids treated Nicole badly. We have good kids that care, and they are good Christian kids."

And as for the game-end tradition, Pastor Summerford said, "It is still a free country we are living in today. And our young people are standing up for their faith as they do this."

This is why I trust True Christians(TM) as far as I can throw them. Evil little fuckers, attacking a 13 year old girl, and oh gosh golly! They didnt do anything! Theyre Good Christian Kids(TM)!

... But if they did, they were in the right!

Liberal Christians, appeaser atheists-- you get these jackasses in line, or shut your damn mouths when people like me deal with them.

Ill add a clip of it to YouTube the second someone uploads it. There was a bit with Richard Dawkins, so Im sure he will put something up!

ID vs ERVs-- Part Ten: The Red Queen Declares "OFF WITH HIS HEAD!"

You all will have to forgive me for totally mixing my 'Alice in Wonderland' and 'Through the Looking Glass' queens, but The Red Queen is the topic of this installment of 'ID vs ERVs'... and well, she whoops Mr. Black Holes ass.

You see, Mr. Black Hole is terribly offended by the very existence of the Dear Queen. Shes a path up Mount Improbable. She is another one of those non-intelligent creative forces that Creationists cannot fathom.

So who is this fiery babe? I hate to say "use common sense", because science rarely works on the level of "common sense", but common sense is a good way to understand the Red Queen. Start with a population of deer. There is a natural variation in how fast each of these deer can run within this population. There is a population of wolves nearby, also with a natural variation in running speed. Faster wolves catch more deer. Faster deer survive generating a population of deer with a natural variation of speed higher than that of the pre-wolf population. Then the wolves get faster, then the deer, etc etc etc. This goes on on a billion different levels. Deer with harder hooves can kick harder-- Wolves with thicker skulls dont get knocked out. Wolves with sharper teeth-- deer with slicker fur. Whatever you can imagine, I bet its wrestling with the Red Queen.

"WAIT!!!" you readers must be thinking. "So why dont we have deer running at the speed of light right now??"

Well the Red Queens sister is The Happy Medium. Lets use HIV as an example for the Happy Medium. HIV is the deer, our immune system is the wolves. HIV needs to evolve at a fantastically high rate to stay one step ahead of our immune system. HOWEVER-- the mutation rate isnt infinitely large. If HIV mutates too much, an infected cell wont produce any infectious progeny. Theyll all be mutant bastards. If it doesnt mutate enough, the immune system catches up. The Happy Medium is where HIV wants to be. But it can never escape the grasp of the Red Queen.

But Creationists dont see the world like you and I. You and I see a process like siRNA, and see an end result of billions years of evolution. Teeny tiny steps, twisting and turning with the Red Queen and the Happy Medium, everything being selfish for itself and accidentally bringing other bits on for the ride. A biological goulash resulting in what we see as siRNA.

Creationists just see the siRNA.

They see the peak of Mount Improbable.

They see magic.

So Im not at all surprised that Mr. Black Hole is completely and totally oblivious to the obvious answer to this 'unanswerable' question:

"One obvious problem with interpreting epigenetic control of REs/TEs as support for the selfish DNA story is the conservation and ubiquity of the phenomenon. Transcriptional and transpositional silencing of TEs are efficient and occur in fungi, plants, and animals. Epigenetic silencing mechanisms can thus be said to be a derived character present in all eukaryotes (a cladistic autapomorphy). It should be noted that the phenomenon is not sequence-specific, as artificial constructs such as transgenes can be inactivated. So in the face of the universality of tight epigenetic regulation of eukaryotic REs/TEs, a valid question, related to the topic of infectious TEs, is: how have any RE/TE families been able to transpose and/or amplify?"
Um. Well, viruses have their own epigenetic profiles. Host cells have epigenetic profiles. They are in a Red Queen race to see whos profile will 'win' (or some other weird messy merge happens). You can change epigenetic profiles through changes in the environment (dietary changes and such). Something that is 'silent' one day can be actively transcribed if, say, you arent getting enough to eat.

Mr. Black Hole doesnt get it. It seems as if he thinks if an ERV is silent NOW it has always been and will always be SILENT. "... How have any RE/TE families been able to transpose and/or amplify?"

His answer:
"A simpler interpretation is that the plesiomorphic epigenetic system determines which sequence will amplify and when, for how long, and at what levels. To put this another way, the multitude of "young" RE/TE families that have amplified in the context of a very conserved epigenetic control system suggests that the latter promotes element "selfishness," not that this system is engaged in an arms race with such sequences."
Post-modernist coagulated word-salad. 'Very conserved epigenetic control system'? What does that mean, 'very conserved'? The 'epigenetic control' of say, your liver cell vs a red blood cell is totally different. The 'epigenetic control' of your liver cell vs a liver cancer cell vs a Hepatitis C infected liver cell is totally different. Epigenetic landscapes change!
Mr. Black Holes data-free answer is that new ERVs have popped up because our epigenetic profiles wanted them to reproduce. Our and the ERVs epigenetic profiles arent competing-- everything happens for pre-programmed 'reason.'

"The crux of the matter is basically this: the currently emerging model of the genome—opposed in all details to the atomistic model—logically entails that selfish DNA as a general phenomenon is an impossibility..."
Selfish DNA is impossible. The Red Queen doesnt exist. Blue isnt a color. Shit tastes like bubble-gum. This paper is a grown man screaming "LALALALALALA VIRUSES ARENT SELFISH! LALALA VIRUSES ARE JUST PINING FOR THE FJORDS!"

What does the Queen have to say to that? "Humph! OFF WITH HIS HEAD! Hes certainly not using it."

May 11, 2004: Best Day Ever

I signed my soul over to David Bowie sometime in elementary school (hey, I was little, I believed in souls and magic and such-- I stand by my decision). Never thought I would be able to see him in concert. Hes like Apollo or Osiris, a god that belonged in a different time. I was born too late to witness His glory. And then, the Reality Tour.I got one of my professors to let me take a final early so I could make it to the concert. I didnt bullshit him with "My grandma is dying" "My aunt is having a baby," I just said "Prof, I have tickets to see David Bowie." That was enough for him.

I cant find a YouTube clip of 'Station to Station'-- one of my favorite songs. Bowie played it for the second time of the tour during the encore. I just started sobbing!! He is as amazing in person as you think he is. So here are a couple Reality Tour clips to celebrate the Best Day Ever.