Intro to HIV Denialism

Tara at Aetiology posted a video interview with John Moore and Jeanne Bergman, two founders of the AIDSTruth website.

Of course, in roll the Deniers. These threads typically go on for 300-600 posts with all the Denier goal-post moving. Have fun playing with them :)

The Denier swarm probably wont move over here though (my black magic frightens them), so you all are more than welcome to leave questions here!

And now for something completely different: MMTV

Mouse Mammary Tumor Virus is a cool little retrovirus, and Ill probably be talking about it a lot more in the future.

MMTV still comes in two forms-- exogenous, and endogenous, which is neat in and of itself. The endogenous guys get passed along as proviruses in germ-line cells, and exogenous versions get passed from a lactating mother to the guts of her feeding pups.

Another reason I think MMTV is neat is that unlike HIV, which has a protein to carry the HIV genome to our cell nucleus (which means HIV can infect terminally differentiated cells), exogenous MMTV doesnt have a nifty nuclear tug-boat. It has to infect diving cells. MMTV waits until the nucleus dissolves during cell division to sneak into the infected cells genome. Berry berry sneaky.

The endogenous guys are also berry sneaky. While they are no longer completely functional they still can transcribe-->translate a superantigen. Its a viral protein, but because it is expressed before the immune system matures, the immune system recognizes the viral protein as 'self.' That means that all the T-cells that would kill an MMTV infected cell are killed, like all T-cells that recognize 'self' proteins. Mice basically lose an arm of their immune system.

Remember the classes of T-Cell Receptors I was talking about with the possums? Endogenous MMTVs (and the infection of pups before their immune system matures) can cause the loss of all T-cells that have certain Variable Beta chains. This deletion increase the mouses susceptibility to new MMTV infections, and also increases susceptibility to other pathogens, like cholera. Yup-- A virus screwing around with how well you can fight off bacteria.

But dont forget, folks, every little ERV is special!

My horrible, horrible secret

With grad school starting in about a month-and-a-half, I cant run from my my horrible horrible secret anymore. Actually, secrets.

1. Ive never taken a course in microbiology
2. Ive never taken a course in biochemistry

Some of you might already know these secrets, but I needed to say it out loud-- I need to start using my blog to learn some basic biochem before school starts.

Im not retarded! Its just that I managed to sneak out of taking micro and took virology instead (micro was a 200 level! virology was a 500 level, and FUN!), and I never had a chance to take biochem because it always filled up before I registered (small school, one biochem), but I got to take advanced eukaryotic genetics!

*sigh* I got street smarts. I gotta get book smarts. So I borrowed Boss Mans biochem book, and Im going to try to use my blog to help me learn! WHOOO!!! hehehehehehehe!

Frankenstein Viruses

When they arent blubbering about 'junk DNA', science journalists predictably go all atwitter when something new or weird happens in the HIV research world. Im not impressed with pop-science HIV articles, but I do like writing posts on the science behind the articles so you all can say "Hey, I heard about that!" and talk about the real research with your friends (everyone incessantly talks about viruses with their friends... right? ... right? hehehe!)

And this is the case with a new finding that you all might have heard: Defense Against Ancient Virus Opened Door to HIV

*sigh* Okay, so get the basics from that article, forget the drama and the problems with equating PtERVs (a gamma retrovirus) becoming endogenous to HIV (a lentiretrovirus) becoming endogenous-- Lets strip the pop-science article down to the basics:

• A component of our innate immunity against retroviruses is a protein called TRIM5a.
• A big difference between humans and our closest relative is our lack of PtERV1 in our genome.
• The evolution of TRIM5a in humans played a part in our resistance to PtERV1, but this same evolution has hindered our ability to fight off HIV.

Now lets flesh this out into a proper analysis of Kaiser et als experiments and findings, and why they did what they did.
When we finally got the chimpanzee and human genomes sequenced, the first thing we did was compare them to one another. A significant finding was that chimpanzees had a class of ERVs not found in humans:

"The larger family (PtERV1) is more homogeneous and has over 200 copies. Whereas older ERVs, like HERV-K, are primarily represented by solo LTRs resulting from LTR–LTR recombination, more than half of the PtERV1 copies are still full length, probably reflecting the young age of the elements. PtERV1-like elements are present in the rhesus monkey, olive baboon and African great apes but not in human, orang-utan or gibbon, suggesting separate germline invasions in these species."

So PtERV1 is a 'young' ERV family, no big whoop. Humans have their HERVs, chimpanzees have their PtERV1s, right? The strange part: exogenous PtERV1 was active when humans and chimpanzees (and gorillas) were still living in the same areas. Why the hell did they get infected with it (and not just infected-- got endogenous insertions), and we were left unscathed?

Like I said before, TRIM5a is part of the innate immune system. It binds to the capsid structure of invading retroviruses and carries them to the proteasome-- the cellular garbage disposal. Well, we already knew that TRIM5a proteins are different between primates. Chimpanzees have one kind, we have another, orangutans have another, etc. And, we already knew that our TRIM5a is a worthless 'defense' against HIV, whereas some other (not all other) primates TRIM5a can help keep HIV infection in check. So they thought a neat experiment would be to see if our TRIM5a played a part in keeping us PtERV1-free.

Minor problem: exogenous PtERVs are extinct. How can you test how well our TRIM5a works against a virus if the virus doesnt exist anymore?

Why by making a Frankenstein virus, of course!

Deniers, take note-- they did not create a zombie virus. They did not bring an ERV back to life. They took parts of an extinct virus, combined them with parts of an alive virus, and created a Frankenstein. Oh they call them 'chimeras', but you know they called it 'Frankenstein' in the lab. You know they did.

They had to make a Frankenstein monster, rather than a zombie, because the +200 PtERV1s have been mutating away from their initial sequence for a few million years. Theyre junk (OMG SHE SAID JUNK!). But, since you have +200 copies to work with, and really youre only interested in the capsid gene (the gene that interacts with TRIM5a), you can reconstruct the original PtERV capsid gene by making a consensus sequence. You can then cut/paste the capsid gene into an 'alive' virus in place of its own capsid, and voila! A PtERV1 brought back to life! Kinda!

They then tested their FrankensteinPtERV against lots of primates' TRIM5a to see if any of them inhibited FrankensteinPtERV reproduction, and lo-and-behold, humans could do it. Our gorilla, orangutan, gibbon, baboon, and African Green Monkey cousins couldnt do it.

But their TRIM5a are great at resisting systemic HIV infection.

So the researchers decided to mutated our TRIM5a to make it more like our cousins, and it lost some of its ability to restrict FrankensteinPtERV, but gained some ability to restrict HIV.

This is one of those horrible, ungodly scenarios that Creationists fear-- a mutation having a benefit in one dimension of a fitness landscape, and having a handicap in another. In this particular case, they never found a mutation that could provide resistance to both retroviruses.

But wait! Theres more!
You know how this whole thing started with researchers looking at why chimpanzees got germ-line infections with PtERVs, but humans didnt? Turns out chimpanzees TRIM5a can inhibit FrankensteinPtERV almost just as well as ours can.

*blink*

ROFL!!!!!

So while TRIM5a plays a part in our susceptibility to viral infection, it is NOT the only factor.

Carl Zimmer at The Loom has a great article on this topic too!

Blogroll Help

I give up. I officially need a blogroll. Im losing track of all the people I read without my old computer, and I definitely want to make sure Im reading everyone who posts here.

BUT!

I want a blogroll widget like what PZ has-- where you have a big lists of blogs, but only, say, 10 are displayed at a time, at random on my ERV homepage. I dont like alphabetical favoritism :P

SO!

Leave a comment here if you think I should or I do read your blog (new computer, I dont have bookmarks for a couple of weeks!) or if you have a blog-blogger-widget suggestion!

Its a tiny fishy, but I finally caught one!

Right now Im happily enjoying the fact that Creationists/Deniers/etc dont post on my blog. Its nice not having to moderate comments (eh a couple Deniers have been creepy, but sitemeter scared them off).

But I am equally as happy to have a nice Creationist stop by to post his/her views of my posts so I can use it as a learning experience for me, the poster, and my readers. So thanks, Webster, for leaving a nice comment. Please dont take this as me attacking you personally-- Im trying to direct my response to the Creationist Claim in general, not you.

ERV, I would be embarrassed to post such nonsense out where anyone can read it.

Nonsense! A little nonsense now and then is relished by the wisest men!

Your first major error is special pleading. Even though no one was there to see it, HERVs must have been inserted millions of years ago, so they were. You don't even offer any evidence besides the bald claims.

Um, actually I did provide a reference--
Differences in HERV-K LTR insertions in orthologous loci of humans and great ape

Again, I will direct you towards PubMed so you can look up references yourself in the future. Some will be available online for free, but if you go to a local library, they should be able to help you get any article you are interested in!
For instance, here is a nice free intro to HERVs! I promise a blog entry on molecular clocks soon, too :)

Retroelements and the human genome: New perspectives on an old relation

Next, you turn to begging the question. From the report that an ERV is necessary for placental formation, you jump to "Mammals gained the function". But that assumes that mammals descended from non-mammals, which is to be proven!

Comparisons of genomes from various organisms creates a phylogenetic tree-- a Tree of Life-- which unquestionably demonstrates that mammals share a common ancestor with 'non-mammals'.

Next, you misrepresent the opposition. "Evolution ... is not accomplished by retroviruses jumping around in the genome" becomes "ERVs cant allow a gain of function." But those two statements are not even close to the same meaning. Dr. Purdom is pointing out that moving data around does not increase its information content, which should be fairly obvious.

Retrotransposition (moving data around) most certainly can 'increase information content.' I just gave an example not a week ago on this very blog-- Marsupials have a T-cell receptor that we dont have because of a retrotransposition.
I would, however, like to caution you against using the terms 'data' and 'information' on this blog. There are several extremely cute and extremely clever mathematicians that read ERV that will jump you for this, if you arent very veeeery certain of your position. Just a heads-up.

Still in the same paragraph, you next slide right into equivocation, claiming that any change in creatures we see today is exactly the same process as that which produced them in the first place, as if studying a car engine could tell you who built the factory.

Genetics is not magic. It doesnt work one day, and work a different way tomorrow. With ERVs, for instance, some retroviruses have endogenous and exogenous components, like MMTV. We can still watch all this stuff happening-- its not some mystical magical process that only could happen millions of years ago.

Next, you unwittingly strengthen your opponents position, by affirming her tentative suggestion of a possible sign of common design over common ancestry. Thanks!

No, not unwittingly-- I addressed that claim immediately after I brought it up. This is a well known Creationist Claim that I have addressed sarcastically on this blog several times (like here!).
You can take the position of common descent or common design through common descent, but not common design only-- unless you can go talk to your designer and ask why they made our genomes to look like apparent descent, when we were specially created.

You finish off by showing that you really didn't read the conclusion very carefully. Dr. Purdom says that "more work needs to be done." You say that her statement is dishonest b/c YECs "dont [sic] do laboratory research." But she didn't say that they do, she said that more work needs to be done. She doesn't even say who should do it! Oh, and did I mention that it took me only about 15 seconds to find a page on YEC research? YEC lab research is limited by the fact that most labs are controlled by evolutionists, many of whom are actively hostile to any YEC attempt to use their facilities, even as students. It's pretty hypocritical to lock them out of the labs, then claim that they can't be taken seriously b/c they don't do lab work!

Bullshit.

The Templeton Foundation begged Creationists to submit research proposals. You know how many they received? None.

Professional Creationists are not interested in doing novel research. They are interested in pirating real research.

'Helping'

'Fr*ming Science' is a lot like UD to me. I cant read one damn article without getting annoyed. This time hes trying to tie atheism in with this survey that says:

Atheists and agnostics emerged as the segment of people least likely to do anything in response to poverty. They were less likely to engage in eight of the nine specific responses measured, and were the faith segment least likely to participate in eight of the nine responses evaluated.

Well, the fact that this is one of the most poorly worded sentences Ive read since I quit TAing about 6 years ago was my first clue that this 'study' was ever-so-slightly less than reliable. I attempted to find their exact findings by clicking on a link that read:

To read about the relationship between faith and a response to poverty, click here

Go ahead. Click there. I shall wait.

...

Uh huh. Think like Jesus, people. Think like Jesus. I completely trust the findings of this 'study.'

I think these were the nine questions:

• giving material resources (such as clothing or furniture) directly to poor people

• donating money to organizations that address poverty

• giving food directly to a poor person or family

• spending a "significant amount of time" praying for poor people

• donating time to personally serve needy people in the community

• visiting institutionalized elderly or sick people who are not family members

• donating money to organizations that address poverty in foreign countries

• serving as a tutor or friend to an underprivileged child

• helping to build or restore a house for a poor family

That is a retarded survey. We're talking Psych 101 'intro to surveys'-- youd get a C on that. Tops. And these are supposedly professionals. Lets knock out an easy one first, how many atheists were surveyed in the first place? Hmm-- no answer? No break-down of stats at all? Did you get a representative sample? How am I supposed to know?

Then we get to the retardation. 'Care more about the poor.' Lets see, give $5 to The Church, knock out a couple of those. Donate a can of corn and an old pair of shoes at Thanksgiving, knock out a couple more. Dont know why the prey, I mean, pray thing isnt 100%, but spend 30 minutes caroling at a retirement home over Christmas, knock that one out...

And then theres the simple fact that Church help isnt in any way 'helping'. They ask for souls before help is rendered. They lie and call that 'helping'. Commit cultural genocide and call them 'charitable missions.' They pocket donated money, spend a percentage on shit, and call it 'helping.' Faith-based 'help' is like Horowitz's 'help.' A bigger mess for me to clean up.

Gee what takes more time, effort, and caring? Playing checkers with an elderly woman once a year because your youth group leader arranges a day and pressures you into doing it, or taking the time to rescue a troubled dog and taking him to training classes for a year to get him certified to be a therapy dog so you can visit the elderly and sick children all the time-- of your own volition? Both just check off one 'caring about the impoverished' item on that checklist.

I mean honestly. How insulting can you get, fr*mer? Degrading my efforts with some radical Christian apologetics piece.

'We need leaders we need leaders whine whine whine!!!' No. I dont need Dawkins or Paul Kurtz to tell me to collect canned goods for a local food pantry. Neither do you. Neither does any other atheist on this planet. There are a billion organizations out there that have secular agendas that you can donate your time and money to. Do it. Stop writing dumb articles that enable, once again, bad theistic behaviors.

Whats this study say to me? These assholes need peer pressure to give fake help to 'Think Like Jesus' and they still have to put out shitty surveys to make one another feel good. Oooh yeah. I wanna be just like them.

Oh dear-- tagged twice!

Okay, still no internet at home. Im probably going to go to the Apple Store tonight to get a laptop (need a Mac for school this fall), and I might as well get it now :)

But Ive been tagged twice for '8 Random Things About You'- so I better get on this!
Here are the rules:

• We have to post these rules before we give you the facts.
• Players start with eight random facts/habits about themselves.
• People who are tagged need to write their own blog about their eight things and post these rules.
• At the end of your blog, you need to choose eight people to get tagged and list their names.
• Don’t forget to leave them a comment telling them they’re tagged, and to read your blog.

1. Even though I was raised in a small farming community in Missouri, my parents still managed to shelter me from religious fundamentalism. I didnt know people actually *believed* Jesus and Moses and all those characters were real until second grade. I didnt know what Creationists were until college.
2. People assume since Im so very anti-theistic I have had a 'bad' experience with religion. Nope. Classmates never bothered me about it in school. Mormon/Southern Baptist/Catholic relatives never tried to convert or ostracize me. Only one classmate tried to convert me (that second grade experience), and my parents didnt let me hang out with her anymore. Turns out that was good. That girl grew up to be an ugly, mean little thing.
3. Our family Sunday-Morning Ritual was watching Star Trek episodes my dad taped from the night before (they were on too late for my bro and I to stay up to watch). We watched the Star Wars Trilogy every Christmas. There was a time in my life I would have seriously considered myself part of the Jedi religion.
4. I went to lots of nerd camps growing up. One camp was 'the top one half of one percent of all high school sophomores in Missouri.' I so impressed the nerdiest of the geeks and the geekiest of the nerds with my knowledge of the Star Wars Universe, I was given the 'Obi Wan Kenobi' award. I was so mortified, that was the moment I ceased to consider myself part of the Jedi religion.
5. Ten years later, I can still quote every line of those movies. Right now. But not the 'prequels'. Those suck.
6. One of my classes at that nerd camp was 'Exploring Religions'. Needless to say, I didnt exactly fit in. One, I already knew all the basic stories that we were learning (most kids hadnt been exposed to religions other than Christianity), and two, I was pissed off we were learning about Christianity/Islam/Hinduism/Buddhism. I wanted to learn about obscure African mythologies and all the reasons to sacrifice someone in South America. Jesus=boring.
7. My one sorta-friend in that class was a Mormon. I didnt know this until I let out this huge rant against Mormonism on her (Mormon cousins had just done something particularly repulsive). She ended up going to the same college as me. Good times.
8. My favorite TV show currently airing is 'Big Love'. Seriously, its good. But its only my favorite until 'Dr. Who' is back on in July. I now consider myself part of the Time Lord religion :P

Im going to have to edit this to tag people tonight-- I gotta work!

EDITED 6-24-07, 8.00 pm--
TAG to The Usual Suspects:
Kris
Tyler
Foxy (you two still count as TWO!)
CAD
Women in Science (8 things about Women in Science?)
Dustin
Factician

And Blake, for COMPLETELY missing my 'Behe vs HIV' post. He should so be ashamed of himself :P

YAY!

Theres beauty in religion

LOL. Naw. Im lying. Its a bunch of shit.

Every Catholic hospital is bound by the ethical directives of the U.S. Conference of Catholic Bishops, which forbid abortion and sterilization (unless they are lifesaving), in vitro fertilization, surrogate motherhood, some prenatal genetic testing, all artificial forms of birth control and the use of condoms for HIV prevention. Baptist and Seventh Day Adventist hospitals may also restrict abortions. Which means that if your local hospital has been taken over — or if you're ever rushed to the nearest hospital in an emergency — you could be in for a surprise at the services you can't get.

Being a former hard-core pre-med, this isnt news to me. Learned lots of neat stuff as a pre-med. Like, 'religious' hospitals would go out of business if it werent for secular funds. From a 2003 American Atheist column:

Despite the religious label, these so-called religious hospitals are more public than public hospitals. Religious hospitals get 36% of all their revenue from Medicare; public hospitals get only 27%. In addition to that 36% of public funding they get 12% of their funding from Medicaid. Of the remaining 44% of funding, 31% comes from county appropriations, 30% comes from investments, and only 5% comes from charitable contributions (not necessarily religious). The percentage of Church funding for Church-run hospitals comes to a grand total of 0.0015 percent.

Oh! Well there you have it, folks! Sell your soul for 0.0015% of your hospitals total funds, and you too can make women go through horrors like this!

She was only 14 weeks pregnant, but her water had broken. Dr. Goldner delivered the bad news: Because there wasn't enough amniotic fluid left and it was too early for the fetus to survive on its own, the pregnancy was hopeless. Hutchins would likely miscarry in a matter of weeks. But in the meanwhile, she stood at risk for serious infection, which could lead to infertility or death. Dr. Goldner says his devastated patient chose to get an abortion at local Elliot Hospital... "I was told I could not admit her unless there was a risk to her life," Dr. Goldner remembers. "They said, 'Why don't you wait until she has an infection or she gets a fever?' They were asking me to do something other than the standard of care. They wanted me to put her health in jeopardy." He tried admitting Hutchins elsewhere, only to discover that the nearest abortion provider was nearly 80 miles away in Lebanon, New Hampshire — and that she had no car. Ultimately, Dr. Goldner paid a taxi to drive her the hour and a half to the procedure.

The doctor was struck by the hoops women had to jump through to get basic care. "One of my patients was a mother of four who had wanted a tubal ligation at delivery but was turned down," she says. "When I saw her not long afterward, she was pregnant with unwanted twins."

In one case that made the local paper, a patient came in with an ectopic pregnancy: an embryo had implanted in her fallopian tube. Such an embryo has zero chance of survival and is a serious threat to the mother, as its growth can rupture the tube. The more invasive way to treat an ectopic is to surgically remove the tube. An alternative, generally less risky way is to administer methotrexate, a drug also used for cancer. It dissolves the pregnancy but spares the tube, preserving the women's fertility. "The doctor thought the noninvasive treatment was best," Dr. Stulberg recounts. But Catholic directives specify that even in an ectopic pregnancy, doctors cannot perform "a direct abortion" — which, the on-call ob/gyn reasoned, would nix the drug option. (Surgery, on the other hand, could be considered a lifesaving measure that indirectly kills the embryo, and may be permitted.) The doctor didn't wait to take it up with the hospital's ethical committee; she told the patient to check out and head to another ER.

Why I have no idea what these people are talking about!

Why do I get this sneaking suspicion that if a Muslim physician refused to treat a Christian Infidel, those warped bastards supporting these measures in that article wouldnt exactly support them anymore?
I bet Padded-Bra Debbie has an example of that for us! She hates her some towlies!

YAY!

When a Muslim abuses a patient, its barbaric. When Christians do it, its beautiful.

What an inelegant understanding of religion I have, to call it all shit.

Rated R for all the Wrong Reasons

Tatarize, from the comments at Pharyngula, pointed out that my blog is rated 'R' on an unofficial online quizzy thingie.

Mingle² - Online Dating

For the words kill (5x), drugs (3x), shit (2x), and dead (1x).

Boo! They must just search your opening page, because I use words much worse than 'shit'-- like my nickname for my favorite person in the universe (which I dont use so much anymore, as someone I want to hire me in 4 years reads this blog :P )

Plus all those words were from those violent Cytotoxic T-Cells and their murderous rampages! I dont just have violence! Here, I have boobies! No violent movie is complete without boobies. I mean common.

Ive got to add more violence, though, this time an explosion. You see, I was overhauling my computer this week... and the motherboard failed. Not at first! Oh I put all my shiny new parts together-- new processor, new memory, new graphics card-- sooooo proud of myself for having not lost my computer skillz since the last time I was elbow deep in computer guts (like, 6 years ago).

So I hit power, everything is running fine........ when I hear a **POP**...... **sssssssssssssssss**

I luckily didnt put the case back together, as I figured Id have to fiddle with something, so I leaned over and noticed a bright flame, billowing with smoke, emanating from my mother board.

Goddammit.

Sooooooo, once again, internet use and blogging will be put on hold for the next couple of weeks as I send that motherboard back, install the new one again, cross my fingers it doesnt burst into flames, plus all my experiments... bleh!

Ah well, no internet means I have a lot more time now to read papers, so I shall be inundating you all with science posts soon, instead of posts on psychic dogs hehehe!

Smartest Dog in the Universe? I think not!

Its rare that one has the opportunity to one-up PZ, so Im taking him to task on this one. He thinks hes found the smartest dog in the universe. Evidently he hasnt traveled on I-70 through Missouri! THERE he would have found the smartest dog in the universe: Jim the Wonder Dog.

Basic math? Basic Christian theology? Lame. Check out what Jim could do!

During the next hour we were treated to a remarkable and completely puzzling exhibition of the dog's extraordinary cleverness. "What would I do," Sam asked, "if I had the stomach ache?" Jim wagged his tail, apparently in sympathy, then trotted over to where Dr. Savage, the town physician, was standing. He nudged the doctor gently. The crowd gasped its astonishment, for this was Jim's first visit to our town, and he had no way of knowing one person from another — no visible way, that is.

He could also:

• Identify cars when given liscence plate numbers
• Speak Greek, German, French, Spanish, and Morse Code
• Identify a variety of trees by species
• Identify members of the audience by their features (black mustache, blue scarf, etc)
• Predict winners of the World Series and the Kentucky Derby, as well as presidential races
• Predict the sex of unborn babies

Oh sure, it could just be a parlor trick that Van Arsdale set up to survive through the Depression... But professors from WashU and UM Columbia examined him! Jim must have been the smartest dog in the universe.

PZ really dropped the ball on this one :P

VIRUS FIGHT!

WHOOO!

Ugh these pics kinda lose their impact in jpeg... Kinda disappointing :(

I screwed up a few infections. I added too much virus, and some cells got dually infected with a red virus and a green virus. Bad. That means that the red-green can recombine.

RED FILTER:

GREEN FILTER:

MERGE-- YELLOW CELL:

Lame. Ah well-- screwing up a couple infections out of 1,000 isnt that bad of a screw-up ratio :P

laughing...toohard...canttakeit...omg...

You cant parody Creationism. YOU CANT DO IT. Reality is ALWAYS funnier than ANY parody you can think of.

Example 1: ID/pleasurian science, see Afarensis and Stranger Fruit

Example 2: From my doppelgangers, regarding the stunning silence from ID Creationists on Behes New Bile.

There have been posts in the anti-ID part of the blogosphere that have taken note of a surprising (from their perspective) lack of attention given to Behe's latest book (The Edge of Evolution) among ID blogs.

......

It is simply a reflection of the fact that a greater number of minds are focused on an issue. It happened in the latter part of the 19th century among Darwinists and is a pattern that has been repeated throughout history. It also explains the decreasing reliance of ID on its founding fathers; accounting for Behe's declining influence among IDists. It is not that he is no longer respected. Only that he has now become one voice among many, albeit still a prominent one.

*blink*

I dare you to find a parody funnier than that.

More Marsupial Madness!!

When I wrote about the new marsupial TCR gene family yesterday, part of which was created by retrotransposition, the last thing on my mind was the latest junk DNA-->crappy journalism scandal*. It was also the last thing on my mind when I did my usual Monday morning PubMed search for 'endogenous retroviruses,' to see what other labs are finding/looking at. And I got well into this paper before I realized, "Oh yeah! This is some of the 'junk' theyre talking about, isnt it?"

Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica.

This paper basically reiterate what Creationists dont want to hear-- We split away from marsupials 170-190 million years ago. Marsupials are an evolutionary branch that connects us to another fully sequenced species (chickens) so we can learn a lot about our evolution by comparing everyone. Transposable elements are great for screwing around with chromosomes (fusions, deletions, rearrangements, etc). And sometimes we co-opt transposable elements for our own use, either as coding genes or non-coding genes (ZOMG SOME JUNK HAS A FUNCTION JUNK HAS A FUNCTION OMGZ!!11!1! GAWD IS REAL!)

The funny part about that last reiteration is that they give a reference that I havent read before:

But an increasingly recognized phenomenon is the co-opting of nonautonomous elements as functional noncoding elements (Bejerano et al. 2006; Kamal et al. 2006). This fulfills the vision originally espoused by McClintock, Davidson, and Britten, that TEs, and repetitive DNA in general, may be critical "control elements" in modern genomes (McClintock 1961; Davidson and Britten 1979).

1961.

1979.

And ID Creationists are 'geniuses' because they discover this fact 30-40 years after everyone else. Fantastic. Congratulations guys. Hey, nobody tell them about siRNA quite yet-- their heads will explode *rolleyes*

So tranposable elements in marsupials (specifically the short-tailed opossum (pronounced 'possum')) is friggen awesome! 52.2% of their genome appears to be transposable elements, as opposed to 44.8% in humans, and 38.6% of the mouse genome. We've got about the same number of ERVs, transposons, and SINES as possums, but they have a TON more LINEs (29.2% vs our 20.4%). Remember LINEs duplicate by copying themselves (instead of hopping around, like transposons) so they make genomes larger, and theyre GREAT at changing the transcription rates of nearby genes (up and downstream) because of their internal promoters, and their ability to screw around with 'normal' promoters.

These researchers also made a cool 'speculation' as to why ERVs appear to be concentrated in certain regions of this possums genome:

It is tempting to speculate that the regions of high ERV density in Monodelphis indicate the location of ancient centromeres and neocentromeres, or that they could play a role in centromere repositioning.

Coooool!



**If science journalists keep calling ERVs 'junk' Im changing the name of this blog to 'The Junk Yard', I will insist upon being referred to as 'The Garbage Lady', and Arnie will be renamed 'Bad Bad Leroy Brown, the Junk-Yard Puppy'. Thanks to the journalists who realize the damage theyre doing and are trying to learn, and shame on the lazy brats who are too proud to admit they royally screwed up.

MORE GMO RICE!! ITS GONNA KILL US ALLLLLLLLLLLL!!!

Take the kids to your bomb shelter, ladies and gentlemen.

Despite my continual pleas to researchers to STOP PLAYING GOD, arrogant (no doubt atheistic materialistic) researchers have created another GMO monster.

This time: Rice.

Rice that can be used... brace yourself... AS A CHOLERA VACCINE.

Rice-based mucosal vaccine as a global strategy for cold-chain- and needle-free vaccination

Now, contrary to what extremely knowledgeable people will tell you about plants as vaccines*, a rice vaccine isnt like, boiling a pot of rice and eating your vaccine. The rice can be used to create the antigen of interest, and rice/plants also make some other proteins/starches that are useful for protecting the antigen until it gets to your intestine to be presented to your immune cells (like when you poop corn).

So really this rice is going to be ground up and put into pill form, which is fantastic on so many levels!
1. Dont need a needle. Ive said over and over and OVER (are you listening, HIV-Circumcision 'researchers'??) its really damn hard to make sure your needles/equipment is appropriately sterilized in the third world. I dont care how many seminars youve had on how to sterilize needles. It doesnt always get done. Plus, I dont think youll hear any kids complaining about a lack of needles ;)

2. Can be kept at room temperature. No refrigeration. Aint gonna always have that in the third world either. Sure you might have a fridge, but it might not have power. And they tested batches that were left at room temp for 1.5 years-- Still worked. AWESOME!

3. Introducing the antigen through the intestinal mucosa. These folks found that introducing the cholera antigen orally works great because cholera normally infects through your digestive tract! Convinces lots of sentinel immune cells to hang out in your intestine and wait for another cholera bug to float by!


Those goddamn bastards. WHEN WILL WE LEARN????



* They used Agrobacterium tumefaciens-mediated transformation to create this GMO rice. Not retroviruses, Davie.

Weeeeeeird! (immune system evolution news)

DOH!

hehehe Im not an immunologist. But this paper Ive been wanting to write about for weeks had too many weird things in it for me to ignore.

A unique T cell receptor discovered in marsupials.

Heres the background-- part of your adaptive immune system is made up of T-cells. T-cells have, well, T-cell Receptors in their cell membranes to recognize when something 'non-self' is floating around. For instance, if a cell is infected with Chicken Pox, it will 'present' bits of virus in MHC molecules. A Cytotoxic T-cell comes along, and is like 'WHOA! What the hell are you doing??' and kills the infected cell.

Well, doesnt 'kill' the infected cell. It persuades the infected cell to commit suicide. Weird, but true.

There are billions upon billions of non-self things that might need to be recognized at some point during your life-- How does your adaptive immune system do it?? When youre a baby you create a huge library of potential adaptive immune cells through various genetic recombinations (you dont really have an adaptive immune system until youre 2-ish). For T-cells, any TCR that recognizes something your body makes is killed-- all the other T cells are left alone.

TCRs are usually made of alpha and beta units, or gamma and delta units. Its very well conserved, evolutionarily. Well researchers found a WHOLE NEW set of genes (eight clusters) that code for TCRs in marsupials (American and Australian) they named mu! Its related to the TCR delta genes and Ig heavy chain genes (used in B-cells). Weird!

AND SOME MEMBERS OF THE MU FAMILY DUPLICATED THROUGH RETROTRANSPOSITION!

Weird!

Which means the recombination steps have already taken place, and there are no introns! It still works, and I dont know how to describe it better than the pic in the paper-- but for those of you without PNAS, the joined VDJ just sort of piggy-backs on another V region. And marsupials use them! These sequences are under positive selection! Its just that one of the possible TCRs has 2 V's. Really weird!

Bleh they needed more pics in this paper though. Im still not sure I totally *get it* Too weird :P Heres UNMs press release that describes the impact of this finding.

How Average Joes do Diets: Alli

So Christians are friggen nuts when it comes to their body image issues ("IM NOT PRETTY CAUSE I DONT LOVE GOD ENOUGH!"), but what is a skeptic to do that wants/needs to get healthier?

The supplement industry is a mess, full of snake oils and caffeine pills-- what does the scientific community have to offer people who are not obese enough to need a physicians help, but still want/need to lose weight?

This week a non-prescription strength version of Xenical went on sale at Walgreens, Targets, and Walmarts near you, Alli. No, not A-leeee, A-lyyyy*.

Alli blocks the absorption of fats in your intestine. Well, technically it blocks the enzymes that break down fats in your intestines, thus the fats dont ever get to an absorbable form. Anyway, if you eat too much fat? S'okay! You arent going to really ever going to 'digest' it.

On the surface this is a great idea for people who have trouble regulating their calories. Everyone knows that weight loss/gain are a function of calories in + calories burned, and here is an aid for people to cancel out calories they accidentally over eat. And it works for the people who use it properly-- they can lose 15 pounds for every 10 pounds a non-Alli person loses.

I am admittedly anti-supplement-- Ive seen drastic changes in my own body with only adding protein powder (I dont eat most meats). And Im going to have to be anti-this-particular-scientifically-tested-supplement too. I think the side effects we will see in the general public is not worth the extra 5 pounds Alli can 'potentially' 'maybe' help 'some' people lose.

This is my problem-- Alli is directed towards people who dont know how to eat. Im not saying this to be 'mean', I didnt know how to eat 5 years ago. Too many simple sugars. Not enough protein. Not enough nutrients in general. This is the US-- we're all over fed and under nourished. People who are drawn to Alli are not eating healthy in the first place, so they arent getting the healthy fats you need, like almonds, olive oil, and salmon. Now Alli is compounding the not-enough-good-fat problem by reducing the uptake of fat soluble vitamins!

Your body needs fat! 'Fat' is not the problem. Bad fats and not eating properly and not exercising are the 'problem'!

The studies that I have seen with Alli are pathetic compared to what I would expect someone to lose eating better and exercising in general. I dont mean half-assing it, I mean really, really trying to get healthy. You can do better on your own than what you can do half-assing it with Allis 'help'.

And Im pissed as all get out that Alli is partnering up with the FDA to offer diet exercise support... if you spend $60 on Alli.

The FDA.

This makes no sense to me. Why do you have to buy a supplement to get dietary and exercise support from the FDA? Im revolted.

*sigh*

I suppose at the very least, you have to be 18 to buy Alli.

I will repeat-- If any of you readers want some help getting healthy (NOT just 'getting thin' or 'getting buff'), drop me a message! Leave a note here (anonymous if youre embarrassed, but you shouldnt be). If I cant answer your question or give you the advice you need, Ill find someone who can. I wont charge you $60. And I promise you wont spontaneously poop.





* Sorry, that annoys me. *rolleyes*

A Quiet Win

You all might remember a while back, McCook Community College was planning on letting a Creationist physicist professor teach a 'physics' course on Creationism.

Well the end of May it got pushed onto the Philosophy department (so sorry, philosophers).

Well my old buddies at Nebraska Citizens for Science (best group of science advocates I have ever had the pleasure of meeting) forwarded me a note from NCSE to announce...

The course has been canceled all together! WHOOO!!! The philosophy department didnt want that garbage dumped in their department either! WHOOOOOOO!

Look, Im not saying you cant let a Creationist teach their point of view. It just needs to be in the appropriate environment. My uni let a Creationist bio professor teach an elective, 1 hour, senior course on 'origins' (course was under 'senior seminar'-- I took one in biotechnology, could take one on 'sex in biology'-- fun stuff. He couldnt flunk kids.) Very good news that a Physics or Philo department wont have to put up with Creationist crap.

My HIV Research

(note: Im still not online at home-- just stopped in the library to upload this post-- be back soon)


Outside of posting cryptic pictures, or barking at people who intrude upon my territory, I dont talk about my research much here.

But Im about to jump into some heavy duty experiments in the next few weeks, and my posting might drop off a bit, so I figure now is a good opportunity to talk a little bit about what I research.

I study the evolution of HIV over the course of time in HIV+ patients, and how changes to the HIV genome effect fitness (replicative capacity).

Unfortunately, 'fitness' of HIV within a patient depends on a LOT of dimensions. If I dont narrow down what Im studying, I could spend the rest of my life studying the evolution of HIV within one patient. So the first thing I have to do is focus on one region of HIV.

Im interested in the gene 'env'. Env codes for the proteins on the outside of the virus that attach to your cells to infect you. Even more specifically, Im interested in a tiny region (500 base pairs) of env that is very important in HIV tropism (what kind of co-receptor it needs to infect).

Heres what Ive been doing the past couple of years:

Isolate viruses from infected patients over the course of their infection-- 3 months post infection, 6 months, 12 months, etc etc etc.

Amplify the region of the genome that Im interested in with PCR.

Cut and paste the region Im interested in over a common background-- the 'white mouse' of HIV called NL4-3. Just think of it as 'laboratory' HIV. The half lab-half patient HIV viruses are called 'chimeras.'

Now-- the cool part. I added GFP and dsRED2 genes to the HIV genome. So when MY chimeric viruses infect a cell, it will glow green or red.

When I put my viruses on cells in a petri dish, all the chimeras basically look equally 'fit'. Its like letting a hungry 10 year-old kid loose in a room full of Cheetos-- The viruses are just going to go to town.

Im not just studying evolution, I actually need to use evolution in my experiment-- specifically a principle called 'competitive exclusion.' So instead of letting a 10 year-old eat all the Cheetos she wants, I put TWO hungry kids in a room... with a snack-size bag of Cheetos.


One kid is going to eat.


One kid isnt.*



When viruses are in the body, they are competing with eachother for host cells. If I 'compete' viruses against one another in a petri dish, I can determine which of the viruses is more fit. Then I can go back and study the biochemistry of the more fit viruses, and the genetic sequences of the more fit viruses, and figure out why they are more fit.

But wait-- I need to remember my assumptions! Ive filtered out allllll the dimensions in the HIV fitness landscape except the impact of the 500 bp region Im interested in, and in an ex vivo environment. How do I know if the 'fitness' Im measuring is real-world fitness?

There is a phylogenetic tree of all of the isolated viruses. So, say I find a super fit virus at the 6 month time-point--- If it REALLY is more fit, it will leave more offspring, and I can find similar sequences at the 12 month time point, and 18 month, etc! We can also go back and test these viruses in a different cell type, with HIV antibodies present in the competitions, with drugs in the competitions, etc to test different dimentions.


Lots of avenues for further research :)


So, anyway, for the next few weeks I will be spending 8 hours a day doing flow cytometry and real-time PCR, so I wont exactly be in the mood to sit at a computer MORE to write posts... buuuuuut we all know a Creationist or a Denier will say something stupid and Ill get pissed off enough to fight through the inevitable computer overload Ill get at work.


And of course, this is all assuming I even have internet access at home.


*(assume the kids are selfish brats and wont share)

Once Again, Technical Difficulties

**sigh**

I have posts just sitting on my computer at home, waiting to be published, but I forgot my flash drive at work.

This also means that I couldnt order my new computer parts this morning (Im gutting my old computer-- gutting it. Im keeping the power supply and the DVD and CD drives, but thats it WHOOOOO!) to have them shipped today so Id get them ~Tuesday. Itll be Thursday before I get them now.

So angry.

Behe vs HIV

I know. I promised no more Behe posts for a while. But a couple of commenters left questions relevant to a Behe excerpt, now posted in an article from Jerry Coyne here:

"HIV has killed millions of people, fended off the human immune system, and become resistant to whatever drug humanity could throw at it. Yet through all that, there have been no significant basic biochemical changes in the virus at all."

Ya know, I try very hard not to take Creationist comments personally. Its bad enough that I have a short fuse with Deniers (especially female math/science/engineering Deniers), and I know I simply dont have the energy to get worked up in a fury every time a Creationist says something dumb. But for the love of Pete, its getting harder and harder not to take Behes new bile, I mean new book, personally, considering his choice of topics, and my choice of research.

Look, I do not expect everyone to be an expert on HIV or fitness landscapes. I hope Ive made it perfectly clear on this blog that if I say something wrong, or something you dont understand, or something youd like to learn more about, I really really want you to say something! I will never, EVER ridicule someone for learning, or telling me Im wrong when Im wrong.

I just expect someone writing a book on HIV or fitness landscapes, pro or anti-evolution, to take 30 damn seconds to do a PubMed search.

30 goddamn seconds. Shit.

Behe is purposefully reaching out of his area of expertise to confuse Average Joes for his own monetary or psychological gain. Every time you start to feel a bit of pity for the wretched creature, as the negative reviews of Behes Bile keep piling up, remember that fact.

Okay, the excerpt. One sentence, but enough to send me into a rage. Remember that YEC segment from 'ID vs ERVs Part 12'?

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.

Behe pulls this same crap in his book! On one hand, he wants to say that 'peaks' on fitness landscapes are traps, or some peaks are unreachable-- yet on the other hand he wants to say that HIV can 'only' mutate to traverse valleys in fitness landscapes when people take anti-retrovirals-- and he pulls a third hand out of his ass to assert HIV hasnt/cant make 'significant biochemical changes,' and you dont want to know where he got the fourth hand to say malarias resistance to drugs is evidence of Design. Heads Behe wins, tails we lose.

Coyne points out the obvious error in Behes logic, paraphrased, "What does Behe expect HIV to do? Grow legs and start tap-dancing?"
And Behe knows damn well that hes being coy-- thats why he used soft language and didnt operationally define his terms. Operational definitions, covered in undergrad Freshman Psychology. Psychology. Common, Behe, what do you mean by 'significant'? What do you mean by 'basic'? What do you mean by 'biochemical changes'? What do you mean by 'changes in the virus'? Structure? Genome? What?

Soft statements so that when someone who knows jack about HIV comes and corrects him, he can backpedal to 'Oh, thats not significant.' 'Thats not the kind of biochemical change Im talking about.'

Then theres that nasty bit about him being totally and irredeemably wrong about the evolution and biochemistry of HIV, no matter how he wants to dance around it. "No significant basic biochemical changes." You sure about that? You sound pretty sure with "THERE ARE NOSIGNIFICANT BASIC BIOCHEMICAL CHANGES, BWA!"

What do you call vif?

Modern lentiviruses sure think vif is a 'significant biochemical change', as it let them be resistant to our APOBEC3G, a cellular antiretroviral. A recently discovered ancient rabbit lentiviral ERV doesnt have vif. I bet its kinda jealous of HIV.

"RAWWRG!" Behe might drool "You just said that all lentiviruses have vif, so omgz Im still right!"

Omgz, drooly Behe. Omgz indeed.

Thus, innate cellular defenses that likely evolved to restrict retroviral replication might have been usurped by HIV to accelerate viral sequence diversification and escape from immune control and inhibition by antiretroviral drugs.

Shit, they talk about fitness variations in that paper, too. Poor drooly Behe viciously rattles his IDC cage, "RAWG! They said MIGHT! MIGHT! JUST SO STORY! RAWG!"

Hes also showing a rather retarded understanding of viruses, and retroviruses in particular. If youll humor me as I personify viruses for a second-- lentiviruses dont *want* to kill you. They are hit-and-stick viruses, as opposed to hit-and-run viruses like influenza. HIV, in particular, wants to be at a happy medium with you because thats how it is most fit. "WWARG! NOOOO! NOOOOOO! More virus equals more pathogenic equals more fit!" squeals Behe, bouncing up and down. "Why doesnt HIV evolve to use a coreceptor found on lots of cells! Infect more! More virus! More fit! WAAAAARG!"
Thats extremely short sighted. Which is more fit, a virus that produces a ton of virus and kills its host before being transmitted, or one that is relatively non-pathogenic, still keeps a high viral load in the host, and is transmitted horizontally AND vertically?
See, if HIV gives you AIDS, youre too sick/too dead to spread the virus. You become a dead-end host. HIV wants you to have babies, and your babies to have babies, so it can be spread vertically as well as horizontally just like it acts in other primates (SIV). It wants to be at a happy medium with us, like it is in other primates. It just wants to cull a few million of us to reach that happy medium, and we arent happy with that 'resolution' to the HIV/AIDS problem. We dont want to co-evolve with HIV because it will kill millions more. So we try to stop it.

And since Behe insists upon blubbering about co-receptor usage-- Ive got a question for him. How do you know there is not a significant biochemical difference between HIV Subtype B env (CXCR4) and HIV Subtype C env (CCR5)? We dont know what Subtype C env looks like, and from preliminary biochemical and genetic analysis, it is vastly different from Subtype B env.

THATS WHAT IM RESEARCHING RIGHT NOW! BIOCHEMICAL EVOLUTION OF HIV. RIGHT NOW. WELL, NOT *NOW*, BUT YOU KNOW WHAT I MEAN.

Hes saying HIV hasnt 'changed', yet we're still in the process of studying HIV. So why is Behe saying this?

Great news on the 'evolution education' front: Explore Evolution

Nonono, not the new, idiotically named textbook from the ID Creationists (IDC are confused by the Google Machine, too. one more similarity to Deniers.).
I mean the 'Explore Evolution' exhibits in natural history museums all over the Midwest. Amidst the depressing statistics on how many schools teach evolution (including human evolution) and how many adults accept and understand basic concepts of evolution, a hopeful paper just came out about the potential effects of 'Explore Evolution' and museums in general in the June issue of 'EVOLUTION'.

Museums Teach Evolution

Natural history museums recognize that they might be one of the few places where children (and sadly, adults) are exposed to evolution. They know they are fighting an uphill battle. So museums know they have to get the biggest bang for their buck. How to do that? Happily for my ego, the way Ive always tried to educate my friends and the public on evolution:

The goals were to show evolutionary research as an endeavor engaged in by real people, to show real data and the experimental process, to engage audiences to learn to think like evolutionary scientists, and to show a range of evolution research projects in a diversity of organisms.

Through interactive and multimedia exhibits, the new permanent exhibit galleries give visitors opportunities to experience aspects of the research conducted by each of the scientist teams. Built around exploration, identification with strong role models, critical thinking, and skill development, the Explore Evolution exhibits create a learner-centered communication, learning, and assessment environment that provides support for evolution learning experiences in school.

Show everyone how we use evolution in our research every day. Show how our research applies to the real world/real people. Show everyone our data in a non-jargony manner so they can take their new knowledge home.

'Explore Evolution' does this by packing a LOT of data and a LOT of real-world examples into one exhibit-- HIV evolution, diatom speciation, ant and fungus co-evolution, fly sexual selection, Darwins finches, comparing human and chimpanzee genomes, whales journey to the sea... All connected with a simple break-down of evolution: variation, inheritance, selection, and time. AWESOME! AHHHH!

But the coolness doesnt stop there! The exhibit organizers are studying peoples understanding of evolution before, during, and after they visit the exhibit to optimize the information and layout. Visitors are given questions like:

During one year, scientists measured the beaks of one kind of finch on a remote island. They found that most of these finch beaks were small. In the following year, a drought wiped out almost all the plants that produce small seeds. Only the plants that make large tough seeds remained. A few years later, the scientists returned to the island and measured finch beaks again. This time they found that more of the finches had bigger beaks. How would you explain why more of the finches had bigger beaks?

Answers were coded as:

• Informed Naturalistic Reasoning (not an expert answer, but theyve still *got it*)

"Well, in that case, I would assume that the birds evolved – well, the birds with the larger beaks were the ones better able to survive, since the larger beaks were more useful in getting the seeds. So that trait is the one that was selected for, and the birds that had the smaller beaks died out over time. . . . They didn't produce as many offspring."

• Novice Naturalistic Reasoning (a naturalistic answer, but not quite right)

"Well, in order to survive, their body parts had to adjust to certain things, similar to the way giraffes' necks probably grew long as they reached for the plants at the top of the trees, so the beak grew longer in order to deal with the tougher seeds..."

• Creationist Reasoning

"Um, first of all I have a problem with your eight million years. I believe in creation in the biblical account, so that pretty well defines how I believe things. God created them and due to the great flood, that is how the diversity came and that would be my explanation …"

While their results so far arent great, theyre encouraging. You can check out a preliminary graph of some data theyve collected so far here: pdf

I dont mind at all that most people gave 'novice' responses to HIV, diatoms, co-evolution, and sexual selection. If Ive said it once, Ive said it a million times-- HIV is weird. Everything about it is weird. Thats why I love it. But I dont expect laymen to know the weirder aspects of HIV off the top of their head at a museum. Diatoms are also weird (common, you know you just Wiki-ed 'diatom'), and co-evolution/sexual selection are weird.
As long as you learn what this stuff is at 'Explore Evolution' and accept that there is a naturalistic explanation to HIV etc, Im happy! Museums are for learning! Good for you for venturing a response!

I am very encouraged at the right side of that graph. What are the basic examples of evolution that you get in high school? Finches. Whales. People. So people who are exposed to these topics *get it*. These three got the highest 'Informed Naturalistic Responses".
WHOOOOOOOOO!

Of course, 'humans/chimps' is where the Creationists freaked out, and even wishy-washy Creationists declared that they didnt come from no monkey.

Get off of my cloud, Creationists! The sane people are *getting* it! WHOO!

Another chunk of data these folks are collecting that I really find encouraging, is how children react to exposure to evolutionary science at a young age. Little kids, of course, use a lot of metamagical thinking to describe/understand 'evolution'. BUT if you expose kids to science, by the time they are pre/early adolescents, they understand 'counterintuitive' evolutionary concepts. Bad news-- kids in Fundy households and schools still grow up to be Creationists despite exposure to science. *wince*

I cant wait until they get all their data together!!

Arnie Puppy: Fear my CERBERUS!

Of course I have a million videos of Arnie being cute. However, all of these videos have me talking in a schmoopy voice that even makes me a little queasy. I do keep my mouth shut in a couple, just because other noises were funnier.

1: Arnie first hearing Rachmaninoff. He also does this with David Bowie. Hes doing it right now as Im typing this and previewing the video. LOL!




2: Arnie pretending a squeaky toy is a baby head.


hehe Okay, I promise, science posts coming up :P

Arnie Puppy: Spawn of Satan

Just so you know, I was asked to post puppy pictures. This isnt just be shamelessly gushing over my awesome dog.

**blink**

Arnie right after I brought him home and cleaned him up a bit. 35 lbs. Covered in scars. Frost-bitten (parts of his ears are still black-- not pink puppy skin).
Since then, he has done nothing sleep, and play, with lots of eating in between.

Play:
Sleep:

Play:

Sleep:

Play:

Sleep:
To avoid that last 'play', we run 5-6 miles a day. Every day. At least.

So then he sleeps during the day.

And, if you need any more proof that Arnold Schwarzenegger the American Staffordshire puppy is an awesome puppy:Now a 70 lb tank.

Technical Difficulties

Sorry, guys-- Havent had internet at home for the past few days, dont blog at work, but Ill be back up as soon as COX gets its act together.

Ugh.

One Last Behe-Bile Post, I Swear!

I am so burnt out on fitness landscapes, but the UD-crew have finally, FINALLY gotten together a review of Marks review of Behes book. Its what we all already predicted, but I feel I need to quote this as even more evidence that I am psychic. Im going to get that Randi prize.

Davie was floored by magnans summary, which isnt surprising because he didnt know how to respond to Mark at all (outside of crying for his mother).

But here is my submission to the Randi Foundation:

ME: Okay, Ive gotta admit, Ive been royally confused at UDs response to Mark Chu-Carrolls review of Behes new book. That they would attack his 'credibility' and pretend thats a rebuttal of his arguments isnt confusing. Whats confusing is that theyre unimpressed with his mathematics credentials. Not his biology credentials. Math.

UD: Though not a biologist I found it interesting to try to evaluate some of his arguments. After all, he isn’t a biologist either but that doesn’t seem to have held him back.

I AM PSYCHIC! WORSHIP ME! FEAR MY ABILITIES TO PREDICT THE ACTIVITIES OF CREATIONISTS! BWAAAAAAAAAHAHAHAHA! I SHALL RULE THE WOOOOOOORLD! AAAAAAAAHAHAHAHAHAHA!

**LIGHTNING CRASH**

Ahem. Also funny:

UD: The Edge of Evolution is quite evidently directed at nonscientist readers and is simplified accordingly, unfortunately glossing over the fine points. So Chu pounces on every relatively simplified description of evolutionary theory as an indication of Behe’s supposed ignorance and stupidity.

Well maybe you should have fr*med your argument better.

ROFL!

Okay, okay, the meat of the 'rebuttal'. First, as a disclaimer, I want to say it really is awesome when non-biologists take it upon themselves to learn about biology. I LOVE it! Thats one of the main reasons I blog-- to practice translating jargony sciency talk into nice practical terms laymen can understand, without dumbing it down. I really appreciate when physicists do that for me. I appreciate it when astronomers do that for me. I always appreciate someone taking the time to explain complex ideas to me, and I know they appreciate me trying to learn.
And, I absolutely commend magnan for sticking his/her neck out to defend his/her views, as he/she understands them. Good for him/her-- thats a great way to learn.

What I find despicable is that a random poster at UD, not a mathematician, not a biologist, has to defend Professional Creationists. Dembski could only caterwaul. Behe is being awkwardly silent against universal negative reviews of his book. So they let a UD commenter give it a go, and he/she naturally doesnt fare so well.

Lets add 'cowards' to the list of reasons why Professional Creationists are dross*, if its not already there.

*sigh* So it is with no pleasure I take the pawn in this game, but it is necessary.

Recombination mainly reshuffles alleles (different mutated versions of genes) during reproduction of sex cells in eukaryotic organisms.

Recombination doesnt only recombine alleles. You can chop out entire segments of chromosomes. You can duplicate huge chunks of chromosomes.
And once again, HIV is an excellent example against this statement: HIV can recombine 'sexually'. If you are infected with two kinds of HIV, Subtype A and Subtype G, some of your cells can get infected with both subtypes. HIV packages 2 copies of RNA/virus, so as the new viruses are budding off, some will get packaged with 1 A RNA and 1 G RNA. When that virus infects another cell, Reverse Transcriptase can hop back and forth between the RNA strands, creating a Subtype AG HIV.

And thats what happened.

Behe’s prime statistical example of the limits of Darwinian evolution with only random variation is the malaria parasite, and this is a protozoan eukaryote (plasmodium) in which meiotic recombination continually occurs. This example gives every advantage to random variations from all types of mutations and recombinational events in a huge population over millions of generations, but the limitations still applied.

And I gave an example of bacterial anti-biotic resistance, which doesnt even include recombination, with only one dimension, with more necessary mutations, that debunks Behes 'IMPOSSIBLE' claim.

Chu goes into a long diatribe over Behe’s use of the “fitness landscape” concept in his argument. It seems to me these criticisms are obfuscations and irrelevant to Behe’s thesis. However many dimensions of different interacting fitness functions, and however this “landscape” changes with time for a species, for any particular reproductive fitness function the species can still be trapped at a local maximum, unable to get across the “valley” to the next, higher peak without an extremely improbable giant leap.

No, magnan, read my post. Its not irrelevant. A 2D/3D/4D graph gives you a false impression of what peaks are actually high and what valleys really are 'impossible.' And you cannot under any circumstances ignore how landscapes change over time.
You cant ignore the fact that the fitness landscape in a recently HIV+ person is entirely different from the landscape after they are late into AIDS! An impossible valley at 3 months infection is an easy hop late in infection.
Behe is completely wrong about fitness landscapes, and he shouldnt have brought them up in the first place.

The reason for this is that the physical genetic loci coding for different fitness functions or factors are generally uncorrelated with each other. Usually they are not even in the same gene. No matter how many other varied genetic changes affect the phenotype in varied ways, certain specific mutational or other genetic changes are needed to make the jump from phenotype structure A to elaborated structure B in time T as evidenced by the fossil record. The probability of this occurring by accumulation of small random changes or by one giant (random) leap is a function of the total complexity of that particular genetic change, the likely presence of steps that are too deleterious to reproductive fitness to spread and fix in the population, and the number of generations. This is regardless of abstract models like the “fitness landscape”.

This is gobbledy gook, and if I was allowed to post at UD I would ask for a clarification. But I cant, so... Can anyone translate?
Im thinking he/she is trying to say the very opposite of what fitness landscapes tell us.
Fitness landscapes tell us that 'bad' mutations at a gene/biochemical level can be pulled along across a valley by other 'good' mutations because its the overall phenotype of the organism that is selected for. Not one individual variation of a gene. Its called network compensation.
It appears as if magnan is trying to say the phenotype doesnt matter, the mutations are impossible. And something about fossils. I dont know.

The malaria parasite drug resistance example (in addition to others) demonstrates these limitations in the living world, regardless of abstract models.

Fitness landscapes arent 'abstract models'. Our technology now allows for empirical testing of fitness landscapes 'in the living world'. Behe should know this.

*sigh* And thats it. Thats the best rebuttal ID Creationists can come up with.

One last funny:

This is just a rhetorical ploy and carefully avoids trying to apply it to explain any particular evolutionary development sequence.

Wait, wait, wait-- so, Mark is supposed to be a biologist AND a mathematician before he can critique Behe? If hes a mathematician, you win, if hes a biologist, we lose.
Look, this is science, magnan. We work in teams. No one can know everything. Mark took care of some math, some more of us took care of the biology, more people took care of more math, more people took care of even more biology... Have you seen the list?
We're a team.
We dont leave our friends and supporters by themselves and expect them to defend us while we suck our thumbs in our closets, like what UD did to you.








* Word of the day: Dross!

BULLSHIT! Breed Specific Legislation

Im a huge fan of Penn & Tellers show 'BULLSHIT!' While I dont agree with everything they say, its a fun show, and I wish something like it were on NBC/CBS/ABC/PBS. Ive got a great idea for an episode, or at least a half episode: Breed Specific Legislation

Most people dont know that BSL is. People who do know probably think its a good idea-- why would policy makers introduce BSL if it wasnt needed?

Im here to tell you, BSL is BULLSHIT.

I admit, Ive got a dog in this fight-- I rescued Arnie Puppy last December (which is why there was no blogging Dec-Jan, nursing the pup back to health). Arnie is an American Staffordshire, one of the many breeds considered a 'pitbull.' Which brings me to BULLSHIT #1.

Find the pitbull.

Did you get it? No? How is a police officer supposed to know whether your dog is a banned breed or not? A mix-up could be clarified with AKC papers, but what happens in cases like mine? What if you rescue a pup off the street or from a pound, and you dont really know what breed your dog is? Im only guessing that Arnie is an AmStaf. He could be any of those black-brown-brindle dogs on that website. He could be a mix (I see lab in him, looks and behaviors, but I have no proof).

"Well," some might say, "we dont let people just buy guns. You cant just find a gun on the street and say 'Oh I found it, its legal!' BSL is necessary to protect society."
Some people, you just highlighted BULLSHIT #2-- Pitbulls are dangerous to society.
The majority of dog homicides are by Pitbulls, Rottweilers, and other hard breeds. But of the 5 million dog bites every year, the number of dog homicides is almost in the single digits. From 1982-2006 there were 264 dog homicides.
But there are problems with how the CDC collected their statistics for dog homicides:

Consider five fatal attacks included in the CDC statistics.

• A man was bitten in the forearm by a Pit bull. The bite was not serious but introduced into the wound was a virulent and fast spreading bacteria. The man died 4 days later from this virulent bacterial infection.
• A teenage girl give birth to a infant, distraught and frightened, she tossed the hours-old infant into a neighboring-junk-strewn yard where two Pit bulls resided. The dogs killed the newborn.
• A German shepherd mixed breed dog went into a bedroom, lifted a newborn out of a crib and carried the infant (by the head) into the living room where the adults were seated.
• A man restrains his girlfriend, while ordering his Pit bull to repeatedly attack her. He is eventually convicted of murder and is serving a 20-year sentence.
• An elderly man attempts to stop his German Shepherd dog from fence fighting with his neighbor's dog, the dog turns on his owner, severely mauling him, inflicting fatal head and neck wounds.

The CDC was right, in that five people died as a result of a dog bite. But were all these bites the result of aggression? Were they the same type or level of aggression? Which behaviors initiated the attack, human or canine? So the number of deaths by dogs (as per the CDC) cannot be used to define aggression, or the aggression of certain breeds, as aggression is not defined or qualified.

And as far as non-lethal dog bites go-- there is no correlation with breeds, other than the most popular breeds in a given area are more likely to bite. That is, in areas where labs are most popular, there are more lab bites. In areas where German Shepherds are more popular, there are more Germy bites. Etc.

If you killed every pitbull tomorrow, the stats wouldnt barely show a blip.


"But I watch the news! Pitbulls are mean. Its just the nature of the breed." BULSHIT #3
Pitbulls (at least AmStafs) were bred to be farm dogs. It hasnt been until very recently that assholes have used them as pit dogs. Dog fighters will fight anything, but their preferred breeds have changed over time, Ive seen the preference for pitbulls to be as recent as the 1960s. Youre telling me you can change 'the nature of a breed' in 50 years?

Lets pretend its been longer. Lets pretend for a second it is 'the nature of the breed' to be aggressive. There should be stats to back this statement up. What do they say?

The American Temperament Test Society has currently tested almost 1000 American Staffordshires, another 1000 American Pit Bulls, and another hundred Staffies (British cousins of AmStafs). The lowest score for those three 'pitts' was given to the AmStafs, with a pass rate of 83.9%. Who has a similar rating? Golden Retrievers, 83.8%. Those vicious, vicious Golden Retrievers.

Lets start banning Goldies and refusing to adopt out Goldies that show up in shelters, choosing to kill them within 24 hours (tons of time for their owners to find them, if they have any, right?). Lets see how suburbia reacts to that.

Thats not an entirely fair analogy. Goldies are a 'soft' breed, and AmStafs are a 'hard' breed. This means that you can teach an AmStaf to not only be aggressive, but to go for 'the kill.'
But there is a key phrase: you can teach them. You have to teach them to be bad through abuse or neglect.

Someone was obviously trying to teach Arnie to be bad when I found him-- he was covered in scars (theyre hidden better now that his hair is full and healthy), but there are several large gashes in his legs that are never going to completely heal. I know someone was trying to make him a fighter. Dog fighting and cock fighting are big in Oklahoma (another reason its the BEST place on earth. Ugh.).

So even the hard-soft breed delineations arent cut and dry. Despite the efforts of whatever asshole owned Arnie before me, he is a sweetheart. To strangers, other dogs (even teeny tiny breeds), and he loves children and will bow submissive to them and take treats gently from their hands (and children flock to him when they know its okay to pet him-- his clownish grin is irresistible to kids). He only shows aggression when its appropriate (note: Arnies fine, Im fine, nothing happened, but it could have).
My brother has rescued two Labradors, and they are red-zone cases. They both want to kill strange dogs, and one (until recently) would attack human visitors. But that does not mean Labradors are mean dogs! It means my brothers dogs had hard fucking lives before he found them! Its not the breed. Its not the dog. Its the humans!

BULLSHIT #3a is another 'characteristic' of the breed-- Myths about pitbull jaws. Like their jaws lock when they bite, or their bite is 1600-2000 lbs psi.
The fellow quoted on on the pitbull rights sites, and the usual expert witness arguing against anti-pit legislation is Dr. Lehr Brisbin, an animal behaviorist at the University of South Carolina.

"The few studies which have been conducted of the structure of the skulls, mandibles and teeth of pit bulls show that, in proportion to their size, their jaw structure and thus its inferred functional morphology, is no different than that of any breed of dog. There is absolutely no evidence for the existence of any kind of 'locking mechanism' unique to the structure of the jaw and/or teeth of the American Pit Bull Terrier."

"To the best of our knowledge, there are no published scientific studies that would allow any meaningful comparison to be made of the biting power of various breeds of dogs. There are, moreover, compelling technical reasons why such data describing biting power in terms of 'pounds per square inch' can never be collected in a meaningful way. All figures describing biting power in such terms can be traced to either unfounded rumor or, in some cases, to newspaper articles with no foundation in factual data."

So be wary of politicians pushing BSL, theyre trying to compensate or distract from something. Fear-based legislation sells, even if its a wild-goose chase (remember the Satanic cults of the 1980s? What happened to those?).
And to most people, BSL seems reasonable on the surface, so theyd be inclined to vote for or support it if it came up. But all dog owners should be held responsible for their dogs behaviors. If you cant handle your dog, whether its a pit or a Pomeranian, dont get a goddamn dog! If you dont have the time to exercise them and train them properly, dont get a goddamn dog!

So pass the word on to your friends: Breed Specific Legislation is BULLSHIT!





And now, a shameless appeal to emotion-- Dont watch this if you dont want to cry:

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Fitness Landscapes: Behe really, really shouldnt have gone there

As I mentioned before, I have to deal with fitness landscapes every day. HIV fitness, relative to the fitness landscapes of their host and the human population, is specifically what I research.

But Behes ideas of fitness landscapes are so incredibly, bafflingly wrong, I started to second guess my own understanding of fitness landscapes. "He cant be this silly. He cant be this oblivious. Maybe I dont really understand this as well as I thought I did. Oh shit. What if I just made an ass of myself in front of PandasThumb and SciBlogs and all their readers? Oh holy shit."

So I spent a little time on PubMed. Youll be pleased to hear that Im not insane. Not only that, but Im learning lots of cool new things, seeing how other biologists are using fitness landscapes.

**evil grin**

If Behe wasnt so fixated on Darwins Black Box, he might have noticed he was opening a Pandoras Box for ID Creationism. Sure on the surface, Pandoras Fitness Landscape Box might look inviting to IDC... a shiny theoretic mathematic veneer, useful for blinding people. But a demon waits for ID Creationists. Empirical research.

I found this oh-so-handy review in Nature:
Empirical Fitness Landscapes Reveal Accessible Evolutionary Paths

Behe seems pleased with himself over the 'probability' of chloroquine-resistance in malaria (wrong about that too), an alteration of two amino acids.

'Empirical Fitness' gives an example of researchers empirically determining probably fitness pathways of bacterial resistance to cefotaxime, and it will blow Behes mind.

FIVE mutations! DUN DUN DUNNNNNNNNNN!

Researchers just used a plug-and-chug method to figure out what kind of pathway bacteria could take to acquire resistance. 32 possible mutants, 120 possible pathways. They tested them all.

Most of the pathways made Behe Evolution Barricades-- dips in fitness keeping the organism from reaching a near-by higher peak.

They found 18 possible pathways that would work just fine. No drops in fitness as the mutations started to pile up. And as the review authors admit, this is extremely conservative. When you take other dimensions of the fitness landscape into account, and the possibility of mutations outside of the 5 building a bridge across a fitness valley then subsequently reverting (epistasis!), there must be many, many more possible trajectories.

Five mutations.

Not two.

This paper also addresses a favorite of ID Creationists in the context of fitness landscapes: ligands and their receptors (biochemistry, what Behe should know). Theyre like locks and keys-- one is no good without the other. And not just that-- How do you make sure the lock is specific for the key, and the key is specific for the lock? You cant have excess keys around, opening locks willy-nilly, or locks that take any key. How could such a thing evolve without God? I mean Designer! How could such a thing evolve without a Designer?

Empirically studying fitness landscapes gives us some awesome examples of how new super-specific ligand-receptors can evolve! How about our hormone receptors? Hormone: key, Hormone receptor, lock. Turns out one of our hormones acts like a master key: 11-deoxycorticosterone. It works on 'ancestral' receptors and modern receptors, which means duplicated receptors (AAAAARG gene duplication! Another IDC bane!) were free to mutate around a bit, and new, more specific keys could evolve, like aldosterone! Then the aldosterone key and aldosterone lock were free to co-evolve with each other and live happily ever after! YAAAAY!

The review calls this process 'molecular exploitation.'

This is only a four page review, but it has some more great examples and describes fundamental aspects of 'empirical fitness landscapes'-- and its a Nature paper! So Im certain you can find this at a local library, or a librarian there can find you a copy. Its worth the hunt if this spike in Behe posts has piqued your interest!

You Win Some, You Lose Some

Last week I rejoiced with everyone else when Guillermo Gonzalez was denied tenure at Iowa State. His support of Creationism didnt play a hand in the departments tenure decision, but its always nice when a crank doesnt get their way. Its even better if they lose their official platform for pushing their crap-- laypeople 'trust' PhDs, MDs, university/med school faculty, etc.

So a couple months ago, HIV/AIDS researchers from around the world got together to send an official statement to the University of Texas- Tyler regarding Blondie and her HIV Denialism.

I am writing to bring to your attention the professional conduct of Dr. Rebecca Culshaw, an Assistant Professor of Mathematics at the University of Texas at Tyler. Dr. Culshaw has recently published a book, entitled Science Sold Out: Does HIV Really Cause AIDS? in which she variously argues that HIV does not exist, cannot be sexually transmitted even if it did, and does not cause AIDS if it did exist and were transmitted. In that book, and in related advertising material, other writings, and interviews, Dr. Culshaw highlights her professional affiliation as a member of the University of Texas at Tyler faculty, using the university’s name to confer authority on her statements. Dr. Culshaw has the right to publish scholarly research, and she may, of course, hold and promulgate whatever views she wishes. But I question whether she has the right to tie the name of the University of Texas to her opinions on HIV and AIDS.

The existence of HIV and its causative role in the development of AIDS is a generally accepted scientific fact, endorsed by the National Institutes of Heath, the National Academy of Sciences, the World Health Organization and many other national and international agencies and scientific societies.

The University of Texas recognizes, as do I, that faculty members should be free to speak their minds. Section Three of the Rules and Regulations of the Board of Regents of the University of Texas stresses that the individual “should be free from institutional censorship or discipline…” Since freedom comes with responsibility, the section continues: the faculty member speaking as a citizen must emphasize that she “is not an institutional spokesperson.” The reason for this stricture is found in the University of Texas Handbook of Operating Procedures, Section 3.01: “The concept of professional responsibility includes recognition by the faculty member that the public will judge the profession by his/her statements.”

I submit that the professions of educator and mathematician suffer from the public statements of Dr. Culshaw, whose book and other works are deeply flawed on a scientific level. Dr. Culshaw, who claims to have studied HIV for over ten years, displays little or no understanding of HIV and AIDS, and her views on various aspects of virology, immunology, pathology and epidemiology are inaccurate and inept, far short of the standards expected of an Assistant Professor at a respected university. Even more disturbingly, her book is riddled with mathematical mistakes and misconceptions that speak poorly to Dr. Culshaw’s competence in her core discipline. With this correspondence is attached a short summary of some of Dr. Culshaw’s more egregious errors in her book; a longer critique is posted at http://www.aidstruth.org/rebecca- culshaw-critique.php.

I am further concerned by Dr. Culshaw’s questionable scholarly practices. First, much of the contents of Dr. Culshaw’s book reflects not her own scholarly research but instead rehashes source material that has long been available on the internet, on websites where Dr. Culshaw herself posts comments regularly; Dr. Culshaw often fails to cite these sources. Second, Dr. Culshaw misrepresents and even manipulates primary data from the scientific literature to support her arguments (see attached Summary, “Scholarly Practices” and following). Third, Dr. Culshaw continued to present her own research on HIV modeling in professional circles for several years after deciding it was based on a fraudulent premise (i.e., after deciding that HIV does not cause AIDS). She has said, “I justified my contributions to a theory I wasn’t convinced of by telling myself these [papers and conference presentations] were purely theoretical… never to be applied in the real world.” This attitude to science is intellectually dishonest; Dr. Culshaw cannot have it both ways.

I reiterate that Dr. Culshaw has the personal right to deny the existence of HIV and its causative role in AIDS. However, I do not believe that the good name of the University of Texas at Tyler should be associated with the views she promotes. The university has a reputation for scientific excellence and stands for the advancement of human health and welfare. Dr. Culshaw’s shoddy research is damaging both to public health and to the university. I am aware that AIDS researchers within the University of Texas system share our concerns on this point, to the point of personal embarrassment.

I therefore request that Dr. Culshaw be instructed that, whenever she promotes her views on HIV and AIDS, be they in a book or on the internet, she do so strictly as a private individual, and not as a faculty member of the University of Texas at Tyler.

I didnt have a hand in this, but I did help Ken a little bit with Blondies claims about HIV and ERVs. And I fully support everything said in this letter. It is completely within Blondies rights to campaign for the death of all puppies in her free time, if she wishes. But she has to state a qualifier/disclaimer that she is not speaking on behalf of UT Tyler, as clearly stated in UT Tylers handbook, as highlighted in yellow above.

Oh you expect the Usual Suspects to act like fools in response to something like this, but here are some excerpts from the 'response' letter all the letter signers got from 'the Provost and Vice President for Academic Affairs at The University of Texas at Tyler', Richard L. Osburn.

To accept the premise that this university, or any other university, should speak against this professor’s opinion is to make a value judgment on what is in the public’s interest and what is not.

Had this professor espoused an opinion in support of your position and had the university received a letter from one who was upset at that opinion by said professor, would you have the university issue such comments decrying that position?

I personally feel that the public interest is best served when there is freedom of expression.

Okaaay. I dont know what to type here that you all arent probably already thinking. So Im just going to blog-scream here real quick.

OMG DID YOU EVEN READ THAT DAMN LETTER, OSBURN?? JESUS!

4 + 7 is zebra. The earth is 6,000 years old. HIV doesnt exist. 'The Once and Future King' is a story about how Gatorade was discovered. Its all a matter of opinion, folks! And how dare you suggest a university go by its own damn handbook! How dare you ask mathematicians to know math, and professors not to encourage plagiarism! Why do you hate freedom so much, AIDS Dogmaists?

I guess Guillermo knows where to look for a job, now.

My encounter with the Vogons of OKC

PROSSER: "This bypass has got to be built and it's going to be built. You should have made your protest months ago."

ARTHUR: "The first I heard of it was when a workman came yesterday. I asked if he'd come to clean the windows, and he said he'd come to demolish the house. He didn't tell me right away of course. First he wiped a couple of windows and charged me twenty quid. Then he told me."

PROSSER: "Look. These plans have been on display at the planning office now for a year."

ARTHUR: "On display? I had to go down to a cellar!"

PROSSER: "That's the display department."

ARTHUR: "I eventually found them in the bottom of a locked filing cabinet in a disused lavatory with a sign on the door saying 'beware of the leopard'."

I had an Arthur Dent morning.

I live on a boulevard with a median, and over the past few months, every intersection of that median has been blocked off. I didnt say anything, I just kept driving one more block out of my way to get where I was going. Then one more block. Then another. But this morning when I was taking Arnie Puppy on a walk, I noticed there were two, brand new 'RIGHT TURN ONLY' signs at the intersection by my house. The very last crossover this median near my house. If they close THIS median off, I will have to go five blocks out of my way to leave/enter my house, and Ill have to make left turns across two busy roads. Instead of having a nice, easy drive into a quiet neighborhood, like there was when I moved in.

So I called the OKC traffic people today to complain. After being transferred three times, they finally found the person I was supposed to complain to. He was in a meeting, but he called me back an hour later when I was in the middle of setting up my Real-Time PCR.

Traffic Guy: "Whats the problem?"

Me: "Well, ya know, there has been a lot of construction going on on the median by my house, and I noticed two new RIGHT TURN ONLY signs at one of the last open intersections we have. I dont know whether you all messed up, or what, but if youre planning more construction, I need to complain. This is getting silly."

Traffic Guy: "That intersection is probably scheduled to be closed."

Me: "WHAT?? Who authorized this?? Who do I complain to? You all cant do that!"

Traffic Guy: "It was funded by private funds. Its already water under the bridge. Theres nothing you can do."

Me: "WHAT????"

Traffic Guy: "Well. You can come to a city council meeting..."

Me: "When and where are these?"

Traffic Guy: "I dont know. But go to a city council meeting and both sides can argue for or against it. They probably wont repave the intersection, though."

Me: "But its not filled in yet! Honestly, whos bright idea was this? This is a hazard! What if my house catches on fire??"

Traffic Guy: "I dont know. It was privately funded. Let me call you back later."

I *know* why my boulevard is getting walled off. I live in a historical neighborhood downtown, which means that there is a combination of rich old white people and... *whisper-- BLACK people!* Rich old people are bored, mean, and have nothing better to do with their money than build a street wall to keep the Darkies away and their property values 'up.' Ive met some of the old people in their neighborhood, and I assure you, it was a reaaaal treat (I should transfer a post I made at IIDB over here on that topic, you all will get a kick out of my adventures).

So Ive been in a tizzy all day (even though my Real-Time turned out beautifully!). And then Traffic Guy calls back.

Traffic Guy: "Oh, we messed up. Those signs were supposed to go on 16th street (one of the recently closed intersections), not 14th. Thanks for telling us."

Me: "Thanks for not closing 14th. You arent closing it, are you?"

Traffic Guy: "I dont think so."

Im sure they are, and the plans are on display in a cellar somewhere, guarded by a leopard...

Look Ma! No math!

Okay, Ive gotta admit, Ive been royally confused at UDs response to Mark Chu-Carrolls review of Behes new book. That they would attack his 'credibility' and pretend thats a rebuttal of his arguments isnt confusing. Whats confusing is that theyre unimpressed with his mathematics credentials. Not his biology credentials. Math. And theyre desperately attempting to give Behe some ethos as a mathematician (eg '... there was more math in chemistry than in computer science.')

This is very, very odd to me.

My boss is a biochemist (BS and PhD). Everything I do is related to biochemistry even though I dont consider myself a biochemist. My boss and I use fitness landscapes.

Behe is a biochemist too. So, whats his excuse for screwing this up so badly? From my point of view this has nothing to do with 'math' at all.

If anything, I thought UD would go after Marks lack of biology credentials. I know that Dawkins WEASLE program (see Dysfunctional Analysis and Greedy Greedy Algorithms) and such use genetic algorithms and all sorts of fun math that are well beyond my Calc I capabilities... but if 'easier' biochemical (non-math) examples refute Behes statements, whats the point in damning someones mathematical credentials?

As I pointed out in a comment on PandasThumb, nothing I do regarding fitness landscapes requires high-level math. And its not just me-- let me go over a recent paper in Journal of Virology to give you all another example of how Behe is being extraordinarily silly (or maybe this is his normal level of silliness, meh.) Nothing in this paper goes beyond simple algebra and statistics (except for the math behind phylogenetic tree programs).

Fitness Landscape of Human Immunodeficiency Virus Type 1 Protease Quasispecies

I know all of you can read the abstract, even if you cant see the whole paper, so you know where Im going to go with this... but lets not play Creationist and say a paper supports our views just from what the abstract appears to say.

Okay, an essential protein to HIV is called 'protease'. Protease is an enzyme responsible for maturing new HIV viruses after they bud off of the host cell. If there wasnt a maturation step like this, there would be nothing preventing new viruses from turning around and infecting the host cell again (all the right receptors are right there). So this makes the protease enzyme a great target for anti-HIV drugs. Youve probably heard of 'protease inhibitors' before.

Unfortunately because of the quasispecies nature of HIV, the second you give someone protease inhibitors, HIV finds a way around that hurdle, so PIs cant knock out HIV for good. What makes this even worse is protease can mutate a LOT and still function just fine... or better than the quasispecies consensus sequence. What Creationists say cannot happen: "... rugged HIV-1 protease quasispecies fitness landscape may be formed by a continuous network that can be traversed by single mutational steps without passing through defective or less-adapted proteins."

So without any slights of hand, this is what these researchers are going to do, no intensive math required:

"We determined the fitness of each variant present in the quasispecies in order to establish the relatinships between genotype, phenotype, and fitness and constructed a phylogenetic-fitness landscape map for each quasispecies."

Step 1: Filter out all the dimensions you arent interested in.
First thing these researchers had to do was get the protease gene out of its natural environment. Take it away from the CD4+ and CD8+ T-cells. Away from the antibodies. Away from in vivo. An easy way to do this with retroviruses is to blow up some infected cells, isolate the cellular DNA, put one copy of cellular DNA per well, and PCR out the gene youre interested in. Each infected cell will yield a different protease gene. Now, the sequence you isolate might be a dud. It was 'good enough' to get in, but the reverse transcription process mutated it out of working order. Thats okay, in this case. We want to see the duds (non-functional proteases) too, to determine why they are non-functional.
Now again, we have to strip all the other dimensions of the fitness landscape away, so you put the isolated protease genes in a common background- in this case a bacteriophage.

Step 2: Test the dimension youre interested in.
Infect cells with phages containing different kinds of proteases (note: theyre using E. coli here to use phages, not eukaryotic cells!). The special bactereophages allow the researchers to compare protease activities-- its a model system instead of directly measuring protease activity differences (they go back and make sure their model predicts normal HIV protease activity. it does).

Step 3: Combine your fitness measurements with your phylogenetic tree.
Ill take this down if JViorl wants, but I think its fair use:Bigger the circle, higher sequence frequency. Longer the line, more different the circle is from other circles. The different colors relate to how active each protease sequence is. Translation: You can be real different from the consensus sequence and still work fine.

Done.

No math.

BONUS!
Breakdown of what percentage of sequences they found that were 1, 2, 3, 4, 5, 6 base pairs different from the consensus sequence!

Diagrams of protease color coded to show where mutations were occuring, and at what frequency!

Relation of fitness in the bactereophage system back to fitness in HIV!

Relation of replication capacity to protease activity in HIV!

Super cool relation of mutation rates and protease activities back to the disease progression in the patients!

No hard math!

YAAAAAAAAAAAAAAAAAY!!!!!!!



Oh wait, Im supposed to write about why Behe is silly, not why this particular paper is cool.

:(

Okay, let me go back to the four points, and put some relevant text from this paper for a rebuttal. *sigh*

1. Evolution can be modeled in terms of a static, unchanging fitness landscape.

"... although the three analyzed quasispecies shared some traits, such as the presence of several fitness optima, every protease quasispecies formed distinctive individual fitness landscapes...
... even quasispecies N and O (two different patients they looked at, ERV), which had similar amino acid diversities, formed very different fitness landscapes."

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.

"... within each quasispecies, there was a large number of fitness optima... Because fitness optima were frequent, the HIV-1 protease quasispecies complexity does not depend exclusively on the enzymes catalytic efficiency..."

3. The fitness function mapping from a genome to a point of the fitness landscape is monotonically increasing.
AND
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.

...Several single substitutions were lethal and led to the master sequence to drop down the peak. However, at other positions, single substitutions sent the master sequence to a new optimum or peak, suggesting that the master sequence may walk through the quasispecies fitness landscape without being trapped at suboptimal alleles...

No advanced super-hard math tricks that no one can understand except for 'math' PhDs.

What am I missing? Why are the UD-crew going after Mark Chu-Carrolls 'math' credentials?

Edited 8.30 pm 6/4/07-- I realize Behe tries to use math to support his views in the chapter Mark is discussing, but Behe should know, as a biochemist, that his arguments are incorrect. No math should be needed... unless hes trying to intimidate his readers into thinking 'Oooh hard math! He must be right!'

No, really-- Where did I mess up?

Im taking full advantage of my 'student' status. When you are a student, its still okay to make mistakes in the lab, accidentally misspeak with your jargon, and not have a clue how, say, SDS-PAGE works... as long as you learn from your mistakes. Really, I learn better from when I screw up (NEVER making a solution without checking its pH again!).

So, um, where are the Creationists who want to correct my Behe post? Its not like I didnt make mistakes-- for instance, I should have been more specific with that second Paint pic. Thats what a quasispecies would look like from a sample of a population. Thats more of a population frequency landscape, as opposed to a general 'EVERYBODY' fitness landscape, and I worry I might have confused some people by not being appropriately specific.

Now, Im sure Bossman could read my post and offer some suggestions and corrections. I know the HIV fitness big-wigs at NIH Los Alamos could chastise my overly simplistic explanations until I turn red from embarrassment. Hell, even the physics and math folks have weighed in on various blogs.

So again, um, where are the Creationists? Why cant they correct my errors and give me constructive corrections?

Ill tell ya why. Its the same problem HIV Deniers have (*GASP!* Creationists and Deniers have something in common?? Say it aint so!!!). Where their personal knowledge stops, the 'magic' begins. DaveScot already demonstrated his willingness to revert to magic with endogenous retroviruses, exactly how Blondie shot her own credibility in the head.

Retroviruses are weird. The whole quasispecies thing is super weird. Combine all this with fitness landscapes, and you might as well be drunk on the tilt-a-whirl. Its confusing as hell. And instead of using this opportunity to learn something new, Creationists 'rebuttal' is 'Evilutionists are MEAN!'

What??

One commenter tried to address the science of Marks posts, and fell flat on his face:

Unfortunetaly for Darwinists, it has been shown that to achieve even a simple modification of a protein, let’s say two amino acid residues, evolution must cross a sequence space of mutations that provide no selective advantage.

Really? Really? You sure about that? Cause I could swear that every day in the lab I compete viruses against one another with one-->five base pair differences that have HUGE fitness differences with all dimensions stripped away but one! And youre really sure that crossing 'simple' stretches of sequence space cant happen unless there is a selective advantage? HIV explores all one and two base pair permutations of the current average 'maximally fit' variant, and some three and four base pair permutations, in one HIV patient, every day.

Every day.

So see, when the fitness landscape is changing every day, and youve got billions of HIV genome permutations floating around, willing and able to shift the quasispecies as necessary... Well, now you all are seeing why HIV is such a bastard for scientists to conquer.

And Im not even getting into Motoo Kimura.

This is reason #21342521 I hate Creationists. They are absolutely worthless to me. I can learn nothing from them, because they dont want to learn themselves, and theyre so damn arrogant that they dont even know when theyre completely wrong-- even the oh-so-educated ones like Dembski. Worthless.

A Nicer, Fluffier Atheistic ERV

I promised to stop picking the low fruit and to start being more positive with my atheism, and I totally did it today.

Again, Im sure a lot of you have 'atheism' as a Google News keyword, so you might have seen this article, 'IN THEORY: Why the uptick in atheism?'

You see where I would have freaked out, in the past. Dumb dumb dumb, and insult to injury, a Rabbi. Ugh. Newbie atheists can chomp up his 'questions'-- Does this mean the Rabbi would go around killing people if he didnt think someone was watching him? If religion is so moral, why are so many of the prescribed laws now considered immoral? Why arent the jails filled with atheists? Why is the National Academy of Scientists, the people trying to solve the worlds problems and contributing positively to humanity, predominantly nontheistic? Do watches mate to make baby watches?

These are the times that I love being an atheist that does HIV and cancer research. Being able to 'stick it' to theists who try to play the morality card didnt exactly play into my decision to go into these fields of research, but its a convenient side effect. Heres my response:

I understand the frustration of the responders who have just been called idiots by someone who knows nothing about them except that they are atheists, I encourage you all to be patient with the Rabbi.
Maybe he has never met an 'out' atheist to have these conversations with before. Certainly thats not an excuse for his bigotry, but patiently answering his 'questions' to the best of your ability would be a better response.

-- Abigail, a stupid atheist molecular virologist trying to solve the problems of HIV and cancer because she has no morals

See! I can be good!

SiCKO Trailer

This is going to be one of those movies, for me. One of those movies, like 'Jesus Camp' and 'Saw' where I know what the plot is, I know whats going to happen, I know its going to bother me, so Im not going to watch it.

I cant watch SiCKO, especially after seeing this preview.


With my recent illness, Ive already spent a lot of money on drugs/office visits/etc... and I havent gotten my official bill from the hospital yet. You all dont know this, but I had a breast cancer 'scare' (ie it was absolutely nothing) that cost me hundreds and hundreds of dollars... and I didnt have breast cancer. Not one cut/biopsy was made. Just the doc visits up to that "Um, youre fine" diagnosis cost me big $$.

And I have 'good' health insurance.

Some people like to bitch and whine about AMSAs position on complementary and alternative medicine (note: bitch and whine, but not actually, you know, do something about it), but AMSA has always been right about universal health care.

I do not know how 'old' physicians can go to sleep at night. Supposedly clever individuals who have convinced themselves that stupid (I mean stupid) 'solutions' to our health care crisis is tort reform, so universal health care is unneeded/dangerous/whatever. Yeah, tort reform works GREAT in the states that have implemented it. Like in my home state of Missouri with one of the 'toughest' tort reform policies in the nation, where malpractice insurance costs are still increasing, patient premiums are still increasing, and doncha know it, but insurance profits are... still increasing, but at record rates. Yeah, lets put a limit on how much a mother can collect after a bad doc (whos been pushed from hospital to hospital, silently, as to not damage the reputation of the hospital that hired him-- could damage profits!) botches her delivery and shes left with a child that needs a lifetime of care. Lets limit that to $25,000. Fuck you.

Look, I know old people are scared of new things like 'remote controls' and 'cell phones' and 'Google', but I really, really dont give a shit that old physicians are scared of learning a new system for universal health care. I think they can deal with it. My problem is the complete denial, and utter lack of action and lack of responsibility physicians take with our health care crisis.

I cant watch SiCKO. It will just make me angry, and Im not in a position to help the people who need it (outside of my vote, of course).