Monday, April 30, 2007

The Ancient Virus World and Evolution of Cells: Part Two,The egg CANT come before the chicken! Oh wait...

Oh as usual, unwanted drama got in the way of science posts-- but finally! Second edition of 'Ancient Viral World'! The paper Im reading is available online for free!

If you asked someone which came first, the virus or the cell, theyd most likely say 'The cell! Viruses need cells to replicate, so they couldnt come first.' hehehe This isnt a trick 'If a rooster lays an egg' question. The Average Joe understanding of viruses might be right in this case! 'Viruses second' is the traditional scientific explanation for viruses, and there are two obvious ways viruses could have arisen after cells:

  1. Unicellular organisms, maybe parasites, lost some of their genes and became obligate parasites.
  2. Renegade genomes - bits of genes/genomes and such escaped from the host genome, selfish bastards that are only looking out for Number One.
But there is a big problem with these hypotheses that surfaced when we started sequencing and comparing viruses: Viruses have lots of genes that arent found in their host cells.

These 'viral hallmark genes' can be found in lots of viruses, spanning the seemingly unconnectable gaps between say, ssRNA to dsDNA viruses. These genes are only distantly related to cellular genes, if a cellular counterpart can be found at all, so they probably arent degraded stolen host genes. Plus, they all have virus-specific uses. For instance, the most widely distributed viral hallmark genes are 'jelly-roll capsid protein' and 'superfamily 3 helicase' (mmm jelly-roll...). Superfamily 3 helicase is a protein involved in genome replication in DNA viruses (and plasmids), whether that DNA virus infects us or an Archaea. The capsid (protein coat) of icosahedral viruses is made of a complex of capsid proteins:Each of the capsid subunits has a 'jelly-roll' domain-- a motif conserved across the viral world.

Viral hallmark genes also include:
  • Archaeo-eukaryotic DNA primase (genome replication)
  • UL9-like Superfamily 2 helicase (genome replication)
  • Rolling-circle replication initiation endonuclease (genome replication)
  • Packaging ATPase of the FtsK family (DNA packaging into virion)
  • ATPase subunit of terminase (DNA packaging into virion)
Now, nobody is saying that because some viruses share genes, all viruses have a LUCA (oh Im sure *someone* is saying it). 'Viruses' as a whole are just too diverse for anyone to humor that idea, so we think that viral phylogenies are polyphyletic, rather than monophyletic. We can tease out a few roots of their tree:
  • Positive strand RNA viruses
  • Retroid viruses and elements
  • Small DNA viruses, plasmids, transposons with rolling circle replication
  • Tailed bactereophages
  • Nucleo-cytoplasmic large DNA viruses
But, if cells arent ancestral to viruses... How could viruses come first?

Sunday, April 29, 2007

Atheism causes anorexia. And obesity.

The author of this article in The Courier (Australia) has discovered something that will not only help her home country of Australia, but also our own countrys battle with obesity and eating disorders in children: Only people of faith are healthy and happy. (dont worry, she didnt support any of her assertions with 'science' so this article is fr*med perfectly)
The Answer: We need to tell children, "If you were a Good Christian, you wouldnt be struggling with your weight or your body image. You would be thin with lips to die for, just like the Good Christian in the articles accompanying pic."

She starts out with a good pop-culture premise, Super-Girl-Syndrome. Luckily I had very supportive parents, so I was never pressured to always be first in grades, looks, eight sports, volunteering, etc etc etc like Ive heard happens to some girls, but I still had a slight case of SGS when I was in school. I always wanted to be the smartest and get the best grade on every test and in every class, and when I didnt get it, a slight internal mental spaz would occur. Alas, I knew damn well I was a scrawny ugly duckling when I was little, so I didnt have body image issues :) "Meh, Im gangly. What ya' gonna do?" I didnt learn until I was in college that I needed to be eating more protein, I needed to lift weights, and Im still learning now that I need to eat a shitload of calories if Im going to do any cardio (running the puppy every morning and every evening) to turn my scrawny-ganglyness into kinda-sexy-in-a-nerdy-wayness. Sure I had health classes and P.E. in school, even in college, but it wasnt until I started experimenting with foods and exercises myself that I really got 'healthy.' Every body is different.

In a perfect world, the 'answer' to some cases of body dismorphia could be letting kids experiment with lots of different eating plans and exercise programs to see how their bodies respond, teach them how to change things up as they get older, different options if they get bored, etc. It would be hard to do, but it would be my ideal solution. There is nothing like giving a Super Girl lots of 'right answer' options to get her to relax.
"Taekwondo is taking up too much time? Thats okay! If you run with your dog in the mornings, you can kill two birds with one stone!"
"Bored eating sandwiches and carrots every day? Lets Google some easy, healthy, lunch recipes!"

NOOOOOOOOOOOOOO dear readers! NO YAY! The answer to life, the universe, anorexia and everything is JESUS!

It is, in truth, all of the above. But there is another profoundly important yet little noticed dynamic at work in the anxious, achievement-oriented lives of perfect girls: they have a sometimes deadly, often destructive, lack of faith. So many perfect girls were raised entirely without organised religion, and most of the rest of us – I admit reluctantly to my own membership in the perfect girl club – have experienced "spirituality" only in the form of mandatory holiday services with a big-haired grandmother, or unconscionably elaborate and expensive bar mitzvah parties, where everything but the Torah is emphasised.

Niiiiice! Even managed to work in a ZING on Judaism!

In fact, our worth in the world has always been tied to our looks, grades, and gifts – not the amazing miracle of mere existence.

Thinness and achievement stand in for qualities of kindness and humility.

Speak for yourself, Biblo. Just because youre pathetic doesnt mean atheists are.

But heres example #2948569146552765 of Religious fundamentalism killing the ability do detect irony.

In essence, they are crying out to our godless culture, showing us just how damaged a child can be who is thrown to the wolves of advertising and amoral media without the protection of any spiritual armour.

There you have it folks. The only kids who have body issues are ones without True Faith. Its not that youre 14 and dont know natural peanut butter is an awesome substitute for Skippy, its that you dont have enough faith. Its not that no one teaches girls how to use free-weights because theyll 'hurt themselves' or get 'bulky', its because you are a complete failure in Gods eyes. If you only trusted Him more, if you only truly gave your heart to Jesus, you would be thin and pretty. Religion is the answer.

**VOMIT!!** <-- non-bulimic

Edited to add: You can leave comments, but they are moderated. Mine didnt make the cut :(

... Or maybe young girls could use some health and exercise courses in school taught by trained individuals. It took me years of self study and trial-and-error to figure out what kind of exercise my body responded to (and I still enjoyed) and what I needed to eat to be healthy.

But yeah, Im sure atheism is the problem, because Lord knows there arent any anorexic or overweight theistic children. Do you think passing judgment on theistic children with body issues, telling them they have problems because they dont have enough 'faith', is 'helping', Courtney? Youre dreadful!

--Abbie, 1.75 meter 61 kg 13% body fat HIV and cancer researcher... and atheist.

Saturday, April 28, 2007

Video dump!!!

Everyone has seen this one, its still real dang funny:

probably will be removed from YouTube soon. Copyright. ;)

Little known fact: I played the cello for 10 years. Had to quit in college, cause for some reason balancing 12 hours of labs, 12 hours of cello practice, coursework, and research was not so much fun. Here is some insight into the cellists psyche:

Usual disclaimer, I know you all read Pharyngula, but I can provide something he cant: an official Jew Seal of Approval! Please note Chris's comment in PZs thread :)

Thursday, April 26, 2007

ID vs ERVs-- Part Nine: IDC Article Etiological Agent in Acute Gumbititis Outbreaks

WARNING: Reading the following post might cause the reader to suffer from acute Gumbititis
(herein referred to as Creationist Induced Gumbititis, CIG).

Much like the 1918 Influenza pandemic (which curiously killed more young, previously healthy individuals, rather than the very young and very old), current CIG outbreaks have victimized an unexpected population. Normally Creationist Claims are targeted towards evolution naive or evolution apathetic populations. The recent outbreak is clearly targeted towards moderate--> experienced Science Defenders in the hopes CIG will be severe enough to cause brain aneurysms. According to the following graph, the only people immune to CIG are non-English speaking, Creationist naive, non-humans.
(note: graph recreated from original data to prevent copyright confusion)

Do NOT read this post in a public area (airplane, library, coffee shop, etc). If you exhibit warning signs of CIG (see below), explaining why you are acting like a Gumby can pass CIG to surrounding individuals.

Please tell your family and friends if you decide to read this post so they can be on the lookout for CIG warning signs.
Mild symptoms:

  • Insistence upon wearing tiny spectacles (even on top of prescription glasses)
  • Insistence upon wearing suspenders and/or sweater vests (note-- sweater vests DO have white shirts underneath. Wearing a sweater vest alone is just sign of bad fashion)
  • Constantly speaking at a socially inappropriate volume
  • Stealing handkerchiefs for use as head wear

Severe symptoms:
  • Sudden appearance of a moostache. Even possible with female victims. Though a sign of severe CIG, easily reversible with proper treatment, as moostache is normally glued on.
  • Fixating on phrases and repeating them ad nauseum (also at socially inappropriate volume)
  • Uncontrollable smashing of personal belongings, others belongings, and nearby people.
  • Will not stop screaming "MY BRAIN HURTS!" Cannot be consoled without anesthesia.
Readers, you have been warned.

So, what is Mr. Black Holes official, damning philosophical argument against Evilutionism?
However, the selfish DNA narrative is not falsifiable in that there is no way to test any statement of DNA selfishness such that the statement could be categorically refuted. Therefore it cannot be a hypothesis. Indeed, the opposite is the case. No matter what data are considered as evidence of RE functionality, the selfish DNA narrative allows the generation of higher-order stories to transmogrify functional roles into genomic selfishness. This irrefutable aspect of the narrative is what permits the idea to prevail in scientific discourse.
Sometimes repetitive elements, ERVs, transposable elements are coopted by the host cell for use. Sometimes they arent. Sometimes birds use wings to fly. Sometimes birds with wings dont fly. That means Evilution is un-falsifiable, thus a scientifically and philosophically unsound theory. A CREATIONIST just told EVILUTIONISTS that their theory is unfalsifiable.



Im okay.

Creationists, who have no idea what ERVs are until I bring them up in conversation (following the insertion of ERVs in genomes is a neat way to connect-the-dots for common descent) ad hoc insist that ERVs are evidence for common design.

Creationists, who have no idea that ERVs mutate differently after 'splits' in the phylogenetic tree until I bring it up in conversation, ad hoc insist that mutations are the result of The Fall.

So, DNA is perfect because it was Designed. Every base pair, every piece of 'junk' is sacred. But any time we do find junk, its because of Original Sin.


More on Evilutions 'Un-Falisfiability' to come.

The PNAS paper that inspired junk

The article referenced in this SciAm article was finally online today in PNAS Early Edition. Its a neat little paper, and I think the SciAm (minus the 'junk DNA') did a nice job summarizing it. Two complaints, still.

  1. '10,000 new uses for junk DNA!' was used out of context. 10,000 sounds like a lot. Its 0.4% of our genome.
  2. It missed a cool point I think pop culture readers might like (but maybe it is too much for a short article).
There are lots of ways to compare the genomes of humans and our nearest relatives-- you can sequence everybody and align as much as your computer can handle to make a phylogenetic tree (HAHAHA! Good luck!), or you can cut your computer (and yourself) some slack and only compare sequences of protein coding regions or specific proteins to generate a tree, or you can translate the mRNA from protein coding sequences into amino acid sequences for comparison... etc etc etc.

So say your lining up all these nucleotide and amino acid sequences and you find a gene we have in common with chimpanzees thats actively transcribed in, say, neurons. You can blow up some human neurons and some chimpanzee neurons and figure out how often the gene we have in common is transcribed by using a microarray.
Turns out that even though we have 98-99% of our protein coding regions in common with chimpanzees, a BIG difference between the two of us is the transcription rates of these genes. Sometimes the in-common-gene is up-regulated in humans, compared to chimpanzees. Or down-regulated. Or the transcribed at the same rate.

You can also study the actual process of transcription with a neato technique called ChIP-on-chip. This assay is used to find the proteins that help transcribe genes, promoters, transcription enhancers or repressors, etc. This paper demonstrates that a portion of unexplored DNA effects the transcription rates of genes associated with system development, nervous system development, and transcription regulatory activity itself.
Minor problem: we ignore repetitive DNA in ChIP-on-chip assays.

Well, thats not entirely unexpected, considering that there is allota genome to explore. However the paper authors gave a rather snippy reason for why we 'ignore' repetitive elements in ChIP-chip assays:
The majority of current whole-genome experimental and computational approaches to gene regulation, such as tiling arrays used on ChIP-chip experiments, and transcription factor-binding site prediction, choose to ignore repetitive regions, for pragmatic reasons, assuming that most if not all are inert.
That sounds curiously similar to a Creationist Claim ("Evilutionists dont study 'junk DNA' because they think its all garbage, but every base pair is sacred!").

A more reasonable explanation is that ChIP-on-chip assays are friggen expensive, and including a few million million unexplored sequences in your assay is not only cost prohibitive, but a lesson in futility. It would be a fishing expedition, and you probably couldnt wade through all the data if you worked on the same assay for years. I mean we're thinking about doing what theyre suggesting with HIV-1, but HIV is only 10 kilo base pairs long. The human genome is ~3.2 billion base pairs long. Little bit of a difference, there.

Now, after more of these regulatory regions are fleshed out, certainly they will be used. But I think that 'conclusion' in the discussion was a touch harsh.

(link for evolgen)

SciAm wants our help with 'Junk DNA'!

For those of you irritated with the treatment of Shelley after she corrected bad science reporting on her blog*, I have some fantastic news to cheer you up!

After evolgen and I posted our irritation at the gratuitous use of 'junk DNA' in a SciAm article, the author (JR Minkle) actually responded to our criticisms in a positive manner!

Cherry on top: He is as horrified at Creationists exploitation of 'Junk DNA' as we are!

x3: "Junk" is taking a beating in the comments. I should have been more aware of how scientists and the public perceive the term. As ERV points out in a juicier piece of context, creationists use the term to cast doubt on evolution. If you Google "junk DNA," the fifth site from the top is called

HUGE high-five to JR Minkle for not taking 'junk DNA' personally and helping us all promote science!! So readers, get your booties over to his article and leave some suggestions!

Im happy to see TR Gregory already responded, but Im hoping Larry Moran and Alex Palazzo and The Pandas Thumb crew will weigh in as well.

* Situation resolved, in Shelleys favor! YAY!

Tuesday, April 24, 2007

Junk DNA Q&A in the works

Sweet! TR Gregory over at Genomicron is putting together a Q&A on Junk DNA!

This soooo needs to be done! We can all have a nice article to reference every time we encounter bad journalism or Creationism.

Go ask questions! Go give suggestions!

Dawkins on FOX: How Others See Us

I think the consensus around the atheistic blagodome is that the Dawkins vs O'Reilly showdown was... well... dull. "Why dont you believe in Zeus?" "Hitler was an atheist!" **YAWN!**

Here it is, if you missed it:

So since certain people are soooooooo concerned (*vomit*) about how Dawkins 'hurts the cause', for atheism and science, I was wondering how others viewed this debate. So I went to an old lair of mine... a bodybuilding forum. Yes, me, bodybuilding. Besides, I think bodybuilders make a great cross section of religion in the U.S. Some bodybuilders are atheists. Some are rabid Christians. Some are actually the scary Muslims the atheists and rabid Christians are afraid of. Jews, Agnostics, even knew a couple pagan lifters. So I checked back into the forum to see what people were saying:

  • I'm pissed. He gets a good guest on and it's about 2 fricken minutes. WTF?
  • oreillys trump card to end the interview was to directly imply that atheism drove hitler and stalin to commit their crimes against humanity.... he must really think his viewers are idiots
  • The absolute worst argument a Christian can make is that people who don't believe in God are all immoral.
  • (Response to Above Comment) I don't see Christians make that argument but I find it funny when Atheists mention morality when on the Atheistic world-view morality is an illusion.
  • (Response to Above Response) What?
    • wtf does that mean?
    • It kind of sounds like atheists believe in the Matrix. The world is just an illusion....
    • Huh? I find it funny when theists try to assign a specific philosophical world view to atheism, and I find it especially funny when someone tells me what my beliefs are.
    • (from a theist) Why do I need to believe in your specific god to know right from wrong and good from bad?
  • I have all of O'Reilly's books autographed and I'm still jumping on the Dawkins bandwagon.
  • Oh and I forgot, when Dawkins replys with "You can't prove Zeus either," O'reilly says "Well uh I just saw Zeus back there and uh he's not lookin so good....."
    • What the hell does that even mean ?!
    • F- for failed attempt at an clever response. (emphasis original)
  • Wow, Dawkins was able to get his message out without causing Oreilly to burst into outrage and cut his mic! Good interview although Oreilly took up 2/3's of it.
  • oreilly "pwned" himself with his dipshit points.
  • That was crap. I was waiting for that interview for days and it only lasted a couple minutes with Bill doing his usual bs.
Huh. Certainly thats only snips from one thread in one forum on the interweb, but it looks like Dawkins made a great impression on the Average Joes who caught the interview.

Yes, Dawkins is really hurting The Cause(TM) [/dripping sarcasm]

Monday, April 23, 2007

More Junk from Scientific American

First this, and now this.

I cant find a publication by Gill Bejerano that includes the term 'junk DNA.' Doesnt help that SciAm didnt reference this groundbreaking publication. I dont know what theyre talking about.

Dawkins on FOX

Oh everyone and their cousin is going to have a post on this, but I just have to say that:

1-- Just like I thought, Dawkins did well. He hasnt ever said anything that has made me wince before, he didnt start tonight. Unlike certain people, Dawkins puts his money where his mouth is and enters the lions-den to reach 'non-traditional audiences.'

2-- I cant believe I didnt go to the gym for that crappy segment. Dawkins did well, but it was like 2 minutes and Bill wasnt even remotely entertaining. Boo.

ID vs ERVs-- Part Eight: Black Hole Swallows Planet of the Straw Men

A continuation of Part Six and Seven.

What follows are the most absurd arguments against evolution I have heard in my entire life. Mr. Black Hole has set up an entire planets worth of 'Darwinist' straw men for himself, and whoooo boy! Hes takin' a battle axe to the poor creatures! But before you burn your eyes reading his powerful refutations of Evilution, let me list the sacrificial straw men:

(a) functional units in the genome consist solely of protein-coding loci ("genes"*) and their associated regulatory regions, with a few exceptions;

(b) all inherited, important aspects of the phenotype are specified by proteins and some RNAs;

(c) the "Central Dogma" holds;

(d) the mapping relation that exists between genotype and phenotype is that of programming instructions (DNA) and the programmed output (phenotype);

(e) genes act and evolve in an independent manner at the DNA level;

(f) higher-order structures such as chromosomes and cells are passive with respect to form-generation, the active agents being genes; and

(g) DNA sequences evolve by a combination of neutral forces and selection pressures.
Not to be a first grade teacher here, but how many of these straw men can you all kill off the tops of your heads? Who is Mr. Black Hole trying to kid with "This is what evilutionists believe!"?

Since ID Creationists love analogies, I also find it interesting that ID Creationists like to alternate degrading the intelligence of their followers with flattery ("Heck even I know how to refute E! Im so smart! Evilutionists are so dumb!"). Just seems familiar, thats all.

So thats your argument, Mr. Black Hole?

siRNA can regulate gene function, and siRNA isnt necessarily in a 'flanking region', therefore Straw-Man-A is dead, therefore evilution is false, therefore your creation myth is true?

Epigenetics exists, 'therefore Straw-Man-B and F are dead, therefore evilution is false, therefore your creation myth is true?

Retroviruses exist, therefore Straw-Man-C is dead, therefore evilution is false, therefore your creation myth is true?

Theres not one gene for 'red hair' or 'good at sports', therefore Straw-Man-D is dead, therefore evilution is false, therefore your creation myth is true?

Genetic linkage exists, therefore Straw-Man-E is dead, therefore evilution is false, therefore your creation myth is true?

Straw-Man-G is gobbldy gook, therefore Straw-Man-G is dead, therefore evilution is false, therefore your creation myth is true? (If anyone can translate Straw-Man-F for me, Id appreciate it)

Thats his logic.

You think Im being simple? Surely this isnt really his argument, right? Shield the eyes of near-by children, readers:

(1) Functional units in the genome do not consist solely of protein-coding loci and their flanking control regions. Instead, functional units of the genome comprise a host of different DNA classes, for example, loci for regulatory RNAs, centromeres, nuclear matrix attachment sites, chromatin boundary elements, transcriptional control sites, and exons, to name but a very few. REs are known to consist of concatenations of functional, nonprotein-coding regions as well as protein/RNA-coding domains. Many cis-regulatory sequences are recognized to be repetitive in that multiple copies of the element are dispersed throughout a genome.

(2) Inherited aspects of the phenotype are specified by more than proteins and RNAs. Following point 1, nonprotein-coding DNA regions have been shown to have an array of direct and indirect phenotypic effects, in addition to providing the systems architecture for protein-coding loci.

(3) The Central Dogma is incomplete. Facets of the Central Dogma are now being seriously questioned, especially since it has been determined that chromatin conformations and cytoplasmic states can be meiotically inherited, a single "gene" can code for many different proteins**, cells can detect and modify exogenous DNA***, and metabolic conditions can (de)activate or modulate a range of mutational processes. Proteins can even impose function on otherwise "functionless" DNA sequences—such as the emergence of neocentromeres from noncentromeric DNA regions. In addition, multiple functions can be layered onto a single DNA segment. Information flow in the cell is hardly the linear specification chain imagined in the 1960s through the 1990s.

(4) A multi-layered mapping relation exists between genotype and phenotype. Cause and effect in phenotype specification are becoming increasingly difficult to discern. The connection between genotype and phenotype is a many-to-one and one-to-many network of mappings, all of which are context-dependent.

(5) Although many alleles do show Mendelian inheritance, genes do not act and evolve in an independent manner. DNA activity and mutational alteration are embedded in the context of chromatin domains, the chromosome, nuclear compartments, the cell, and epigenesis. There is no such thing as autonomous DNA unit action or evolution.

(6) No justification can be provided for ascribing greater ontological significance to one set of cellular components (e.g., protein-coding regions) over another (e.g., the cytoskeleton). Indeed the line between the "genome" and the "encoded cell" has blurred. The fact that ciliates literally engineer their "somatic" chromosomes, and phenomena like RNA editing and position-effect phenomena, readily gives the lie to the notion of DNA being the sole active, "directing agent" in the cell.

(7) DNA sequences change by more than a combination of neutral forces and selection pressures. Models of DNA sequence evolution that recognize only neutral and selection-driven genomic changes persist in biology textbooks, phylogenetic models, and population genetics, but these are now seriously outdated. Many routes of genomic alteration, even point mutations, are actually or potentially under some form of metabolic control. There thus appears to be a spectrum of "mutational control" in the cell, ranging from the strictly targeted (site-specific) to the "random," operating at a stage before screening by natural selection or genetic drift.
.... Ta dah?

Readers, I expect you all to mail me boxes of wine (BOXES, not bottles) for reading this crap. I need it. To use my favorite descriptor, this paper is like a coagulated word salad:
What all of this means is that the postulates of the genome model supporting the selfish DNA narrative are either false or need to be modified out of recognition. The genome definition based on points 1–7 goes beyond simply DNA ≠ genome; it rather indicates that DNA genome, and quite possibly (DNA + chromatin proteins) genome. If we want to maintain the metaphor of a book, then the genome is an interactive, semiotic, and super-sophisticated text that has, at this time, no other physical counterpart. It is a genomic book where, for instance, a sentence can take on a hundred related but different meanings, depending on the epigenetic context, all of which are compatible with the whole text. Furthermore, the genome-book contains many cryptic writings that, when transposed, rearranged, or read with an epigenetic decoder, reveal their meanings.


* Yeah, he puts "gene" in quotes through the entire paper. Creationists dont believe in "genes", evidently.
** Once again, Mr. Black Hole is convinced HIV operates through magic.
*** Okay, you know that 'Fundies Say the Darndest Things' where a Creationist almost discovers the sun? Mr. Black Hole, a biologist (**WINK!!!**) has just discovered restriction enzymes. EcoRI exists, therefore Creationism is true. ROFL!!! I hurt myself laughing so hard at this one!

Saturday, April 21, 2007

Why do I blog?

Blog brother Kris tagged me with the 'Why do I blog meme'!

Well originally it was a way to force me to learn about other kinds of microbiology besides viruses. Im going to be getting a PhD in micro, and Ive never taken a general micro class, lol! Virology Im set on, but bacteria? Ek. Trypanoso-what? Eh.

I also wanted to fill a blog niche. I didnt see a lot of virus blogs around (which reminds me, I need to post more info on general virology!), and certainly no ERV or epigenetics blogs. Ive got some weird stuff in my brain to offer the blog community.

I also wanted a place to gush about lab stuff, because honestly, I have the coolest job and coolest research project on the planet :P

But I stopped for a month or so when I was applying to grad school and nursing baby Arnie back to life. I might have abandoned ERV then. But after a series of encounters with Deniers and Creationists occurred in rapid succession, I couldnt keep my yapper shut anymore. I physically couldnt. So I credit those morons with twisting the nerdy old ERV blog into the ERV you know today! Hurray for Creationists and Deniers! lol!

This is the only outlet I currently have for countering 'those types.' Im hoping you all read something here that you didnt know before, and might remember something I say and be able to counter a Creationist/Denier you encounter in real life. I mean I do this so I can learn too. Learning something well enough to explain it reasonably to someone else is how things *stick* in my brain. Correcting others errors helps everything *stick* too.

I do want to thank you all for listening to my rants and ramblings. Id do this even if no one was reading cause its good for me intellectually and psychologically, but its fun having discussions with real people on these topics :)

Friday, April 20, 2007

Another potential Evil GMO! *cue thunder, lightning*

Those shady GMO plants, what with their complete carotenoid biosynthetic pathways and their home-made defenses against invasive species. Thinkin theyre all hot 'feeding starving people.' I mean look at this guy! What a little snot!

Looks like the usual suspects could have a new buddy. In a recent PNAS paper, a group of Frankensteins playing GOD figured out how to get rice to take up Fe3+ again by MUTATING the rice genome. A long time ago, the ancestor of rice could take up either Fe3+ or Fe2+ from the soil it was grown in. It only really wanted the Fe2+, but it figured out how to make it out of Fe3+. Modern day rice is grown in rice paddies where Fe2+ is abundant, so it lost the ability to take up Fe3+. Meh, no big whoop. Like salamanders/fish in dark caves that have 'lost' their eyes- If you dont need a gene and you lose it through mutation, meh!

Except... what if you need to grow rice in a low-Fe2+ environment? I mean not every farm is as rich as the Missouri River bed-- you just have to grow food where you can, so you just end up with sick, low yielding plants. Its the best you can hope for. Or is it?

Like in their lost-a-trait cousins, all the right parts are still in the rice genome for taking up Fe3+. These guys just mutated the rice genome back to its ancestral state, and hurray! Rice can grow under low Fe2+ conditions again! Man could you imagine GMO rice with this gene AND the ability to make Vitamin A?

Start painting your protest posters now!

**I realize there are valid complaints against GMOs. However the hysteria over GMOs is scientifically unfounded (eg Frankenstein glowing man eating plants). Read more over at Conspiracy Factory!

April fun! YAY!

April doesnt totally suck! Dad, bro, like 17 of my 293 Baptist cousins have birthdays*, first human in space and tons of other cool space events, Earth Day and Arbor Day, start of the American Revolution, the Curies isolated their first bit of radium, first cell phone call (1973 LOL!), James Watsons birthday, American Natural History Museum opened, Kodak cameras, roller skates, TV dinners, and Twinkies were invented! TWINKIES!

*My birthday is tomorrow too. I know I only have like 4 regular readers, but I expect you guys to type out 5,000 birthday messages for me so Dawkins will be jealous :P

Thursday, April 19, 2007

April fun. Ugh.

So I swear there are some good things about April, but with the Virginia incident, OKC bombing, Branch Davidian mess, Lincoln and MLK Jrs assassinations, Hitlers and Pope Benedicts birthdays (zing!), 1906 earthquake, Titanic sinking, Rodney King verdict riots, Columbine, Chernobyl, um, Im sure Im missing some.

So heres a depressing anti-theistic video to... depress you some more...

Ive always had a fancy for mismatched scenery/music. Like video footage of us bombing Iraq with 'Dancing Queen' playing in the background. Ugh but no one gives ABBA a blank check as an answer to The Problem of Evil. Heres a link to the fellow who made this video, and if you need cheering up hes got some great smackdowns of the ID Creationist Carnival.

I swear tomorrow will be better :)

Wednesday, April 18, 2007

ID vs ERVs-- Part 7: This is never going to end, is it?

This next post covers the first 6.5 pages of Sternbergs groundbreaking paper on 'junk DNA' and 'epigenetics.'

So groundbreaking, in fact, its release upon the earth in the year 2002 created a black hole in New York which sucked this paper into The Void. You and I went about our daily activities for 5 years, not knowing this beautiful paper existed. But through means unknownable to modern man, with our clunky 'materialistic thinking', Sternbergs paper finally reemerged in our dimension through the brain of Sal Cordova. Behold its beauty!

For a 'biologist' (**WINK!**), Sternberg doesnt seem to mind replacing things he personally doesnt understand with magic/philosophy/incorrect logic/BS. Take this classic misrepresentation of epigenetics:

"This belief, namely, that DNA=genome and that genome+developmental program, has nonetheless been seriously thwarted by the realization that chromosomal sequence data must be placed into the framework of epigenetics. The paragenetic function of chromosomes is also apparent. But all of this is an indirect admission that the DNA=genome=developmental program formula is incorrect in principal."
No. Epigenetics does not 'thwart' the idea that your genes make you. Epigenetics is an evolved mechanism for controlling gene expression, just like siRNA. Just like positive/negative feedback loops. How does Mr. Black Hole think epigenetic landscape changes are mediated? Sing along everyone, you know the words: MAGIC! YAY!
"Where is the decision-making locus (sensu lato) that determines with messenger RNA (mRNA) will arise from RNA editing and/or alternate splicing of hnRNA (heterogeneous nuclear RNA)?"
Oh dear. 'Decision-making locus'? Ugh.
Lets look at a nice small genome for an example of how mRNA isnt magic. How about HIV:OMFG! The HIV genome contains overlapping/alternate splicing! Look at all those overlapping genes!! HOW DOES HIV DO IT???? How does it KNOW how to splice????

Positive/Negative feedback. See? No magic required.

After listing a few more equally idiotic 'subquestions' (dont ask, I dont know whats up with 'subquestions'), he finally brings up ERVs.
"One sub-question looms so prominently that it desrves immediate attention, namely: what is the function of the repetitive DNA fraction of chromosomes?"
The function? Dont you mean 'what are the functions'? Surely he doesnt think all repetitive DNA only has one, THE, function? Ah, but he does! They all have A function, or they all have NO function, NO other options! He breaks scientists down into three groups:
  • Selfish DNA Narrative
  • REs are integrally functional components of the genome, cell, and epigenetic process
  • Appeasers (lol)
Guess which group ID Creationists fall in! Every little sperm/base pair is sacred!

Group 1 is made up of those evil Darwinists and Neo-Darwinists. Selfish DNA, he says, is 'an endless source of just-so stories.' These Neo-Darwinists who say RE have no function, theyre only selfish bits of DNA, are so prevalent he had to go all the way back to 1980 for a reference. Thats like saying Aristophanes was stupid because he didnt know how to use a computer. Lame. But you know ID Creationists, if they couldnt beat up their straw men, theyd have no one to beat up at all.

Group 2. Ah, angelic Group 2! They understand that REs are integral (his word) parts of 'the software system.' Common, you didnt think youd get to read an ID Creationists paper without an inappropriate analogy, did you? Mr. Black Hole then laments this group has few proponents, mostly 'theoreticians with a commitment to explore the possibility of integral function.' ROFL! All the scientists that figure out an RE has a function are tainted by Group 1 and create Group 3.

The last group is made up of Save-able scientists brainwashed by Neo-Darwinists-- The appeasers. Some REs have been cooped by their host genomes (Mr. Black Hole speaks of this option with obvious disdain) for direct use, a different function entirely, chromosomal rearrangement, etc. And, some REs are just plain old garbage. Seems reasonable, right?

WRONG, dear readers! This stance is 'tepid'! Either REs ALL have A function or they ALL have NO function, says Mr. Black Hole! Jesus, readers, grow a pair! Take a stance! ALL OR NONE!


Cause thats how biology works, right?

Up next: 'Part Eight: Nothing Escapes the Black Hole of ID!'

Tuesday, April 17, 2007


This is why I think the 'Frame' is absolutely retarded! Read me! READ MEEEEEE!!!

Censorship at Darwin vs. Design conference

Below is a dialogue through e-mail between Ken Ueda, Sarah Levy and Dr. Wise from 4/11/2007 6:43 p.m. - 4/12/2007 5:20 p.m..

Ken to Dr. Wise:

Hello Dr. Wise. I hear good things about you among my peers. You seem to be very well liked. I stopped by your office earlier today but unfortunately you were not there. I was talking to Dr. Scalise in the physics department and was wondering (since I hear no professor plans on debating against the Discovery Institute) if I were to be able to speak among those 15 minutes that they plan on giving us. I plan on not debating against the Discovery Institute (as this would seem to suggest that I am giving them the same epistemic worth of legitimate science) but giving a speech on the history of Intelligent Design (such as the Dover Area School District trial). I fear that many of my peers may actually believe some of the terrible arguments that the Discovery Institute plans on talking about and since I know that no professor would have anything to do with the conference, I would like very much as a student to be able to speak to the public. I promise it will be in good taste. Thank you.

-Ken Ueda '09

Math, Physics, Philosophy Major

Dr. Wise:


I don't control who gets invited to the DI's event, so I cannot say you can do it. You would have to ask the organizer or perhaps Sarah Levy ( of the Christian Legal Society. Ms Levy invited the DI to come here. There are some biology students who also may attend. I will talk with them today.

Best regards,

J. Wise

Ken to Sarah Levy:

Howdy. I have heard that the Discovery Institute has supposedly invited some of the faculty of SMU to debate against intelligent design. I have also heard from members of the SMU faculty that none of them plan on attending so I was wondering if I may speak on their behalf. All I ask is for really a small amount of time on stage so I may refute their claims and I think that isn't too much to ask since the conference is 2 days and I'm sure they will have plenty of time to argue against me.

-Ken Ueda '09

Sarah Levy:

Mr. Ueda,

I am not in charge of the schedule of events, but have forwarded your message on to those who are in hopes that they will contact you shortly. May I ask if you are a faculty member, or are somehow connected with the university?

Thank you,

Sarah Levy

Ken to Sarah Levy:

I am a student of SMU.

Ken Ueda '09

Anika Smith:

Dear Ken,

Sarah Levy sent your question to me this afternoon regarding your request to debate the speakers for the Darwin vs. Design conference. It is true that we invited representatives from the anthropology, biology, and geology departments at SMU to debate our speakers as fellow scientists and peers. These men are on even footing in education and experience, and we invited them to help illuminate the debate between Darwinism and Design. They have declined to engage in the debate.

These departments were challenged because they had called for the conference to be removed from campus. We wanted to see them put their money where their mouth is, so to speak. While I understand your desire to present your view for 15 minutes, the format does not allow the time or the patience for the audience to do so. I suggest that you attend the conference with your questions and really stick it to the speakers during the Q & A, if you like. Encourage your friends and anyone else who is concerned (including the professors who chose not to debate) to do the same, and hopefully the Q & A will be engaging and provocative.

Whatever you decide to do, I sincerely hope you continue to pursue these questions and wish you well in your education.


Anika Smith

Ken to Anika Smith:

Well that is strange because I believe the reporter from the Dallas Morning News revealed that the Q&A session will be pre-screened. If this is true, I wonder how is it even possible to "really stick it to the speakers" if they are able to dodge the more important questions. It is not just the faculty who believe that the conference should have been removed from this campus but the students as well so I as a student (and I should say at least a somewhat educated one) should be completely adequate to represent this opinion.

-Ken Ueda '09

Anika Smith did not reply back.

So who's doing the censoring?
THIS is a real problem with science communication! THIS is what we need solutions to! HOW are you going to attack a student for 'not leaving his Ivory Tower' to address the Creationists on his back porch when he tried to? HOW are you going to attack a student for 'not fraaaaaaming' his approach to this situation 'better'? HOW are you going to attack a student who never got a chance to 'fraaaame'?

ARG! *stomps off in a multicolored huge font all caps huff**

Ken Witwer eats Denier Culshaw ALIVE

And I helped!

See, Culshaw wrote this great expose on the HIV LIE (turns out you can uncover a massive world-wide multi-decade conspiracy in fewer pages than a Nancy Drew novel!) . I refused to buy the book and I couldnt find it in a local library (though Ill still read it if a Denier sends me a copy!), but Ken Witner had a firm enough grip on his sanity and temper to write a patient (though appropriately sharp) rebuttal to Culshaws claims. Cherry on top: he wrote it in a language accessible to Average Joe readers. I dont know Ken all that well, but Im really proud of this final product. Its beautiful.

Science Outsold? Correcting the falsehoods of Science Sold Out: Does HIV Really Cause AIDS?

Oh, and after he dismembered her claims, he delivered a bonus roundhouse kick to her ethics. Turns out Blondie plagiarized other papers/Deniers, and Ken could pick up on some of them through a casual reading.

An examination of Dr. Rebecca Culshaw’s scholarship

And you know how it goes with plagiarism-- for every phrase you catch, theres at least one you missed. Shes setting a great example for her students.

Its not every day you meet a timberwolf

I was strolling around town the other day with a friend, and we stumbled upon a timberwolf. Well, half timberwolf, half aikita.

Absolutely beautiful creature. And better manners than the Creationists Ive met down here too!

Sunday, April 15, 2007

Im done with the Frame.

After a comment on Pharyngula, my question as to whether Mooney and Nisbet are that naive has been answered.

Quotes are from Nisbet, Post#28:

The question is this:

Over the next five, ten, fifteen or twenty years, in a diverse and pluralistic society that has to reach collective decisions relatively quickly regarding political debates over global warming, the teaching of evolutionary science in science class (and only evolutionary science), stem cell research etc...what's the best way to engage the broader public by way of the media?

Our answer:

While remaining true to the underlying science, you have to recast messages in a way that connect to people's social identity. And yes, in the United States, that means connecting to people of diverse faiths.
Duh. Duh. Duh. Duh. DUH.

Do you honestly think this is news? You think youre bringing novel ideas to the table? What??

I guess this is our major difference in opinion. If I understand you correctly, you see this as appeasing religion. I don't see it that way.

Dawkins will always play an important role. As we write at the Washington Post, we agree with him on evolution and admire his books. Indeed, our credentials as skeptics and defenders of science are well established.
Here is a real problem, that you and Chris are either unable or unwilling to address. Brace yourself here: I am not Richard Dawkins.

I am a 5'8" chick with blue eyes, long brown hair, and (Ive been told) a *cute* voice, that wears polo shirts from Old Navy. Im not how most Christians/Muslims/etc would picture an 'atheist', so I can slide in cognito through even the most fundamentalist theistic environments.

And I have difficulty getting past the Iron Curtain gate keepers.

Stop enabling their behaviors by 'blaming' atheism. Oh, or even better idea, why dont you all focus your energies on solving the Iron Curtain problem, rather than pointing out the sky is blue.

One tool is to understand how to frame issues--not spin the facts--but recast a complex topic in a way that makes it meaningful to a non-traditional audience. In addition, you have to figure out the media platforms that reach these non-traditional audiences.
Like blogs. Like books. Again, thanks for that fantastic revelation.

As Ive said before, this blog is an outlet for my frustration at being stopped over and over and OVER by the Iron Curtain. Its currently the only way I can reach non-traditional audiences.

That means for example the religious news beat, entertainment media, blockbuster movies, targeted documentaries, and places on the Web where people are not expecting to find science-related information. It even means reaching people interpersonally, as I layout in my latest column for Skeptical Inquirer Online.
Fine. Ive already offered to help these endeavors. Wheres your script? Wheres your director? Lets go.

In these contexts, it is often most effective, to remain true to the science, but sometimes not actually talk about it.
We're just gonna pretend you didnt say that.

Not all of the themes addressed here can be sorted out in the blogosphere. After all, every medium has limitations. Indeed, Chris and I are trying to work across mediums--including magazines, newspapers, blogs, radio, and public presentations--to raise attention to what we see as a partial answer to a very specific question that a lot of people are trying to figure out.

We even want to go the old fashioned route and talk about it over beers or over the phone.
This is the phrase that would have made me throw my drink at you if we were 'talking about it over beers.'

Aw gee, Chris and you are trying to work across mediums. If only other people would take your lead! If only there were science magazines! If only there were science sections in newspapers! If only there were science blogs! If only there were science podcasts! If only there were science public presentations! If only scientists talked with their friends about science over beers and over the phone!

Lets raise our glasses to Matt Nisbet and Chris Mooney, True American Science Pioneers!

My question has officially been answered. Nisbet and Mooney are that naive.

ID vs ERVs-- Part Six: An Unexpected Epilogue

Check out this 'news' from my doppelgangers at 'Intelligently Sequenced':

A post at Uncommon Descent entitled, 'NY Academy of Sciences peer-reviewed paper acknowledges ID proponents,' contains the following remark:

"Most Darwinists erroneously predicted that 98.7% of the DNA was devoid of function (“junk”), while the ID/ET theory correctly predicted some yet to be decoded function of junkDNA."
Oh wow! NY Academy of Sciences! Well cool! Thats a real journal, not 'Medical Hypothesis'! So I click around, trying to find a link to this paper, and I accidentally give UD a hit. Seems they just posted on this topic too:
I’ve been delayed in reporting that a peer-reviewed paper in the annals of the New York Academy of Sciences by Richard Sternberg gives an acknowledgement to several ID proponents. In 'On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic-Epigenetic System' it says:

I also thank Drs. Paul Nelson, Stanley Salthe, Jonathan Wells, and Todd Wood (alphabetical order)for their very helpful criticisms of the manuscript.

Congrats to all those involved.

So I clicked around a bit more. When was this paper published?


ROFL!!! What the hell?? 'Delayed in reporting' is a bit of an understatement there, Sally Baby. And that 'Richard Sternberg' name sure sounds familiar... Hmm where have I heard this name before...

The Sternberg Affair! YAY!!

After a preliminary perusal of this groundbreaking 2002 paper (that has been ignored, even by ID Creationists), its exactly what you all would expect. Misuse of real words, use of non-words, no data, *yawn*

I wish I had found this before I started writing up my 'Viral World' posts-- I would have held off on those. And Ive still got to fisk Horowitzs 'peer reviewed' paper. Ak! lol!

Saturday, April 14, 2007

Okay, Chris, Matt-- Stop digging. Stop it.

Chris, Matt-- you arent making things better. I have no idea why you think this is "helping." Youve dug a hole, deal with it, but for the love of Pete, stop digging. Its getting painful for me to read this stuff.

Ive stated this same thing several times, and I think you all are missing it, so let me be very, very clear:
Saying stupid things like this-

If the defenders of evolution wanted to give their creationist adversaries a boost, it's hard to see how they could do better than Richard Dawkins, the famed Oxford scientist who had a bestseller with "The God Delusion." Dawkins, who rose to fame with his lucid expositions of evolution in such books as "The Selfish Gene," has never gone easy on religion. But recently he has ramped up his atheist message, further mixing his defense of evolution with his attack on belief.

Leave aside for a moment the validity of Dawkins's arguments against religion. The fact remains: The public cannot be expected to differentiate between his advocacy of evolution and his atheism. More than 80 percent of Americans believe in God, after all, and many fear that teaching evolution in our schools could undermine the belief system they consider the foundation of morality. Dawkins not only reinforces and validates such fears -- baseless though they may be -- but lends them an exclamation point.

...eables Creationists/Deniers/etc. You are not helping. Youre validating anti-science talking points ("Richard Dawkins is a MEANY!") instead of confronting them.

You say arguments like evolution-->immorality are stupid, but instead of cutting that argument off at the knees ("If evolution leads to immorality, why am I the one doing HIV and cancer research, while Good Christians are shuffling funds around to prevent victims of sexual abuse from collecting awarded funds? I mean certainly that doesnt mean theism=amorality, its just that your claim makes no sense."), you say "Dont be an 'out' atheist"?

What the hell?

Another weird comment:
In 2000 Americans didn't pore over explanations of President Bush's policies; they asked whether he was the kind of guy they wanted to have a beer with.
And more people would rather have a beer with me than Billy Dembski (probably including his ID buddies). Im sorry, Im completely missing the point, here. You keep saying "Oh I dont mean to dumb things down" but thats exactly what it sounds like youre suggesting with trite comments like this.

Another one:
Making complicated issues personally meaningful will activate public support much more effectively than blinding people with science.
Well thank you for the news flash. Thats exactly what I do, quote:
Another reason would be to get these kids to transmit this information to their parents. Like Ive said over and over and over, Average Joe Creationists slide right off that Creationist-Wagon when they realize how evolution is directly connected to their quality of life. Its not just about 'dogs turning into cats'-- its about Mom not having to go on chemo when she gets breast cancer because her genotype matches the cancer that can be treated with radiation alone. Its about inventing new drugs and vaccines to make our lives better. Get high school kids to write about these kinds of real-world benefits, and suddenly Mom and Dad dont mind evolution being in the curriculum anymore. Might even be inclined to start fighting against Creationism.
I dont know why Chris isnt believing me, but Im exactly the kind of scientist hes viewing riding in on a horse over the horizon... And Im having extraordinary difficulty getting 'the message' out through traditional means! Chris, Matt, you all are the one missing the point! Ive said it over and over and OVER! We have this mystical cadre of 'science communicators'. It already exists. But WE arent the ones being asked to speak about evolution/vaccinations/etc on CNN! Talk to your journalist buddies, buddy! Stop digging yourselves in a deeper hole, and stop validating anti-science proponents! Just stop!

Discrimination Against Blacks=24-Hour Outraged News Coverage. Discrimination Against Atheists=Meh.

Um so I got a message from David Mills last night telling me to tune into ABCs program 20/20-- My fellow Oklahoman Chester Smalkowski was going to have a segment on the horrors his family experienced when his daughter had the audacity, the audacity I tell you, to insist upon saying the Pledge before their basketball game instead of a creepy Christian prayer.

*note Nicoles friends giving her a hug afterwards... but they still said the prayer with everyone else anyway. Several of my best friends are theists, but I know they would have stood with me in protest.

Their family has been tormented from that day since, and you can read about their first-hand experience of Christian Love(TM) in 'Just Another Salem.' (for a taste of the Loving Christian(TM) view on terrorizing an entire family, check out this fine post! I cant tell whether this site is parody or not...). So I tune in, watch a segment on a guy who lives with wolves (used the opportunity to teach Arnie how to howl). Watched a segment on how THE SECRET to weight loss is weightlifting (to which I say 'duh,' but thats another post). Got ready to go out during the segment on Protestant leaders sexually abusing kids (In other news, dog bites man! Sky is blue! Music is good! More at 10!).

No segment on the Smalkowskis. You know, never mind this happened... 9 months or so ago? Never mind this incident is several orders of magnitude more horrifying than Don Imus saying 'nappy.'

Ugh. Looks like my open offer to CNN has extended to ABC. I hope David just got the dates mixed up, or it was a different Dateline/60-minutes/whatever show.

Thursday, April 12, 2007

The Ancient Virus World and Evolution of Cells: Part One, Intro

Hey how about a series of posts on some cool science, instead of clueless Creationists and megalomaniac Deniers? hehehe!

So we had a visiting professor come this week to give a few presentations-- Jim Van Etten was one of the first people to discover a Giant Virus (hes also a really great guy, even to a lowly pre-grad student like me). These guys are monstrous in viral and genome size, with some surpassing particle/genome size of organisms we would consider 'alive'! Giant viruses have turned the way we look at viruses upside down. 'De-evolved' creatures? Used to be bacteria, but lost the ability to reproduce on their own? Renegade bits of genome and protein?

hehehe Right. And histones dont do anything but neutralize DNA :P As our ability to identify and sequence new viruses increases, the hypothesis that viruses are ancient... maybe even ancestral to all life on earth... is starting to be taken seriously.

Humor me for a sec as I personify some inorganic molecules/viruses:
Okay, RNA world. Pool of neucleotides, proteins, enzymes and such, just floating around... Selfish bits of RNA protecting themselves with a protein coat could be what we call an RNA virus today. Then you could keep your RNA around longer if you stored it as a more stable DNA genome, with a little reverse transcriptase. Retrovirus? Still have a lot of mistakes with that, though, hmm-- How about keeping everything as DNA, all the time? Well there youve got a DNA virus.

But hey, this is science, not magic! We've got questions, we can use the scientific method to figure out answers (or get closer to some answers... or get more questions... but still, you go somewhere!). So Im going to go through a paper here that you all can get for free online:

The Ancient Virus World and Evolution of Cells

I picked this one in particular because Koonin is one of the Giant Virus dudes hehe Sweet.

Skeptic's Circle #58 -- I've got a whole lot of woo for you...

Yay! I took Kristjans advice and submitted to The Skeptic's Circle, and heres the latest edition!

Skeptic's Circle #58 -- I've got a whole lot of woo for you...

Wednesday, April 11, 2007

I no longer feel so alone!!

Oh I know you all probably read Pharyngula, but just in case you missed PZs endorsement of John Dennehy at Evilutionary Biologist, heres a link! PZ was happy for the Evilutionist company, Im happy about the virologist company!

John studies bacteriophages! You know, the sweet lunar lander guys! Ive always had a crush on bacteriophages, but its never been enough to pull me away from my syncytia :P

Tuesday, April 10, 2007

An answer better than that damn 'Frame'

Im glad to see Im not the only one who is still baffled as to the purpose of 'The Frame'. And Im glad to see Im not the only one trying to do something, and that others are better organized than I am.

An astute reader sent me a link to this kick-ass group (which is predictably British):
Sense About Science

Sense About Science is an independent charitable trust. We respond to the misrepresentation of science and scientific evidence on issues that matter to society, from scares about plastic bottles, fluoride and the MMR vaccine to controversies about genetic modification, stem cell research and radiation.

Our recent and current priorities include alternative medicine, MRI, detox, nuclear power, evidence in public health advice, weather patterns and an educational resource on peer review.
Maaaaaaaaaaaaan! I wanna join! Look at these cool pamphlets they have up for order/download:
Making sense of the weather and climate
Sense About... Homeopathy
Maaan even tips for celebrities speaking about science!

And look at this program, specifically for young researchers!

These are people Im going to go to for help and suggestions communicating science to the public.

They grow up so faaaast! **SOOOOOOB!!!**

My baby graduated from kindergarten tonight :(

When I first brought him home last December, teeny tiny and covered in scars:

Now, fat and happy:

Everyone go adopt a puppy.

Monday, April 09, 2007

lol! What would Jesus eat?

Haha! Perfect timing, on MSNs part! I was just about to write about God diets!

I went to a local health-food store this weekend to pick up some liquid vitamin goop. As some of you may or may not know, Im really into body building and powerlifting. Really. Me. And in the past 6 months or so, with the stress of moving/getting Arnie/running Arnie 6 miles a day/being sick... Ive accidentally lost 15 pounds. When youre already muscular-skinny, losing 15 pounds kinda makes you look like an anorexic Xena, so Ive been looking into ways of pumping more healthy calories into my diet. So, thats why I went to the health food store.

It was a nice little place, chock full of the overpriced snake oils that you come to expect from health-food stores, but I knew what I was shopping for. I could skip right past the liver flushes and prostate cancer cures. Made my way to the checkout for my overpriced liquid zoysia, and the kind ol shop keep put a ton of fliers in my sack (just in case there was some form of potion I didnt know I needed).

Thank GOD he did! Uuuuugh!!! As a fitness enthusiast, I really get angry at people like Dr. Phil/the Ab Doer/etc who take advantage of desperate people to make some $$$. Ugh. You know, the bb/diet industry is well known for their worthless supplements, but youd think 'Christians' would be above exploiting their 'beautiful faith' to sell crap to their fellow 'Christians'.

But hey, maybe they really do know what theyre doing! Lets see what they tell me to do to gain that 15 lbs back! Lemme fill out this little free health analysis! (Note, dont do this yourself-- the advice is shit and youll just get junk email too)
Okay, Question 1: "What is your main goal? lose weight, feel and look healthier, live a more spiritual life"
Hmm. Well, one and three are certainly not my goals. I guess 2? Wheres 'gain weight'?

Question 2: Erm, same question, in check box form... Not checking anything.

Question 3: "Which of the following is true about your lifestyle?"
"I'm usually in bed before midnight." Yup! And home by 1! Zing!
I have lots of relaxation time, I put red-heads to shame in the paleness department... uh oh. Not checking this next box is going to come back to haunt me "I incorporate prayer into my daily life." lol No!

Question 4: "Which of the following is true about your diet?"
hehehe Theyre going to hate this too-- I dont eat fast food or drink sugary drinks, but I eat non-organic food! GMO food! I drink a gallon of milk a week... milk from Wal-Mart! I am so screwed.
lol And I dont take a 'megavitamin' once a day. What the hell is a megavitamin? I bet Mr. Maker can sell me some megavitamins! Lets wait and see!

How is my health, according to God?
Good news everyone! Mr. Maker says Im doing great with sleep (I dont think the bot understood my joke...), relaxation, and sunlight! Alas, I need help with prayer :(

"Studies on the importance of prayer are becoming abundant. Hospitals across the land have bolstered their "prayer therapy" for the sick and recovering. By taking care of your physical and spiritual needs, you will be living the way that God intended. Let The Maker's Diet help you incorporate this vital element of health into your daily life."
Yeaaah, about that 'prayer therapy.' Um, it doesnt work. And when you tell a patient theyre being prayed for, they actually do worse than control groups. Turns out sick people freak out when their doctors ask complete strangers to pray for them. Yeah...

How is my diet, according to God?
OH I SO got pwned! I totally thought Mr. Maker was going to try to sell me megavitamins!
Vitamins and minerals that have not been incorporated into an organic matrix may actually be harmful to the body. It is better to supplement healthy food and beverage choices with living food supplements that are in a balanced form, which is easy for the body to absorb and utilize.
I TOTALLY forgot about the organic matrix! Duh! lol! Wait... waaaait.... BINGO! HAHAHA! I knew they wouldnt miss an opportunity to sell something!

Blech! Okay, some funny stuff from the article in my grocery sack-- When Mr. Maker first met his wife, he thought she was 'healthy' because she didnt eat chocolate. On the next page, 'Nicki' says that on one of their first dates, Mr. Maker brought her a box of chocolates, and she ate them all... Jesus doesnt have a problem with binging, evidently. Nicki, hon, eating an entire box of chocolate, by yourself, and telling everyone you dont eat chocolate, is an eating disorder.

Their list of things God doesnt want you to eat is really strange, too:
  • pork
  • shellfish and fish without fins and scales
  • hydrogenated oils
  • artificial sweeteners
  • white flour
  • white sugar
  • soft drinks
  • pasteurized and homogenized skim milk
  • corn syrup
  • hydrolyzed soy protein
  • artificial colors and flavors
  • excessive alcohol
Well, a couple make sense, Biblically. A couple make sense nutritionally. But... Jesus hates skim milk? Jesus hates soy protein? ROFL!!!

If any of you really want some diet/exercise advice, leave a comment-- Ill give you some tips for free, or point you in the direction of some reputable folks who can help. Even if youre Christian. Blech.

Sunday, April 08, 2007

Hey, at least theres a dialogue going on this issue now :P

Some have said that my reaction to the Nisbet/Mooney paper was 'hostile' or 'harsh'. Well folks, if you think its harsh, its because Im kinda ticked off. This 'answer' to the woes of our societies scientific illiteracy is stupid. There, I just said it. Its stupid. "Throw more scientists at the problem." Oh wait, not just scientists, scientists with super special training in the art of communication. (And boobs. And sweet bow staff skills. Wouldnt hurt if they also trained dragons. *rolleyes*)
Look, I went to a liberal arts university-- I took speech/communication classes, I took art appreciation classes, I took philosophy, I took writing courses etc etc etc. Certainly on this blog I have to fight the urge to type in txt spk, and I never use apostrophes appropriately, but outside of a 'How to Communicate Science' course, I would say Im the kind of *scientist* that is supposed to 'cure' this communication problem (complete with boobs, bow staff, and dragon).

And in my current environment, I feel completely ignored. What is making 200 more of me supposed to do? 200 more people to be ignored. Super. I mean are we to believe that I am the only scientist on the planet that already has these super special qualifications? Im the only person being ignored? Thats idiotic! This cadre of Super Communicator Scientists already exists, especially within my internet-video game-Red Bull generation! But we're being ignored, and we have very few outlets by which we can cut our communication teeth, so to speak. Our talents arent being utilized to their full potential. This blog has been a much needed stress-release valve for me.

Suggestions like Science Cafes and speaking at local schools are helpful. I didnt find the N/M article helpful. I kinda took it personally, though Im sure N/M only wanted to help. And Id love to have a post-presentation critique from Chris Mooney! I know I still have a lot to learn about public presentations!
But until I, or others, can slide past the Iron Curtain of ignorance that some desperately want (need) to maintain, I maintain my stance that if N/M really, really believe that our scientific illiteracy problem is a result of few 'good' science communicators, they are incredibly naive, and enabling the perpetrators of the real barriers to productive communication.

Friday, April 06, 2007

Nisbet, Mooney cant possibly be this naive

Okay, great, once again us hoity-toity 'scientists' in our Ivory Towers are getting lectured about how we *should* communicate with the public. Fantastic.


This is like an article in Dungeons and Dragons Digest*: "GUYS: 10 Great First Date Ideas!"

See, its all fine and dandy to give advice to scientists for speaking to the public... but if theyre never/rarely invited to speak to the public, what does it matter? Whats your point?

Ive been working my ass off trying to arrange little Wednesday seminars at local churches on why evolution is important since Ive moved to an area where Creationism is a very real problem. Ive approached radical churches, liberal churches, UU churches... Guess how many times Ive gotten to speak. Guess. Guess. Uh huh. Oh Ive never been shot down immediately-- they pretend theyre interested while Im standing in their church-- "Oh yes! Teach both sides! Sounds neat!" Then they stop returning my calls. Then they stop returning my emails. Then it would be stalking, if I bothered them any more about it.

Id like to think that when I do have the opportunity to address the public on some form of science, I do a decent enough job, but how about some real advice, journalist friends? How about some advice as to how to get invited to speak about science? Hell, Im at a major research institution, and the only after work presentation weve had is some jerk-off talking about 'God and Science.' I mean Jesus, Im a young, relatively attractive, cutesy female, and I cant get a science speaking gig around here. You think burly old professors get invited inside church walls to speak about evolution?
How about getting your journalist friends to talk to scientists when speaking about science, and not getting a fully loaded panel of idiotic Creationists/Deniers/Skeptics/Anti-Vaxers/etc with one actual scientist (who gets talked over the entire 'conversation')? Scientists arent in Ivory Towers, the people who need to hear what we have to say are behind Iron Curtains. You two cant be naive enough not to know this.

Considering the number of times Mr. Mooney has spoken in Oklahoma, Im not sure he is in the position to be giving the above advice, though maybe he will understand my point of view and my frustration. I dont need lectures. I need help getting my voice heard. THEN you can bitch about my communication strategy.

*I apologize for making fun of D&D. I know a lot of people think its fun, and they date just fine. Just trying to make an analogy.

[Insert Maniacal Mad-Scientist Laughter Here]




*lighting crash*

Ahem. Um, sorry, kinda excited about those pics. Erm, sorry about that... I cant tell you what these are yet, though some of you might be able to figure out the basics :) Once again, Im hoping these glowing buggars are going to start a knowledge revolution.

Thursday, April 05, 2007

Lazy Linking-- Funny Business

I have the best friends on the planet. One friend in particular is very very Catholic, knows Im very, very atheistic, and we both have a lot of fun with it (I do the sign of a cross before I drink cheap red wine, she gives me a Darwin Fish to put on my car when I turned 16, and so on). She just sent me an Easter present! (the link, not the shirt, lol!)

(Edit: I put the wrong link here before-- you all were totally missing the joke!)

HAHAHAHA! With a note: "My students asked me to buy this t-shirt. I thought of you. Who in their right mind would put a fetus on a t-shirt! Its not cute - its doesnt make me want to save it - it makes me want to run away!" It makes me hungry. Mmmmm... fetus.....**Homer Simpson drool**


After a recent series of events, spurned by the Harvard 'chaplain' of Humanism, Im questioning whether I am 'allowed' to still call myself a Humanist. I found this comic through Humanist Network News, but Im still going to keep reading it, even if Im not a True Humanist(TM).

And Im sure you all have seen these on Pandas Thumb and Pharyngula, but:

Wednesday, April 04, 2007

Moble Elements, Drivers of Genomic Evolution Part Deux

I didnt mean to make this a two parter (obviously, as 'Part One' was written several months ago), but I just came upon this article, and TEs impact on genomic evolution obviously needs another post. Its not just the TEs themselves that have directed the evolution of our genomes-- how our genomes have reacted to TEs has also had far reaching effects.

As my blogs subtitle goes, if we're made in Gods image, 'God' is made of gag, pol, and env. Up to 50% of our genome is made of transposable elements. Theyre egotistical bits of parasitic DNA that only care about themselves. Invite themselves into our genome, eat all our brownies, and leave the place a mess-- inserting themselves in protein coding regions, breaking chromosomes, rearranging genes and chromosomes, messing up splicing, and screwing up transcription levels.

So, how are we still alive right now? If ~50% of our genome is made of these bastards, how is everything still working? Cause our genome evolved ways to make 'God' shut up. Lots of ways, actually, as Ive alluded to in my posts to Creationists and Deniers that want ERVs, in particular, to be active.

RNAi - A cellular function probably almost as old as TEs themselves. Maybe... *maybe*... RNAi was initially 'invented' strictly for control of TEs, and was eventually co-opted for use by the cell itself. See, most TEs have a little inverted repeat at the beginning and the end of their genome, so a transcript would invert itself into an RNA hairpin-- exactly what dicers love to eat.
Experimental evidence of this control mechanism is that if you screw up RNAi proteins in eukaryotes, transcript levels of TEs jumps up. It also appears that C. elegans use the RNAi pathway as their main means of keeping TEs quiet.

Epigenetics -
Making changes to histones causes DNA to twist up around them tight, or loosen up. Keep your DNA locked up tight, and genes arent transcribed, including TEs.
You can also make DNA wrap up around histones tighter by making little changes to DNA, called DNA methylation. Again, keeping the DNA wound up tight keeps the transcription machinery from getting in and making TE transcripts.
And, you can use chromatin remodeling proteins (like SWI/SNF in plants) to alter the structure of your chromatin, changing the loops and supercoils of your double-stranded DNA.

RNAi AND Epigenetics, Wondertwins, UNITE! - In some eukaryotes, RNAi is required for chromatin modifications, like in fission yeast. Sometimes RNAi and chromatin remodeling combine to actually cut out TEs, like in Tetrahymena and Paramecium!

So I missed half the picture in that first post!