Monday, January 29, 2007

Lab Lesson of the Day: Check Your pHs

All last week I was trying to optimize my Western Blot procedure. This is what Westerns are supposed to look like:


This is what my Westerns looked like:



I was doing all of these elaborate set ups to figure out the problem. I tried other labs antibodies, I tried other labs blotting apparatuses, I tried other labs membranes, I tried different blocking agents, nothing was working! I mean, this is a really simple procedure, and I was just trying to get a cellular control (actin) to work! There was no reason for this to be so hard! I could teach a 10 year old to do this protocol (well, not 'me' technically because mine were screwing up, but still).

I figured out what the problem was today. I was mixing some other solutions, and I realized I didnt check the pH of my PBS. Its supposed to be 7.4. I measured mine: 4.7.

4.7.

*blink*

AAAAAAAAAARRRRRRRRRGGGGGGGGGG!!!

If you dont work with chemicals much and dont know what that means, think of it this way-- Its like trying to grow an oak tree on Mars. It just aint gonna work right.

So I tell my boss what the deal was. He was speaking with a couple other professors at the time. He turned to them and said, "ERV designed some wonderful experiments last week to diagnose why our Western Blots werent working, and she figured out what the problem was today. (turning to me) But thats not going to happen again, right?"

Hes a good boss :)

Friday, January 26, 2007

Because Im Young

Orac posted a nice little Bowie tribute to Mr. 99. I thought it was sweet, and certainly a representation of Oracs classy behavior in the face of Creationists, HIV Deniers, Holocaust Deniers, etc. However, Im still young enough that I can get away with a bratty snip every now and again, so I choose to be snarky now. Heres my dedication to Mr. 99.

Thursday, January 25, 2007

Creationists with Credentials

Would someone PLEASE teach Creationists how to use credentials properly.

Right: "You need computer help? Let me look at it, Im a computer science major!"

Wrong: "You need computer help? Let me look at it, Im a third degree WTF black belt and I breed golden retrievers!"

Real World Example from ID Creationists: "Im an MD and I graduated number one in my class and I scored in the 99th percentile on the boards, and I doubt evolution."

"WAAAAAAIT ERV!!" you might say. "That might not be wrong! Maybe he really does have valid scientific reasons for doubting evolution! Listen to what the man says!"

Okay, fine. What does Mr. 99 have to say for himself?

Perhaps you can explain, in molecular biological terms, listing the stepwise sequence of DNA changes (simplified, of course, so my poor moronic brain can grasp it), which occurred to bring about the development of a hand, finger, or knee from, say, the paw or limb of a lemur-like precursor (or whatever form you wish to posit as mammalian (making it easy on you; no need to go back to jellyfish or something which didn't even have limbs) ancestor to humans.

*shudder* Im sorry, why was there an obnoxious list of accomplishments before his little letter? They obviously mean nothing because Mr. 99 knows jack shit about basic biology. Basic biology. If you look on page 650 of 'Principles of Genetics' Edition 3, my introductory genetics textbook, you can figure out the answer to that devastating question, Mr. 99.
If a used textbook is too expensive for Mr. 99, as others pointed out in the thread at Respectful Insolence, you can even look up papers in PubMed. *blink* How can you be an MD and not know how to use PubMed? I mean, its no Google, but shit, dude!

UD specifically states
His example empirically disproves the false claims of Dawkins, Harris, KCFS, NCSE, and others who insinuate that exposure to criticism of the Darwinian orthodoxy will deteriorate scientific understanding.


No! No, UD, its a wonderful example of how Creationism turns you into a complete retard! You can have ALLLLL of Mr. 99s accomplishments, and you can still be mocked by someone half your age with half your education. And hes a role model for Creationist Kids? Hes not even being mocked for his beliefs (so he cant play persecuted martyr), he is being mocked for flaunting his credentials, then falling flat on his face.

Thats your role model, ID Kids. Thats your role model. You sure you wanna be an ID Kid?

Wednesday, January 24, 2007

Atheists Anthem



For me, great bands are like gods: All the good ones were popular 5000 years before I was born. The gods I love-- Led Zeppelin, Grateful Dead, Jimi Hendrix... theyre all long gone. Two of these bands are kings of Mount Olympus for me: Pink Floyd, and David Bowie. No one can compare to their song writing skills. No one can compare to their musical skills. End of story. But for the most part, theyre gone. They belonged to a different time... But at least Ive got their CDs and concert bootlegs. *sigh* I figured that no mortals would have the ability to tame Pegasus to join the pantheon, much less join the monarchy.

Boy, have I been pleasantly surprised by Muse. Proudly, openly atheists, but can still use religious themes to write kickass albums. Political songs that are vicious, without being preachy. And get this guys-- Totally into sci-fi and aliens and stuff.

If youre atheist, politically motivated, and dont think talking about aliens is odd, give em a listen. Support your local atheists :)

*sigh* I tried so hard not to be scary.

Man, the undergrad I was so excited about? She quit after two days. *sigh*

I tried so hard not to be intimidating, too! Normally I am kinda intimidating because I take my research very seriously, and if someone isnt pulling their weight, I take it personally. But I know what its like to be an undergraduate in a scary real-world lab for the first time. I know how hard it is to be a female in a male dominated field (she was a chem major) and I was really hoping to mentor her into a badass researcher like me.

*sigh* She is only a sophomore, and jumping into a lab at that age requires a lot of balls. Not everybody has them, I guess. *sigh* Well, we might be getting a summer undergraduate student. Those are kinda better anyway, as theyre usually juniors (WHOO! Know how to use pipettes!), and theyre in the lab all day (so they can do more fun experiments).

Ugh I had all these solutions for her to make on Friday, too. Arg...

Tuesday, January 23, 2007

Creationists Behaving Badly

Oh thank goodness! I thought Creationists behaving nicely was a sign of the apocalypse!

Looks like the Creationists in Drag cant take the heat from a 23 year old girl! OH BOO HOO HOO!! **LAUGH!!** Id also like to point out to the self-proclaimed "Neville Chamberlain" atheists that you can be painfully polite and stick to science with these people, and they STILL act like little brats. My comments were nothing if not congenial, and after I patiently wrote a huge post smacking down some very wrong things said in this UD article, Baby Bradford wouldnt publish that comment, though he published the two I wrote to his sycophants. He then promptly closed comments for the thread.

If these people cant impress a 23 year old kid, how are they going to overthrow Evilution again? lol Gawd theyre losers.

Conversation saved for posterity:

At 7:07 PM, ERV said...

There is a difference between endogenous retroviruses, Alus, L1s, SINES, etc, and you conflated each of these terms in your review.

Read this and try again:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15016989&query_hl=1&itool=pubmed_docsum

Sorry, all of the above are an excellent indicator of common descent.

At 7:21 PM, William Bradford said...

Hello Erv. I don't believe I "conflated" the terms if by that you mean that I gave the impression there was no distinction between them. One of the studies stated the following:

"These results have major repercussions for phylogenetic analyses based on SINE insertions, indicating the need for caution when one concludes that the existence of a SINE at a specific locus in multiple individuals is indicative of common ancestry. Although independent insertions at the same locus may be rare, SINE insertions are not homoplasy-free phylogenetic markers."

The paper does not exclude the possibility of a common descent inference. Rather it calls for a cautious approach when the data indicates this to be the prudent course. I've encountered reckless "extremists" representing different points of view who rush to judgement in spite of the particulars that make each instance unique. I'll take a look at your reference though.

At 1:02 PM, ERV said...

Yes, I believe you did conflate terms. For instance, immediately following the quote from TO on nonfunctional endogenous retroviruses, you began discussing Alus. I can whole heartedly assure you that while portions of endogenous retroviruses are functional, you do not want fully functional ERVs. That would guarantee body-wide cancer.
Alus do indeed have a function-- as their sequence similarities added to our chromosomes' ability to rearrange and duplicate, but they are in no way absolutely necessary. I have Alus you dont have. A kid in India has Alus we dont have. The same goes for LINES.

You then go on to conflate ERVs with SINES in the article, and again here in the comments. I realize you arent a retrovirologist, so they all look like bits of DNA hopping around, however they all behave differently. That journal I listed before can help clarify the differences between different kinds of mobile elements. Additionally, I know of no one who only uses SINES for constructing phylogeny (especially in mice), but if there is difficulty at a node, taking a closer look at SINES (among other variables) would be a good idea, due to the behavior of SINES.

And, as far as the last paragraph goes, that viruses were around before cells is not a novel idea invented by ID or writers on UD. Please look up Patrick Forterre. However, I still dont see how any of this is in any way an argument for Intelligent Design, or an argument against evolution.

At 6:45 PM, William Bradford said...

Conflate- to combine (as two readings of a text) into a composite whole. The format followed was the sequence laid out in the linked UD article and my comments were linked to the sequence of comments made in that article. ERVs were frequently cited in discussion groups focused on evolution and intelligent design. The archives of many Yahoo groups are public record. It was not uncommon to encounter the cliche argument that the existence of non-functional elements in a genome was both expected of an evolutionary process and an indication that a designer would have to be stupid to so design life that way.

At 5:47 AM, ERV said...

William Bradford: It was not uncommon to encounter the cliche argument that the existence of non-functional elements in a genome was both expected of an evolutionary process and an indication that a designer would have to be stupid to so design life that way
Thats a false dilemma.
Your god could have put ERVs and various other mobile elements into organisms' genomes to lead humanity to the obvious conclusion of descent with modification. I can see why it wouldnt want to include molecular genetics in the Bible, and why it would trust in our eventual technologies and abilities.
Im just having more and more problems with your, and the UD post, every time I read them. They are positively riddled with errors, but again, I dont blame that on you, because mobile elements are pretty alien to non-virologists or non-geneticists. But yet again, to suggest that mobile elements dont point to common descent with a flashing neon sign is silly, and I dont quite see the point of these articles.

At 9:07 AM, Nathan Munson said...

Yes, I believe you did conflate terms. For instance, immediately following the quote from TO on nonfunctional endogenous retroviruses, you began discussing Alus. I can whole heartedly assure you that while portions of endogenous retroviruses are functional, you do not want fully functional ERVs. That would guarantee body-wide cancer.

No kidding Erv. Nice strawman. It was nowhere suggested that William would want fully functional ERVS.

Alus do indeed have a function-- as their sequence similarities added to our chromosomes' ability to rearrange and duplicate, but they are in no way absolutely necessary. I have Alus you dont have. A kid in India has Alus we dont have. The same goes for LINES.

And your point is what? You can beat up strawmen?

And, as far as the last paragraph goes, that viruses were around before cells is not a novel idea invented by ID or writers on UD.

Neither William nor UD claimed to have invented the concept. Is imputing motives and statements to others that are not factual, a habit of yours?

At 9:19 AM, William Bradford said...

William Bradford: It was not uncommon to encounter the cliche argument that the existence of non-functional elements in a genome was both expected of an evolutionary process and an indication that a designer would have to be stupid to so design life that way

Thats a false dilemma.

No, it's a false argument. It makes no more sense than the argument that a designer would be stupid to design the inevitability of death.

Im just having more and more problems with your, and the UD post, every time I read them. They are positively riddled with errors,

If they were riddled with errors you would have pointed out something more substantial than "conflating." Given that most of my post referenced research papers and UD quotes where are the errors?

At 9:34 AM, Cephus Rocks said...

I can see why it wouldnt want to include molecular genetics in the Bible,

You can see why a historic book, meant to instruct on moral precepts and reveal God, would not want to include molecular genetics? Then again if that subject matter were included, prebiotic pathways to a genome would have been too; don't you think?

As an aficionado of books by Dawkins maybe you can shed some light on this UD quote:

"DNA researcher Andras Pellionisz has found unwitting friends in the ID community. He observed that while Darwinists like Richard Dawkins are dismissive of his field of scientific research..."

Was Dawkins dismissive? If so why?

At 7:42 PM, ERV said...

Nathan Munson: No kidding Erv. Nice strawman. It was nowhere suggested that William would want fully functional ERVS
I believe it was. Immediately following a paragraph from TO saying ERVs are not fully functional, William Bradford said:
"The next reference is further evidence cautioning against the assumption of dysfunction."

Clearly indicating that Mr. Bradford would like someone to discover a fully functional ERV to support his other assertions that all DNA is useful.

Nathan Munson:And your point is what? You can beat up strawmen?
Mr. Bradford seems to think that Alus are functional and necessary, given his citations in this article.
Alus are useful for things like duplicating an arm of a chromosome and alternate splicing and such, so over a long period of time they are in retrospect 'necessary' though at the time they were not.
The fact that you and I have different Alus illustrates that point. If all Alus are necessary, one of us would be dead. In a few million years, maybe your Alu will co-op something fun, and not having your Alu would be deadly.

Nathan Munson:Neither William nor UD claimed to have invented the concept. Is imputing motives and statements to others that are not factual, a habit of yours?
To the casual observer, it absolutely looks like this is an idea invented by ID, and look at the silly Evolutionists that didnt know.
I realize that blog writing is very casual. If Mr. Bradford did not mean it that way, Im sorry. Perhaps me pointing this out will help better your alls writing skills so this sort of confusion is prevented in the future.

At 7:57 PM, ERV said...

Cephus Rocks: You can see why a historic book, meant to instruct on moral precepts and reveal God, would not want to include molecular genetics? Then again if that subject matter were included, prebiotic pathways to a genome would have been too; don't you think?
*laugh!* Could you imagine how thick it would have to be to include all of that?? LOL My biology books would add a good 50 lbs at least, and theyre paperback! Ugh add in all the physics and chem... I would have hated to be the guys making copies of the Bible before the printing press!

Cephus Rocks: As an aficionado of books by Dawkins maybe you can shed some light on this UD quote:

"DNA researcher Andras Pellionisz has found unwitting friends in the ID community. He observed that while Darwinists like Richard Dawkins are dismissive of his field of scientific research..."

Was Dawkins dismissive? If so why?
Im afraid I was not present when these two individuals met, so I have no idea whether Dr. Dawkins was dismissive, much less why he was dismissive or not.
Perhaps it would have been prudent for Dr. Pellionisz to ask Dr. Dawkins himself if he felt slighted? That certainly would have made things easier.

At 9:03 PM, Nathan Munson said...

William Bradford said: "The next reference is further evidence cautioning against the assumption of dysfunction." Clearly indicating that Mr. Bradford would like someone to discover a fully functional ERV to support his other assertions that all DNA is useful.

Cautioning against the assumption of dysfunction does not equate to wanting a discovery to support an assertion that all DNA is useful. Worse yet Mr. Bradford did not claim that all DNA is useful. In making that allegation you are lying. Anyone reading the post can see you are putting words in his mouth.

Nathan Munson:And your point is what? You can beat up strawmen? Mr. Bradford seems to think that Alus are functional and necessary, given his citations in this article.

That's an unwarrented assumption on your part. He does not believe that and the "evidence" you cite reflects your projections.

If all Alus are necessary, one of us would be dead.

There was never a claim to the contrary. As I've indicated you are good at demolishing strawmen.

Perhaps me pointing this out will help better your alls writing skills so this sort of confusion is prevented in the future.

The confusion is a creation of your mind. You need a remedial reading comprehension course or a course on ethical behavoir depending on the source of your problem.

At 2:23 AM, Cephus Rocks said...

Cephus Rocks: You can see why a historic book, meant to instruct on moral precepts and reveal God, would not want to include molecular genetics? Then again if that subject matter were included, prebiotic pathways to a genome would have been too; don't you think?

*laugh!* Could you imagine how thick it would have to be to include all of that?? LOL My biology books would add a good 50 lbs at least, and theyre paperback! Ugh add in all the physics and chem... I would have hated to be the guys making copies of the Bible before the printing press!

A description of documented prebiotic pathways to a functional genome would take up no space at all. If you had confimation of such pathways you would be Nobel eligible.

Cephus Rocks: As an aficionado of books by Dawkins maybe you can shed some light on this UD quote: "DNA researcher Andras Pellionisz has found unwitting friends in the ID community. He observed that while Darwinists like Richard Dawkins are dismissive of his field of scientific research..." Was Dawkins dismissive? If so why?

Im afraid I was not present when these two individuals met, so I have no idea whether Dr. Dawkins was dismissive, much less why he was dismissive or not. Perhaps it would have been prudent for Dr. Pellionisz to ask Dr. Dawkins himself if he felt slighted? That certainly would have made things easier.

The claim was that Dawkins was dismissive of a field of scientific research; not that anyone felt slighted. Regretably you have twisted the words of others since you began posting comments. You don't need to do that.

At 3:38 AM, William Bradford said...

This post is closed to further comments.

Sunday, January 21, 2007

Creationists behaving nicely

In contrast to my usual encounters with Creationists, William Bradford over at Intelligently Sequenced is being really nice about a post he did on ERVs thats just, well, really really wrong. I left a comment on this article, and though comments are moderated, he is being polite and letting my posts be published. Unfortunately, after reading that article several more times, in addition to the UD post he linked to, I keep finding more and more little mistakes. Technically, the UD post is terrible, hijacking basically all viral research and pretending it supports ID in an attempt to 'discredit' Talk Origins.
Im tempted to do a smack-down. Ive been in a smack-down mood.

But William Bradford has been nice, and Dr. Cook was most definitely not, so Dr. Cook gets to go first.

Saturday, January 20, 2007

Readers Decide! Whos the biggest asshole in this Denier article?

I cant decide who is the biggest asshole in this scenario. Ill just list all the characters and let you all decide.

Wangari Maathai - Nobel Peace Prize winner

WHAT, ERV? Why would you call a Peace Prize winner an asshole? Well, cause she spouts shit like this:

"Depopulation has been a pivotal agenda of the neo-conservative American Eugenics Movement, in order to 'free-up' resources for rich elites, and away from 'inferior groups'"

“Us black people are dying more than any other people in this planet [from AIDS]"

“Why has there been so much secrecy about AIDS? When you ask where did the virus come from, it raises a lot of flags. That makes me suspicious.”

Oh man! So HIV was invented by American Neo-Conservatives to kill black people!
Well, Ms Maathai, if you want to know where HIV comes from, try a little Google search. Hell, Ill cut out all the work for you and link you to the site, Ms Maathai!
LINKY!!!


But shes not an asshole just for saying stupid shit about science. Lots of people do that. Shes an asshole because she is an African woman that many MANY Africans, adults and children look up to! Does she have any idea how much damage she is doing?? To the stigma of HIV patients, to the treatment efforts of foreign workers (Tripoli Six, anyone?), and the research efforts of foreign workers as well. Yeah, your BLACK, Ms Maathai, and the people trying to help you are BLACK. And YELLOW. And WHITE. And RICH. And POOR. And YOUNG. And OLD. And you just told them ALL to FUCK OFF. Ms Maathai, you are an asshole.

Executive Intelligence Review - Looks like just a weird 'publication' like the 'Canadian National Newspaper'.
Hacks quoting hacks, how nice. I suppose they should be dismissed from being in the running for biggest asshole. But theyre still assholes. Yeah, there are low cost techniques to significantly reduce the spread of HIV. BUT THE HOSPITALS IN THE THIRD WORLD DONT DO IT. Tripoli Six-- Totally innocent, children were infected with unsterilized needles. My Irritating the CDC post.


Cheap ways to prevent HIV transmission are well known and taught. Why dont you all stop pretending like youve uncovered these AWESOME ideas and sit there and watch the hospitals sterilize their needles so it gets done? Thanks in advance.

Dr. Boyd E. Graves - A lawyer. A LAWYER.

Yes, the fine 'Doctor" is a LAWYER. A LAWYER who doesnt mind using the handle DOCTOR so retarded journalists think they have some sort of scientific training. Thats fantastic! Even the Creationist lawyers arent that brazen! His biography touts "THE MAN WHO SOLVED AIDS" (caps original).
Hey, Graves, you might not know this, not being a molecular biologist, or having taken a biology class since high school, but WE CANT MAKE VIRUSES. We dont have the technology to do that, sorry. How the hell would you even go about doing that without being able to sequence anything? We didnt know how to sequence DNA when HIV first emerged, much less to RT PCR! Youre an asshole, Lawyer Graves.

William Campbell Douglass, M.D. - A real doctor.
Oops! Hes still an asshole!
“The truth of the matter is”, Dr. Douglass further elaborates, “AIDS is a man-made disease; AIDS is not a homosexual disease; AIDS is not a venereal disease; AIDS can be carried by mosquitoes; Condoms will not prevent AIDS; And there are a least six different AIDS-related viruses loose in the world.”

Well, Dr. Douglass, you are an IDIOT. 'AIDS can be carried by mosquitoes'? Really? AIDS? You dont mean HIV, you mean AIDS? A mosquito can carry a syndrome? Dumbass. Lets pretend you meant HIV. Is that why all the HIV aid workers have come back with malaria, but not HIV?
And you arent faring much better than the Dr. Lawyer. How ya gonna make a virus, Dr.? How ya gonna do it if you cant sequence? How ya gonna make a retrovirus? Idiot.
And condoms dont prevent AIDS? Right, condoms prevent HIV infection, which prevents AIDS. Ugh, lets pretend you meant condoms dont prevent HIV infection. Really? Cause I only wear a pair of latex gloves when I work with virus. I dont have AIDS. Im not infected with HIV. Oh, but by all means, asshole-- spread that rumor so people dont wear condoms.

Unknown person - Possibly journalist, bad referencing
"It is very strange. Because Gallo, Montagnier and those other virologists know that the AIDS/HIV virus doesn’t occur naturally in monkeys. In fact it doesn’t occur naturally in any animal."

No, HIV doesnt occur in 'monkeys'. Its HUMAN immunodeficiency virus, tard. 'Monkeys' get SIV. Cats get FIV. Cows get BIV. This source doesnt compare to the other assholes, I just had to correct that idiotc remark.

Toni Lawson - Irresponsible journalist who wrote the article.
Now, I would be willing to forgive a journalist for this sort of thing. Sure, its irresponsible. Sure, its pretentious. But I dont expect every journalist on this planet to know enough science to know better than to publish shit like this.
Heres the problem. I left a comment, as you are encouraged to do. It was along the lines of "Wangari Maathai has no education on virology to speak of, this article is a slap in the face to people all over the world who have dedicated their lives to curing HIV infection, and that the author should be more responsible in the future."
Turns out that comments are moderated. So, time went by, I kept checking the page, and wouldnt ya know, my comment never showed up! Well, maybe they have some intern approve the comments, but he really just sits there and plays World of Warcraft. But funny enough, a comment from Edward Haslam, a professional Denier, in full support of the article!
Well then, Toni, youre officially in the running for biggest asshole! On the bright side, I only found this article because I have 'HIV' in my Google News, so this idiotic piece will disappear in time with the 'crop circle' and 'alien' articles. Have fun being a nobody, asshole.

So Im tired. Thats all Im going to write-- so I leave it up to the two people who read my blog: Vote for the biggest asshole.

How to wake a hibernating bear: Lesson 1, Dont wake a hibernating bear

This blog has been slumbering for a while. The end of October and all of November, I was freaking out over applying to graduate school.

December, I accedentally adopted an American Staffordshire puppy. We had this huge ice storm the beginning of the month, and we got two days off of work. Work is ALL I DO, so I was bored out of my skull. Luckily, the gym was open, so I trekked on over. Outside, I was greeted by this adorable little puppy! Now, sometimes people take their dogs to the gym, tie them to the bike rack while they work out, and run with them home, so I told the gym workers "Hey! Someones puppy got off of his leash!" They were like "Nooo.... that puppy has been out there for days..." Like I said, this was during a snow storm big enough to shut down the University... it was terrible outside. The gym workers were going to call a shelter for him, they couldnt let him stay out in that weather any longer. The problem is, this puppy was an AmStaff. AmStaff=Pit Bull to shelters, and pit bulls arent adopted out. No matter how sweet they are, theyre killed.

So I bawled through my entire workout, walked downstairs, and ask if anyone has a rope so I can walk him home.

And, all January Ive been working my ass off at work, because this special facility I have to use to do all my viral work was finally open the first of January, after being closed for two months to fix a friggen vent. UGH!

All these stories end well:
1--"I am happy to report that the admissions committee for Microbiology and Immunology has accepted you into our graduate program."

2--


3-- Work is going at light speed now-- we might have a new cohort for studying differences in HIV transmission, a vital experiment for our cancer project turned out better than we could have imagined (we might really be on to something), and we got an undergrad to help me out around the lab with little things (doing dishes, making solutions, passing cells-- little things that take up 1/3 of my week).

WHOOOOO!!!

So, what had the ability to rouse this blog from its slumber? The election results? No! The crappiest season of 'Americas Next Top Model' ever? No! To quote Penn and Teller: This asshole. And this asshole. Posts coming up.