brb, sry

Sorry, guys-- family emergency this weekend = no blogging.

Glad I am not a physician, glad other people are, and nurses are the best people on Planet Earth.

While Im sitting here in the ICU, Id really appreciate some funny videos/links/anything to distract me. Everything is fine (fine-ish?) now, but Im going nuts. Everything is taking longer than the physicians initially said (not for 'bad' reasons, just because shit doesnt always go as planned), and when you combine that with my natural impatience, and my extreme frustration in situations where I cant do anything (Im a doer, not a talker, especially not a sit-and-waiter) I am going fucking nuts.

(might do some posts on genetically manipulating humans to fight HIV-1 and endogenous non-retroviruses in bats just to distract me later)

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Skeptics of Oz was great-- Sean Gillespie asked me if I had any requirements/requests to speak, I gave him my usual rider: Sean didnt just fill a brandy glass with brown M&Ms... He filled huge Richard Dawkins Foundation coffee mug with brown M&Ms! AWESOME! Sean was just a fantastic…
Endogenous retroviruses are weird, but how they got into our genomes and what they mean, evolutionarily, isnt too hard to understand (unless youre an IDiot). A retrovirus has to not only accidentally infect a germ-line cell (sperm/egg), that particular egg/sperm has to successfully mediate…
I guess Im going to have to change the name of 'ERV'. Before I was just concerned. Now, ERVs are officially not so special at all. Viruses, all kinds of viruses, are all over the place in genomes-- from insects to humans. Endogenous Viral Elements in Animal Genomes Carl Zimmers take: Your inner…
Time will explain it all. He is a talker, and needs no questioning before he speaks. - Euripides

I'll try to find you some good shit later today, I don't have anything in the till right now. :(

If I understand correctly you are a dog person but perhaps you would enjoy Procatinator, anyway:

http://procatinator.com/

I wish you well.

If you haven't already been there, done that, Angry Birds is an excellent timewaster.

Hope everything turns out well.

So what do you think of the recent announcement by Roche Germany about them finding XMRV in 7/8 CFS patients using Next Generation Sequencing (which is not susceptible to contamination)?

Take your time responding..I am sure you have a ton of egg on your face to wipe off.

>dancing in the endzone

I'll leave the virology to Abbie, but from what I can see: 1.) the study was not actually sanctioned by Roche and 2.) it's a fairly poor looking study from and exclusively statistical perspective, with unbalanced target and control groups and extremely small sample sizes and 3.) it conflicts with all the other research except Mikovitz's.

Wishing you and yours all the very best, Abbie/ERV, and I hope things conclude as successfully as possible.

Tyler..what makes you think it wasn't sanctioned by Roche? Didnt they use Roche's equipment?

Sue, the institution's name isn't attached to the study in any of the stories I've read, even if the equipment is used. I also couldn't find any press release mentioning the study in their website's media archive.

Tyler, I am just not sure how the equipment could be used without Roche being involved. Hopefully, we will hear more soon.

Sue,

Just my opinion, but it feels tasteless of you to post that here given there are appropriate threads elsewhere on this blog to post it.

The claim doesn't âread rightâ to me; it reads like a badly written PR piece.

As far as I can make out on short noticeâcorrect me if Iâm wrongâthis originates from an oral presentation at an IACFS/ME meeting given by Dr. David Strayer who is listed as the âMedical Directorâ of Hemispherex Biopharma, and it is his work he is reporting (i.e. not something âdone by Rocheâ). Mikovits also is listed as a speaker at this meeting, FWIW.

There is some sort of webinar on the company website, but you have to register to view it; Iâm not about to.

Strayerâs company appears to be involved in a legal standoff with shareholders over a claim of FDA approval to conduct a trial on âan experimental drug being developed for the treatment of chronic fatigue syndromeâ, which, apparently, the FDA has not approved at the time. (Iâm guessing the shareholders bought stock based on the claim of approval and are peeved on learning itâs wasnât true or something along those lines.)

I am just not sure how the equipment could be used without Roche being involved.

Usually you just buy the equipment and use it as you want to, like buying anything else.

Funny links you say? You should check out fark.com

By tripencrypt (not verified) on 08 Dec 2011 #permalink

Grant..given the fact that the owner of this blog routinely calls dr. mikovits a "c--t", being tasteful is not something i am worried about.

Tyler...now if XMRV was indeed found in human blood samples using next generation sequencing, isn't sample size sort of irrelevant? I mean...if XMRV is defintely not a human pathogen but a contaminant, it would not be found even once using this method, right?

I have more Iâd say, but it seems to me that you are âhijackingâ the thread.

Grant..cant blame you for mistrusting strayer or anyone at Hemispherex

it was my impression that Roche actually conducted the tests...perhaps a publication will be out soon.

Like I said, I'll leave the virology to the virologists and others with relevant expertise. I was only commenting on the statistics, which is my area of expertise.

Sue,

I'm finishing my PhD at a university with one of the US's main sequencing centers. Next gen sequencing is not only susceptible to contamination from sample/library prep, but it's known to happen and is not that uncommon. The primary application of NGS thus far has not been as a diagnostic, though, so it's been less of an issue thus far.

I say this from the perspective of having been involved with tech-dev teams here for Solexa (before it was purchased by Illumina, and after that purchase, as well), Ion Torrent, and have talked to people involved in method development for Pac Bio and SOLiD. I'm not just blowing smoke. Roche NGS is likely 454 or maybe Nimblegen? I'm legitamately curious and yet I can NOT find the primary disclosure of these data anywhere. Do you happen to know where this was announced/published?

Anyway, given that it does happen, what does it mean when you find the needle in the haystack with that frequency? Well, you ask the next set of questions: what was the relative representation? Were they in the healthy controls? I was able to find 2/17 healthy controls had XMRV. So those numbers look better but I can't find a primary source, only other ME/CFS forums. Where is this data coming from? I want to see the paper or the press release that it comes from, because I have other questions about the sample / library prep. IF it came from samples from the WPI that could have been contaminated, then NGS is irrelevant. How were these data collected and prepared is still issue 1.

My favorite part of the article I saw so far is this gem:

NGS is not susceptible to mouse contamination and demonstrates that XMRV is in fact integrated into human DNA which means it is a human virus.

and

I expect that Next Generation Sequencing or NGS, which does not have the flaws of PCR technology in evaluating a poorly understood human virus(es), will be the best way forward to a consensus as to the question of association of CFS with XMRV/HGRV.

Except for, you know, pretty much every single method for sequencing requires PCR in some capacity. Sanger, Illumina, 454, ion torrent, any method at all that uses amplification is using PCR. How someone can say the method is free of a contamination issue betrays lack of understanding of the system. This is really quite unfortunate.

Sue, that wouldn't have been a presentation by a Hemispherx Biopharma researcher, of Ampligen "fame"? Those guys make the WPI look like a temple of science. I think ERV might have to wipe her face so, because it's improper to blow coffee out your nose laughing in the ER.

Hi Abbie Smith,

I have written a long theory here on endogenous RNA viruses and ME. It's much like the purposed theory of endogenous RNA viruses and multiple sclerosis (the famous HERV-W research). What I'd love for your to do, is play the role you play the best: "The devils advocate" (don't get that the wrong way). If you could tell me some reason why one would *know* I am wrong, than it would get me a leap forward.

http://forums.phoenixrising.me/showthread.php?10775-It-s-all-in-the-Gut…

Telling me that I don't have the facts to back everything up, is different from saying this and that ***can't*** be so because of this and that. You're smart. I guess that really goes without saying.

Jason...I see. I didn't know they could still have contamination. well, carry on then.. LOL

Mu..LOL

ps..i got the info from the Cheney Clinic website. There isnt any more info out there about this.

I'm seconding Order of the Stick by eric s. More webcomics:

He is Dr. McNinja - heals with one hand, kills with the other. Lots of archives to read through, be sure to check out the alt text too:
http://drmcninja.com/

For slightly more serious comics you may try Goblins and Erfworld. Both have a fair bit of material to read through but also appeal mostly to gamers and fantasy buffs. Goblins in particular gets much, much better than its initial art and plot suggest:
http://www.erfworld.com/book-1-archive/?px=%2F001.jpg
http://www.goblinscomic.com/06252005/

Axe Cop is surreal, definitely distracting; it's worth checking the "about" page as it explains a lot:
http://axecop.com/index.php/acepisodes/read/episode_0/

Project Rho is kinda awesome and engrossing to the average non-physicist, it discusses how you could really build a rocket to visit Pluto (and more importantly, how TV gets it wrong):
http://www.projectrho.com/rocket/prelimnotes.php

TVTropes can give you endless hours of wikipedia-style binging and it's limited only by the number of windows and tabs your browser can manage at once. It's basically a list of every pop-culture cliche on the planet:
http://tvtropes.org/pmwiki/pmwiki.php/Main/HomePage

Hope things get better.

Hi Abbie Smith,

I've written a long theory about teapots in orbit around the Sun. It's much like a lot of other stuff. Can you tell me some reason why one would *know* I am wrong?

Oh yeah, laugh all you want, you genomicist. This is "Next Generation" sequencing we're talking about. When Picard, Jordy and Data show up to give you a demonstration (and kick your butt), you won't be laughing.

http://www.youtube.com/watch?v=7aLHJXokuzw

Watch it. You might learn something.

By sasqwatch (not verified) on 09 Dec 2011 #permalink

@erk. The HERV-W theory is well known in some autoimmune diseases, and now that ME also seems to have a strong autoimmune component (i.e. the RTX research), I think very well could be that a parallel could the case. Comments like "tea pots in orbit around the Sun" only shows how little you understand (or want to understand). Proving a theory wrong could be done e.g. with statements such as "endogenous RNA viruses can't be triggered by those events because [input something], therefore it must be wrong". There has come so much bile out of the blog owner (not talking about the facts reported, those which hold true are welcomed, I am talking about the juvenile potty mouth way of expressing ones opinion, which drowns all the points, valid or not) that although the owner might be well educated about ERVs, it might not be possible to get something meaningful out.

I thought he was from New Castle, but the accent had been muddied through time. Now I learn he's not a Geordie; rather, a pitiful Jordy. Pshah.

(I guessed on the name, actually. I don't think I've ever seen any Trek episode all the way through, after the original series [when I was a kid])

By sasqwatch (not verified) on 09 Dec 2011 #permalink

theshortearedowl,

ditto - I just wanted to spell out the problem in my reply.

I'm not sure why Sue said, "LOL" after... I feel like she thinks I'm making that part up?

Oh, I know you were, Justicar. Just trying to find some extremely random silliness and trying not to freak out too much about Abbie's situation. ...and hoping some extra-terrestrial genomics is what the doctor ordered. I've been lurking in the slimepit from time to time, and have been enjoying your commentary there and elsewhere. Hopefully I can get the time to contribute more substantively, but have emergencies of my own unfolding at the moment, sadly enough.

By sasqwatch (not verified) on 09 Dec 2011 #permalink

Crack pot business plan

1 Don't comment on relevant posts about XMRV where key XMRV researcher is shown to be more fucked up than a football bat.
2 Wait till blog owner posts about family medical problems and asks for distractions then post reams of XMRV related crap
3 ????????
4 profit!!!!

Jesus fucking Christ I wish you parasitic little cock-holsters could hold down your schadenfreud boners for long enough to think about how crass and fucked up it is to be asking for advice on your crackpot theories and probably contaminated Next generation sequencing paper specifically on a post about family medical problems rather than on the million and a half XMRV threads and ERV posts.

#3... insist on using the word "theory" inappropriately.

E.g., could you look at this paper I just wrote. There's a theory in there, which is mine, which is as follows: er... ahem... uh, er... ahem. (etc.)

http://www.youtube.com/watch?v=FOzVkSFnKxI

By sasqwatch (not verified) on 09 Dec 2011 #permalink

#5

That Liam Neeson improv sketch is brilliant. Can't believe it could be so funny to listen to some guy saying he contracted AIDS from a prostitute from an African country ravaged by starvation, whose only financial recourse was to sell her body.

Jesus fucking Christ I wish you parasitic little cock-holsters could hold down your schadenfreud boners for long enough to think about how crass and fucked up it is to be asking for advice on your crackpot theories and probably contaminated Next generation sequencing paper specifically on a post about family medical problems rather than on the million and a half XMRV threads and ERV posts. Posts.

YES.

Hey, XMRV can be funny too...

For instance, if you look at the docket entries of Judy Mikovits's civil trial (vs WPI), you'll note that Mikovits's latest entry, the "DEFT ANSWER TO COMPLAINT FOR BREACH OF CONTRACT, SPECIFIC PERFORMANCE TRADE SECRET MISAPPROPRIATION CONVERSION, BREACH OF IMPLIED CONVENANT OF GOOD FAITH AND FAIR DEALING AND REPLEVIN", has been approved by...

...ASMITH

http://www.ccwashoe.com/public/ck_public_qry_doct.cp_dktrpt_docket_repo…

(on a slightly more serious note, I find it "funny" that Mikovits is (still) apparently defending against a breach of replevin)

@Erk. Just to clear it out, the reason I put an emphasis on can't was to show clearly that there's a difference between saying it isn't so because it isn't proven (as I wasn't proposing to "have the whole truth", it's rather a working hypothesis), and saying it can't be so because of this and that - it'd the latter I was after, hence the emphasis on "can't". And, just to note, ERVs have nothing to do with Mikovits, the WPI, XMRV, MLVs, Lombardi or any of the other. Absolutely nothing to do with it. It's research done in MS and schizophrenia, and to my knowledge the only ERV proposed to play a role in human disease. When the title of the blog is "ERV", I assumed that a discussion of ERVs, triggers and autoimmunity could be a topic, but I guess I was wrong.

@67, do you really think that Sue is displaying schadenfreud by discussing what she is? I think you need to calm down, take a breather.

@sasqwatch. Well, if you run out of arguments, I guess acting obnoxiuos is your response. Well done.

@ Jason #64

You have way more patience than I.

@ sasqwatch #60

Sequencing: THE NEXT GENERATION [daaah dah-dah-daaah dah-dah-daaaaaaaaah...]

I was just thinking the other day, what are they going to call the NEXT next generation sequencing tech? Kind of run themselves into a corner there...

@ ben #67

True it is a bit creepy to suddenly have all this XMRV stuff, but the way I read it was that Abbie was looking for distraction, not just amusement. I could see it as being moderately engaging to knock out some casual dismantling of Redo's nutty theory, in between filling in old Cosmo surveys and reading dog-eared copies of National Geographic.

@Abbie - sincerely hope you/family are out of the medics' grasp.

@sasqwatch. I know you didn't. I assumed it was a crass response to me using the word theory instead of working hypothesis, and a way of saying the working hypthesis had to be non-sense without any reasoning. If I was wrong, than I do apologize, and I hope you'll have a great weekend. And our health is the most important thing we have, so fingers crossed for AS close ones.

Little update--
Thank you, folks. A hidden bonus of asking you all to post links was that I also got to occupy myself cleaning out the spam trap :) I really appreciate it, everyone :)

So what happened was one of those things you always hear about on the news? Young, healthy, athlete keels over from an undiagnosed heart condition. We caught it *just* in time though, so no one is dead. They just had 9 hours of open heart surgery (after having never even broken a bone, much less any kind of surgery in their entire lives) on Monday.

Thursday sucked monkey balls, but yesterday was a REALLY good day-- totally off the Oxygen mask, got out of bed in the morning (with a lot of help), walked around the bed later in the day (with a lot of help), talking a lot better, and finally got to have some food (well, liquid food, but a win).

I havent slept/eaten since Sunday evening, but now that things are on the upswing, I actually slept last night. YAY! This week I was in the ICU, but next week I *have* to get back in the lab, so Ill be balancing work and ICU, so I will try to get back to blogging, but it might be slow for a bit.

Thanks again for your patience and all your comments :)

Except Sue. You can go fuck yourself, Sue.

Great to hear that things are going well!

By Yakivegas (not verified) on 10 Dec 2011 #permalink

Glad things are looking a little better now.

How about some stupid tortoise tricks!
youtu.be/qWZRGZInJkw
or a tragic story of forbidden love:
youtu.be/6R3BYCT5oWw

Glad everyone is okay, and glad that you're doing ok dealing with everything.

Best of luck to everyone involved by you, Abbie.

"So what happened was one of those things you always hear about on the news? Young, healthy, athlete keels over from an undiagnosed heart condition."

When I was a sophomore in college, a girl I knew in High School died like that. While running the Marine Corps marathon. At around the 25th mile. Tragic. She had been heavy in high school, but was Navy ROTC in college, so presumably was in better shape.

Your friend is lucky.

Whoa. Nasty news about the heart, great to hear it all got caught in time and operated on immediately!

Am happy and relieved to hear things are improving for her Abbie. Sounds like you will both be needing plenty of rest now.

Bad night last night.

In the ICU since 2.30 this morning.

Im hoping its one of those "get better get better GET WORSE get totally better" things.

Breath bated once more. Having been on the ICU roller-coaster before, I really wish there was more I could do. So sorry.

By sasqwatch (not verified) on 11 Dec 2011 #permalink

Oh, now you can do better than that, can't you?

Sue

well shit. Hope everything works out!

I just had the weirdest 17 hours ever.

Apparently, someone who was awake for the past 4 days was not actually awake, and is now actually awake and is like totally back to normal personality-wise and has no idea wtf just happened to them.

Im creeped out that I have basically been caring for a zombie for the past week, and Im a liiiiiiiiiitle tired, so Im going to sleep now...

No, no theyre not a zombie anymore. Zombie apocalypse began and ended in a week.

I AM LEGEND!!!!

ERV@#101

"No, no theyre not a zombie anymore. Zombie apocalypse began and ended in a week.

I AM LEGEND!!!!"

In more ways than you know.

Sorry about your week. I hope this one is better.

If Schadenfreude is your bag (and we know it is)I got to spend the whole weekend in a new parent class.

I am 45. I have diapered angry new world monkeys, can perform most minor surgeries and have no gag reflex.

Picture Hannibal Lecter being talked down to by a "lactation coach".

The Bride looked at her and said..."Lady,one we aren't breastfeeding, my funbags my call, two my husband will murder you if you bother him."

One of the benighted husband/hipsters in the room asked me about bonding with my child.

I told him we were going professional since I knew several bondsmen and figured the judge would only require the baby to post twenty grand. Besides how many hospital staff can it maim before I dart it and get it in the cage?

He didn't get it.

By Prometheus (not verified) on 12 Dec 2011 #permalink

Young, healthy, athlete keels over from an undiagnosed heart condition. We caught it *just* in time though, so no one is dead.

If anyone is still reading, and since nobody else has:

Anyone not current on CPR? And your excuse is ...?

(Brought to you by your friendly net-neighborhood first responder.)

By D. C. Sessions (not verified) on 12 Dec 2011 #permalink

D.C. Sessions: alas, CPR would have been useless in this particular situation. But it is generally good advice that one remain current, because it's helpful in some situations.

The most common cause of "young athlete collapses from cardiac condition" is a simple bradycardiac arrest. CPR is not only lifesaving but may be the only intervention required in the short term.

So: maybe not this time -- but if you're betting the odds ...

Disclaimer: I'm a 60ish overweight male. Getting y'all up to speed on CPR is in my own selfish interest ;-)

By D. C. Sessions (not verified) on 12 Dec 2011 #permalink

CPR is not only lifesaving but may be the only intervention required in the short term.
So: maybe not this time -- but if you're betting the odds ...

I do not dispute any of that. But I will note that young athlete collapses and dies from heart thingy has causes other than that, and there are certain heart things that amount of mechanical compression is able to overcome - unfortunately.

I was bee bopping around town one day going by a local hospital as a matter of fact when a late 50 to early 60 something overweight gentleman collapsed in the parking lot. So, I dash over and start doing CPR on him.

Well, it wasn't really the parking lot. More like parking lot adjacent; there's a field there on the hospital grounds where people walk their dogs the like.

Anyway, it took almost 8 minutes from the first notification until an ambulance arrived. So long it took them, that by the time we got old dude in the back, we passed the ER people heading down to the field.

The gentleman didn't survive. I'm not saying that he wasn't potentially savable for any reason I earlier alluded to - just that given the response time and what not (while on the grounds of a hospital even), poor guy didn't stand a chance.

But hey, it's not the first time I've had a mostly dead person vomit on me! I think he had potatoes for lunch judging by the taste of it.