Monthly Archives: March 2010

Black Ninja Monday is When the Commenter Trolls Get Their Due [Comments]

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Several star commenters have noted recently that the troll factor is rising again. This post is reminder that all comments wasting words and the comment moderator's time wondering about such issues as "why does gizmodo love/hate/get paid by company XYZ?" may result in zero warnings and then a ban. And whatever happens to your comment account, remember: it's not my fault if you lose your account because you said something stupid. Black Ninja Monday is when the action goes down, so you've got two days to turn things around. The obvious choices: You can have fun in troll hell, or join the ranks of the thoughtful, starred, proud and clever commenters everyone appreciates. Again, Monday: that's when there'll be internet blood everywhere. But it won't be mine. More »


The problem with Comparative Whole Genomics……

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I have been having this debate with a good friend and mentor.


I think Complete Genome Comparison could be a Killer App.

He thinks it could be a legal and scientific nightmare.

I think he's right.

Let's really think about this for a second. If history has anything to say about human behavior we need look no further than the secrecy with which gene sequences were hunted.

Hell, even Science makes mention of it several times. The Article "Data Hoarding Blocks Progress in Genetics" might be a good read if you are interested.

Guys like Daniel MacArthur over at Genetic future point out some good points about the difficulty in making sense of all the noise that exists in genomes. But the problems go even further than that. Hell, CNV can differ in IDENTICAL TWINS!!!! Say Wha?

So what do we have to say about this? Phenotype and comparison are kings. Databases of "normals" and disease afflicted need to be developed. They need to be curated, they need to be "shared"

Ahem, excuse me? Did you say "shared?"

Yes, I did say shared.

Exec/USGOVT/BGI/UK/Etc- "Well, sure we would like to give that idea more credence and study it. And the implications it may bring. Would you be so kind as to forward your attorney's information so that our attorneys can consult with yours in order to bankrupt you and send you away with you radical thinking?"

He has me convinced (a tough thing to do) that the level of collaboration amongst human geneticists and Venture Capitalists might not be exactly the level of their physician brethren....

What happens when you get access to a database, but not "all of it"

Who pays? Who benefits? Who gets rights of discovery? Who pays the Nosferatu? (sorry Dan)

With Sequencing as a Service, do you have these problems licked? Probably not.

So when Daniel points out every geneticist afflicted with a disease feel good discovery, there are about 100 nightmare scenarios of chasing down rare variants that turn out to be nothing except a good excuse to burn through 10 million dollars........

I begin to say, well how can we pick that up quicker? Comparative Whole Genomics.

Great, which database do I start with? Do I have to use 20 or 200 databases? How can I afford such work? Which one of the 200 won't make a play legally to own my discovery?

Ahh, yes. It is a good time to be a genome centric attorney. But a nightmare to launch a business where you depend on someone else's database.........

The Sherpa Says: Yes, sugar plums, ponies and lemon drops for as far as the eye can see for Genomics! I hope Andy will bring this back to earth........Or maybe Glenn Close can show us where the fruit punch swimming pool is?

Re polarizing ceramic magnets.

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This may be an easy one for the right person but for me up to this point I have yet to ever do it on purpose.

Can the ceramic magnets in servo motors be re polarized, have their polar orientations moved, simply by brute force from a stronger electromagnetic field?

Reason being I have a lar

The FDA, 2c19 and the ACC

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Did anyone see the FDA issuance of the better warning that as many as 14% of patients will not benefit from Plavix/Clopidogrel?

Did anyone see the cold shower being poured on by the press and the cardiologists?

Christopher Cannon Assoc. Prof at Harvard says:
The ACC will need to develop protocols, "Thus a real conundrum"

He then says "I expect mass confusion in response to this FDA warning"

Well Chris, It's not as if we haven't been shouting from the rooftops about this for over a year now.......

"The test costs about 500 USD according to Courtney Harper PhD, Director of the FDAs division of chemistry and toxicology devices. But cost isn't the only issue."

Which BTW is false 23andME is cheaper......But wait, isn't that medicine?

"The time to get a result varies. It may be a few hours to a day or two, or other labs may take a few weeks"

This is absolutely true. It takes me 3 weeks for a test from Quest. I am certain that there has to be some lab to do it quicker.......

BUT, the FDA has only approved AmpliChip for this testing.....

This sounds to me like the FDA needs to approve some kits and PDQ with the ACC meeting coming up like,

My guess

1. The ACC will address and release its prelim algorithm

2. The ACC conference will have even further data regarding this released.

3. The last step is to FDA in some kits to do this test, quicker and more standardized.

We need a company that can direct us to

So the question, why all the cold water on this killer app? Well, because it is getting lumped in with DTC genomics, which is feeling a backlash from hype and failed promises. Or trying to play medicine.
As well as a flat disregard for medicine. So when the press and the healthcare providers are against you, you can feel it.

But this is what I have been frustrated about all along. I saw this coming. Doctors blowing off PGx thinking it is SNPChip Hype. Journalists pouncing on overpromising and intellectually dishonest DTC Genomics companies.....

This is why I was so mad about the blimp.

When something really awesome comes around, people are burned out from Open Bars......

The Sherpa Says: Let's really do this. Genomics and PGx IS medicine. Let's say it proud, Let's ay it loud. Quit screwing around to avoid regs. Let's how the world how we can use this to help mankind!

NCBI ROFL: What kind of erotic film clips should we use in female sex research? An exploratory study. | Discoblog

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2518795978_f11dbdce5c“INTRODUCTION: Erotic film clips are used in sex research, including studies of female sexual dysfunction and arousal. However, little is known about which clips optimize female sexual response. Furthermore, their use is not well standardized. AIMS: To identify the types of film clips that are most mentally appealing and physically arousing to women for use in future sexual function and dysfunction studies; to explore the relationship between mental appeal and reported physical arousal; to characterize the content of the films that were found to be the most and least appealing and arousing. METHODS: Twenty-one women viewed 90 segments of erotic film clips. They rated how (i) mentally appealing and (ii) how physically aroused they were by each clip… RESULTS: The most appealing and physically arousing films tended to exhibit heterosexual behavior with vaginal intercourse. The least appealing and least physically arousing films tended to depict male homosexual behavior, fellatio, and anal intercourse. CONCLUSIONS: Erotic film clips reliably produced a state of self-reported arousal in women. The most appealing and arousing films tended to depict heterosexual vaginal intercourse. Film clips with these attributes should be used in future research of sexual function and response of women.”

woman_porn

Photo: flickr/thebittenword.com

Related content:
Discoblog: NCBI ROFL: The pressing question this Penis Friday: how hard is hard enough?
Discoblog: NCBI ROFL: The logic of Ménage à Trois.
Discoblog: NCBI ROFL: Boys and girls, please open your textbooks to page 69…


Same Test Results: 23andMe is Myriad is BRCA is Medicine

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Same Test Myriad 23andMe

Myriad’s BRCA breast cancer genetic test “Multisite 3 BRACAnalysis” is the same test as 23andMe’s BRCA breast cancer genetic test “BRCA Cancer Mutations (Selected).” Both services test for the same mutations to produce the same diagnosis medical diagnosis justified by the same medical research.

See the exhibit above which depicts genetic test results for 23andMe’s BRCA genetic test and Myriad BRCA genetic test.

The contested 23andMe claim is published by 23andMe online at 23andMe’s Terms of Service, Section 3.

Contested 23andMe Claim

23andMe Service Is For Research and Educational Use Only. We Do Not Provide Medical Advice, And The Services Cannot Be Used For Health Ascertainment or Disease Purposes.

The objections to this claim are that this same test is already defined for use as “health ascertainment or disease purposes” and that the use of this test is already included in standard medical practices in the United States. One implementation of this test for use as “health ascertainment or disease purposes” includes the Myriad “Multisite 3 BRACAnalysis” test.

Thus, either the 23andMe “BRCA Cancer Mutations (Selected)” test is medicine, or the the Myriad “Multisite 3 BRACAnalysis” test is not medicine.

Note: The 23andMe and Myriad reports depicted in this exhibit have been reformatted for publication on the Internet. Email me if you would like an unformatted copy of either report depicted in the display.

Spooky “Dark Flow” Tracked Deeper Into the Cosmos; No Word on What’s Tugging at Galaxies | 80beats

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ComaClusterA year and a half ago, the team led by Alexander Kashlinsky of NASA proposed the controversial and ominously named “dark flow,” a massive gravitational force that is tugging at galaxy clusters, and that Kashlinsky says could be coming from beyond the limits of our own visible universe. Now the team is back with a follow-up study in The Astrophysical Journal Letters, and Kashlinsky says the team has tracked the dark flow out twice as far as before.

A quick note on dark flow: The reason Kashlinsky noticed it thanks to the cosmic microwave background, a signature left over from 380,000 years after the Big Bang that permeates the universe. “The hot X-ray-emitting gas within a galaxy cluster scatters photons from the cosmic microwave background (CMB),” the NASA press release says. “Because galaxy clusters don’t precisely follow the expansion of space, the wavelengths of scattered photons change in a way that reflects each cluster’s individual motion.” Using data from the Wilkinson Microwave Anisotropy Probe (WMAP), which mapped the microwave background, the team managed to find this tiny effect when they looked at huge clusters of galaxies, and found something totally unexpected.

What the 2008 find showed was that these galaxies were moving in a way that the distribution of matter in our visible universe couldn’t explain, traveling a million miles per hour in a particular direction. Says Kashlinsky: “This is not something we set out to find, but we cannot make it go away” [US News & World Report]. The new study confirms this weird effect, and finds that it extends farther out, to at least 2.5 billion light years away. Where Kashlinsky’s first study relied upon three years of WMAP data and 700 galactic clusters, the new study grows those numbers to five years of data and double the number galactic clusters. The clusters appear to be zooming along on one particular line aimed at Hydra, Kashlinsky said, but “right now our data cannot state as strongly as we’d like whether the clusters are coming or going,” to or from Earth [USA Today].

While the universe itself keeps on expanding and expanding in all of the directions it can whiz, no one direction should be preferred, which is why the dark flow is to damned interesting. According to our best understanding of how the matter in the Universe was distributed, there’s no way of accounting for this flow. The obvious alternate explanation is a little unnerving: something outside of our visible universe is pulling on the matter that we can see [Ars Technica].

For another explanation of dark flow, check out Phil Plait’s at Bad Astronomy, written after the initial 2008 study.

Related Content:
80beats: Mysterious “Dark Flow” Is Tugging Galaxies Beyond the Universe’s Horizon
Bad Astronomy: Trans-Cosmic Flow Broadens Our Horizon

Image: NASA, the Coma Galaxy Cluster