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Comment: Re:The same way many global warming papers got pub (Score 4, Informative) 109

The vaunted peer review - supposed to eliminate problems like this - failed.

Not really. Peer review is designed to catch holes in their logic or spot errors, such as if the incorrect analysis method was applied or if their scientific evidence doesn't fully support their claim. When it comes to outright fraud, a peer reviewer really has very limited means of spotting it. In exceptionally rare cases they will request that a claim be replicated by an outside researcher, but that is exceedingly rare and I don't think I've ever heard of a reviewer actually attempting to replicate research themselves as part of the peer-review process.

What normally happens is that other people in the field will read the paper and say "I don't really buy this" and attempt to replicate it themselves. If a consensus of groups can't replicate their findings, then the question becomes whether there was fraud involved or if it was just another example of "winnners curse" or maybe something unique about their study that was different from all the rest (like if they were looking at a different cell line or global population than everyone else). In no case is it really feasible for the peer-reviewer to catch outright deceptive fraud, but usually it gets spotted sooner or later. And the bigger the scientific claim, the bigger the bulls-eye becomes on your back.

Comment: good and bad (Score 3, Interesting) 136

by eli pabst (#46339447) Attached to: Major Scientific Journal Publisher Requires Public Access To Data
Will be interesting to see how this is balanced with patient privacy, in particular with the increasing numbers of human genomes being sequenced. I know a large proportion of the samples I work with in the lab have restrictions on how the data can be used/shared due to the wording of the informed consent forms. Many would certainly not allow public release of their genome sequence, so publishing in PloS (or any other journal with this policy) would be impossible. So while I think the underlying principle is good, I think an unintended consequence might be less privacy for patients wanting to participate in research (or less patients electing to participate at all).

Comment: Re:Mechanics (Score 1) 1264

by eli pabst (#41174211) Attached to: US Doctors Back Circumcision

Only if you overlook the claim that "Langerin is a natural barrier to HIV-1 transmission by Langerhans cells."

No, not really. Cells can express a lot of different proteins that are innately antiviral, but that doesn't mean that the cell still can't be infected. Infection of Langerhans and other classes of dendritic cells by HIV is a well established fact. Not to mention that on immune activation Langerhans cells become mature dendritic cells and stop expressing Langerin.

Comment: Re:Mechanics (Score 1) 1264

by eli pabst (#41160997) Attached to: US Doctors Back Circumcision

(Speaking as a man with a foreskin, who can't quite imagine what it would be like not to have one... uncomfortable?)

I occasionally see reports about circumcision affecting cancer outcomes, AIDS transmission, things like that.

What completely mystifies me, is the mechanics of these effects. Perhaps a foreskin can lead to increased transmission of AIDS. How? By what mechanism?

The foreskin is known to be highly enriched for the types of peripheral immune cells that carry the specific receptors used by HIV for entry into the cell, such as Langerhans cells and macrophages, while the rest of the penis is not. So by removing the foreskin you are limiting exposure to the specific cell types that HIV can infect.

Comment: Re:Bad research reporting is worth forfeiting mod (Score 2) 1264

by eli pabst (#41160907) Attached to: US Doctors Back Circumcision

I'm forfeiting a mod point for this, sorry to whoever I modded up... The actual abstract of the actual paper backing up this claim (BOLD IS MINE):

ABSTRACT. Existing scientific evidence demonstrates potential medical benefits of newborn male circumcision; however, these data are not sufficient to recommend routine neonatal circumcision. In circumstances in which there are potential benefits and risks, yet the procedure is not essential to the child’s current well-being, parents should determine what is in the best interest of the child. To make an informed choice, parents of all male infants should be given accurate and unbiased information and be provided the opportunity to discuss this decision. If a decision for circumcision is made, procedural analgesia should be provided.

IOW, no, we're not recommending anything, we're simply saying there are POTENTIAL medical benefits. Well there are potential medical benefits to getting my appendix removed, or my tonsils cut out, it doesn't mean I should be forced to make that decision.

Stupid journalists, we need to seriously trim the fat in that industry and start with these jackasses who misrepresent science for political gain.

You're quoting the American Academy of Pediatrics report published in 1999, not the one from this year. There has been a lot of research published on this since then.

Comment: Re:Usually you run as root (Score 1) 84

by eli pabst (#39653575) Attached to: Critical Flaw Found In Backtrack Linux

The issue is, that one would expect a distro specifically built for security and penetration testing would not have a discoverable security flaw. No matter how obscure. It might make one wonder what else has been missed?

Do you really think that's a reasonable standard? Even OpenBSD has had security flaws in it.

Comment: Re:Handwringers & luddites (Score 1) 224

by eli pabst (#38771950) Attached to: Mutant Flu Researchers Declare a Time Out

When they screw up and it is released, and they will f*ck up, they are humans, i hope your the first one infected.

Right. That's why we've had all these epidemics and plagues that came out of USAMRIID and similar institutions. Oh, wait, that's right, you haven't. Because we know how to store and contain weaponized or highly contagious pathogens.

There have been 3 separate instances in the last 10 years where BSL3 pathogens have escaped from a lab and infected people, including one in Beijing where a small local outbreak occurred and one person died of SARS. My biggest concern isn't so much the publication of the knowledge, but rather that this pathogen is actually not being kept at a USAMRIID-like facility, but a BSL3 at University of Wisconsin, Madison.

Comment: Re:Handwringers & luddites (Score 1) 224

by eli pabst (#38771858) Attached to: Mutant Flu Researchers Declare a Time Out
No, really it's not stupid. In fact there was an article in Nature this week written by several experts in the field that basically argued the same point. They estimated the likelihood of accidental release through lab-acquired infection is around 30% within four years, based on recent rates of lab-acquired infections. Keep in mind that one of the biggest concerns is that this modified pathogen is *NOT* being stored in a USAMRID-grade BSL4 lab, but rather a BSL3 facility. Do a google search for laboratory-acquired SARS (also a BSL3 agent) for a wake up call. Release of a highly transmissible pathogen with 50% mortality would be a catastrophe unlike anything we've ever experienced.

Comment: Re:Drops in NGS Costs Outpacing Storage Costs (Score 1) 239

by eli pabst (#38247632) Attached to: Genome Researchers Have Too Much Data
Yeah, this problem really sank in with us when we realize it was faster to download the data onto 2TB external drives and ship it to collaborators rather than transmit it over the internet (even with Aspera). Seemed so bizarre to be surrounded by all this high tech equipment and yet we're putting stamps on our data so we can give it to the mailman.

Comment: Re:This doesn't look good (Score 1) 126

by eli pabst (#28358015) Attached to: Revived Microbe May Hold Clues For ET Lifeforms

Pathogenity requires extensive adaptive mechanisms from a microbe, otherwise it isn't able to live in an organism with an immune system. Microbes that cause human illnesses have through countless generations developed traits that enable them to grip molecules on human cells, thrive in tissues, and resist the immune cells' attempts to destroy them.

I don't know if I really agree with that. Some of the more dangerous pathogens are those that have recently jumped from other species and have had little time to evolve into coexistence with their new host. SIV infections are symptomless in their natural host, but deadly in related primate species (including HIV in humans). Same thing with herpesviruses, relatively minor symptoms in their natural host, but often deadly when they make a zoonotic jump (herpes B amd AlHV are good examples). Plus 120,000 years ago is not very long at all on an evolutionary time scale and it could have easily been exposed to other primates/mammals (even humans) at that time. In fact the age of it really only guarantees that a human host would have zero protective immunity against it, so it would be like smallpox blowing through native American populations.

A continuing flow of paper is sufficient to continue the flow of paper. -- Dyer

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