A paper about spread of bird flu. I think.

"calculated the arc cosine of the scalar product of the migration matrices."

Actually, that sounds like something a slightly inept graduate student would have written, because he asked his advisor what he should do, and his advisor gave him instructions on what to calculate and how to do the calculation. The student did it, but still doesn't really understand what he was doing.

Thanks for this, reveres. I read the AFP story yesterday and went "wha?" Some of us are also condemned to think like editors. I think it is genetic.

Revere, sometimes, just once, a TKO would bring rapid and full closure.

I read the posted, longish news release, and I thought it was yet another publish or perish product; you and the readers here who know academe recognize they gotta put out something or their job advancement, never mind their jobs, are at stake. Do you know if these authors are tenured?

Niman posts sequence reporting often. His response at Flutrackers.com is that it's coming out of Northern China, out of Hubei, most recently.

The reality is quite obvious. It's coming out of the migratory pathways, and the sequence changes can occur anywhere along those pathways. Qinhai's E627K. Gharbiya's N294S. etc.

What they're really arguing is over who gets to wear the albatross necklass. It's distracting, fractionating, and meaningless, imo. But for those who want entertainment, UCI is ready to please.

That's "necklace", not "necklass". Sorry.

A simple observation on the paper and the science. Past is prologue as they say. No one really knows how H1N1 started and really where because it roared across the planet in six months. Situation is nearly the same. They called it Spanish Flu but found indications of it really starting in Kansas. Massively at least. The dribbling of cases of some unknown pneumonia also was indicated for at least 5 years prior to this from China, Russia, Turkey, Italy, and France during the war. No great load of cases that could be attibuted to "Spanish Flu" only that men got very sick in the trenches and died astoundingly quick.

Here is the observation. Since the missionaries, the mandarins, the Turks, Italians and the French all recorded weird pneumonias and in quantity but not huge kills back then, wouldnt the only possible vector back then be birds? Wouldnt it just be better to accept that endemically infected birds are the main vector with subs springing up from them? Some like the mice are already found to magnify the virus so to me its an almost no brainer. The problem is that to make the connection to birds its going to have to go high path.

Another bragging rights thing if and when it comes.

Re: 13 March, 2007, PNAS ("PENIS") paper -- yawn, who really gives a flyin' frack 'bout where a recombining transgenic RNA virus "geographically originated" (the tedious "create a mythical patient zero" and media-kick its head-in syndrome). What 'bout the how part of it all!?!

Revere: "[Wallace et al] speculate further on general evolutionary mechanisms suggesting that the virus switches between different genetic combinations to allow it to infect various hosts species in the same and different localities. This may be true, but at best it is only consistent with but not a result of their analysis..."

I'd like to point out China has dabbled in genetic engineering -- throwing GM crops and trees into the general environment -- within the same timeframe as the West. Hello, duhh -- is everybody out there as asleep as the Bush administration, or should I just seriously rethink my coffee-nicotine addictions!?!

C21*S*E*Research -- The Politics of Horizontal Gene
Transfer (How did H2H H5 evolve!?!)

I suspected genetic engineering was dangerous way back
in the late 90s when first digesting a tv news item on
H5N1 contamination in Hong Kong -- six people (adults
and kids) "cytokine storm" died of this transgenic flu
during a late 1997 outbreak in Hong Kong's Special
Administrative Region.

Even a major pharma company, Roche, was worried back
in 1997 bout the global implications -- in its Media
News 16 (May 2006) Roche says:

"Roche has been in discussions with governments as
early as 1997 regarding pandemic preparedness..."

www.roche.com/med-cor-2006-05-16

So how did H5N1 get here?

H5N1 is a transgenic polymorphic pathogen -- a highly
mutable cross species multi-strained virus probably
CaMV 35S promoter gene flow originating from genetic
engineering.

Since the mid 90s, dietary consumption of GM
(genetically modified) crops by birds, animals and
humans (who eat crops, birds and animals) has
increased dramatically. It is very probable GM crops
containing CaMV 35S transcription promoter are the
horizontal gene transfer (HGT) causation vector thru
which transgenic viral pathogens (eg. H5N1) are
recombining (homologously) into existence with such
ease, speed and spread.

The "homologous recombination" process has, according
to Recombinomics.com, always been the explanation for
viral evolution and not "random mutation". But, the
thang bout the technology of potpourri tweaking GM
organisms sees "hyper-acceleration" entering natural
DNA evolution -- thangs move a durn sight faster...

Recombinomics -- Random Mutation Explanation of Flu
Genetics Is Fatally Flawed (March 30, 2006) @

www.recombinomics.com/News/03300602/Random_Mutation_Flawed.html

The defence against evolving polymorphic viruses is
rather simple and has been repeated many times by
numerous scientists worldwide -- cease the corporate
controlled release of genetically modified organisms
within the global environment.

Prior to the end of 2005, efforts in sequence tracking
the genesis of H5N1 were criminally lackluster -- we
now know transgenic strains are present in birds and
mammalian populations...

But still, the question remains unanswered, how did a
transgenic virus appear out of nowhere?

The probable (but unproven) cross species vector is
GM/GE feed fed to domestic fowl from the mid 1990s to
present, HGT recombining H5N1 (via CaMV 35S promoter)
into a transgenic polymorphic pathogen, now infecting
and killing humans...

So,basically I'm saying gene flow has occurred as a
consequence of transgenic crops doing a CaMV 35S
promoter recombination hotspot remix in the bellies
(and bodies) of all organisms consuming such crops.

Prof. Joe Cummins was the first to warn against using
the CaMV 35S promoter or any viral genes in plants
because it had been shown that such viral transgenes
in plants could gene flow recombine with naturally
occurring viruses to generate, in some cases,
super-infectious viruses.

Subsequently, the CaMV 35S promoter has been found to
substitute for the promoter of many plant and animal
viruses to produce infectious viruses.

* Remixed excerpt ISIS Press Release 29/11/04 -- Fluid
Genome & Beyond @
www.i-sis.org.uk/Fluidgenomeandbeyond.php

Jon, I followed that fluid-genome link. Although my credentials in molecular biology are far from stellar, they are sufficient to have left me suspicious after reading the paper in question. Particularly given that it trails off into a poetic and somewhat incoherent meditation which likens the operations of cellular genetics to jazz music, and invokes "universal love" as an organizing principle of biology.

I note also that the organization which hosts the paper in question, ISIS, has published other papers with which I am familiar. I recently read a piece of theirs on nuclear power, a field in which my intellectual footing is far more sure than in DNA twiddling, and that paper, although it eschewed silly philosophical meanderings, is best described as having been a conglomeration of bunk, superstition, and reassertion of the premise.

I am certainly willing to hear serious science which backs up the notion that transgene crop plants may have larger genomic side effects. Have you got anything which might have been actually peer reviewed and published in a reputable journal?

--

Several points I would like to bring up:

First, I think it is important to obtain as much information about the virus as possible so as to understand both the how and the why of it moving into humans (and other mammals). Knowing where it started and how it moved along those migratory paths (and away from them if it is now doing so), will help in doing that.

Second, am I wrong in remembering that the last two pandemics (1957 and 1969), both started in southern China in or near the same province?

Third, I have done phylogenetic analysis to some extent (on fossils, not RNA or DNA), but I am aware that a lot of what determines the tree you get are the characters you choose. That is why you need to use as many characters as possible rather than picking and choosing. One of the very few legitimate reasons for excluding characters is that they are unknown for more than about 5 percent of your samples. Not doing this can greatly affect your results. In addition, excluding species (specimens in this case) from your analysis without good reason can also alter the results. So, I'd like to know what characters were used and what were not used, and why strains outside of southeast Asia were excluded. What do you guys think?

What Niman just posted at Flu Trackers. He calls the report "clueless".

Should the penis review panel itself be in need of review?

Asked of Niman: > Originally Posted by Scottmcpherson
Are they reading your travel logs? Apparently not.

Niman's reply: > No, they are using amino acid sequences instead of nucleotide sequences and have left out the most important sequences, which were those from NORTHERN China from 1997. Moreover, phylogenetic analysis tries to pull together many components[,] and the programs literally can't see the forest through the (phylogenetic) trees.

Lenn: This was a convenience sample (what they had available to them) of 192 sequences. They used locality as a character at the tree tips but it is hard to know what they did from what I had available. I didn't find the paper very clear (I guess I said that already). One of my colleagues says that real peer review begins after publication, so it will be interesting to see what others say. Southern China is indeed the putative origen of the other pandemics, so this isn't startling news. They claim to be able to pinpoint it more precisely to Guangdong in the south, however. In the comment that follows yours there is notice that Niman disagrees with the paper. He should publish his work in a scientific journal. An opinion on a website that does not allow review or comment is insufficient as is a blog comment. But we've been over this territory already.

This site is interesting to me because I'm working at the progressive end on raising awareness among health officials re bird flu and disaster planning, and a very serious problem is illustrated.

My experience is that the poultry and pharmaceutical industries control the conversation about avian influenza, and that they believe that is as it should be because they believe they are best qualified. However, when science tells us something that is true and contrary to the financial interests of these industries, a conflict sometimes ensues. For example, we know that the great majority of outbreaks occur in industrial poultry production, such that a moratoriam on that production is the strongest possible measure that could be taken at this time, or, in other words, shutting down factory farms at this time would probably give the world enough time to prepare for pandemic effectively. The conflict here is obvious, and I've seen statements from the poultry industry that suppresses this info.

In the study discussed here, there is the assertion that "explosive growth in the production of factory farm poultry" is a cause of the avian influenza danger, and the editor describes this as "neither new nor [known as] the result of their analysis".

Do you see my problem? I'm sure the scientists do: Anonymous bloggers claim to be "senior public health scientists and practioners", but are spreading unsubstantiated and meaningless assessments of a scientific paper that is indistinguishable from the meaningless spin and disinformation we might expect from the poultry industry. Specifically, the science gives us that avian influenza is caused by "explosive growth in the production of factory farm poultry", which is an incredibly valuable finding, but anonymous bloggers imply that we ought to disregard this info because it isn't new or original, as if novelty mattered.

This hurts science, and scientists, and, in this case, could cost lives very soon.

kparcell: We have discussed the factory farm issue quite a lot here in the last two years plus, so it isn't new for our readers. More importantly, there are still open questions about the relative roles of small distributed holdings and large farms, and while we have expressed our general opinion that industrial farming is a likely explanation there is no consensus or adequate demonstration this is so as yet. If you know of such a demonstration we'd be pleased to share it.

We've said plenty here about the spin of the poultry industry and also about the disgraceful way they treat their workers. Like everyone else we are trying to make our way through difficult, contradictory and confusing data about what is happening and why. It is not at all clear to us the world would be saved from a pandemic if we shut down factory farms, although it is a possibility (but not one likely to be tested).

Regarding the statement in the post about whether the study showed this to be true or not, it did not nor did it shed any light on it. It isn't even clear the study correctly describes what is happening. I read the paper and I reported as well as I could what I found. If you have read it and think otherwise feel free to say so here. It most definitely is not a finding of the paper. That is for certain. Would you have be falsely say it is? My emphasis was on what we have learned from this paper and this is not anything we learned from it. I don't see how that hurts science. You may feel it is a problem for a particular position, but I disagree.

Regarding our anonymity, we have explained it frequently here. We are trying to protect our students, colleagues and institution from the demonstrably punitive practices of this US administration. Since we all depend on federal funding for our research, we don't feel it proper to put them at risk for what we say here. In terms of your point I would also think it is easier to dismiss the rantings of anonymous bloggers than the considered statements of senior scientists (which is what we are).

Your point, then, seems to be that we didn't say things the way you wanted us to and the way you think they are. You have an open invitation to make your case here in the Comment thread. It is always most helpful when you give us some citations rather than make general statements, but we'll accept any kind of reasoned argument.

In the first place, you called your post a rant, and rants do serve a purpose, so I don't mean to pick on you personally. I appreciate your rejoinder and respect you enough to answer you, as I suppose I should, whatever/whoever you are, in the absence of evidence of bad will. Many peer reviews are no better than rants, sometimes rather worse, and they're anonymous too. But they're private, not published on the internet as the opinions of anonymous senior scientists, because they don't deserve the space in the public debate, by definition.

Moreover, I'm glad to go on record opposed to anonymous bloggers claiming to be senior scientists protecting children, because this is perhaps the penultimate of insidious industry practices, to put it politely, perhaps only exceeded by an appeal to patriotism, which you skirt. And here you make the repeated assertion that the content of the scientific paper is old news, as if that discredits it, which is what we might expect from industry but just the opposite of what we expect from scientists. An industry propagandist might say that a moratorium on factory farming is just the same old idea everybody has heard before and not likely to be tried, which is what you say. A scientist might say that because most outbreaks occur on factory farms and spread from there, closing factory farms would probably give us enough time to prepare for pandemic, which is what I wrote. An industry propagandist might say that there are still open questions about the role of factory farms, which is what you say. A scientist would say that there are always open questions but perhaps no time left for excuses. Seriously, "revere", if your name was on this, would you go on record that we need to settle all those open questions? Tell me, what administration do you fear would withhold funds from you for further study?

All that being said, I think an industry propagandist would have transgressed more with personal attack because they're hacks, as would kids because they're kids. So I don't believe that you personally are an industry hack. My guess is that you and perhaps those you describe as your regular readers have simply bought the industry propaganda, which is no sin, but is exactly why we need people to stake their names on their work. You can say anything, absolutely anything, and not be held accountable because you are a phantom. That's not science, that's wikipedia.

Now, I hope you'll forgive me if I end my part of this conversation here, but the good will be done by people who do stake their names on their work, and I choose to concentrate my energy there.

kparcell said (loose translation) : "Yikes! You know what you're talking about. I'm outta here before I humiliate myself."

The comments sure do take strange turns on this blog. Here we have a really nice rant on an extremely annoying problem--dense, turgid, tangled prose in scientific papers--and nobody (hardly) seems to notice.

Rant on, Revere! If people would just say what they mean, the scientific journals wouldn't waste so much paper. Scientists resort to jargon like you quote above when they really don't know what they're talking about.

Rob, Revere covered this one so thoroughly that he left no questions to ask and no additional comment to be asserted, except, "me too." They do that sometimes.

http://www.youtube.com/watch?v=BcYRm0wxgOw

kparcell,

Cheers:*) to you for taking the time posting YouTube's vid advert for Dr. Greger's book "Bird Flu: A virus of our own hatching". The "recombination paradigm" (mentioned in my above posting re: the recombining transgenic RNA virus aka H5N1") is, in Greger's "Bird Flu", presented as a possible technical mechanism for H5's evolution. Indeed, when this probable mechanism is viewed in context with contemporary international "factory farming" protocols -- well, you've pretty much outlined the "score" in your v articulate post above...

Cheers:*) and Aloha pumehana -- Jon

thank you Jon, and I apologize if the link amounts to an ad for a book, I took it as a humane society release about the link between factory farming and bird flu, not a promotion.

Rob and Greg, good for you for sharing your opinions, but Greg, I wonder if it's appropriate to engage in a personal attack on someone posting with a real name on a site that claims to exist to protect scientists from personal retribution. This illustrates the main flaw in this forum: anonymous attacks have a place in private peer review but not in the public debate.

kparcell: The anonymity business is tiresome. You claim this is your real name. I don't know if it is or it isn't, and if it is, I don't know you from a hole in the wall so your use of your "real name" adds nothing here. One thing anonymity adds is allowing the reader to concentrate on what is said. You are have it backwards regarding peer review. Many journals are now moving to open review (including the journal which I edit), not anonymous review, for exactly the reason that accountability is important there. Here, the emphasis is on what is said without confusing it with who says it.

In fact, peer review remains appropriately anonymous because reviewers need to speak without fear of retribution, and they remain private because anonymous critics cannot be held accountable. I take the time to criticize what you're doing here because you created a forum for misinformation, like Wikipedia, and if there is anything to your claims of authority, then all the worse because this then lends credibility to abusive sites.

In any event, I'm surprised that "revere" has engaged in a personal attack on me by questioning my honesty regarding my name. I assumed that you understood that using anonymity to protect yourself while you engage in attacking someone not anonymous is a very low act. Perhaps you do.

kparcells: LOL. You are one weird character. Sensitive, too. I wasn't claiming you were lying, only pointing out that whether you used your real name or not (and how do I know you did; because you said it was?) was irrelevant. I don't know what you know about peer review, but I've done lots of them and been both a reviewer (too often) and now an Editor in Chief, and I can tell you that open peer reivew is much better than the blind variety. If you have had experience with both, I'd be interested to hear why you think blind review was a better experience. Maybe we have just had different experiences.

Regarding the misinformation I've allegedly spread here, I hadn't understood that's what you were accusing me of. Since I am anxious to correct errors of fact, I would appreciate it if you would spell out exactly what misinformation we have spread here. If we have, I'll be glad to own up to it and correct it. I have to know what it is, first. From what I understood, you felt I didn't come down hard enough on factory farms in that particular post (although I have in other posts) and I didn't give the authors of the PNAS report enough credit. Perhaps. Since this implies you read the paper, I'd be glad to know where I slighted their contribution. Regarding how a particular post is written, feel free to get your own blog. You'll find it's hard work and you don't please everybody and sometimes you don't do as good a job as you'd like, although in this case I don't see the problem. Educate me and everyone else.

You've misunderstood. I'm not personally offended by your anonymous personal attack on me with continued namecalling. That's ordinary and no decent person will credit it. The surprise proceeds from the form of your attack being most contrary to your creed. However, there's nothing more obviously an enemy of rational thought than ad hominem, and I fully expect you "reveres" to employ it to defend your baseless position that your anonymous attacks are justified because they're safer for you than scrawling grafitti at the subway. As for spreading misinformation, yes you are, and I know I've already been clear about that. But really, attacking my name!

kparcell, I had forgiven you for ending your part of our conversation, and overlooked the minor slight of your withdrawing your kind attention to our befuddlement. I take back the forgiveness since I see there is nothing to forgive and.. I suppose the only polite course is to continue to overlook the overlooked. Naturally, I remain willing to forgive you again, when appropriate.

But, please, before you go, most of us here are pretty serious, I take what I learn here to my family, to my community health center, and to my city councillors. If you can correct any errors on the part of the Reveres, I and many others here, including the Reveres, will be forever in your debt.

I don't think I can help people who are so deliberately obtuse, but my recommendation is that you google demagogue, apologies to your poor suffering family, and see what Wikipedia has to say.

kparcells: I don't believe I called you a single name, not once. Your failure to engage in rational discussion says it all, I'm afraid.

I guess "attacking the man", which is argumentum ad hominem, by referring to him as a "weird character", is permissable in the courts of the glorious state of Kazakhstan, where anyone who objects is described as suffering from being "sensitive". But not in science.

Stop Factory Farming = Stop Bird Flu. See: WHO, UN, Worldwatch, Humane Society, Lancet, etc.

Stop Factory Farming = Same Old Idea Not Likely To Be Tried. See: Poultry Industry Journals, Effect Measure, Grafitti.

Why don't you give it up?

kparcell: I'm afraid you have overstepped the bounds of rational and civil discourse. Your position is so irrational it makes me suspect you wish to discredit opponents of factory farming by your immature behavior. The "conversation" is over.

Hey, your sandbox. But just to be clear, you discredit yourself through your words, and I support an immediate global moratorium on factory farming.

Kparcell has a history of vegetarian/factory farming
fanaticism in many places on the Internet . If you allow it
he will waste hours of your time and be extremely rude .
Do a google search on "Kparcell" for confirmation.

Ross: I warned him the last time. HUnfortunatley he/she/it/they doesn't engage in civil discourse so I'll have to take that into account.