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Plant RNA Paper Questioned

Remarkable findings of ingested plant miRNA in animal liver and blood draw speculation about the study’s validity.

By | April 16, 2012

Paddy fields in the northeast of ChinaWIKIMEDIA COMMONS, CHARLIE FONG

When the news broke last September about a study identifying small RNAs from ingested plants in animals, the focus shifted unexpectedly and quickly to potential implications for genetically modified (GM) food safety. But some experts in the field of RNA interference (RNAi) feared that the GM-related concerns were misplaced, and that there were more fundamental issues with the research.

The research team, led by Chen-Yu Zhang of Nanjing University, China, reported finding small RNA molecules from ingested rice and other plants in the bloodstream of both mice and humans and in mice livers. One of these RNAs from rice, they found, could inhibit a mouse protein that usually aids in removal of LDL or “bad” cholesterol from the blood.

The controversy surrounding the results started even before publication. An editor at Science, for example, rejected the manuscript because the discovery was “too extraordinary,” Zhang says—a response the group also received from Cell and Molecular Cell. The journal Cell Research accepted the report after a 2-year effort that included, according to Zhang, eight months of added experimental work to address reviewer critiques. Then, publication of the findings triggered concerns that small RNAs ingested from plants could affect how our bodies function, and unpredictable alterations in these molecules in GM plants might have unpredictable effects.

But RNAi expert Phillip Zamore, investigator at the Howard Hughes Medical Institute and Gretchen Stone Cook Professor of Biomedical Sciences at the University of Massachusetts Medical School, thinks that rushing to any conclusions about GM relevance is premature. “If you could dream up a molecule that you would worry about [for GM foods], this wouldn’t be it,” he said.

The deeper question, Zamore said, lies in the assertion that single-stranded RNA molecules like these microRNAs, or miRNAs, which silence expression of their RNA targets, can survive the digestive tract. They are “very fragile,” he said. The idea that these RNAs would not be immediately destroyed by the digestive enzymes of the gut “is controversial, to say the least,” he added. “Hundreds of millions of dollars have been spent trying to stabilize single-stranded nucleic acids in the bloodstream, let alone the digestive tract, and unmodified RNA has never been found to survive.”

But Zhang disagreed, pointing to a 2008 paper in which he and his colleagues demonstrated that endogenous animal miRNA could exist stably in the bloodstream, suggesting that blood-borne miRNAs somehow resist being broken down. So the new findings that miRNA from plants can be stable in blood or other tissues are not unprecedented, he argued. These latest results also raise the “surprising possibility that miRNAs derived from plants are especially stable, although this will need to be confirmed by others,” said plant biologist Eric Lam, a professor at Rutgers State University. Lam also noted that the miRNAs in question were ingested as part of plant tissues, not as unprotected RNAs, a possible explanation for their ability to survive the animal digestive tract.

Zamore is also concerned about the potential for cross-detection between plant and animal RNA sequences, given the short length of miRNA molecules, which average about 22 nucleotides, he said. “There’s a real likelihood that there will be at least one sequence in (the mouse or human) genome that matches the sequence from the plant.” As a result, the Zhang team’s findings could reflect degraded animal RNA sequences, rather than plant miRNA, he said, adding that the study design allowed for one mismatch within the detected sequences, increasing the likelihood of a fortuitous cross-detection.

Lam believes otherwise. While mismatching is “possible,” he said, it’s “not very likely.” Zhang added that the group performed an analysis for a chemical signature specific to plant miRNAs that “clearly demonstrated (that) serum miRNAs we detected were the exogenous plant miRNAs.”

Even if one accepts the premise that the RNAs identified in the study were, in fact, of plant origin, however, Zamore questions whether the levels detected have any meaningful impact on the animals. For miRNAs to be effective as interfering RNAs, Zamore said, they must be present in a quantity sufficient to match the quantity of the RNA targeted for silencing. “MicroRNAs function in cells at remarkably high levels,” he said. “For example, miRNA-122, which controls cholesterol production in the liver, is present at a half million molecules per cell.” The Zhang paper describes detecting the equivalent of just 853 copies per cell.

But Zhang argues that even these low levels are relevant, referring to previous studies that have identified “biologically active” levels of miRNAs ranging from 700 to 4,450 copies per cell. Lam noted that the relevant number probably depends on the specific RNA molecule. “It is at least possible that some small RNAs are more potent than others,” he said.

One thing that Zhang, Zamore, and Lam seemed to agree on is that unanswered questions remain, such as whether the RNAs are further modified in some way to pass digestion and how they affect human physiology. Indeed, Zhang says that the editor who rejected the paper as “too extraordinary” expressed interest in the group’s “next similar story.” Given the interest the first installment has generated, the editor won’t be alone in that interest.

Zhang et al., “Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA,” Cell Research, doi:10.1038/cr.2011.158, 2012.

Clarification (April 16, 2012): This story has been updated from its original version to clarify that plant miRNAs were found in the bloodstream of both mice and humans and in mice livers.

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Avatar of: Shi V. Liu

Shi V. Liu

Posts: 1457

April 16, 2012

I found the rejection by Zamore rests more on dogma than on reality.  Why doesn't he perform a similar experiment to see if the textbook statements really hold true before he launches such a harsh criticism on the new discovery?
On the other hand, Lam's comments do make some sense.
Attitude matters in dealing with extraordinary scientific discoveries.
In that regard, Science’s attitude in selling and still protecting a ridiculous “discoveryâ€쳌 of Arsenic Life should deserve more attention from scientific communities. 
And, CNS’s collective effort in consistently suppressing a fundamental discovery on cell reproduction and continuously promoting cell division fakery is a more serious problem in today’s science.

Avatar of: Dr. Keith R. Brunt

Dr. Keith R. Brunt

Posts: 1457

April 16, 2012

These are all legitimate and expected scientific questions that are part of the scientific process. Reproducibility and determination of physiological relevance. I would imagine that there is also some rejection-remorse. Should this turn out to be the seminal finding implicated, it could add another level of nutritional complement with vitamins, minerals, carbohydrates, and amino acids. I can only imagine the impact it will carry in citations, not to mention the implications to health, disease and pharmacology.

Avatar of: Guest

Anonymous

April 16, 2012

Well said.  So awfully much remains yet to be learned.  And the interplay between immune and auto-immune mechanisms -- may we never fail to consider -- show no signs of being either perfected, nor, as yet perfectible, nor predictable. 

We must be open to the need for ruling out potential roles of such variable miRNA transfer possibilities as might well be played by such vectors as biting insects, parasites of all kinds, bacteria, viruses, prions and some of the multifarious kinds of life forms we humans carry around in our various individual alimentary systems, symbiotically, merely tolerantly, or otherwise. Some such factors have indeed been found to bridge gaps which circumvent certain common rejection mechanisms and incompatibility blocks which have applied to the typical host, but which apply in atypical individuals. In fact, we don't even know which symbioses tend, under what conditions, to become pathogenic in some individuals -- hence such syndromes as IBS and Crones remain classified as idiopathic. And the dynamic among flora and fauna in one portion of one individual's alimentary canal can vary drastically from the set in another.  Over the entirety of life morphological variation history, many strange phenomena are unaccounted for etiologically, such that we we have little by way of empirical certainty to justify our preferred rationales for explaining either the typical host or the anomalistic one. 

Then too, take the example of such disparate phenomena as the disappearance of marsupialism across multiple species, in one geographical area, and the conservation of that complex set of traits in the same species in a widely separated geographical area. The popular notion that advantageous (or tolerated) random mutation explains how such a complex set of morphological changes can occur from WITHIN a single species, over many, many generations. But it falls far short of explaining how it would occur ACROSS multiple species in one locality, and not occur across those same separate species, over time, in another. 

Take, also, host graph rejection phenomena, some of which are anomalistic. Unknown to many outside research, and even some physicians working inside it, many surgical graph introductions in humans in the early days before tissue matching became the norm, were NOT REJECTED, despite tissue mismatches. To experiment with humans who are mismatched today would be a known risk of unconscionable proportions. But some non-rejections are recorded as having occurred early-on, and seem to have been forgotten, if not systematically hushed up.  But their occurrence suggests there is much remaining to be learned about host-graph rejection, and non-rejection factors, beyond those of tissue matching boundaries alone. (And if these rare cases of mis-match non-rejection did not occur as recorded, then they were reported by some otherwise highly credible individuals, I have read.)   

But, in any case, much criticism has been heaped on publishers in recent days -- some of which may be corrective, but much of which overlooks (I think) the great stimulus to thought and development of new questions and ways to test them, which have started out as unpopular, or maverick, or even goofy-sounding ideas... until they worked. And, even if not for the fact that some genuine quality of thought sometimes comes from trying out what may only have seemed to be goofy ideas, an occasional publication of something that may indeed prove out, over time to be genuinely goofy, this does not take away the entertainment value of discovery of such a faux pas by the reader who has a healthy appreciation of the benefit of occasional comic relief.

(: >)

Avatar of: mem_somerville

mem_somerville

Posts: 1457

April 16, 2012

I am eager to see another unrelated group confirm this. I had trouble getting even past figure 1, where there were no negative controls for the PCR.

But it seemed to require so many unusual steps: getting past stomach acids, persisting in serum, and then acting on the gene in a far-downstream place, uncharacteristic of this mechanism. Things that make you go: hmmm.

Avatar of: Hilary Butler

Hilary Butler

Posts: 1457

April 16, 2012

The article makes perfect sense.

Why would it make you go "hmmmmm"?  After all, if chemicals, and other viruses which we swallow or inhale, which don't get 'degraded' then enter the body and methylate DNA, then why couldn't food?

The real reason this is being questioned, is that it brings real meaning to the old wive's phrase which science disses which goes, "We are what we eat".  Perhaps the consequences of studies like this, could be massive litigation against the purveyors, and supporters of sugar, refined and fast foods, which can literally....  "make" a person what they eat all the time.  The medical literature is full of articles which show that over consumption of certain "food" can make you sick.  Maybe this is why. 

Proving that, might be something certain scientists want to avoid, because... the flow down effect will also be to seriously question the nutritional nouse of people who currently call themselves "doctors".

"An apple a day, you know, keeps the doctor away".  And just maybe, some day, someone will find "epigenetic" proof of that "old wives tale".  And just maybe, someday, people will realise that certain foods keep cancer away, precisely because micro RNA methylates DNA, keeping the "eater" more healthy.

While it's possible to "chose" what we eat, it's just unfortunate that we can't "chose" to avoid exposures to the huge numbers of environmental, agricultural and pharmaceutical toxins which also methylate genes, ... which that august body of science considers "safe", because they don't realise how those things also methylate genes and promote "non-health".

Avatar of:

Posts: 0

April 16, 2012

These are all legitimate and expected scientific questions that are part of the scientific process. Reproducibility and determination of physiological relevance. I would imagine that there is also some rejection-remorse. Should this turn out to be the seminal finding implicated, it could add another level of nutritional complement with vitamins, minerals, carbohydrates, and amino acids. I can only imagine the impact it will carry in citations, not to mention the implications to health, disease and pharmacology.

Avatar of:

Posts: 0

April 16, 2012

Well said.  So awfully much remains yet to be learned.  And the interplay between immune and auto-immune mechanisms -- may we never fail to consider -- show no signs of being either perfected, nor, as yet perfectible, nor predictable. 

We must be open to the need for ruling out potential roles of such variable miRNA transfer possibilities as might well be played by such vectors as biting insects, parasites of all kinds, bacteria, viruses, prions and some of the multifarious kinds of life forms we humans carry around in our various individual alimentary systems, symbiotically, merely tolerantly, or otherwise. Some such factors have indeed been found to bridge gaps which circumvent certain common rejection mechanisms and incompatibility blocks which have applied to the typical host, but which apply in atypical individuals. In fact, we don't even know which symbioses tend, under what conditions, to become pathogenic in some individuals -- hence such syndromes as IBS and Crones remain classified as idiopathic. And the dynamic among flora and fauna in one portion of one individual's alimentary canal can vary drastically from the set in another.  Over the entirety of life morphological variation history, many strange phenomena are unaccounted for etiologically, such that we we have little by way of empirical certainty to justify our preferred rationales for explaining either the typical host or the anomalistic one. 

Then too, take the example of such disparate phenomena as the disappearance of marsupialism across multiple species, in one geographical area, and the conservation of that complex set of traits in the same species in a widely separated geographical area. The popular notion that advantageous (or tolerated) random mutation explains how such a complex set of morphological changes can occur from WITHIN a single species, over many, many generations. But it falls far short of explaining how it would occur ACROSS multiple species in one locality, and not occur across those same separate species, over time, in another. 

Take, also, host graph rejection phenomena, some of which are anomalistic. Unknown to many outside research, and even some physicians working inside it, many surgical graph introductions in humans in the early days before tissue matching became the norm, were NOT REJECTED, despite tissue mismatches. To experiment with humans who are mismatched today would be a known risk of unconscionable proportions. But some non-rejections are recorded as having occurred early-on, and seem to have been forgotten, if not systematically hushed up.  But their occurrence suggests there is much remaining to be learned about host-graph rejection, and non-rejection factors, beyond those of tissue matching boundaries alone. (And if these rare cases of mis-match non-rejection did not occur as recorded, then they were reported by some otherwise highly credible individuals, I have read.)   

But, in any case, much criticism has been heaped on publishers in recent days -- some of which may be corrective, but much of which overlooks (I think) the great stimulus to thought and development of new questions and ways to test them, which have started out as unpopular, or maverick, or even goofy-sounding ideas... until they worked. And, even if not for the fact that some genuine quality of thought sometimes comes from trying out what may only have seemed to be goofy ideas, an occasional publication of something that may indeed prove out, over time to be genuinely goofy, this does not take away the entertainment value of discovery of such a faux pas by the reader who has a healthy appreciation of the benefit of occasional comic relief.

(: >)

Avatar of:

Posts: 0

April 16, 2012

I am eager to see another unrelated group confirm this. I had trouble getting even past figure 1, where there were no negative controls for the PCR.

But it seemed to require so many unusual steps: getting past stomach acids, persisting in serum, and then acting on the gene in a far-downstream place, uncharacteristic of this mechanism. Things that make you go: hmmm.

Avatar of:

Posts: 0

April 16, 2012

The article makes perfect sense.

Why would it make you go "hmmmmm"?  After all, if chemicals, and other viruses which we swallow or inhale, which don't get 'degraded' then enter the body and methylate DNA, then why couldn't food?

The real reason this is being questioned, is that it brings real meaning to the old wive's phrase which science disses which goes, "We are what we eat".  Perhaps the consequences of studies like this, could be massive litigation against the purveyors, and supporters of sugar, refined and fast foods, which can literally....  "make" a person what they eat all the time.  The medical literature is full of articles which show that over consumption of certain "food" can make you sick.  Maybe this is why. 

Proving that, might be something certain scientists want to avoid, because... the flow down effect will also be to seriously question the nutritional nouse of people who currently call themselves "doctors".

"An apple a day, you know, keeps the doctor away".  And just maybe, some day, someone will find "epigenetic" proof of that "old wives tale".  And just maybe, someday, people will realise that certain foods keep cancer away, precisely because micro RNA methylates DNA, keeping the "eater" more healthy.

While it's possible to "chose" what we eat, it's just unfortunate that we can't "chose" to avoid exposures to the huge numbers of environmental, agricultural and pharmaceutical toxins which also methylate genes, ... which that august body of science considers "safe", because they don't realise how those things also methylate genes and promote "non-health".

Avatar of:

Posts: 0

April 16, 2012

I found the rejection by Zamore rests more on dogma than on reality.  Why doesn't he perform a similar experiment to see if the textbook statements really hold true before he launches such a harsh criticism on the new discovery?
On the other hand, Lam's comments do make some sense.
Attitude matters in dealing with extraordinary scientific discoveries.
In that regard, Science’s attitude in selling and still protecting a ridiculous “discoveryâ€쳌 of Arsenic Life should deserve more attention from scientific communities. 
And, CNS’s collective effort in consistently suppressing a fundamental discovery on cell reproduction and continuously promoting cell division fakery is a more serious problem in today’s science.

Avatar of: Guest

Anonymous

April 16, 2012

This is in response to the article in "The Scientist," titled, "Plant RNA Paper Questioned."

Questioning any paper is healthy, provided it doesn't result in tossing out silverware with the dishwater.  If a research paper is honest about the methodology applied, the resulting data, and the author's interpretation of results, what has ordinary or extraordinary to do with whether it should be published?  And, if a conjectural interpretations of (honestly cited) methods and results later turn out to be false, that is how scientific progress in the real world keeps the good stuff and filters out the bad, is it not?

Perhaps what best describes what I wish to impart here is that distinctions are in order as between what is absurd versus what is "extraordinary" with respect to whether it should be published.

I, for one, have many areas of skepticism about some current presumptions in the sciences which seem to raise no objections when cited, because they have become  relegated to consensuses du jour.  (See elsewhere my observations on the necessity of essential working hypotheses, so long as they do not wax into dogma.)

Here are just a few such presumptions:

1.  Why do so many papers in bio-evo theory go unchallenged when they speak of species adaptations over time, caged so as clearly to imply that individual organisms which make up a species, proactively inform their gametes somehow to come up with an appropriate mutation or -- especially -- a series of appropriate mutations which target a solution to a specific environmental challenge?  (For example, what are the odds that a species under stress as a consequence of a substantial change in milieu, don't come up with so many mutations that are deleterious or inappropriate that astronomically overwhelm the chances of accidentally coming up with a situation-appropriate mutation... much less a series of same which not only must simply occur but, also, must occur in precisely the right order?)  Incidentally, I do not assert that, when pinned down on it, any serious scientist would claim to have specific knowledge of such an assumption, but literally thousands of published sentences in research papers imply or make explicit statements which leave no other alternative interpretation.

2.  Should the Michelson-Morley experiment in physics be treated as a finding so perfectly and exhaustively reliable as to be a fully authoritative establishment of  the presumption that light does not require any medium through which to be propagated?  No dark matter or quasi-particles were so much as perceived to apply at the time this classic experiment was originally run?  This is not to say the consensus that light does not require any medium through which to be propagated is wrong?  It is, rather, to express some doubt that Michelson and Morley established it as a certainty, much less that it should not be subjected to question at all (the definition of a dogma is something that is not to be questioned). 

3.  Should the work of Watson and Crick have been denied publication on grounds that their claims were "extraordinary?"  (This one is facetious, and made only to support a point.)

4.  But, zeroing in on the immediate research issue here -- whether we should take seriously even the remotest possibility that there could be transference of segments of miRNA or RNA or entire genes from other life forms to a human cells (whether to somatic or gametic cells) -- are we wise to reject the possibility summarily?  Actually, if there were to be any substance to it, it would certainly open up some avenues whereby some evolutionary phenomena might be made more sense of.

5.  Many papers on bio-evolution, imply or in some instances make bold statements which lend themselves to no other alternative conclusion, than that purely fortuitous mutations (or, more recently, fortuitous non-coding sequences) account for "adaptation."  Most mutations that occur to individual organisms in a species are either deleterious to coping of those organisms, or overwhelmingly inclined to be inappropriate to any specific new milieu change, or both.  And, even where such mutations occur in somatic cells, the gametic cells are a separate ballgame (no pun intended), so for adaptation-appropriate mutations to occur other than randomly, suggests that the gametic cells are capable of "reading" and "proactively responding to" specific environmental stresses to the somatic cells. The implications in writing, seem to be that the exponentially great odds against a fortuitous serendipitous random mutation (which would have to be in the gametic cells to be heritable) are able to occur due to having an enormous amount of time, and an enormous number of organisms to be distributed over and among.  But, if that rationalization is the best we can come up with, then it sets a precedent -- does it not -- to justify the possibility that, given a comparably elongated span of time, and an enormous number of individual organisms in a subject species, odds in the billions, trillions, or more of distributing all the other random chance mutations, such that bio-evo occurs.  (Now, I am not saying it does not occur, as there is overwhelming evidence that it has, and does.  My point is that, IF, AND TO THE EXTENT THAT, this rational is sufficient grounds for the assertion that all adaptation has no other etiology than this theoretical astronomically unlikely model to "justify" its having become a
consensus, then the very SAME principle can be applied to a rationalization of how transfers of miRNA could be transferred from one life form to another.  And, thence, to argue that no specific example has yet been established by way of experiment, is without merit.  (That is to say that if astronomical odds are acceptable for the purposes of deriving a bio-evolutionary model consensus, then they cannot, with any consistency of reason, be treated as ruling out the other.)

I do not offer these observations as argumentation for or against any current assumption made in biology.  I merely wish to assert that it would be inconsistent to allow research papers to state, or imply, that what cannot be demonstrated to be the consequence of experiments, and yet is sufficient basis for a consensus in one field of study, should not be treated as grounds for ruling out a hypothetical postulation in another.   Also, if results of the experimentations in the instant case are even remotely suggestive that miRNA may be transferred from another life form to another, we have a precedent for saying, "It probably does occur, even if only in one instance out of an astronomically large number of samples over many millions of generations.

Our best models in science are always open to being upgraded, are they not. 
So, these things considered, let me suggest again, that as long as there is no misrepresentation made by a researcher as to details of methodology or results obtained from it, no publisher should be too hasty in denying publication on grounds of something's being extraordinary, or not yet fully demonstrated experimentally, should it?

(Please forgive a few errors of spelling, grammar and syntax here. One's reasoning can be at once clear and rational and, also, difficult to articulate. And if the essence is communicated, allow, please, a few typos and such... ( : < )

Avatar of:

Posts: 0

April 16, 2012

This is in response to the article in "The Scientist," titled, "Plant RNA Paper Questioned."

Questioning any paper is healthy, provided it doesn't result in tossing out silverware with the dishwater.  If a research paper is honest about the methodology applied, the resulting data, and the author's interpretation of results, what has ordinary or extraordinary to do with whether it should be published?  And, if a conjectural interpretations of (honestly cited) methods and results later turn out to be false, that is how scientific progress in the real world keeps the good stuff and filters out the bad, is it not?

Perhaps what best describes what I wish to impart here is that distinctions are in order as between what is absurd versus what is "extraordinary" with respect to whether it should be published.

I, for one, have many areas of skepticism about some current presumptions in the sciences which seem to raise no objections when cited, because they have become  relegated to consensuses du jour.  (See elsewhere my observations on the necessity of essential working hypotheses, so long as they do not wax into dogma.)

Here are just a few such presumptions:

1.  Why do so many papers in bio-evo theory go unchallenged when they speak of species adaptations over time, caged so as clearly to imply that individual organisms which make up a species, proactively inform their gametes somehow to come up with an appropriate mutation or -- especially -- a series of appropriate mutations which target a solution to a specific environmental challenge?  (For example, what are the odds that a species under stress as a consequence of a substantial change in milieu, don't come up with so many mutations that are deleterious or inappropriate that astronomically overwhelm the chances of accidentally coming up with a situation-appropriate mutation... much less a series of same which not only must simply occur but, also, must occur in precisely the right order?)  Incidentally, I do not assert that, when pinned down on it, any serious scientist would claim to have specific knowledge of such an assumption, but literally thousands of published sentences in research papers imply or make explicit statements which leave no other alternative interpretation.

2.  Should the Michelson-Morley experiment in physics be treated as a finding so perfectly and exhaustively reliable as to be a fully authoritative establishment of  the presumption that light does not require any medium through which to be propagated?  No dark matter or quasi-particles were so much as perceived to apply at the time this classic experiment was originally run?  This is not to say the consensus that light does not require any medium through which to be propagated is wrong?  It is, rather, to express some doubt that Michelson and Morley established it as a certainty, much less that it should not be subjected to question at all (the definition of a dogma is something that is not to be questioned). 

3.  Should the work of Watson and Crick have been denied publication on grounds that their claims were "extraordinary?"  (This one is facetious, and made only to support a point.)

4.  But, zeroing in on the immediate research issue here -- whether we should take seriously even the remotest possibility that there could be transference of segments of miRNA or RNA or entire genes from other life forms to a human cells (whether to somatic or gametic cells) -- are we wise to reject the possibility summarily?  Actually, if there were to be any substance to it, it would certainly open up some avenues whereby some evolutionary phenomena might be made more sense of.

5.  Many papers on bio-evolution, imply or in some instances make bold statements which lend themselves to no other alternative conclusion, than that purely fortuitous mutations (or, more recently, fortuitous non-coding sequences) account for "adaptation."  Most mutations that occur to individual organisms in a species are either deleterious to coping of those organisms, or overwhelmingly inclined to be inappropriate to any specific new milieu change, or both.  And, even where such mutations occur in somatic cells, the gametic cells are a separate ballgame (no pun intended), so for adaptation-appropriate mutations to occur other than randomly, suggests that the gametic cells are capable of "reading" and "proactively responding to" specific environmental stresses to the somatic cells. The implications in writing, seem to be that the exponentially great odds against a fortuitous serendipitous random mutation (which would have to be in the gametic cells to be heritable) are able to occur due to having an enormous amount of time, and an enormous number of organisms to be distributed over and among.  But, if that rationalization is the best we can come up with, then it sets a precedent -- does it not -- to justify the possibility that, given a comparably elongated span of time, and an enormous number of individual organisms in a subject species, odds in the billions, trillions, or more of distributing all the other random chance mutations, such that bio-evo occurs.  (Now, I am not saying it does not occur, as there is overwhelming evidence that it has, and does.  My point is that, IF, AND TO THE EXTENT THAT, this rational is sufficient grounds for the assertion that all adaptation has no other etiology than this theoretical astronomically unlikely model to "justify" its having become a
consensus, then the very SAME principle can be applied to a rationalization of how transfers of miRNA could be transferred from one life form to another.  And, thence, to argue that no specific example has yet been established by way of experiment, is without merit.  (That is to say that if astronomical odds are acceptable for the purposes of deriving a bio-evolutionary model consensus, then they cannot, with any consistency of reason, be treated as ruling out the other.)

I do not offer these observations as argumentation for or against any current assumption made in biology.  I merely wish to assert that it would be inconsistent to allow research papers to state, or imply, that what cannot be demonstrated to be the consequence of experiments, and yet is sufficient basis for a consensus in one field of study, should not be treated as grounds for ruling out a hypothetical postulation in another.   Also, if results of the experimentations in the instant case are even remotely suggestive that miRNA may be transferred from another life form to another, we have a precedent for saying, "It probably does occur, even if only in one instance out of an astronomically large number of samples over many millions of generations.

Our best models in science are always open to being upgraded, are they not. 
So, these things considered, let me suggest again, that as long as there is no misrepresentation made by a researcher as to details of methodology or results obtained from it, no publisher should be too hasty in denying publication on grounds of something's being extraordinary, or not yet fully demonstrated experimentally, should it?

(Please forgive a few errors of spelling, grammar and syntax here. One's reasoning can be at once clear and rational and, also, difficult to articulate. And if the essence is communicated, allow, please, a few typos and such... ( : < )

Avatar of:

Posts: 0

April 17, 2012

We are talking about the paper with the "inadvertently" duplicated images... If they submit sloppy papers to Science, how can they expect the Editor to take them seriously. Extraordinary claims require extraordinary evidence - not sloppy figures. http://t.co/SrXwAXYQ

Avatar of:

Posts: 0

April 17, 2012

Immunologists should remember in 1960s immune RNAs (iRNAs) were used to treat diseases in animals, which were also termed as regulatory RNAs. It is likely that some RNAs are resistant to the degrading evironments of the digestive tract and blood. Why not the miRNAs from GM food?

Avatar of:

Posts: 0

April 17, 2012

I think they were lucky to have it deemed too extraordinary by the knowledge gate keepers of Science (and Nature), more often they reject papers on the basis that it is not of general (i.e. their) interest...

Avatar of:

Posts: 0

April 17, 2012

The article made perfect sense to me in the context Ms. Butler mentions. I cited it in "Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors" http://dx.doi.org/10.3402/snp.... to bolster my across-species argument.

Other cited works suggest that viruses may drive evolution via the molecular mechanisms for pre-existing variability in intracellular signaling, effects on nutrient metabolism, and subsequent effects on the production of pheromones that standardize nutrient-dependent reproduction and control speciation. For example, a gene that codes for the mammalian olfactory
receptor, OR7D4, links food odors to human hunger, dietary restraint, and
adiposity. OR7D4 also exemplifies a direct link
from human social odors to their perception and to unconscious affects
on human behavior associated with human olfactory-visual integration.

It has also become clearer that nutrient chemical/odor receptors, like OR7D4 provide a clear evolutionary trail that can
be followed from unicellular organisms to insects to humans. It should surprise no one that organisms must acquire nutrients containing small RNAs required for the calibration of individual survival and that the small RNAs also serve a purpose in standardization and control of species survival via their metabolism to pheromones in accord with the basic principles of biology and levels of biological organization.

One study or proposal of cause and effect does not an across-species model make. But there is a model that accommodates the important findings that Zhang et al., provide, and no model I know of for evolution via pre-existing genetic variability that doesn't. It may be frightening for those who think this will force them to choose between pre-existing genetic variability and random mutation when they attempt to explain natural selection, but perhaps they can take comfort in the thought that viruses and/or small RNAs from plants cause either the genetic variability, the random mutations, or both.

Avatar of: jvkohl

jvkohl

Posts: 53

April 17, 2012

The article made perfect sense to me in the context Ms. Butler mentions. I cited it in "Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors" http://dx.doi.org/10.3402/snp.... to bolster my across-species argument.

Other cited works suggest that viruses may drive evolution via the molecular mechanisms for pre-existing variability in intracellular signaling, effects on nutrient metabolism, and subsequent effects on the production of pheromones that standardize nutrient-dependent reproduction and control speciation. For example, a gene that codes for the mammalian olfactory
receptor, OR7D4, links food odors to human hunger, dietary restraint, and
adiposity. OR7D4 also exemplifies a direct link
from human social odors to their perception and to unconscious affects
on human behavior associated with human olfactory-visual integration.

It has also become clearer that nutrient chemical/odor receptors, like OR7D4 provide a clear evolutionary trail that can
be followed from unicellular organisms to insects to humans. It should surprise no one that organisms must acquire nutrients containing small RNAs required for the calibration of individual survival and that the small RNAs also serve a purpose in standardization and control of species survival via their metabolism to pheromones in accord with the basic principles of biology and levels of biological organization.

One study or proposal of cause and effect does not an across-species model make. But there is a model that accommodates the important findings that Zhang et al., provide, and no model I know of for evolution via pre-existing genetic variability that doesn't. It may be frightening for those who think this will force them to choose between pre-existing genetic variability and random mutation when they attempt to explain natural selection, but perhaps they can take comfort in the thought that viruses and/or small RNAs from plants cause either the genetic variability, the random mutations, or both.

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Kamoun Lab @ TSL

Posts: 1457

April 17, 2012

We are talking about the paper with the "inadvertently" duplicated images... If they submit sloppy papers to Science, how can they expect the Editor to take them seriously. Extraordinary claims require extraordinary evidence - not sloppy figures. http://t.co/SrXwAXYQ

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JXG

Posts: 9

April 17, 2012

Immunologists should remember in 1960s immune RNAs (iRNAs) were used to treat diseases in animals, which were also termed as regulatory RNAs. It is likely that some RNAs are resistant to the degrading evironments of the digestive tract and blood. Why not the miRNAs from GM food?

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Lessofthesame

Posts: 3

April 17, 2012

I think they were lucky to have it deemed too extraordinary by the knowledge gate keepers of Science (and Nature), more often they reject papers on the basis that it is not of general (i.e. their) interest...

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azar123

Posts: 11

April 18, 2012

 Science and natures are the bullys  of science, most retracted articles comes from them as they have a close nite of reviewers and institutional mafia. They should be disbarred,  as in many case they do worst then good as their contribution ot the current scientific advancement are  minimal/null . The are holding the lamp post of the flavour of the month while scientific truth is only secondery, will it make noise that their  guiding light. Most retractable papers come from them

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Stefan Jaronski

Posts: 1

April 18, 2012

dsRNa CAN successfully survive ingestion by insects and be absorbed to affect the insect's target genes. This has been demonstrated by Baum et al 2007 Nature Biotechnology 25(11): 1322-1326; and Tian et al 2009 PLoS ONE 4(7): e6225. doi:10.1371/journal.pone.0006225  and currently both Monsanto and DOW Pioneer are actively researching potential and implementation in GMO crops to succeed or complement current Bt-gene technology. Granted, the coleopterans and lepidipterans used have generally alkaline midgut fluids in contrast to acid gut fluids in vertebrates, but the insects have full complement of digestive enzymes. The key necessary datum is whether or not dsRNA will survive acid hydrolysis.  

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Q

Posts: 1457

April 18, 2012

The mature miRNA is single strand. How about the pre-miRNA? There should be lots of pre-miRNA in the plant????

April 18, 2012

How about plant based vaccines where the RNA contamination might directly get injected to humans????

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tbmd

Posts: 2

April 18, 2012

 potentially worse are the animal cultured vaccines with DNA contamination or possible prion contaminated from using bovine serum for the passages of vero cells. We already know what introduction of SV40 into the population created. there are more (maurine and porcine) viral contaminated vaccines in which the long term exposure and impact is unknown

April 18, 2012

True, but this just adds another lever of uncertainty.

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Posts: 0

April 18, 2012

 Science and natures are the bullys  of science, most retracted articles comes from them as they have a close nite of reviewers and institutional mafia. They should be disbarred,  as in many case they do worst then good as their contribution ot the current scientific advancement are  minimal/null . The are holding the lamp post of the flavour of the month while scientific truth is only secondery, will it make noise that their  guiding light. Most retractable papers come from them

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Posts: 0

April 18, 2012

dsRNa CAN successfully survive ingestion by insects and be absorbed to affect the insect's target genes. This has been demonstrated by Baum et al 2007 Nature Biotechnology 25(11): 1322-1326; and Tian et al 2009 PLoS ONE 4(7): e6225. doi:10.1371/journal.pone.0006225  and currently both Monsanto and DOW Pioneer are actively researching potential and implementation in GMO crops to succeed or complement current Bt-gene technology. Granted, the coleopterans and lepidipterans used have generally alkaline midgut fluids in contrast to acid gut fluids in vertebrates, but the insects have full complement of digestive enzymes. The key necessary datum is whether or not dsRNA will survive acid hydrolysis.  

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Posts: 0

April 18, 2012

The mature miRNA is single strand. How about the pre-miRNA? There should be lots of pre-miRNA in the plant????

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Posts: 0

April 18, 2012

How about plant based vaccines where the RNA contamination might directly get injected to humans????

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Posts: 0

April 18, 2012

 potentially worse are the animal cultured vaccines with DNA contamination or possible prion contaminated from using bovine serum for the passages of vero cells. We already know what introduction of SV40 into the population created. there are more (maurine and porcine) viral contaminated vaccines in which the long term exposure and impact is unknown

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Posts: 0

April 18, 2012

True, but this just adds another lever of uncertainty.

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Posts: 0

April 19, 2012

I am surprised the paper was published without simple experiment  - feeding the mice and then analyzing the stomach content for the presence of the miRNA. Even cleaner experiment - in vitro mixing extract from rice and mice stomach secret for 10-20 min and testing for the presence of the miRNA=> if detected as intact - then there may be a possibility for the validity of the paper. I doubt. If the above-mentioned experiments were not done, then this is all a bull... no matter what; just because without these control-experiments everything else is a pseudo-paper & pseudo-science.  Chris, Ph.D. in Molecular Genetics.

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Posts: 0

April 19, 2012

....Continuing:  On the other hand - there may be a chance for some conservative sequences to be present (and expressed) in the plant genomes and animal genomes. This is a known fact especially concerning short nucleotide sequences.  Since I did not bother to read the paper, I hope the particular miRNA had been hybridized to a labeled genomic (human & mice) DNA (or else appropriate detection was performed) in order to investigate if this miRNA was from endogenous (human/mice) or exogenous (rice) origin. 

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Hristem

Posts: 1457

April 19, 2012

I am surprised the paper was published without simple experiment  - feeding the mice and then analyzing the stomach content for the presence of the miRNA. Even cleaner experiment - in vitro mixing extract from rice and mice stomach secret for 10-20 min and testing for the presence of the miRNA=> if detected as intact - then there may be a possibility for the validity of the paper. I doubt. If the above-mentioned experiments were not done, then this is all a bull... no matter what; just because without these control-experiments everything else is a pseudo-paper & pseudo-science.  Chris, Ph.D. in Molecular Genetics.

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Hristem

Posts: 1457

April 19, 2012

....Continuing:  On the other hand - there may be a chance for some conservative sequences to be present (and expressed) in the plant genomes and animal genomes. This is a known fact especially concerning short nucleotide sequences.  Since I did not bother to read the paper, I hope the particular miRNA had been hybridized to a labeled genomic (human & mice) DNA (or else appropriate detection was performed) in order to investigate if this miRNA was from endogenous (human/mice) or exogenous (rice) origin. 

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Posts: 0

April 29, 2012

  keepitlegal said, First:
"Questioning any paper is healthy, provided it doesn't result in
tossing out silverware with the dishwater.  If a research paper is
honest about the methodology applied, the resulting data, and the
author's interpretation of results, what has ordinary or extraordinary
to do with whether it should be published?  And, if a conjectural
interpretations of (honestly cited) methods and results later turn out
to be false, that is how scientific progress in the real world keeps the
good stuff and filters out the bad, is it not?"

    "Ordinariness" may rightfully influence publication. A high-profile journal -- or any journal that receives many more submission than it can print, and certainly "broad-range" journals like Science and Nature -- has every right to select only those papers that are most likely to be of interest to a broad readership.  Second, a journal certainly has the right to accept only papers which advance fundamental understanding in a field, or -- as was Cell's original policy -- report a novel advance in a field. Finally, I firmly believe that a journal has a responsibility not to publish work which is redundant, contributes nothing new, or repeats previous work without taking it further.

Unrelated to this, keepitlegal added:
"1.  Why do so many papers in bio-evo theory go unchallenged when they
speak of species adaptations over time, caged so as clearly to imply
that individual organisms which make up a species, proactively inform
their gametes somehow to come up with an appropriate mutation ..... "
 and
"5.  Many papers on bio-evolution, imply or in some instances make
bold statements which lend themselves to no other alternative
conclusion, than that purely fortuitous mutations (or, more recently,
fortuitous non-coding sequences) account for "adaptation."  Most
mutations that occur to individual organisms in a species are either
deleterious to coping of those organisms, or overwhelmingly inclined to
be inappropriate to any specific new milieu change, or both."

  These statements seem closer to Intelligent Design propaganda than to reasoned criticism of scientific publishing. Furthermore, it is both obvious from genetic principles, and well-established experimentally, that *most* single-nucleotide mutations have little or no phenotype. It is also probable that *most* large-scale genomic rearrangements are not deleterious. (This is less certain because, although most observed rearrangements are not very harmful, I think it is not known how frequent are the lethal rearrangements which are not observable.)

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pgegen

Posts: 1

April 29, 2012

  keepitlegal said, First:
"Questioning any paper is healthy, provided it doesn't result in
tossing out silverware with the dishwater.  If a research paper is
honest about the methodology applied, the resulting data, and the
author's interpretation of results, what has ordinary or extraordinary
to do with whether it should be published?  And, if a conjectural
interpretations of (honestly cited) methods and results later turn out
to be false, that is how scientific progress in the real world keeps the
good stuff and filters out the bad, is it not?"

    "Ordinariness" may rightfully influence publication. A high-profile journal -- or any journal that receives many more submission than it can print, and certainly "broad-range" journals like Science and Nature -- has every right to select only those papers that are most likely to be of interest to a broad readership.  Second, a journal certainly has the right to accept only papers which advance fundamental understanding in a field, or -- as was Cell's original policy -- report a novel advance in a field. Finally, I firmly believe that a journal has a responsibility not to publish work which is redundant, contributes nothing new, or repeats previous work without taking it further.

Unrelated to this, keepitlegal added:
"1.  Why do so many papers in bio-evo theory go unchallenged when they
speak of species adaptations over time, caged so as clearly to imply
that individual organisms which make up a species, proactively inform
their gametes somehow to come up with an appropriate mutation ..... "
 and
"5.  Many papers on bio-evolution, imply or in some instances make
bold statements which lend themselves to no other alternative
conclusion, than that purely fortuitous mutations (or, more recently,
fortuitous non-coding sequences) account for "adaptation."  Most
mutations that occur to individual organisms in a species are either
deleterious to coping of those organisms, or overwhelmingly inclined to
be inappropriate to any specific new milieu change, or both."

  These statements seem closer to Intelligent Design propaganda than to reasoned criticism of scientific publishing. Furthermore, it is both obvious from genetic principles, and well-established experimentally, that *most* single-nucleotide mutations have little or no phenotype. It is also probable that *most* large-scale genomic rearrangements are not deleterious. (This is less certain because, although most observed rearrangements are not very harmful, I think it is not known how frequent are the lethal rearrangements which are not observable.)

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Anonymous

May 7, 2012

To say that any of my statements comes close to "intelligent design" is both a false accusation of my ideas, and an intellectual cop out on your behalf. My statements are my statements, and are not derivatives of any dogma. If you are unable to add value by way of showing me wrong in what I HAVE said, then the least you could do is avoid attributing to it something I have NOT said. Let me assure you that any fact or any compelling argumentation against one or more of my statements is WELCOME by me, as a person who seeks correction, and who views learning as being BOTH a process of being given access to further ADDED VALUE to reconsider by AND as a cybernetic process, whereby discourse enables corrections in directions of the learner's thinking. (I do not share the popular view that learning means memorizing only the facts and arguments provided by others, and then defending those facts and arguments against any new information or reasoning -- an infirmity found even among many who have graduated from some universities whose professors, surely, surely, know better.

So, your cheap shot attempt to "explain away" a statement of mine (to wit, my statement number 5)on basis that YOU DISCERN some dogmatic intent on my part, indicates actually that you, yourself, may be entertaining a dogmatic bias in your own thinking.

With perhaps a fuller appreciation for advanced issues of scientific certainty, in context of unfalsifiables, and with perhaps a far more advanced appreciation of the limits of epistemic and ontological access of the human experience than you indicate awareness of, I balk at the suggestion I would treat as a certainty any side of any question for which there is not, to my knowledge, any empirical grounds for knowledge certain to resolve which alternative belief in its regard, is certain to the absolute exclusion of the other.

From where I sit, philosophically, it is appalling to me to observe how many inside science academia and in research,AS WELL AS how many of various meta-physical dogmatic persuasions -- fail to discern the difference between knowledge certain, on the one hand, and convenient, but uncertain, assumption, on the other.
Dogmatism, in my view, is the insistence that ANY uncertain thing is certain and true (or that it certainly is NOT true) where neither or none of the alternatives is by humans, as yet, empirically established with certainty.

Simply because something does not suit one's own intuition, or the intuition of one's fellows in stance, does not a certainty provide. What is "true" about nature, or untrue about nature, is neither determined by popular vote of many, nor even by popular vote of an elite esoteric community who perceive themselves to have a license to "know" things they have no actual means of knowing.

Much in scientific assumptions is convenient to assume, and useful in being applied in a constant struggle to upgrade and to update tentative syntheses. Much in scientific assumptions is NOT falsifiable and, therefore, is NOT known for a certainty to be "true" or valid or knowable. And, if everything taught in academia were subjected to the rule it must be proved for a certainty, then it would not appear in any textbook. Take, for example, Newton's First Law. Where was the confirming experiment performed? It had to have been performed where no outside force was present... not even the force of gravity from a star thirteen billion light years distant. Newton (whom I much respect, even as I much respect Charles Darwin) argued out of one side of his mouth the standard that nothing can be known but that it can be empirically confirmed, yet argued out of the other side of his mouth that his "laws" are "self-evident. In all due respect, let us be CONSISTENT. Let us not take that which is supported by non-exhaustive, non-empirically testable, circumstantial evidence and -- because it is useful to us, and serves as a pragmatic working hypothesis, and make and EXCEPTION for it, and call that EXCEPTION by the name of "self-evident." Or, if we wish to press the case for self-evidence, then let us not use the "empirical standard" to exempt ANYTHING CLAIMED BY ANYONE, to whom it is "self-evident." To recognize and acknowledge this conflict of standards, as being something one can, by virtue of being educated (inculcated with the double standard) apply it when we wish to assert one thing, and deny its application when we wish to argue against another.

This point is not offered to question the wonderful tool of having WORKING HYPOTHESES,nor to TREAT any useful working hypothesis or methodology as "in error." It is merely offered in evidence that there is SUBJECTIVITY, alone, that allows a double standard for including one thing and excluding another. But, UNLIKE EITHER the "intelligent design" dogmatist or the bio-science dogmatists, it is my contention that what is established as empirical CERTAINTY, should be labeled accordingly, and what is NOT empirical certainty should not be stamped with the same stamp when, and if, it suits any individual or group of dogmatic thinkers who may happen to have some clout in so doing.

Even consensuses are tentative in science. That is historical fact. One day "dark matter" was not embraced as existent, and following a vote, it was "science." So, indeed, I would not support an argument that, because something is or is not currently in fashion with the bulk of the scientific community, therefore, it is anti-science, any supporter of it a maverick, and it is admissible for use in textbooks, whereas, one day earlier it was anti-science.

But do I subscribe to the formal school of thinking called "intelligent design?" Most emphatically, NO! Why not? Because its formal assertions strike me as radical, logically inconsistent and its arguments for its case strike me as poorly informed and eclectic. That is, it would seem to argue in favor of including its own empirically unfalsifiables in formal education, but not, also, the disparate unfalsifiables of other religions. They would, it seems, open a Pandoras box to pry their way into education and then quickly shut it before a crowd of other opinions join the fray. Again, let us be CONSISTENT. But, then, do I share at least a few of the stances in belief with the "intelligent design" school of thinking? Yes. I do; and, as I have pointed out elsewhere, SO, TOO, DO A NUMBER OF scientist acquaintances of mine, both inside and outside family. Like me, these, several, many of them PhDs, are offended by atheistic professors who avow their own unfalsifiable belief stances in classrooms, even as they insist that "intelligent deisign" thinkers do not. So, the great question for me, waxes into, "Why do not those of various opinions on what should and should not be included in science in academia, seek to agree upon CONSISTENT criteria -- in recognition that the issue of what is and is not falsifiable does not seem to suit anyone. The issues CANNOT be logically nor reasonably based upon what is empirically ascertainable and what is not, lest much that is of value in science would not pass that standard.

(Anyone who doubts this cannot have studied or understood the most rudimentary arguments in formal epistemology, and surely could not be familiar with the vast bulk of the discourse called "The Science Wars" that took place between self-styled scientific realists and postmodernist critics during the 1990s. (Oddly, many in the sciences are grossly unaware of how many claims made, even to this very day, among members of the scientific community, did not, and do not now, stand up to scrutiny, and are HIGHLY reliant upon philosophical assumptions that are neither logically consistent nor empirically verifiable.

Today, many who fancy themselves to be capable of making a case for what should and should not be included in education, as science, and as meta-science, repeat mindless questions, and cite ridiculous aphorisms, on each and both sides of the issues. Radical argues with radical; dogmatist, with dogmatist. And I disavow the ignorant banter of each and both, and long for an open-minded discourse that shows no sign yet of approaching.

Let that which is called science apply the same standards to ITS OWN convenient and internally preferred myths as are applied to any OTHER myths. (And no claim is made by me that, just because something is a myth it is concomitantly, categorically untrue. It merely is UNFALSIFIABLE, unproved, and undisproved for a certainty.

Let me be on the front lines of those who argue that science could not move forward on any other basis than objectivity, nor objectivity on any other basis that self-honest admission of what we have established as CERTAIN, on the one hand, and what we strongly "believe" to be good and practical myth as TENTATIVE. That is the ax I would grind, and the only ax. Let none have license to go unchallenged in positing what he chooses to believe without absolute proof, as obvious or as "self-evident," and what he does NOT choose to believe without absolute proof, as absurd until proven.

And, any who would claim to be at once both "scientifically literate," and empirically grounded in all his "beliefs" about nature, and does not recognize how thin, if even existent, be the ice he stands on, under what definition of literacy falls such a lack of familiarity with the very ideal of science (by which ideal, it is open to new information and to change of stance, and, by that virtue alone distinguishable from DOGMATISM.

To adopt one view that suits one's self, and refuse to acknowledge or even consider another as worthy of being studied, without even allowing that there is a contradiction in that, is not only dogmatism, it is self-based (or group concensus-based) bigotry.

It is my contention, here and in all other places, that dogma is never science, and science is never dogma. Science is open, or it is not science, but dogma. (And lest anyone cite the so-called term "The Central Dogma of Bio-science," as an exception, let him verify it, that Frick, himself, allowed that his choice of words for it was unfortunate.

If I challenge one field of science, on grounds it proffers myth as reason that is superior to that of admitting, "We do not know," when indeed we do not... then I do not hesitate to challenge another field, if it make a similar claim. Neither do i believe all evidence that shall ever be on the table is yet on the table.

Neither do I "believe" every currently preferred majority stance of ANY unfalsifiable assertion or consensus of ANY field of scientific endeavor. For example, it is my personal stance (variously referred to by some as a tentative "belief" or working hypothesis) that there are multiple emergent dynamics in physics, and not just the two emergent scale-level ones most physicists acknowledge presently: the classical-scale dynamic and the quantum scale dynamic. I have no proof, and thence no certainty that other dynamics occur at larger and smaller scales of "existence." But I perceive and believe and have taken the TENTATIVE stance that they do. (This view departs from the currently popular multiverse view, but it is more intuitive to me, and in no way damages my life nor anybody elses, and I am TENTATIVELY satisfied that it does not contradict ANY empirical evidence, and does not defy any rule of logic.

(All logic, by definition, leads back to whatever assumptions (postulates) one begins with, by way of operations assigned to the task, and CANNOT falsify those assumptions, nor certify them. Hence, until and unless an assumption is found certainly false, it remains an ALTERNATIVE possibility. And it would be a shame for any scientist, or philosopher of science, to be ignorant of the limits of logic, much less the non-exhaustion up to present date, at least, of all there is to be known, tried, or discovered about nature, or the potentiality for anything to exist outside nature.

Science is hamstrung by any self-deception or self-persuasion that the scientist knows anything he does not know to be certain is certain, or that anything he does not know to be impossible is impossible.

So, while some stances are USEFUL and may have held up under all (science history indicates most, rather than all... vis a vis the compelling argumentations of Thomas Cuhn and others, science rules assumptions in on basis of incomplete evidence -- never all the evidence -- and were we to have "all" the evidence to be found in nature, we could never have CERTAINTY we had it all... a deep, deep paradox, is it not?

Stance becomes dogmatism at precisely the point at which it is asserted as the only possibility, barring any other, where no empirical falsification (as yet) exists to rule it completely in, or completely out.

An example of something I, that comes from no dogma, and which I cannot certify and recognize and acknowledge I cannot certify -- but CHOOSE to believe, is that matter and energy are granular (that the universe is not seamless) but that each particle of mass or energy is of quantum uniqueness, and that time passes in discrete increments, not unlike the ticking of a clock, with each quantum of change in time allowing at some level of resolution no further travel of any particle to any farther increment than the adjacent quantum unit away (essentially a quantum time unit) with each such time unit increment providing a new configuration of all the particles, such that none has moved more than one increment, by the special distance, relative to each unique frame of space-time, by a single Planck unit length (unless that, too, be divisible. (This is too brief a space to put it in. My apologies for the resulting garble.)

But do I perceive that, because this physical view is intuitive to me, even if a thousand physicists were to gather into a consortium and vote in favor of it, that any OTHER view would thereby be rendered unlikely, or unrealistic, or unreasonable, or naive, or just not worth being considered... Not I.

Who would be WRONG in such a variant view, by my standards, would be one who would "explain away" any view but his own, whether I share that view, or whether I do not share that view. The dogmatist is he who will not allow credence or consideration of any conclusion UN-RULE-IN AND UN-RULED OUT, but his own, and of those who buy in with him on his own.

If you, pgegen, would wish to offer additional value to my statement number 5, you would do well to address what it SAYS, and not what you, in your own dogmatic bias, perceive it to border upon saying. That I would welcome.

Being one who seeks additional facts, more compelling argumentations, and thus opportunities to self-correct -- and who perceives THAT to be what learning is all about, let me assure you that you are welcome to upgrade or update my thinking. On the other hand, if the best you have to offer me is an attempt to "explain away" what I said on basis that it strikes you as bordering upon one of your own dogmatic biases, then you add no value no opportunity for ANYONE to progress in learning anything.

A mind fully open to learning -- rather than defending dogmatism -- is a mind open to at least the possibility that one's unfalsifiable opinions, no matter how widely shared with others who hold themselves out to have superior vision about such things, knows one iota more about nature than he ACTUALLY knows about it. Were nature capable of caring what you think, or what I think, or what anyone else THINKS, I doubt it change itself to conform to that; so it is my best guess that our science, as the study of it, can at best attempt to do the conforming -- the adamant egos insistence notwithstanding. Let us take care that we recognize our best scientific potential, therefore, to continue to conform our thinking to it, or simply wallow in dogmatically conserved ignorance.

(And, by the way, all certainty, borne of experience, is borne of experience that is local, and perceptions that are subjective. So, the claim of certainty by another, on basis of what experimental or observational findings may have resulted is, locally heresay, until and unless we have done that experiment or observation FIRST HAND. And many of us -- including, I dare say, you, have NOT conducted first hand every experiment or observation you presently BELIEVE to have revealed what you have been told about "science." (Have YOU personally replicated Michelson and Morley's experiment in resolving whether light requires an aether through which to perpetuate? They did not factor in "dark matter," or any other more recent possible media (some of which have not been precisely corroborated but which fit nicely, in the interim as fudge factors.) Do you dare to question to current wisdom that the proxy evidence that something MUST exist, lest our formulas are wrong,as
being compelling. And do you, turn right around and deny that some individuals utilize the VERY SAME ARGUMENTS in support of a believe in a "great banger?" Let us have CONSISTENCY!

And though one inspect a trillion swans, and find not one black one, that does not rule out the possibility that at least one black one exists. So, you must repeat each experiment and observation, and get the same result, an infinite number of times, and have gotten, each time, the same result, or you do not have CERTAINTY. Additionally, science (as so often is said) without INTERPRETATION is nothing more than a accumulation of facts... and interpretation is local and subjective.

But, if you wish to make an effort to persuade me or any reader that a statement of mine is flawed, or is not worthy of being considered, you will not persuade us by attempting to sweep it under the table of something that conflicts with a dogmatic bias of your own. I "believe" you can do better than that.

Prove me wrong, if you can, by contesting what I have said, as I said it, on its merits, and you will do me a favor, as I seek correction. If you do a good job of THAT, I shall gladly embrace your added value, and alter my stance on what you refute.

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Posts: 0

May 7, 2012

To say that any of my statements comes close to "intelligent design" is both a false accusation of my ideas, and an intellectual cop out on your behalf. My statements are my statements, and are not derivatives of any dogma. If you are unable to add value by way of showing me wrong in what I HAVE said, then the least you could do is avoid attributing to it something I have NOT said. Let me assure you that any fact or any compelling argumentation against one or more of my statements is WELCOME by me, as a person who seeks correction, and who views learning as being BOTH a process of being given access to further ADDED VALUE to reconsider by AND as a cybernetic process, whereby discourse enables corrections in directions of the learner's thinking. (I do not share the popular view that learning means memorizing only the facts and arguments provided by others, and then defending those facts and arguments against any new information or reasoning -- an infirmity found even among many who have graduated from some universities whose professors, surely, surely, know better.

So, your cheap shot attempt to "explain away" a statement of mine (to wit, my statement number 5)on basis that YOU DISCERN some dogmatic intent on my part, indicates actually that you, yourself, may be entertaining a dogmatic bias in your own thinking.

With perhaps a fuller appreciation for advanced issues of scientific certainty, in context of unfalsifiables, and with perhaps a far more advanced appreciation of the limits of epistemic and ontological access of the human experience than you indicate awareness of, I balk at the suggestion I would treat as a certainty any side of any question for which there is not, to my knowledge, any empirical grounds for knowledge certain to resolve which alternative belief in its regard, is certain to the absolute exclusion of the other.

From where I sit, philosophically, it is appalling to me to observe how many inside science academia and in research,AS WELL AS how many of various meta-physical dogmatic persuasions -- fail to discern the difference between knowledge certain, on the one hand, and convenient, but uncertain, assumption, on the other.
Dogmatism, in my view, is the insistence that ANY uncertain thing is certain and true (or that it certainly is NOT true) where neither or none of the alternatives is by humans, as yet, empirically established with certainty.

Simply because something does not suit one's own intuition, or the intuition of one's fellows in stance, does not a certainty provide. What is "true" about nature, or untrue about nature, is neither determined by popular vote of many, nor even by popular vote of an elite esoteric community who perceive themselves to have a license to "know" things they have no actual means of knowing.

Much in scientific assumptions is convenient to assume, and useful in being applied in a constant struggle to upgrade and to update tentative syntheses. Much in scientific assumptions is NOT falsifiable and, therefore, is NOT known for a certainty to be "true" or valid or knowable. And, if everything taught in academia were subjected to the rule it must be proved for a certainty, then it would not appear in any textbook. Take, for example, Newton's First Law. Where was the confirming experiment performed? It had to have been performed where no outside force was present... not even the force of gravity from a star thirteen billion light years distant. Newton (whom I much respect, even as I much respect Charles Darwin) argued out of one side of his mouth the standard that nothing can be known but that it can be empirically confirmed, yet argued out of the other side of his mouth that his "laws" are "self-evident. In all due respect, let us be CONSISTENT. Let us not take that which is supported by non-exhaustive, non-empirically testable, circumstantial evidence and -- because it is useful to us, and serves as a pragmatic working hypothesis, and make and EXCEPTION for it, and call that EXCEPTION by the name of "self-evident." Or, if we wish to press the case for self-evidence, then let us not use the "empirical standard" to exempt ANYTHING CLAIMED BY ANYONE, to whom it is "self-evident." To recognize and acknowledge this conflict of standards, as being something one can, by virtue of being educated (inculcated with the double standard) apply it when we wish to assert one thing, and deny its application when we wish to argue against another.

This point is not offered to question the wonderful tool of having WORKING HYPOTHESES,nor to TREAT any useful working hypothesis or methodology as "in error." It is merely offered in evidence that there is SUBJECTIVITY, alone, that allows a double standard for including one thing and excluding another. But, UNLIKE EITHER the "intelligent design" dogmatist or the bio-science dogmatists, it is my contention that what is established as empirical CERTAINTY, should be labeled accordingly, and what is NOT empirical certainty should not be stamped with the same stamp when, and if, it suits any individual or group of dogmatic thinkers who may happen to have some clout in so doing.

Even consensuses are tentative in science. That is historical fact. One day "dark matter" was not embraced as existent, and following a vote, it was "science." So, indeed, I would not support an argument that, because something is or is not currently in fashion with the bulk of the scientific community, therefore, it is anti-science, any supporter of it a maverick, and it is admissible for use in textbooks, whereas, one day earlier it was anti-science.

But do I subscribe to the formal school of thinking called "intelligent design?" Most emphatically, NO! Why not? Because its formal assertions strike me as radical, logically inconsistent and its arguments for its case strike me as poorly informed and eclectic. That is, it would seem to argue in favor of including its own empirically unfalsifiables in formal education, but not, also, the disparate unfalsifiables of other religions. They would, it seems, open a Pandoras box to pry their way into education and then quickly shut it before a crowd of other opinions join the fray. Again, let us be CONSISTENT. But, then, do I share at least a few of the stances in belief with the "intelligent design" school of thinking? Yes. I do; and, as I have pointed out elsewhere, SO, TOO, DO A NUMBER OF scientist acquaintances of mine, both inside and outside family. Like me, these, several, many of them PhDs, are offended by atheistic professors who avow their own unfalsifiable belief stances in classrooms, even as they insist that "intelligent deisign" thinkers do not. So, the great question for me, waxes into, "Why do not those of various opinions on what should and should not be included in science in academia, seek to agree upon CONSISTENT criteria -- in recognition that the issue of what is and is not falsifiable does not seem to suit anyone. The issues CANNOT be logically nor reasonably based upon what is empirically ascertainable and what is not, lest much that is of value in science would not pass that standard.

(Anyone who doubts this cannot have studied or understood the most rudimentary arguments in formal epistemology, and surely could not be familiar with the vast bulk of the discourse called "The Science Wars" that took place between self-styled scientific realists and postmodernist critics during the 1990s. (Oddly, many in the sciences are grossly unaware of how many claims made, even to this very day, among members of the scientific community, did not, and do not now, stand up to scrutiny, and are HIGHLY reliant upon philosophical assumptions that are neither logically consistent nor empirically verifiable.

Today, many who fancy themselves to be capable of making a case for what should and should not be included in education, as science, and as meta-science, repeat mindless questions, and cite ridiculous aphorisms, on each and both sides of the issues. Radical argues with radical; dogmatist, with dogmatist. And I disavow the ignorant banter of each and both, and long for an open-minded discourse that shows no sign yet of approaching.

Let that which is called science apply the same standards to ITS OWN convenient and internally preferred myths as are applied to any OTHER myths. (And no claim is made by me that, just because something is a myth it is concomitantly, categorically untrue. It merely is UNFALSIFIABLE, unproved, and undisproved for a certainty.

Let me be on the front lines of those who argue that science could not move forward on any other basis than objectivity, nor objectivity on any other basis that self-honest admission of what we have established as CERTAIN, on the one hand, and what we strongly "believe" to be good and practical myth as TENTATIVE. That is the ax I would grind, and the only ax. Let none have license to go unchallenged in positing what he chooses to believe without absolute proof, as obvious or as "self-evident," and what he does NOT choose to believe without absolute proof, as absurd until proven.

And, any who would claim to be at once both "scientifically literate," and empirically grounded in all his "beliefs" about nature, and does not recognize how thin, if even existent, be the ice he stands on, under what definition of literacy falls such a lack of familiarity with the very ideal of science (by which ideal, it is open to new information and to change of stance, and, by that virtue alone distinguishable from DOGMATISM.

To adopt one view that suits one's self, and refuse to acknowledge or even consider another as worthy of being studied, without even allowing that there is a contradiction in that, is not only dogmatism, it is self-based (or group concensus-based) bigotry.

It is my contention, here and in all other places, that dogma is never science, and science is never dogma. Science is open, or it is not science, but dogma. (And lest anyone cite the so-called term "The Central Dogma of Bio-science," as an exception, let him verify it, that Frick, himself, allowed that his choice of words for it was unfortunate.

If I challenge one field of science, on grounds it proffers myth as reason that is superior to that of admitting, "We do not know," when indeed we do not... then I do not hesitate to challenge another field, if it make a similar claim. Neither do i believe all evidence that shall ever be on the table is yet on the table.

Neither do I "believe" every currently preferred majority stance of ANY unfalsifiable assertion or consensus of ANY field of scientific endeavor. For example, it is my personal stance (variously referred to by some as a tentative "belief" or working hypothesis) that there are multiple emergent dynamics in physics, and not just the two emergent scale-level ones most physicists acknowledge presently: the classical-scale dynamic and the quantum scale dynamic. I have no proof, and thence no certainty that other dynamics occur at larger and smaller scales of "existence." But I perceive and believe and have taken the TENTATIVE stance that they do. (This view departs from the currently popular multiverse view, but it is more intuitive to me, and in no way damages my life nor anybody elses, and I am TENTATIVELY satisfied that it does not contradict ANY empirical evidence, and does not defy any rule of logic.

(All logic, by definition, leads back to whatever assumptions (postulates) one begins with, by way of operations assigned to the task, and CANNOT falsify those assumptions, nor certify them. Hence, until and unless an assumption is found certainly false, it remains an ALTERNATIVE possibility. And it would be a shame for any scientist, or philosopher of science, to be ignorant of the limits of logic, much less the non-exhaustion up to present date, at least, of all there is to be known, tried, or discovered about nature, or the potentiality for anything to exist outside nature.

Science is hamstrung by any self-deception or self-persuasion that the scientist knows anything he does not know to be certain is certain, or that anything he does not know to be impossible is impossible.

So, while some stances are USEFUL and may have held up under all (science history indicates most, rather than all... vis a vis the compelling argumentations of Thomas Cuhn and others, science rules assumptions in on basis of incomplete evidence -- never all the evidence -- and were we to have "all" the evidence to be found in nature, we could never have CERTAINTY we had it all... a deep, deep paradox, is it not?

Stance becomes dogmatism at precisely the point at which it is asserted as the only possibility, barring any other, where no empirical falsification (as yet) exists to rule it completely in, or completely out.

An example of something I, that comes from no dogma, and which I cannot certify and recognize and acknowledge I cannot certify -- but CHOOSE to believe, is that matter and energy are granular (that the universe is not seamless) but that each particle of mass or energy is of quantum uniqueness, and that time passes in discrete increments, not unlike the ticking of a clock, with each quantum of change in time allowing at some level of resolution no further travel of any particle to any farther increment than the adjacent quantum unit away (essentially a quantum time unit) with each such time unit increment providing a new configuration of all the particles, such that none has moved more than one increment, by the special distance, relative to each unique frame of space-time, by a single Planck unit length (unless that, too, be divisible. (This is too brief a space to put it in. My apologies for the resulting garble.)

But do I perceive that, because this physical view is intuitive to me, even if a thousand physicists were to gather into a consortium and vote in favor of it, that any OTHER view would thereby be rendered unlikely, or unrealistic, or unreasonable, or naive, or just not worth being considered... Not I.

Who would be WRONG in such a variant view, by my standards, would be one who would "explain away" any view but his own, whether I share that view, or whether I do not share that view. The dogmatist is he who will not allow credence or consideration of any conclusion UN-RULE-IN AND UN-RULED OUT, but his own, and of those who buy in with him on his own.

If you, pgegen, would wish to offer additional value to my statement number 5, you would do well to address what it SAYS, and not what you, in your own dogmatic bias, perceive it to border upon saying. That I would welcome.

Being one who seeks additional facts, more compelling argumentations, and thus opportunities to self-correct -- and who perceives THAT to be what learning is all about, let me assure you that you are welcome to upgrade or update my thinking. On the other hand, if the best you have to offer me is an attempt to "explain away" what I said on basis that it strikes you as bordering upon one of your own dogmatic biases, then you add no value no opportunity for ANYONE to progress in learning anything.

A mind fully open to learning -- rather than defending dogmatism -- is a mind open to at least the possibility that one's unfalsifiable opinions, no matter how widely shared with others who hold themselves out to have superior vision about such things, knows one iota more about nature than he ACTUALLY knows about it. Were nature capable of caring what you think, or what I think, or what anyone else THINKS, I doubt it change itself to conform to that; so it is my best guess that our science, as the study of it, can at best attempt to do the conforming -- the adamant egos insistence notwithstanding. Let us take care that we recognize our best scientific potential, therefore, to continue to conform our thinking to it, or simply wallow in dogmatically conserved ignorance.

(And, by the way, all certainty, borne of experience, is borne of experience that is local, and perceptions that are subjective. So, the claim of certainty by another, on basis of what experimental or observational findings may have resulted is, locally heresay, until and unless we have done that experiment or observation FIRST HAND. And many of us -- including, I dare say, you, have NOT conducted first hand every experiment or observation you presently BELIEVE to have revealed what you have been told about "science." (Have YOU personally replicated Michelson and Morley's experiment in resolving whether light requires an aether through which to perpetuate? They did not factor in "dark matter," or any other more recent possible media (some of which have not been precisely corroborated but which fit nicely, in the interim as fudge factors.) Do you dare to question to current wisdom that the proxy evidence that something MUST exist, lest our formulas are wrong,as
being compelling. And do you, turn right around and deny that some individuals utilize the VERY SAME ARGUMENTS in support of a believe in a "great banger?" Let us have CONSISTENCY!

And though one inspect a trillion swans, and find not one black one, that does not rule out the possibility that at least one black one exists. So, you must repeat each experiment and observation, and get the same result, an infinite number of times, and have gotten, each time, the same result, or you do not have CERTAINTY. Additionally, science (as so often is said) without INTERPRETATION is nothing more than a accumulation of facts... and interpretation is local and subjective.

But, if you wish to make an effort to persuade me or any reader that a statement of mine is flawed, or is not worthy of being considered, you will not persuade us by attempting to sweep it under the table of something that conflicts with a dogmatic bias of your own. I "believe" you can do better than that.

Prove me wrong, if you can, by contesting what I have said, as I said it, on its merits, and you will do me a favor, as I seek correction. If you do a good job of THAT, I shall gladly embrace your added value, and alter my stance on what you refute.

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