One month of stonewalling

| 52 Comments

In early February, a number of bloggers brought to your attention a peculiar paper on mitochondrial proteomics, a paper which was obviously odd on even casual inspection, containing grandiose claims of a theoretical revolution that were entirely unsupported and ludicrous assertions of evidence for God in the genome. Deeper examination revealed that much of the paper had also been plagiarized from various sources. To the credit of the journal, the paper was quickly retracted one month ago today; however, the retraction was entirely based on the plagiarism, and none of the other failings of the paper were addressed, nor were any of the patent errors in the review process at the journal Proteomics discussed. This is strange, especially in light of the fact that the Warda/Han paper was the most accessed article in the journal. This is not an issue that should be swept under the rug!

Today, several of us — Steven Salzberg, Lars Juhl Jensen, and Attila Csordas — are repeating our call for an explanation of the events that led to the leakage of such an egregiously ridiculous paper into print. Bad papers are a dime-a-dozen, and we aren't so much concerned with the detailed discussion of the flaws in this one paper as we are with seeing the integrity of the peer-review process maintained, or better, improved. The Warda/Han paper had obvious red flags that marked it as potentially problematic in the title, the abstract, and scattered throughout the body, and it's hard to imagine how any reviewer or editor could have let them simply slip by without comment, yet that is exactly what seems to have happened.

We want to know how this paper slipped through the cracks, because we want to know how large the cracks in the peer review process at Proteomics are. It's a journal with a good reputation, and we are not presuming that there was any wrong-doing or systematic failure of peer review there, but we do think that a lack of transparency is of concern: there is no assumption of a crime, but the ongoing cover-up is grounds for suspicion. Let's see some self-criticism from the journal editor, and an open discussion of steps being taken to prevent such errors from occurring again.

Alternatively, if the journal wants to outsource its quality control to a mob of bloggers, that works, too … but we tend to be less formal and much more brutally and publicly critical than an in-house process might be, and we're also going to be less well-informed than the actual principals in the review process. Better explanations are in order. Let's see representatives of the journal provide them.

52 Comments

PZ Myers, would you think this paper more credible than the one at the heart of the scandal? I wrote this myself, so I’d like you to critique it:

A critical test of common descent (evolution) While there are ways to experimentally test the process of evolution, known as natural selection, by mimicking it artificially, ways to test the historical issue of evolution, known as common descent, must rely on making observations and making predictions of the outcome of those observations.

Inside the cells of all Eukaryota (plants, animals, fungi, and protists) are organelles called mitochondria. Likewise, inside the cells of plants are organelles called chloroplasts. Both mitochondria and chloroplasts have their own DNA and are thought to be descended from bacteria that took up residence inside the larger cells. In any case, the DNA in those organelles are completely different from the DNA in the nuclei of those same cells.

We can take the DNA of cell nuclei and check them to see if the differences between those of various organisms can enable us for build a family tree of those organisms. The more similar their nuclear DNA is, the more closely related they are. But since mitochondria and chloroplasts also have DNA, we could also take them and check to see if we could build up a family tree that is the same as the one we would build up with the nuclear DNA.

Indeed, there is no reason, if all life was produced by a single recent act of creation, for the DNA of the mitochondria of all animals to be significantly different from each other. So if I was a Creationist, especially of the young Earth kind, I would predict that it would be impossible to make a family tree from mitochondria DNA, or if I did, it would be completely different from the nuclear DNA. But if I was testing the theory of common decent, I would predict that the readings in animals of both their nuclear and mitochondrial DNA would produce the SAME FAMILY TREE in all cases! This would make perfect sense if the mitochondria and the rest of the cells have been evolving together ever since they first came together over a billion years ago.

Mitochondrial DNA is already used in forensics to determine who the mother of a child is, while nuclear DNA must be used to determine the father of that same child. This would only be an extension of that function, since the parents of the child must be of the same species, or at least very closely related, to even produce offspring at all.

No plagerism and no claims that cannot be backed up with testing!

There is an innocent possibility here.

Obviously the paper got in due to either careless or biased editorial performance. Either someone was bored with it and skimmed too fast to pick up the crazy parts, or a closet creationist let it in despite the incoherence.

I don’t know how many editors per paper that journal uses, but let’s say it’s one or a few, at least for review papers, and one or more of those editors are no longer serving as editors, due to this incident.

That would fix the problem. There is no ethical obligation for the journal to reveal such a step.

A careful reading of the lists of editors for various issues might reveal a name that ceases to appear, of course.

However, for a variety of valid reasons, Proteomics might choose to keep the dismissal of individuals from its list of potential editors private. The problem is fixed. If bloggers choose to closely follow the journal, that’s more or less a plus, not a minus.

Of course the reputation of Proteomics could be even further repaired by openly stating how the problem was dealt with, but the net benefits of making public a dismissal may be outweighed by the legitimate problems with doing so, especially when the only issue is that a bad paper was let into the journal.

Dale: No, that’s not a more credible abstract, and I’d reject it as well. It doesn’t say anything other than to propose a test (one that has already been done, many times), it’s far too basic, and the creationist take on the issue is so far off base and so simply refuted that it doesn’t even merit mention in a science paper.

Harold: I suspect that the most likely explanation is error rather than malice, and sure, there is no ethical obligation to reveal in-house measures taken. There is a practical obligation, however – it would correct the perception that the journal has something to hide.

I just read the paper. Who the heck reviewed that trash? How did any editor let it by? Either the editor and the reviewers failed to read the thing or they agreed with the authors’ message.

Plagiarism? That’s the least of the problems.

I think what’s disturbing about this is that it smells so very creationist. Just like the Sternberg case, or the Leonard PhD committee case, or key 1-vote majority on state school board cases, creationists are masters at engineering PR wins. They typically do this by getting a very few key people into key positions at critical times to execute a one-time ambush. Yeah, they know someone will notice after the fact and try to blow the whistle, but meantime they have managed something valuable, such as a martyr (like Gonzalez or Sternberg) or a “peer reviewed” paper, which they can then spread across thousands of websites and cite endlessly in support of their agenda. Doesn’t take many ambushes.

The stonewalling is also quintessentially creationist. A responsible journal would immediately and publicly investigate, identify what happened, and take immediate (and again, public) steps to rectify whatever went wrong. Just as happened in the case of the Korean stem cell fraud. I very strongly suspect that if it were possible to track down the individual whose actions could break this logjam and start the ball rolling but who is carefully not doing so, we’d find ourselves a creationist. It’s how they operate.

There is an innocent possibility here.

I have been going against the blogging crowd in arguing for innocent possibilities and allowing sufficient time for a proper inquiry before releasing anything but the tersest of statements. However, IMO sufficient time is up, and it does not look like we’re going to get the necessary thorough explanation. I suspect Proteomics can now be declared dead as an outlet for scientific research. I certainly wouldn’t submit anything there (unless I were a crank in search of an outlet with low standards).

Sorry, Proteomics, but you’ve had a fair chance to redeem yourself, and you didn’t. Don’t blame someone else as you slide down the tubes of history.

I am a computer scientist and I don’t really know which journals are reputable as far as proteomics and genomics research goes. Is this journal widely accepted as authoritative? If so, I don’t think using a broad brush and painting the journal as a mouthpiece for ID is appropriate. Obviously this paper was not vetted by someone who was interested in presenting an actual scientific paper – or possibly the reviewer did not grasp the level of lunacy delivered by the weird side statements ( which seems plausible if the reviewer was cogniscient of the science but might not be a very good English speaker ).

Don’t blacklist the journal unfairly because of an obvious black eye on their part ( unless they claim the paper WAS properly vetted and they claim it was science - then toss em out. )

Don’t blacklist the journal unfairly because of an obvious black eye on their part ( unless they claim the paper WAS properly vetted and they claim it was science - then toss em out. )

I agree.

They should instead be blacklisted for not providing a prompt disclosure of how the black eye came about and what they are doing to prevent another one in the future.

We could have titled this: Hunting for our next Sternberg

…We want to know how this paper slipped through the cracks, because we want to know how large the cracks in the peer review process at Proteomics are.…

Alternatively, if the journal wants to outsource its quality control to a mob of bloggers, that works, too.…

A couple of points. Peer review publication is not the end of peer review and not a good house keeping stamp of bona fide science. It is a first step in the process.

There are at least two schools of thought. Do you want to set up a peer review firewall that does not allow the publication of ideas others cannot yet understand (think Einstein working as a patent clerk while the world ever so slowly recognized the genius of his paper), or do you want to allow the occasional “bad” paper through with the hope that a good paper won’t be censored? Devout evolutionists are in general against the later, since it could lead to, gasp, the publication of an intelligent design paper.

The second point is: Maybe the journal doesn’t want to disclose its failures exactly because the PT-mafia will work a mob of bloggers into a feeding frenzy; the sharks have detected the fragrant scent of blood.

Bruce in Finding Nemo

Bruce: [Catches faint whiff of Dory’s blood; his eyes turn black] Ooooooooo, that’s good…

Just remember: Proteomics “…are friends, not food”.

I think the failure to have any effective review process is the number one reason to blacklist a journal. After all, selecting papers with merit is their primary purpose. Not only multiple reviewers but a highly placed editor and multiple staff members *should* have read this paper in detail. The fact that they either didn’t, or thought it was high quality, is not a minor issue. A paper is not one of thousands of widgets going down a conveyer belt, where a few will obviously slip by–it is a painting hanging on the wall of the gallery. Any decent gallery should know what they are hanging and take, and be seen to be taking, steps if they end up with a fake.

William Wallace Wrote:

We could have titled this: Hunting for our next Sternberg

Speaking of Sternberg, on your own blog you made some pretty ill informed statements about the case and then it became apparent you were relying at best on secondary sources, and it is not even clear to me that you have read the appendix with the actual emails. Remember how you called the fact that an employee had looked into Sternberg’s library records, an act worthy of the German Stasi (i am paraphrasing now) and how I pointed you to the original email?

Here is the exact quote

WW Wrote:

Looking into what Sternberg checked out from the library is something right out of the East German Stasi play book.

To which I responded

Another email from Marilyn Schotte: Whatever I said about Sternberg seems not to have affected Dr C’s objectivity (Coddington) because I do remember in October , Dr C was reasssigning research associates to newly formed visitor spaces, after a staff move, and he said that he “wanted to make sure that Dr S (Sternberg) was treated fairly”.

About the books

“He had over 50 books and periodical checked out and ignored repeated requests to either turn them in or renew them. After the third recall notice and a prompt from me via email he returned a book needed by someone else and told me that he “notified the library staff about the others”. The next day I queried the staff about those remaining overdue books and was told that Rick had contacted no one and that the books and periodicals were still overdue”

And PvM is a contributor to PT? The mind boggles.

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PvM:

WW Wrote:

A couple of points. Peer review publication is not the end of peer review and not a good house keeping stamp of bona fide science. It is a first step in the process.

True, we have seen how peer reviewed (sic) ID publications still manage to publish vacuous papers. However, peer review that missed the obvious signs seems rather problematic

There are at least two schools of thought. Do you want to set up a peer review firewall that does not allow the publication of ideas others cannot yet understand (think Einstein working as a patent clerk while the world ever so slowly recognized the genius of his paper),

Again, an overly simplistic view of Einstein’s work.

or do you want to allow the occasional “bad” paper through with the hope that a good paper won’t be censored? Devout evolutionists are in general against the later, since it could lead to, gasp, the publication of an intelligent design paper.

How can you speak for ‘devout evolutionists’ when you have no idea how they think or believe. The publication of an ID paper, a contradiction in terms really, is indeed problematic because a formal retraction like in the case of Meyer’s paper, does not seem to stop the ignorance from being continued amongst Christian believers, exposing them to foolish science.

The second point is: Maybe the journal doesn’t want to disclose its failures exactly because the PT-mafia will work a mob of bloggers into a feeding frenzy; the sharks have detected the fragrant scent of blood.

PT Mafia, there you go again with making Christianity look foolish.

Do you oppose that the journal explains its failures in peer review? Why

And PvM is a contributor to PT? The mind boggles.

That presumes a lot.

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William Wallace:

PvM wrote:Do you oppose that the journal explains its failures in peer review? Why?

That’s better, you’re back on topic.

You might want to ask an employment attorney. Employment laws might be involved. Also, while plagiarism might not have been the worst of the paper’s problems, it was sufficient.

Additionally, as I already communicated, why feed the sharks?

PvM wrote:Do you oppose that the journal explains its failures in peer review? Why?

That’s better, you’re back on topic.

You might want to ask an employment attorney. Employment laws might be involved. Also, while plagiarism might not have been the worst of the paper’s problems, it was sufficient.

Additionally, as I already communicated, why feed the sharks?

WW Wrote:

That’s better, you’re back on topic.

Who brought up Sternberg :-) Especially since your original claims about Sternberg seemed ill informed… I understand you may not want to discuss this at PT.

You might want to ask an employment attorney. Employment laws might be involved. Also, while plagiarism might not have been the worst of the paper’s problems, it was sufficient.

Please explain your employment law arguments. It sounds interesting, or purely speculative? It was not plagiarism that caught the eyes of so many, it was the poor arguments proposed. Plagiarism is much harder to detect.

Should we not get to the ‘bottom of this’?

ps: this site has a preview button…

Additionally, as I already communicated, why feed the sharks?

Because Proteomics needs to explain itself. It has a reputation which has been damaged by what appears to be poor peer review practices.

Yes, it is one early step in the process. But it should at least weed out the obvious garbage, and this paper was obvious garbage. Unless you’re advocating that there should be no assessment at all before accepting a paper for publication, in which case, please, don’t push for that. There’s too much to read as it is.

There is also plenty of controversy and difficulty within science that can be productively discussed in the pages of a journal. We “devout evolutionists” (whatever that might be; the phrase says more about your biases than ours) are opposed to seeing publication of ID because it is also obvious garbage. Do you have a reason for wanting a decrease in the signal-to-noise ratio in scientific publications?

PvM:

ps: this site has a preview button…

Is this for my sake, or yours?

Is this for my sake, or yours?

Both, just sharing knowledge my friend. What you do with it is beyond my control however.

PZ Myers:

Do you have a reason for wanting a decrease in the signal-to-noise ratio in scientific publications?

The internet is much more useful today than it was with 1993’s Gopher.

The internet’s signal has more energy today. But the noise has even more energy, in my opinion. The signal to noise ratio has gone done.

Is it worth it? …worth thinking about.

Do you want to allow the occasional “bad” paper through with the hope that a good paper won’t be censored?

Again, worth thinking about.

Dale Husband:

There are a few points you may want to consider:

1)Gene trees are not species trees. Of course ideally good multi-gene phylogenies should overcome this. 2)Organelle sequences are routinely, and have been used, to reconstruct phylogenies of the host organism 3)Phylogenies of mitochondria and bacteria place mitochondria as been most closely related to the alpha-proteobacteria 4)Similarly chloroplasts bear strong similarity to cyanobacteria

I do not see what sort of leg William Wallace’s alleged arguments have to stand on, other than it is crippled with rickets.

Among other things, literally every other post of his consists of

“Wah, wah, the PT Mafia is persecuting me, even though they let me post whatever fact-free crap my little heart desires!”

Really, if he was honestly being persecuted “Mafia” style here, he would not be barred from commenting at Panda’s Thumb, nor would he have PvM try to help him make posts without screwed up html, as, instead, William Wallace would probably have his ability to type with his fingers violently taken away from him.

Secondly, this paper was a poorly written paper whose writers did indeed plagiarized other papers. And the paper made two claims, 1) that mitochondria were not descended from endosymbiotic bacteria, and 2) that this was proof of God. The paper did not provide evidence for either claim. So, exactly what is William Wallace protesting here? If the paper does, in fact, provide such evidence, but, has been hidden from all, save for William Wallace, then, why isn’t he pointing out the exact passages where the evidence is hidden?

Really, if he was honestly being persecuted “Mafia” style here, he would not be barred from commenting at Panda’s Thumb, nor would he have PvM try to help him make posts without screwed up html, as, instead, William Wallace would probably have his ability to type with his fingers violently taken away from him.

I appreciate William’s contributions, however ill informed I believe they are, they help in getting the message across.

Yeah “they help get the message across”. Too well if you ask me!

Do you think people have not guessed WW is a http://en.wikipedia.org/wiki/Intern[…]n_sockpuppet ??? Owned!

To build upon what PZ said, in the case of a research paper the point of peer review is to ensure that the statements and conclusions of the manuscript are supported by the results and that all relevant literature is cited properly. For literature reviews, which present no new data (which was the case both for Warda and Han and for Meyer in the Sternberg case), the statements and conclusions should be based on the literature cited. Using a review to invoke nonscientific concepts instead of making a commentary within the bounds of science is completely inappropriate. If people wish to make philosophical or theological arguments, other media are available for that; keep it out of scientific journals.

Of course, the Warda and Han case was also marked by rampant plagiarism (see http://udel.edu/~mcdonald/wandahan.pdf). They are also guilty of plagiarism in another paper they published in the Glycoconjugate Journal, (Warda et al., “Is human placenta proteoglycan remodeling involved in pre-eclampsia?” Dec 27, 2007) spotted by Sarah W. on Pharyngula:

From Warda et al.:

“Detailed characterizations indicate the placental basement membrane tissue predominantly contains HS PGs, whereas CS/DS PGs are mainly located in the intervillous space of the ECM”

From Chen, C.-P. et al., Placenta 28:97-106 (2007):

“Detailed characterizations indicate the placental basement membrane tissue predominantly contains heparan sulfate proteoglycan (HSPG), whereas chondroitin sulfate and/or dermatan sulfate proteoglycans (CS/DS PGs) are mainly located in the intervillous space of the ECM”

From Warda et al.:

“HS, the constituent of up to 50% of the total expressed GAG in endothelial cells, is unique among GAGs in the ability to bind a large number of different proteins with complex role in the extracellular matrix, regulating a wide variety of biological process, including hemostasis, inflammation, angiogenesis, growth factors, cell adhesion…”

From Tersariol, I.L.S. et al., Brazilian Journal of Medical and Biological Research 35:135-144 (2002):

“Heparan sulfate and heparin are particularly important among glycosaminoglycans in their ability to bind a large number of different proteins. Heparin-like glycosaminoglycans play a complex role in the extracellular matrix, regulating a wide variety of biological processes, including hemostasis, inflammation, angiogenesis, growth factors, cell adhesion, and others.”

I notified the EIC, Prof. J.F.G. Vliegenthart, on February 24 - still no response.

On the theme of plagiarism, I came across another example just today, where this article

http://www.ncbi.nlm.nih.gov/pubmed/[…]med_RVDocSum

rips off several complete, word-for-word paragraphs of this one

http://www.ncbi.nlm.nih.gov/pubmed/[…]Discovery_RA

I have already contacted the author of the 2002 paper and the editors of the journal that published the plagiarized version. If anyone’s feeling bored, feel free to dig through the Koizumi paper for other plagiarized bits.

The irony is that I caught it because one of my students plagiarized the same sections as the the second paper - and my sleuthing pulled up BOTH published sources.

How the h*ll am I supposed to require academic integrity of my students when the very papers they review as part of their coursework are ripped off?

gabriel,

It’s scientific misconduct, pure and simple, and must be dealt with by the journal editors. Granted, it’s impossible to guarantee that a manuscript is free of plagiarism; no reviewer can know every single sentence of every relevant piece of published literature. As a researcher and reviewer, I take the default position that what I’m reading is the authors’ own work (although I would like to learn more about the online searches used by those who rooted out the Warda and Han plagiarism, I might start using that on every paper I review). When random events bring plagiarism to light, an example must be made and a strong message relayed that it is not acceptable behavior. You did the right thing by altering the editor and the authors whose work was stolen.

William Wallace -

Since I was in the minority “there may be an innocent explanation” camp, I would like to firmly differentiate the honest opinion I expressed from what you expressed.

Basically, I said maybe they fired or discontinued using one editor, but for some reason decided not to tell the world about that.

However, I also said…

Of course the reputation of Proteomics could be even further repaired by openly stating how the problem was dealt with

So essentially, the only difference between me and other posters is a matter of degree. Others have made the excellent point that at this stage, the reputation of the journal may NEED to be further repaired.

Meanwhile, you wrote…

There are at least two schools of thought. Do you want to set up a peer review firewall that does not allow the publication of ideas others cannot yet understand (think Einstein working as a patent clerk while the world ever so slowly recognized the genius of his paper), or do you want to allow the occasional “bad” paper through with the hope that a good paper won’t be censored? Devout evolutionists are in general against the later, since it could lead to, gasp, the publication of an intelligent design paper.

I assume I am one whom you would describe as a “devout evolutionist”. I find that description inaccurate; the theory of evolution has nothing to do with devotion and is evidence-based. The use of that slur immediately alerts any reader to the probable quality of your argument.

The false dichotomy you describe does not exist. Naturally I am adamantly opposed to any form of actual biased censorship of evidence-supported scientific publications, including, of course, publications which include no original research whatsoever but formulate defensible hypotheses or predictions based on an accurate understanding and acknowledgment of data that already exists in field.

But some papers are so bad that to accept them is to abandon any standards whatsoever, and this is a clear example.

Naturally every crackpot with a demonstrably worthless idea claims that others “cannot understand” it.

Your comments about Einstein are also inaccurate. Einstein had four papers published in a single year, 1905, in a major physics journal. His position at the patent office was related to his physics education. His career continued to improve. While the extreme genius of his contributions may not have been recognized at first, he was never “censored” by scientific editors. This is relevant, since the entire gist of your post is that journals must allow creationist nonsense or risk rejecting works of genius. But the example you use actually suggests that true works of genius will not be missed.

It’s also important to note that your tone would change in a most hypocritical way if someone were fired or censored for supporting mainstream science. Rather than choosing a side based on reason or ethics, you merely find some argument to defend “your side”, however inconsistent you may be.

Edward Jackson is just trying to derail what I said

But if not, here it is in (hopefully) plainer English: Plagiarism was sufficient. The bellyaching about poor peer review seems to be motivated not over legitimate concern over junk science but about suppressing dissent from the T.o.E. and a desire for another internet execution a la Sternberg. While I am not arguing that peer reviewed journals should become the free for all we have on the internet, increasing the noise can result in increased signal, too. So which is more important: increasing the signal, or maintaining a signal to noise ratio? I think it is an interesting question, the desire for blood not withstanding.

gabriel wrote:

…How the h*ll am I supposed to require academic integrity of my students when the very papers they review as part of their coursework are ripped off?

Gabriel, have you seen Butler University’s Understanding plagiarism ? You could require your students to read it.

harold wrote: Your comments about Einstein are also inaccurate. Einstein had four papers published in a single year, 1905, in a major physics journal. His position at the patent office was related to his physics education. His career continued to improve. While the extreme genius of his contributions may not have been recognized at first, he was never “censored” by scientific editors.

I never said Einstein was censored. One point was what if his paper had not been published?

To respond to your latest canards, Einstein wasn’t given a position at a university, either, and it strains your credibility if you’re suggesting Einstein’s promotion at the patent office was because his boss was impressed with the special theory of relativity paper he had written. (Though if you insist this was the case, I will look into it further).

This is relevant, since the entire gist of your post is that journals must allow creationist nonsense or risk rejecting works of genius.

Entire?

But the example you use actually suggests that true works of genius will not be missed.

If we allow enough time. In modern physics, only a few years may be required. In renaissance astronomy, a lot longer: Copernicus re-interpreting long existing data for a heliocentric model, Tycho Brahe discounting it and insisting upon a geocentric model.

“True works of genius will not be missed.”

Except in the case of Copernicus until Kepler. Or Mendel until Hugo de Vries and Carl Correns.

It’s also important to note that your tone would change in a most hypocritical way if someone were fired or censored for supporting mainstream science.

It would not.

Plagiarism was sufficient.

On the contrary, plagiarism was an outcome of increased scrutiny based on some strong indicators that suggested that there was something wrong with this paper. Indicators which are clearly visible.

And this has nothing to do with Sternberg, other than perhaps that it shows your documented ignorance on these matters.

And PvM is a contributor to PT? The mind boggles.

should we remember you said that the next time you project “ad-hominem” on the rest of us?

What Wallace, and other idiots like him, keep failing to grasp is the difference between “revelation”, and what appears to be revolutionary science, but is still based on pre-existing observation.

they want to compare creationist arguments like intelligent design, to revolutionary theories in science, but they keep missing the fact that no matter what “revolutionary” hypothesis you examine, the reason it was accepted within the scientific community is because it was still based on PREVIOUS observations, and ended up doing a better job of explaining previously observed data, as well as making more accurate predictions for future observations.

ID goes farther back than Paley, but let’s say it didn’t. that still gave it essentially equal time with Darwin’s theory to “revolutionize” science by having more explanatory and predictive power.

However, since it has NONE of either, it’s no surprise we rightly reject it as nonsense at best.

there simply is no comparison.

you morons can cry “victim” all you want, but anyone with any sense can quickly see there is no basis for your whining… other than you are just a bunch of fearful jagoffs; afraid your ignorance will no longer be tolerated by society at large. It’s time for society to put to the torch the concept that because you call your ignorance “religion”, it deserves some kind of free pass in the world of ideas.

However, know that the louder you scream your ignorant protestations, the more gas you throw on the fire.

There are at least two schools of thought. Do you want to set up a peer review firewall that does not allow the publication of ideas others cannot yet understand (think Einstein working as a patent clerk while the world ever so slowly recognized the genius of his paper), or do you want to allow the occasional “bad” paper through with the hope that a good paper won’t be censored? Devout evolutionists are in general against the later, since it could lead to, gasp, the publication of an intelligent design paper

No, you over- (or under-) state the case. The problem isn’t “an occasional ‘slip’ that lets an ID paper through”. The problem is that some utter nonsense got through. We’re talking about so bad that there was initially some speculation as to whether the journal had been sokaled.

And contrary to your paranoid fantasies, not everyone is dead set against the publication of an ID article in a respectable journal. What I and many others are against is the publication of pretend science in a respectable science journal. If the proponents of ID ever started doing some honest science on the topic, then for my money they could and should publish along with other scientists.

However, the behavior of the leading IDologists leads me to believe they never will do any honest science on the topic. The utterly predictable rank displays of incorrect ‘facts’ and sloppy thought suggest that they are either utterly dishonest or else utterly incompetent.

You are, of course, free to point out any examples of honest ID science that I may have missed. (Take your time; I certainly will not be holding my breath.)

PvM:

William Wallace Wrote:

We could have titled this: Hunting for our next Sternberg

Speaking of Sternberg, on your own blog you made some pretty ill informed statements about the case [snip]

“Hunting for our next Sternberg” is probably correct, in the sense that WW is hunting for another case that can be exploited via misrepresentation in the same manner the Sternberg case was.

After all, his posts in this thread seem to indicate that he thinks the problem with the Proteomics case was that an ID paper got published.

What I find ironic is how in both cases there appeared to be reuse of existing articles, the difference is that in this case the authors had not written the original articles.

Fascinating design inference however…

Question for William. Is plagiarism sufficient for a paper to be retracted and how do you define plagiarism?

What about self-plagiarism

In academic fields, self-plagiarism is a problem when an author reuses portions of his or her own published and copyrighted work in subsequent publications, but without attributing the previous publication.[7] Identifying self-plagiarism is often difficult because of legal issues regarding fair use.[8] Some professional organizations like the Association for Computing Machinery (ACM) have created policies that deal specifically with self-plagiarism.[9] As compared to plagiarism, self-plagiarism is not yet very well-regulated. Some universities and editorial boards chose to not regulate it at all; those consider the term self-plagiarism oxymoronic since a person cannot be accused of stealing from himself.

For authors wishing to avoid potential issues when authoring new papers, the authors are strongly encouraged to follow these “best practices”:

1. Provide full disclosure — mention in the introduction that the new or derivative work incorporates texts previously published. 2. Ensure there is no violation of copyright. 3. Cite the old works in the references section of the new work.

PZ Myers:

Dale: No, that’s not a more credible abstract, and I’d reject it as well. It doesn’t say anything other than to propose a test (one that has already been done, many times), it’s far too basic, and the creationist take on the issue is so far off base and so simply refuted that it doesn’t even merit mention in a science paper.

Well, I learned something new tonight! Most science journals seem to be way out of my league!

Daniel Gaston:

Dale Husband:

There are a few points you may want to consider:

1)Gene trees are not species trees. Of course ideally good multi-gene phylogenies should overcome this. 2)Organelle sequences are routinely, and have been used, to reconstruct phylogenies of the host organism 3)Phylogenies of mitochondria and bacteria place mitochondria as been most closely related to the alpha-proteobacteria 4)Similarly chloroplasts bear strong similarity to cyanobacteria

I knew all that already. Thanks for confirming it here!

Well, I learned something new tonight! Most science journals seem to be way out of my league!

you could polish that into an editorial piece, though.

Dale Husband:

Well, I learned something new tonight! Most science journals seem to be way out of my league!

You could always start your own journal. After all, even if you’re starting with zero credibility, that’s still ahead of some of the competition. :)

It would be fun to contemplate a spoof creationist journal, except it’s impossible to out-parody Casey Luskin et al. On top of that, no matter how stupid an article is, Luskin and Wells will quote-mine it. Have they quoted articles from Playboy? They probably think that it’s a peer-reviewed journal, since their target audience reads it (or at least looks at the pictures.)

WW said: “A couple of points. Peer review publication is not the end of peer review and not a good house keeping stamp of bona fide science. It is a first step in the process.”

True, to the extent that publication simply means it is of at least casual interest to the scientific community.

“There are at least two schools of thought. Do you want to set up a peer review firewall that does not allow the publication of ideas others cannot yet understand (think Einstein working as a patent clerk while the world ever so slowly recognized the genius of his paper),”

What is it with kooks and Einstein?

A number of people understood S.R. I’m not sure what you mean by ever so slowly; in 2-3 years, S.R. was widely accepted. Journals didn’t travel as far and wide, and as quickly they do now. You attempt to project an air of erudition you don’t possess.

“or do you want to allow the occasional “bad” paper through with the hope that a good paper won’t be censored? Devout evolutionists are in general against the later, since it could lead to, gasp, the publication of an intelligent design paper.”

Intelligent design is not even wrong.

“The second point is: Maybe the journal doesn’t want to disclose its failures exactly because the PT-mafia will work a mob of bloggers into a feeding frenzy; the sharks have detected the fragrant scent of blood.”

No scientific journal is safe from scrutiny.

On what basis do you assert that rigorous peer review would have prevented Einstein’s paper from being published? You must provide a clear logical connection here otherwise you are just attempting to make some random fearmongering illogical argument.

With respect to Copernicus and heli-geo centrism.. I wrote this in another thread. But its applicable in this one too.

WW writes:

“A point I deem worthy of consideration in the Ptolemy/Copernicus/Tycho/Kepler progression is that it took centuries to get from a Ptolemaic epicyclic/geocentric theory to Copernican heliostatic/heliocentric/epicyclic/constant-velocity model, and even after that, the venerated (as an observational astronomer) Tycho Brahe asserted that the data better matched a Ptolemaic model over the falsified Copernican model.”

This isn’t so strange as it seems in hindsight. Although the epicylic method was based on an incorrect theory, it did offer an algorithm that could be used to compute orbital phenomenon of arbitrary precision limited by the number of “cycles” that could be determined and used.

I believe (someone correct me if I am wrong) that Copernicus claimed that the orbits of the planets were circular (now I think old Nic knew better, but circular orbits may have been a nod to certain religious authorities). It could be that Tycho could see from his detailed observations that circular orbits couldn’t cut it. Hence, although a Copernican paradigm was ultimately a better picture of the solar system, epicycles allowed one to compute more precise timing of astronomical phenomena. So from a 16th century perspective, I would argue that epicycles were the better model.

With Kepler’s laws came a more precise view of the nature of planetary orbits, and a more concise algorithm for computing orbits. At that point, epicycles were doomed to a footnote in history.

“By falsified, I mean, from a sixteenth century perspective: No 1000+ mph wind at equator due to Earth’s axial spin; no observed parallactic displacement of stars. Subsequently, Kepler seems to have simultaneously recognized the scientific value of Tycho’s data as well as the harm in Tycho’s dogmatism, and decided that the ends justified the means. Kepler deceived Tycho and his heirs. But Kepler ultimately produced the heliocentric/elliptical/changing velocity planetary orbit model we so clearly recognize as “true” today

Assuming this progression and regression is not unique, where in this drama is evolution?

I think sometime before Kepler; that is, we currently have a Ptolemaic/dogmatic theory of evolution.”

Not a chance. At worst it may be between classical mechanics and QM.

“The truth is mighty, and will prevail (eventually).”

The “truth” has already prevailed. What we are trying to do is get a more precise description of the “truth”

They probably think that it’s a peer-reviewed journal, since their target audience reads it (or at least looks at the pictures.)

Playboy has pictures? Whoda thunk it?

Stuart Weinstein: “A number of people understood [special relativity]”

Do you think his boss at the patent office did? Do you think a manager at a patent office promoted Einstein for his S.R. paper, while nearby universities continued to not offer Einstein a position?

SW: “I believe (someone correct me if I am wrong) that Copernicus claimed that the orbits of the planets were circular (now I think old Nic knew better, but circular orbits may have been a nod to certain religious authorities).”

Copernicus’ model used epicycles too, in an attempt to reduce discrepancies between his mere mathematical model and actual observations.

Tycho later successfully argued that the geostatic models produced as accurate if not more accurate predictions, and were less complicated than Copernicus’s. Both models were wrong, but Tycho’s model, the more incorrect one that still lined up with observations (think Coulter’s “story to fit the facts”), prevailed for some time, primarily because Tycho was the premiere observational astronomer of his day. [Note: Tycho was born about three and a half years after Copernicus died.]

Incidentally, Copernicus’ book actually had a little fluorescent orange sticker that cautioned readers: ~”Heliocentricism is just a scientific theory; a mere mathematical model.” And yet science survived. And, the warning was correct.

Okay, the warning was in a preface, was not fluorescent orange, and it was inserted by a sympathetic Lutheran at the printing house. And as far as I can tell, Copernicus was a Catholic priest, though modern secularists like to marginalize if not mask this fact.

William Wallace

The problem isn’t “an occasional ‘slip’ that lets an ID paper through”. The problem is that some utter nonsense got through.

This deserves to be underlined, we are discussing the peer review process which in turn is part of the larger process, not ID specifically.

WW knows its about larger processes but seem to claim that the process (and its growing relationship with the internet) is set up to weed ID out. Paradoxically he claims that the journal may have been overly protective because the paper was ID.

Knowing that ID is intended as a vacouos strawman to be paraded as close to science and education as possible, there is no doubt in my mind that forensic design detection was used when discovering this failure of peer review.

But so what? The existence of natural design detection methods, the lack of previous ID testing and the use of failure of peer review to push papers through only accentuates that ID isn’t science and that cdesign proponentsists makes every effort to withhold testing.

Why would anyone opposed to a transparent scam on top of a fundamentally flawed world view need to use sock puppets?

Unless creationism is diminishing which I seriously doubt. Besides that, DI seems to be currently transforming themselves to an “academic freedom/scientific integrity” movement, or at least producing such floaters, so there is still an identifiable producer of BS.

Guess they couldn’t set up a new “institute” while keeping the old useful idiot donors. Dembski and Luskin is trapped in their own ineptness (Dover) and public recognition; we will probably see a new generation of scammers soon. Luckily Sternberg choose to commit public seppuku, so there is one less candidate out there.

WW Wrote:

Do you think his boss at the patent office did?

What has this got to do with the peer review of Einstein’s work?

WW Wrote:

Do you think a manager at a patent office promoted Einstein for his S.R. paper, while nearby universities continued to not offer Einstein a position?

Strikeout.

Einsteins manager was interested in physics and supported Einstein’s work:

Abraham Pais, Subtle is the Lord..., pp 47 - 48 2nd ed Wrote:

Einstein did well at the patent office. He took his work seriously and often found it interesting. There was always enough time and energy left for his own physics. In 1903 and 1904 he published papers on the foundations of statistical mechanics. On September 16, 1904, his provisional appointment was made permanent. Further promotion, wrote Haller, ‘should wait until he has fully mastered machine technology; he studied physics’.

No one before or since has widened the horizons of physics in so short a time as Einstein did in 1905. His work of that year [IIRC 5 papers, whereof 4 seminal, my note] will of course be discussed at length in later chapters. Here I note only that in March he completed a paper which was to earn him the Nobel prize and that in April he finished an article that finally gained him the PhD degree from the University of Zürich.

On April 1, 1906, Einstein was promoted to technical expert second class with a salary raise to SF 4500. He now knew enough technology and, writes Haller, ‘belongs among the most esteemed experts of the office’. At the end of 1906, he finished a fundamental paper on specific heats. He also found time to write book reviews for the Annalen der Physik. At the end of 1907 Einstein made the first important strides towards the general theory of relativity.
Here the sketch of the young man’s life ends. Einstein’s days in Bern are not yet over, but a new phase is about to begin; his academic career. [References and notes removed.]

Einstein had no problem to publish peer reviewed papers, and was doing research during a long period of years. His immediate academic career revolved around finishing his PhD. (But no doubt he had eventually gotten hired on the strength of his other papers alone.)

And his manager took an interest in his studies and helped Einstein as necessary, even to the point that professional promotion was intentionally delayed.

WW Wrote:

And, the warning was correct.

Strikeout.

In the 16th century the scientific method, as it where, wasn’t yet as powerful or as recognized as in later times.

Stuart Weinstein Wrote:

in 2-3 years, S.R. was widely accepted.

Another problem for kooks is IMHO the observations that identified cosmological expansion acceleration, and revolutionized cosmology to arrive at the current concordance model where very little mass and energy is the previously observed. I’m not really up to the history (and both dark matter and dark energy had several years of prehistory), but I believe acceptance come very quickly.

To the comments modulo vacuous spelling errors, as it were, I would also like to add the observation that the revolution of cosmology wasn’t paradigmatic as the models and methods resembles the earlier ones. Take that, Kuhn!

Incidentally, Copernicus’ book actually had a little fluorescent orange sticker that cautioned readers: ~”Heliocentricism is just a scientific theory; a mere mathematical model.” And yet science survived. And, the warning was correct.

Okay, the warning was in a preface, was not fluorescent orange, and it was inserted by a sympathetic Lutheran at the printing house. And as far as I can tell, Copernicus was a Catholic priest, though modern secularists like to marginalize if not mask this fact.

I never knew the parallels between the idiocy of the 16th century church view and todays was so great. The same reason of “it’s just a point of view, just like ours” pleading we see today. Of course just like we laugh at the retards of Copernicus time, future generations will be laughing at the ID’ers (except some of us have already started)

The fact Copernicus was a catholic priest is of no importance. What point do you think “modern secularist” trying to hide?

About this Entry

This page contains a single entry by PZ Myers published on March 12, 2008 10:17 AM.

Expelled: the Denial was the previous entry in this blog.

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