ARN Misrepresents a Scientific Paper. Surprise!

| 35 Comments

The good folks over at the Access Research Network have this post up about some recent work published in the PNAS. The paper in question is entitled “Nitrate Assimilation in Plant Shoots Depends on Photorespiration” and is available here. A readable summary of the paper's findings can be found here.

The primary finding of the paper is that the photorespiration system in plants, which decreases the efficiency of photosynthesis, also serves an important function in allowing plants to convert nitrate into organic forms of nitrogen. Prior to this work it was commonly thought that the photorespiration was just an evolutionary vestige from a time when the atmosphere contained more carbon dioxide than it does today.

The ID's are presenting this as an indictment of evolutionary theory. The ARN summary concludes with this observation: “Evolutionary presuppositions stood in the way of scientific progress. A design model would have simply tried to determine the reason for the phenomenon. ”

To put it kindly, this is hardly the only interpretation of the facts. I have posted a complete reply to this piece of ID silliness over at EvolutionBlog. While crafting my reply, I contacted Dr. Arnold Bloom of UC Davis, the lead author of the paper. I showed him the summary of his work at ARN. He was not amused, and he gave me permission to use his reply in my posting. Check it out!

35 Comments

A bunch of creationists misrepresenting evolution…christ…I’m going to have to take off a few days from work and reevaluate life…everything I know was just upended.

Magnuson is funny. I bet a month ago he would have said that a design model predicts that God wanted plants to not function optimally.

Evolution has predictive power. ID has astounding postdictive power.

A few weeks ago in a post on “junk DNA” I brought up this same issue: it was real scientists puzzling over details that did this research and made these discoveries, not IDists boldly out investigating the world.

In that post, I quoted a letter from Harold Brown, who said, “Closely constrained communal research may be a more effective long-term means of pursuing knowledge than research in which resources are continually diverted to following up any apparent lead. The idea [is] that tightly organized research leads (despite itself) to the recognition of anomalies that generate new approaches …”

I’d like to reiterate this point here: that scientists, as the article stated, have puzzled over the topic of this paper and have pursued the close study of how photosynthesis works. In doing so - in pursuing “closely constrained communal research,” they gained the understanding of the details that enabled them to comprehend and solve the problem of the anomaly of photorespiration.

What would an “ID-oriented” working scientist (if there were any) done differently?

There is a point here that I am struggling to express. If one is an armchair thinker, about virtually anything, it is possible to imagine scenarios where some as-yet-understood phenomena might have meaning and purpose. But as long as one is unconstrained by the reality of details, one has a vastly greater chance of being wrong than right in one’s imaginings - bad ideas (or just wrong ideas) are a dime a dozen, and good ideas only reveal themselves after the work is done.

So this point of the IDists - that “a design model would have simply tried to determine the reason for the phenomenon,” is lazy, cheap, after-the-fact armchair science.

There is an inherent contradiction from the IDists here. They claim that evolutionary scientists are blinded by their dogmatic adherence to a failed paradigm, but every time those evolutionary scientists demonstrate their freedom from that dogmatism by discovering something new, the IDists berate them for not have figured it out sooner.

If the “design model” is so darned nifty and powerful, then let’s see some ID scientists get to work and figure some of this stuff out themselves, instead of sitting on the sidelines and taking backhanded credit for the work of others.

The PNAS abstract starts like this:

“Photorespiration, a process that diminishes net photosynthesis by 25% in most plants, has been viewed as the unfavorable consequence of plants having evolved when the atmosphere contained much higher levels of carbon dioxide than it does today.”

The presupposition is that photorespiration is the result of some past evolutionary process under different conditions, and was considered currently unfavorable. This resulted in a decision to genetically alter the plant genome to reduce the effect of photorespiration. This current paper shows that nitrate assimilation depends on photorespiration, and the decision to genetically alter plants to disable this process was the wrong path.

What signs led down this path? This article describes some. “An Early Arabidopsis Demonstration. Resolving a Few Issues Concerning Photorespiration”

by Chris Somerville in Plant Physiology

“Ogren went one step further to suggest that photorespiration was not biologically necessary,that it had evolved only to recycle carbon from phosphoglycolate back into the Calvin cycle and that the CO2 loss was the cost of recycling the other three carbons back into the Calvin cycle. The evidence for this was that plants grown in low levels of O2 or high levels of CO2 were more productive than plants grown in air despite strongly reduced levels of flux through the photorespiratory pathway. Thus, the implication was clear: Plant productivity could be strongly enhanced by identifying mutants with reduced amounts of photorespiration.”

This article in Science also discuss the signs.

“Genetic Engineers Aim to Soup Up Crop Photosynthesis”

“William Ogren, a now-retired RuBisCO researcher from the University of Illinois, Urbana-Champaign, says with only slight exaggeration. Enzymatic rates are often on the order of 25,000 reactions per second; RuBisCO turnover in higher plants can be as little as two or three reactions per second. “Not one of evolution’s finest efforts,” says Ogren.”

RuBisCO (ribulose-1,5-bisphosphate carboxylase-oxygenase) is the enzyme which triggers the photorespiration reaction.

“The oxygenation reaction is–as far as we can tell, and a lot of research over decades has gone into it–just a complete waste,” says Andrews. “It doesn’t do anything for the plant.”

This striking inefficiency was no handicap when photosynthesis first evolved 3 billion years ago, because the atmosphere was almost devoid of oxygen. After photosynthesis filled the air with oxygen and RuBisCO’s weakness was revealed, it may have been too late for evolution to fix the problem, says Murray Badger, a RuBisCO specialist at The Australian National University.

“If genetic engineers could find a way around RuBisCO’s slowness and inefficiency, they might reap a double benefit. A faster, more efficient enzyme could help crops grow and increase their biomass, letting them produce more grain at a faster rate.”

“More efficient RuBisCO could thus lower crops’ need for nitrogen, now mainly supplied by fertilizer in many countries.”

The PNAS abstract starts like this:

“Photorespiration, a process that diminishes net photosynthesis by 25% in most plants, has been viewed as the unfavorable consequence of plants having evolved when the atmosphere contained much higher levels of carbon dioxide than it does today.”

The presupposition is that photorespiration is the result of some past evolutionary process under different conditions, and was considered currently unfavorable. This resulted in a decision to genetically alter the plant genome to reduce the effect of photorespiration. This current paper shows that nitrate assimilation depends on photorespiration, and the decision to genetically alter plants to disable this process was the wrong path.

What signs led down this path? This article describes some. “An Early Arabidopsis Demonstration. Resolving a Few Issues Concerning Photorespiration”

by Chris Somerville in Plant Physiology

“Ogren went one step further to suggest that photorespiration was not biologically necessary,that it had evolved only to recycle carbon from phosphoglycolate back into the Calvin cycle and that the CO2 loss was the cost of recycling the other three carbons back into the Calvin cycle. The evidence for this was that plants grown in low levels of O2 or high levels of CO2 were more productive than plants grown in air despite strongly reduced levels of flux through the photorespiratory pathway. Thus, the implication was clear: Plant productivity could be strongly enhanced by identifying mutants with reduced amounts of photorespiration.”

This article in Science also discuss the signs.

“Genetic Engineers Aim to Soup Up Crop Photosynthesis”

“William Ogren, a now-retired RuBisCO researcher from the University of Illinois, Urbana-Champaign, says with only slight exaggeration. Enzymatic rates are often on the order of 25,000 reactions per second; RuBisCO turnover in higher plants can be as little as two or three reactions per second. “Not one of evolution’s finest efforts,” says Ogren.”

RuBisCO (ribulose-1,5-bisphosphate carboxylase-oxygenase) is the enzyme which triggers the photorespiration reaction.

“The oxygenation reaction is–as far as we can tell, and a lot of research over decades has gone into it–just a complete waste,” says Andrews. “It doesn’t do anything for the plant.”

This striking inefficiency was no handicap when photosynthesis first evolved 3 billion years ago, because the atmosphere was almost devoid of oxygen. After photosynthesis filled the air with oxygen and RuBisCO’s weakness was revealed, it may have been too late for evolution to fix the problem, says Murray Badger, a RuBisCO specialist at The Australian National University.

“If genetic engineers could find a way around RuBisCO’s slowness and inefficiency, they might reap a double benefit. A faster, more efficient enzyme could help crops grow and increase their biomass, letting them produce more grain at a faster rate.”

“More efficient RuBisCO could thus lower crops’ need for nitrogen, now mainly supplied by fertilizer in many countries.”

Contrast this with Bill Dembski the self-anointed New Newton/Einstein who will not apologise even for a flubbed quote.

If any proof is required that ID is fake science this is it.

Contrast this with Bill Dembski the self-anointed New Newton/Einstein who will not apologise even for a flubbed quote.

Self-anointed? Has William Dembski referred to himself as the “Newton of Information Theory?”

If any proof is required that ID is fake science this is it.

Non sequitur.

O’brien: Self-anointed? Has William Dembski referred to himself as the “Newton of Information Theory?”

No, technically the quote is attributed to Robert Koons (whose grasp of science is apparently insufficient to distinguish an Isaac Newton from a PT Barnum). But the difference between Dembski humbly allowing that bit of silliness to adorn the dust cover of his book, and actually making the claim himself, strikes me as kind of a technicality.

Syntax Error: mismatched tag at line 1, column 180, byte 180 at /usr/local/lib/perl5/site_perl/5.16/mach/XML/Parser.pm line 187.

No, technically the quote is attributed to Robert Koons (whose grasp of science is apparently insufficient to distinguish an Isaac Newton from a PT Barnum).

I do not know why you included the link to Perakh; his opinion and a dime would not get me a gumball from a gumball machine (as for Paul Gross, he comes off like a clown).

But the difference between Dembski humbly allowing that bit of silliness to adorn the dust cover of his book, and actually making the claim himself, strikes me as kind of a technicality.

It is common to include cheerleading on the back of books to encourage people to buy them, so I see no reason to fault Dembski for including Koons’ praise.

O’Brien: “I do not know why you included the link to Perakh” Mainly to bug you.

O’Brien: “… as for Paul Gross, he comes off like a clown” … in the highly respected opinion of Robert O’Brien, of course. How many of those will it take to purchase a gumball?

O’Brien: ”… I see no reason to fault Dembski for including Koons’ praise.”

No, I don’t suppose you do. Still, I contend that adorning his book’s dustjacket with such ludicrous aggrandizement is only technically distinct from making the claim himself.

Dembski loves the encomiums handed out to him by his fellow-“intellectuals”. It is one thing to be complimented by a crony or facttotum. It is another thing to puff up your chest and crow about it. Dictators and assorted cranks down history have been fond of letting the “people” know what the “people” think of them. The leading lights of the ID(iocy) movement aren’t any different. O’Brien might want to read thru the works of Perakh and Gross - who between them have over 40 years of published research in the sciences - before passing judgement. Perakh is one of those scientists who knows what freedom and tyranny actually mean having lived through and survived the best hospitality the USSR can offer a person with a conscience.

Dictators and assorted cranks down history have been fond of letting the “people” know what the “people” think of them. The leading lights of the ID(iocy) movement aren’t any different.

Hyperbolic nonsense.

O’Brien might want to read thru the works of Perakh and Gross - who between them have over 40 years of published research in the sciences - before passing judgement. Perakh is one of those scientists who knows what freedom and tyranny actually mean having lived through and survived the best hospitality the USSR can offer a person with a conscience.

You serve Perakh and Gross well, loyal chamcha, but I remain unimpressed by them. I know doctors who far surpass both of them, including those who suffered under the Soviet regime.

O’brien: “I know doctors who far surpass both of them, including those who suffered under the Soviet regime.”

Now here’s a good example of a really useless post. We have two specific individuals, with a history of publications dealing with specific topics, referring to a documented, published network of facts observations and thoughts, that you can look up, read, criticize if you like, maybe learn something from…

juxtaposed to an anonymous collection of indeterminate size of “doctors” who have - for unknown reasons - impressed an unknown (dare I say it?) insignificant nobody. Wow. Suddenly I lost all respect for Perakh and Gross.

Durbin Wrote:

Now here’s a good example of a really useless post. We have two specific individuals, with a history of publications dealing with specific topics, referring to a documented, published network of facts observations and thoughts, that you can look up, read, criticize if you like, maybe learn something from …

Your compatriot was engaging in what is known as asinus asinum fricat, which is all too common here (excepting you, of course, Russell). I simply let him know that I would not be genuflecting before Perakh and Gross.

Wow. Suddenly I lost all respect for Perakh and Gross.

Welcome to the light, brother.

But, you see, this is just an extension of the uselessness I’m talking about. For you to refer to Perakh, Gross and or shiva as asini without explanation or justification, and then to generalize - with no reference to any specifics - to the whole of Panda’s Thumb… there’s just no information there; it’s just playground-level name-calling. (Though, of course, we’re all impressed that you can be vacuous in Latin as well as in English.)

Somehow, I find this tune running through my head whenever I see an O’Brien comment:

“…too much of nothing, it just makes a fellow mean”

O’Brien has shown why Gross and Perakh are feared amongst ID proponents. For good reasons I may add

Robert O'Brien Wrote:

Your compatriot was engaging in what is known as asinus asinum fricat, which is all too common here.

Pim van Meurs Wrote:

O’Brien has shown why Gross and Perakh are feared amongst ID proponents. For good reasons I may add

Quod erat demonstrandum

While Obrien seems to have some grasp of Latin, he seems to be unable to address the claims made in any logical form or manner.

It is clear that O’Brien’s contributions seem to be limited to name calling.

Not surprising since his claims remain poorly supported. But that seems to be a trend amongst IDers.

Russell Durbin Wrote:

But, you see, this is just an extension of the uselessness I’m talking about. For you to refer to Perakh, Gross and or shiva as asini without explanation or justification, and then to generalize - with no reference to any specifics - to the whole of Panda’s Thumb … there’s just no information there; it’s just playground-level name-calling. (Though, of course, we’re all impressed that you can be vacuous in Latin as well as in English.)

I agree, Russell, that my insults, however clever, are ultimately “empty calories.” I also agree with your compatriot who said I have not provided any evidence for ID or some such. However, I have yet to commit to any ID position so I cannot be faulted for not meeting the “burden of proof” for something I did not assert.

O’Brien backpedalling: However, I have yet to commit to any ID position so I cannot be faulted for not meeting the “burden of proof” for something I did not assert.

O'Brien Wrote:

Because I have experienced God in my life, that is why. I refuse to turn my back on Him like many do when they become disillusioned with their respective religions. I also believe that there is strong evidence for intelligent design in all the sciences and mathematics.

or has Robert changed his mind?

Another gem

1) You are correct in that we don’t know the conditions of the primordial earth. So, why speculate about abiogenesis at all, when Pasteur did such a great job of refuting it? 2) The “math argument” against evolution is correct; evolution is only reasonable with a Creator guiding it.

Vah! Denuone Latine loquebar? Me ineptum. Interdum modo elabitur. :-)

What I posted to another messageboard, far removed from this one in both theme and time, has no bearing here. If you wish to participate in that discussion, I suggest you jump in a time machine or through the nearest menhir portal.

But you stated

However, I have yet to commit to any ID position so I cannot be faulted for not meeting the “burden of proof” for something I did not assert.

When I pointed to the obvious fact that you did in fact commit to an ID position, you now want to avoid discussing it? The discussions at that site are closed, it would be interesting to explore them on this site especially in light of your claims about commitment to ID positions.

Is your statement now that you are committed to a particular ID position but that you when you made your above statement you were discussing a much narrower position?

PvM Wrote:

When I pointed to the obvious fact that you did in fact commit to an ID position, you now want to avoid discussing it?

I have not committed to or argued for an ID position here, and that is what counts. You are welcome to mine that past discussion to your heart’s content, but I am not willing to argue for any position that I have not committed to here.

PvM Wrote:

Is your statement now that you are committed to a particular ID position but that you when you made your above statement you were discussing a much narrower position?

The closest thing I have to a statement is contained in my reply to Dr. Wolpert, which I posted to another thread.

Interesting, so what is O’Brien interested in ‘discussing’? He seems to arbitrarily reject rebuttals of Dembski’s work by people he considers to be ‘unqualified’ without addressing their claims, he makes some unsupported assertions about some of the contributors to this forum but when he makes the statement that he has not committed himself to any ID position and I show that this is incorrect the issue becomes a much narrower one namely that he is committed to a particular ID position, just unwilling to discuss it on this forum.

Does this mean that he is also not committed to Dembski’s arguments? And yet he seems to reject criticims based on an appeal to ‘you are not qualified’.

Interesting. So what is Robert’s position on Dembski’s arguments I wonder?

Anything beyond “The myopia and pedantry you display in evaluating William Dembski’s mathematical contributions is characteristic of people in your field.” I wonder :-)

I mean, is Robert objecting to what he sees as pedantry or myopia in people’s objections to Dembski’s mathematical contributions. If so, could he show that these objections qualify as such and are not in fact valid scientific objections?

Pim, I believe what Mr. O’Brien is trying to tell you is that he really does have nothing to say. (But he can say it in multiple languages!)

He did assert, however, that critiques of Dembski’s work by Perakh and Gross were without merit, cast aspersions on their scholarship and integrity, and slandered everyone here who’s expressed a contrary opinion. All without a single word of backup.

This “God” that he’s experienced in his life… perhaps it was Ares or Hermes - a deity all about feistiness or chicanery.

”… too much of nothing, it just makes a fellow mean.”

If, before they get here, I could warn creationists of one thing, I would warn them against setting themselves up to be Navy Davied. Being Navy Davied is when, after you take a strategically agnostic position on an issue, a Panda’s Thumb regular tracks down a contrary statement you made on a different site in the past. Usually humiliation follows.

Actually, I wouldn’t warn them, because the creationist usually disappears shortly after being Navy Davied, thus improving the local property values.

PvM Wrote:

…but when he makes the statement that he has not committed himself to any ID position and I show that this is incorrect the issue becomes a much narrower one namely that he is committed to a particular ID position, just unwilling to discuss it on this forum.

No, my statement was correct. I have not committed myself to a ID position here. The purview of this discussion is Panda’s Thumb. What I posted to another venue six years ago is irrelevant to my participation here.

Interesting. So what is Robert’s position on Dembski’s arguments I wonder?

I have no position on his arguments, although I am sympathetic to them. I do, however, have a position on William Dembski as a person; I admire him.

PvM Wrote:

Anything beyond “The myopia and pedantry you display in evaluating William Dembski’s mathematical contributions is characteristic of people in your field.” I wonder :-)

I mean, is Robert objecting to what he sees as pedantry or myopia in people’s objections to Dembski’s mathematical contributions. If so, could he show that these objections qualify as such and are not in fact valid scientific objections?

You are confusing issues here. I posted that remark to Shallit’s thread concerning Dembski’s contributions to mathematics as a whole. The thread had nothing to do with specific ID arguments.

Robert: You are confusing issues here. I posted that remark to Shallit’s thread concerning Dembski’s contributions to mathematics as a whole. The thread had nothing to do with specific ID arguments.

Let’s put things in their perspective

Me: Interesting how o’Brien seems to be moving the goalposts. First it was ‘Dembski’s mathematical contributions’ now it is mathematical prowess …

Robert Wrote:

Nope. I do not think non-mathematicians are qualified to address either.

Me: Rather than disputing that non mathematicians are qualified to evaluate Dembski’s claims, why not address the arguments presented by these ‘non-mathematicians’?

Robert Wrote:

or the same reason a neuroscientist would be loath to waste time on a phrenologist.

Robert Wrote:

Quality is more important than quantity, and I do not think anyone here (whom I’ve seen thus far) is qualified to comment on the quality of William Dembski’s work.

Since much of the work by Dembski IS related to ID, I wonder about the contradictions. Is Robert saying that while non-mathematicians cannot comment of the quality of Dembski’s work, they are qualified to comment on specific flaws in his arguments?

It’s time that Robert presents an exact description of his claims since so far his claims seem to be suffering from ‘moving goalposts’ First the claim that he has not committed himself to any ID position, which quickly became ‘here’ when it was pointed out to him that his statement seemed to contradict earlier statements made by Robert.

Pim, you’re wasting your time on this guy.

Bene diagnoscitur, bene curatur. Cuiusvis hominis est errare Cura, ut valeas!

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This page contains a single entry by Jason Rosenhouse published on July 29, 2004 5:43 PM.

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