From PNAS: What’s wrong with peer review

_{News
December 22, 2014

News, Peer review

2}_{Categories
News
Peer review}

Share: Facebook; Twitter/X; LinkedIn; Flipboard; Print; Email

From a recent article’s Significance statement:

Our research suggests that evaluative strategies that increase the mean quality of published science may also increase the risk of rejecting unconventional or outstanding work.

You don’t mean stuff that is true but no elite source can afford to admit? Shocka! Abstract

Peer review is the main institution responsible for the evaluation and gestation of scientific research. Although peer review is widely seen as vital to scientific evaluation, anecdotal evidence abounds of gatekeeping mistakes in leading journals, such as rejecting seminal contributions or accepting mediocre submissions. Systematic evidence regarding the effectiveness—or lack thereof—of scientific gatekeeping is scant, largely because access to rejected manuscripts from journals is rarely available. Using a dataset of 1,008 manuscripts submitted to three elite medical journals, we show differences in citation outcomes for articles that received different appraisals from editors and peer reviewers. Among rejected articles, desk-rejected manuscripts, deemed as unworthy of peer review by editors, received fewer citations than those sent for peer review. Among both rejected and accepted articles, manuscripts with lower scores from peer reviewers received relatively fewer citations when they were eventually published. However, hindsight reveals numerous questionable gatekeeping decisions. Of the 808 eventually published articles in our dataset, our three focal journals rejected many highly cited manuscripts, including the 14 most popular; roughly the top 2 percent. Of those 14 articles, 12 were desk-rejected. This finding raises concerns regarding whether peer review is ill-suited to recognize and gestate the most impactful ideas and research. Despite this finding, results show that in our case studies, on the whole, there was value added in peer review. Editors and peer reviewers generally—but not always—made good decisions regarding the identification and promotion of quality in scientific manuscripts. (paywall)

As Retraction Watch explains, “Put another way, peer review rewards mediocrity at the expense of breakthroughs.” Hat tip: Retraction Watch Follow UD News at Twitter!

Comments

Oh Mungy, I gave little Joey a few papers on the evolution of ATP synthase in response to his claims that no one has provided evidence of its evolution. He didn't read them, and even if he did, I doubt he would understand them. In this conversation, Andre (another genius here at UD), decides to put his two cents in which adds up to pretty much nothing. He has nothing to say that even resembles a scientific thought despite there being plenty of opportunity from the posts I have already made. Instead he asks a question I have already answered numerous times for jazzy and then asks another ridiculous question that shows his complete lack of knowledge on the subject of evolutionary biology.AVS_{December 23, 2014
December
12
Dec
23
23
2014
05:37 PM
5
05
37
PM
PDT}

It certainly is hilarious when people who have been here to UD time and again find it hilarious when IDers claim there’s no “concrete evidence” for something when it's almost beyond doubt that these people have been asked by the ID'ers here, yes even encouraged, repeatedly, to provide the evidence they claim exists, and consistently fail to do so. It certainly is hilarious when IDers claim there’s no “concrete speculation” for something. No, we see that here all the time.Mung_{December 23, 2014
December
12
Dec
23
23
2014
04:03 PM
4
04
03
PM
PDT}

It certainly is hilarious when IDers claim there's no "concrete evidence" for something. And evolution is guided by selection.AVS_{December 23, 2014
December
12
Dec
23
23
2014
02:36 PM
2
02
36
PM
PDT}

AVS the function search? So evolution is by your own admission very much guided then?Andre_{December 23, 2014
December
12
Dec
23
23
2014
01:54 PM
1
01
54
PM
PDT}

Good grief. Lots of twaddle from AVS and Zach but no concrete evidence to back their claims. Anything on where the information came from gents?Andre_{December 23, 2014
December
12
Dec
23
23
2014
01:50 PM
1
01
50
PM
PDT}

Yes, as I already said these ribozymes with catalytic activity were generated by the function search carried out by chemical evolution. When the first RNA molecule was able to catalyze a reaction, the sequence became the information for a catalytic molecule. Many RNA molecules are capable of catalytic activity, it was the job of chemical evolution to search for useful molecules and the right combination of useful molecules, of course this was no simple task. And look, the protocols of the RNA evolution experiments were specifically designed to mimic the process of natural selection, if you disagree, you should take it up with the scientists themselves or maybe carry out your own experiments. Something tells me you've wandered a little too far into the realm of experimental biology to really understand how nonsensical the claims are that you are making. "All of the proper functions in the right place at the right time" is a phrase commonly thrown around by IDers despite us not knowing what these functions even are. Who knows how many there are or how many of them are temporally sensitive. And no, only one molecule that can catalyze a peptide bond is needed to potentially synthesize a protein. And wrong again, a random RNA sequence certainly can provide a function. This was a requirement for the some of the experiments that we have talked about. The investigators started off with random sequences, induced random, mutations, and selected for certain active molecules. These active molecules have developed a function and their sequence is the information for the synthesis of this molecule.AVS_{December 23, 2014
December
12
Dec
23
23
2014
12:58 PM
12
12
58
PM
PDT}

jazzcat: -Prebiotic experiments generally show that some of those required for life can arise but not nearly in sufficient quantities for a prebiotic soup. Based on what we have discovered so far, but the epoch in question is very ancient, and we have only just begun to explore the history. jazzcat: -Random strands of nucleotides would not produce any information therefore function so there could be no selection. That's not necessarily the case. Even simple sequences can have catalytic functions. jazzcat: -RNA is capable of catalyzing some reactions and capable of storing some information but it is inadequate for producing a living cell. Once you have replication, then you have evolution. A membrane is usually considered essential in order to isolate the replicase, but simple membranes can form spontaneously. jazzcat: -Furthermore functional RNA contains information which would be the thing we are trying to explain in the first place. Where did the information come from? Random RNA sequences can have function. But you are right. There are many open questions. jazzcat: Really? Then you wouldn’t mind showing me how? It's called adaptation. See Darwin 1859. jazzcat: Since there is a vast number of possible sequences theorists must resort to chance, at which odds defy any reasonable chance of happening in the entire universe. That is your claim, however, there's no a priori reason for that claim. It's quite possible that it is inevitable given the appropriate conditions. No one knows at this time. humbled: RM + NS has never produced a new system or body part. Legs. jazzcat: a random RNA sequence won’t provide a function. That is incorrect. See Sassanfar & Szostak, An RNA motif that binds ATP, Nature 1993.Zachriel_{December 23, 2014
December
12
Dec
23
23
2014
12:47 PM
12
12
47
PM
PDT}

AVS @59 If you are going to presuppose ribozymes catalyzing reactions you would in effect presuppose the presence of biological information, which is what we're trying to explain the origin of. Yes I meant polypeptide synthesis, amino acids linking together, sorry about that. It's funny you don't see the irony in intelligent agents artifically synthesizing RNA strands and through intelligent selection, selecting those for functions that COULD be a plausible pathway to the first life. Even if some "function" was found, it would be no help to the origin of life, which needs ALL of the proper functions in place at the right time. An RNA that can catalyze one or two reactions does not lead to the synthesis of a protein I agree structure begets function as soon as you have function, but a random RNA sequence won't provide a function. ONly a very very small number of sequences among the VAST combinatorial possibilities provide any function. And I don't appreciate the tone towards Meyer's book. Have you read it? Critiquing a model is not pseudoscientific.jazzcat_{December 23, 2014
December
12
Dec
23
23
2014
12:33 PM
12
12
33
PM
PDT}

I'm sure the book has plenty of pseudoscientific nonsense in it, jazz. Anyways, 1. I assume you're talking about polypeptide synthesis, not amino acid synthesis. Either way, the presence of ribozymes that catalyze this reaction would overcome this problem. In accordance with this, it's no surpise to find the ribosome, which is the site of polypeptide synthesis is largely made up of RNA and active site is entirely made up of RNA. 2. Does it really matter how the experimental strands came about or how they select for them? In the end you are using random sequences and looking for function. This is exactly what would have happened in chemical evolution, it is a model of chemical evolution. Preventing cross reactions is a necessity in experiments like these, variables must be controlled. Who knows, maybe not allowing cross-reactivity is what is keeping us from finding more efficient self-replicators. 3. "Structure begets function" applies as soon as you have a function. The function is controlled by the structure. You can have many structures many of them will have function to some degree, some will not. Chemical evolution found these structures, likely with low level function, and chemical evolution built upon it. Don't fall into the trap of think that evolution looks for a single "correct" sequence, it does not.AVS_{December 23, 2014
December
12
Dec
23
23
2014
12:22 PM
12
12
22
PM
PDT}

Evolution does NOT produce information, not in reality anyway, it only corrupts existing information. Come on folks, this is 101 stuff. RM + NS has never produced a new system or body part. Nothing naddah zilch. Since RM + NS cannot do what the Darwin faithful claim it can, but worshipped and defended regardless, Darwinian evolution is exposed as yet another belief system.humbled_{December 23, 2014
December
12
Dec
23
23
2014
12:19 PM
12
12
19
PM
PDT}

AVS @56 Thank you for your reply. "Signature in the Cell," has chapters of debunking the current OOL models such as metabolism first, RNA world, clay hypothesis, etc..although I have not gotten that far in the book so I will take a look at your model. Thank you for presenting it. Three points we could continue the conversation with: 1) Water is a poor (thermodynamically unfavored) environment for amino acid synthesis because the reaction releases a water molecule. 2) Intelligent agents are artifically synthesizing strands and then intelligently selecting them for certain functions. They are also preventing interfering cross reactions that would otherwise not be prevented in a mixture of chemicals. 3) "structure begets function" does not apply before life. In order for function to arise in the first place the correct sequence must be found. Since there is a vast number of possible sequences theorists must resort to chance, at which odds defy any reasonable chance of happening in the entire universe.jazzcat_{December 23, 2014
December
12
Dec
23
23
2014
11:57 AM
11
11
57
AM
PDT}

Jazz, look into the surface metabolism model. Concentration of the necessary molecules likely occured near or on the hydrothermal vents, providing environments suitable for chemical evolution. Neither of these models are likely to be completely correct but they are small steps toward the generation of the first cell. random strands most certainly can produce function as has been demonstrated in experiments that use millions of random sequences and then select for certain catalytic activity, some of these I just mentioned. And as I said, the sequence of these strands themselves is the information for their replication (similar to DNA) as well as function. The production of the first living cell no doubt also involved other molecules that have been generated in early earth experiments, one of the most important being lipids, which are capable of forming a bilayer on their own. "Self-replication requiring more than RNA" is your opinion, as I said we have already shown the evolution of ribozymes that can add short sequences of template directed nucleotides. The information is inherent to the sequence and resulting shape of the molecule. "Structure begets function." This is one of the most important ideas of biology. Early ribozymes synthesize random strands of nucleotides, some of these strands will have catalytic activity, this has been demonstrated time and time again. What we have to figure out is which of these catalytic reactions were important for early life and which evolved later.AVS_{December 23, 2014
December
12
Dec
23
23
2014
11:38 AM
11
11
38
AM
PDT}

Zachriel @53 I can see we're getting nowhere. "the counterexample is evolution, which is a natural process." Really? Then you wouldn't mind showing me how?jazzcat_{December 23, 2014
December
12
Dec
23
23
2014
11:27 AM
11
11
27
AM
PDT}

AVS @51 We may be getting somewhere. A few points of rebuttal: -Prebiotic experiments generally show that some of those required for life can arise but not nearly in sufficient quantities for a prebiotic soup. -Random strands of nucleotides would not produce any information therefore function so there could be no selection. It is the specific sequence that is needed. -RNA is capable of catalyzing some reactions and capable of storing some information but it is inadequate for producing a living cell. -Self replication requires much more information then just an RNA molecule. -Furthermore functional RNA contains information which would be the thing we are trying to explain in the first place. Where did the information come from?jazzcat_{December 23, 2014
December
12
Dec
23
23
2014
11:22 AM
11
11
22
AM
PDT}

jazzcat: Natural processes have NOT shown the ability to produce new information. There is no counter example. The counterexample is evolution, which is a natural process.Zachriel_{December 23, 2014
December
12
Dec
23
23
2014
11:15 AM
11
11
15
AM
PDT}

Zachriel @50 Yes Natural processes have NOT shown the ability to produce new information. There is no counter example. This is why the inference to ID works especially at the origin of life, before Darwin's theory of evolution can "take hold." Once you provide a counter example of how the information in DNA or RNA in the first life could arise through a wholly natural process, you let us know mmk?jazzcat_{December 23, 2014
December
12
Dec
23
23
2014
11:13 AM
11
11
13
AM
PDT}

Ok, so you want to talk about the origin of information in cells. This is a hot-topic for IDers because of the gaps in origins research. It is extremely difficult to study the earliest forms of life so we have to do our best with what we already know. So what do we know? We know that nitrogenous bases and sugars can arise from early-earth experiments, minerals bind preferentially to ribose sugars, these minerals were prevalent at the sites of proposed chemical evolution and are capable of catalytic activity, activation of nucleotides has been seen in early-earth experiments, these experiments have produced nucleotide strands up to 100 nucleotides in length even without nucleotide activation, RNA molecules are capable of both information storage and catalyzing a number of chemical reactions, the evolution of ribozymes that join two nucleotides together into a ribozyme that is capable of adding multiple nucleotides has been shown, molecular evolution of ribozymes that catalyze the binding of base to sugar has been demonstrated. This is some of the information behind the RNA world, with the key being that RNA is capable of storing information and catalyzing reactions. The evolution of RNA molecules that were capable of catalyzing chemical reactions conducive to life as we now know it also have the information for their replication stored within them. How exactly these molecules evolved and along with other molecules formed the first cell is certainly a mystery and there is still much we don't know, but we are piecing the puzzle together.AVS_{December 23, 2014
December
12
Dec
23
23
2014
11:12 AM
11
11
12
AM
PDT}

jazzcat: Since we’re talking about the origin of life most of your comment does not apply Ignoring the evidence doesn't mean it goes away. Evolution provides information about early life, which helps shed light on its origin. Furthermore, you base your position on the false claim that "Natural processes have NOT shown the ability to produce new information, they can merely transmit existing information." Evolution is the counterexample.Zachriel_{December 23, 2014
December
12
Dec
23
23
2014
11:08 AM
11
11
08
AM
PDT}

Zachriel @48 Since we're talking about the origin of life most of your comment does not apply, however you said this, "As for the very first life, there are a number of ideas; and while there is no complete theory, there is some tentative evidence supporting abiogenesis, with no evidence of a designer." You did not answer my question which where did the information necessary to produce the first life come from? "Evolution can result in new information." Irrelevant to the origin of life. Before life there is NO evolution because there is no biological information transmitted from parent to offspring. There is no mutations in copying DNA because this is BEFORE DNA. Please provide just ONE example of a natural process producing functional digital information?jazzcat_{December 23, 2014
December
12
Dec
23
23
2014
11:04 AM
11
11
04
AM
PDT}

jazzcat: Where did the information necessary to produce the first life come from? Evolution provides us some clues. The evidence implies branching descent and adaptation through natural selection, adaptation roughly translating into an increase in "information". As we have a natural mechanism whereby this information can increase, it's reasonable to suppose that similar mechanisms were involved before the most recent common ancestor. As for the very first life, there are a number of ideas; and while there is no complete theory, there is some tentative evidence supporting abiogenesis, with no evidence of a designer. jazzcat: From our uniform and repeated experience only intelligence is the cause. That is incorrect. Evolution can result in new information.Zachriel_{December 23, 2014
December
12
Dec
23
23
2014
10:56 AM
10
10
56
AM
PDT}

AVS @45 "Proteins simply interact with the DNA to copy it, transcribe and express it, correct it, induce mutations, etc. based solely on molecular interactions." Careful now, it is NOT SOLELY based on molecular interactions it is based on molecular interactions WITH the information contained in the sequencing of the nucleic acids. The sequencing of the nucleic acids are NOT due to any molecular, chemical, or physical interaction. You have also highlighted what origin of life researchers call the "DNA enigma." DNA contains instructions for building proteins, but proteins are required to build DNA strands. It is a chicken & chicken egg dilemma. The mere presence of this closed loop suggests a purposeful arrangement of parts to suit a specific goal.jazzcat_{December 23, 2014
December
12
Dec
23
23
2014
10:54 AM
10
10
54
AM
PDT}

AVS @45 You're mischaracterizing Meyer's argument. No where does he make the case that the actions DNA carries out are due to a conscious mind. Computers perform software functions without conscious activity. A photo-copier copying the information in a book does not require an intelligent design. What he seeks to explain is the ORIGIN of such information. "Evolution at the molecular level is the alteration of these functions that make small changes in an organism which selection can act on." I agree but this is presuming organisms before the origin of life. There is no natural selection with random variations BEFORE the origin of life which involves selection and variation. "The basic function of DNA as information storage is comparable to these things, but that is where the similarities end." I'll grant you that statement for the sake of argument. You have admitted that DNA functions as information storage...it stores information. Where did the information come from? It can transmit from organism to organism but the FIRST organism could NOT have the information transmitted to it without first assuming another living organism before that one. Where did the information necessary to produce the first life come from? From our uniform and repeated experience only intelligence is the cause. Natural processes have NOT shown the ability to produce new information, they can merely transmit existing information. If my premises are true as you have admitted, then my conclusion would HAVE to be true.jazzcat_{December 23, 2014
December
12
Dec
23
23
2014
10:44 AM
10
10
44
AM
PDT}

Do you not see how superficial those comparisons are to DNA and its functions in the cell, jazz? The biggest difference is that the functions of DNA are carried out without the need for a conscious mind. Proteins simply interact with the DNA to copy it, transcribe and express it, correct it, induce mutations, etc. based solely on molecular interactions. Evolution at the molecular level is the alteration of these functions that make small changes in an organism which selection can act on. The basic function of DNA as information storage is comparable to these things, but that is where the similarities end. And I think you're giving a little too much credit to the design of those molecules. They are just slightly modified versions of naturally existing molecules, although this is no small task.AVS_{December 23, 2014
December
12
Dec
23
23
2014
10:33 AM
10
10
33
AM
PDT}

AVS- I am OK with intelligent design EVOLUTION producing DNA and ATP synthase. What cannot be tested nor modeled is unguided evolution doing it. There aren't any testable hypotheses for such a thing. It cannot be measured, there aren't any equations, it is all bluff and willful ignorance of your opponents' positions.
Did you take a look at those papers I told you about on the other post that talk about the evolution of ATP synthase by the way?
Yes, nothing that relates to unguided processes and nothing that can be demonstrated scientifically.Joe_{December 23, 2014
December
12
Dec
23
23
2014
10:28 AM
10
10
28
AM
PDT}

I don't see the relevance in this AVS. You don't dispute the premise of ID that humans (who are intelligent) have the ability to produce digital information do you? Is there a problem with the standard method of historical scientific reasoning you disagree with? We are trying to explain the origin of an event in the remote past: the origin of the information necessary to produce the first living cell.jazzcat_{December 23, 2014
December
12
Dec
23
23
2014
10:25 AM
10
10
25
AM
PDT}

AVS @39 "What is the closest human-designed thing to DNA?" blueprints, computer software, hieroglyphic inscriptions, pages of text. "Can you give me some examples of molecules designed by humans while you're at it?" I cannot name the molecular structures off the top of my head but I can name some abstractly: Ribozyme and protein engineering, GMOs, medicines...etcjazzcat_{December 23, 2014
December
12
Dec
23
23
2014
10:22 AM
10
10
22
AM
PDT}

It is exactly what you are saying Joe. "Evolution hasn't explained the existence of ATP synthase," "evolution hasn't explained the existence of DNA," etc. It's all the same argument, you're just picking at the current gaps in knowledge and ignoring what is already known. Did you take a look at those papers I told you about on the other post that talk about the evolution of ATP synthase by the way? I doubt it. Ignorance is bliss.AVS_{December 23, 2014
December
12
Dec
23
23
2014
10:20 AM
10
10
20
AM
PDT}

AVS:
Once again, Joe, you have resorted to the “evolution hasn’t explained it yet, therefore evolution is wrong” argument.
That is your opinion and doesn't follow from what I have posted. Also ID is not anti-evolution and your ignorance of the debate is still meaningless.Joe_{December 23, 2014
December
12
Dec
23
23
2014
10:16 AM
10
10
16
AM
PDT}

This is the problem, jazz. The molecular world is very different from the macro-scale world that we are much more familiar with. My question was worded poorly, I'm basically asking what is the closest human-designed thing to DNA. I think that if you give your answer to it, I will be able to point out some significant differences between it and DNA. Can you give me some examples of molecules designed by humans while your at? Just off the top of your head. ThanksAVS_{December 23, 2014
December
12
Dec
23
23
2014
10:14 AM
10
10
14
AM
PDT}

AVS Would it help if the argument were re-phrased as such?: Digital Information as a function ONLY arises from an intelligent source from our uniform and repeated experience. Natural processes such as chance, necessity, or a combination of the two are inadequate and have never been shown to produce the function of digital information. Because DNA functions as information we can logically infer to the best explanation that ID is the origin of the function of Digital Information in DNA.jazzcat_{December 23, 2014
December
12
Dec
23
23
2014
10:09 AM
10
10
09
AM
PDT}

Prev 1 2 3 4 Next

You must be logged in to post a comment.

Leave a Reply