Evolution and the myth of "scientific consensus"

[RickG]

http://www.reuters.com/article/2012/03/28/us-science-cancer-idUSBRE82R12P20120328


A former researcher at Amgen Inc has found that many basic studies on cancer -- a high proportion of them from university labs -- are unreliable, with grim consequences for producing new medicines in the future.

During a decade as head of global cancer research at Amgen, C. Glenn Begley identified 53 "landmark" publications -- papers in top journals, from reputable labs -- for his team to reproduce. Begley sought to double-check the findings before trying to build on them for drug development.

Result: 47 of the 53 could not be replicated. He described his findings in a commentary piece published on Wednesday in the journal Nature....

Bayer and Amgen found that the prestige of a journal was no guarantee a paper would be solid. "The scientific community assumes that the claims in a preclinical study can be taken at face value," Begley and Lee Ellis of MD Anderson Cancer Center wrote in Nature. It assumes, too, that "the main message of the paper can be relied on ... Unfortunately, this is not always the case."

(emphasis added)

Yes, that's why we see TV ads by lawyers sewing pharmaceutical companies. Now, how does that relate to the mainstream journals of the Earth Sciences? Show me an example where this has occurred in the Journals Nature, Science, and the numerous journals of the American Geophysical Union. How about comparing apples with apples.

 

[Zosimus]

Yes, that's why we see TV ads by lawyers sewing pharmaceutical companies. Now, how does that relate to the mainstream journals of the Earth Sciences? Show me an example where this has occurred in the Journals Nature, Science, and the numerous journals of the American Geophysical Union. How about comparing apples with apples.

I hate it when lawyers sew people...

http://www.newyorker.com/magazine/2010/12/13/the-truth-wears-off

In 1991, the Danish zoologist Anders Møller, at Uppsala University, in Sweden, made a remarkable discovery about sex, barn swallows, and symmetry. It had long been known that the asymmetrical appearance of a creature was directly linked to the amount of mutation in its genome, so that more mutations led to more “fluctuating asymmetry.” (An easy way to measure asymmetry in humans is to compare the length of the fingers on each hand.) What Møller discovered is that female barn swallows were far more likely to mate with male birds that had long, symmetrical feathers. This suggested that the picky females were using symmetry as a proxy for the quality of male genes. Møller’s paper, which was published in Nature, set off a frenzy of research. Here was an easily measured, widely applicable indicator of genetic quality, and females could be shown to gravitate toward it. Aesthetics was really about genetics....

Then the theory started to fall apart. In 1994, there were fourteen published tests of symmetry and sexual selection, and only eight found a correlation. In 1995, there were eight papers on the subject, and only four got a positive result. By 1998, when there were twelve additional investigations of fluctuating asymmetry, only a third of them confirmed the theory. Worse still, even the studies that yielded some positive result showed a steadily declining effect size. Between 1992 and 1997, the average effect size shrank by eighty per cent.

And it’s not just fluctuating asymmetry. In 2001, Michael Jennions, a biologist at the Australian National University, set out to analyze “temporal trends” across a wide range of subjects in ecology and evolutionary biology. He looked at hundreds of papers and forty-four meta-analyses (that is, statistical syntheses of related studies), and discovered a consistent decline effect over time, as many of the theories seemed to fade into irrelevance. In fact, even when numerous variables were controlled for—Jennions knew, for instance, that the same author might publish several critical papers, which could distort his analysis—there was still a significant decrease in the validity of the hypothesis, often within a year of publication. Jennions admits that his findings are troubling, but expresses a reluctance to talk about them publicly. “This is a very sensitive issue for scientists,” he says. “You know, we’re supposed to be dealing with hard facts, the stuff that’s supposed to stand the test of time. But when you see these trends you become a little more skeptical of things.”

(emphasis added)

 

[RickG]

I hate it when lawyers sew people...

No doubt lawyers are the lowest scum of the earth, except for politicians, many of which are lawyers as well. For lawyers, it is all about winning, rather than justice.

 

[Zosimus]

No doubt lawyers are the lowest scum of the earth, except for politicians, many of which are lawyers as well. For lawyers, it is all about winning, rather than justice.

I was actually having a bit of fun at the use of the word "sew." I'm sure what is meant is that the lawyers are SUING the pharmaceutical companies, not sewing them.

 

[Zosimus]

http://retractionwatch.com/2014/08/01/another-nature-stem-cell-paper-is-retracted/

Another stem cell paper has been retracted from Nature, this one a highly cited 2008 study that had already been the subject of what the journal’s news section called a "furore" in 2010....

This is the seventh retraction in Nature this year.

 

[RickG]

Zosimus, you may be interested in this one.

http://www.mdpi.com/2072-4292/3/9/2002/pdf

 

[RickG]

http://retractionwatch.com/2014/08/01/another-nature-stem-cell-paper-is-retracted/

Another stem cell paper has been retracted from Nature, this one a highly cited 2008 study that had already been the subject of what the journal’s news section called a "furore" in 2010....

This is the seventh retraction in Nature this year.

Thus the peer review process doesn't end with publication. When problems are found, they get corrected.

 

[Zosimus]

Thus the peer review process doesn't end with publication. When problems are found, they get corrected.

Your faith is impressive. I, however, have another point of view.

 

[RickG]

Your faith is impressive. I, however, have another point of view.

And I respect that. I think an important thing to take from the discussion is that breakdowns in the process do occur but they are not the norm and generally get corrected. Once published, it is out there for the entire scientific community to review. If you ever search for papers through a scientific search engine you will notice with the returned search results are also citations attributed to those papers. Few to no citations generally indicates a work of little or no significance. Also pay attention to who is citing. When the majority of citations are by the actual author citing his own work from another paper, that's a red flag. That of course doesn't mean that citing ones self is improper, it just shows that if little or no citations are by other scientists, generally indicates little or no acceptance of the research findings.

 

[sfs]

I hate it when lawyers sew people...

http://www.newyorker.com/magazine/2010/12/13/the-truth-wears-off

The ironic thing is that the author of that New Yorker piece was subsequently fired for fabricating things in his writing.

There is indeed a serious problem with peer reviewed research, and quite a lot of all published research is simply wrong. In some fields, the fraction is probably more than half. Particle physics is very careful, at least these days, and they rarely claim to have observed something that doesn't hold up. Psychology seems to to really bad. Biomedical research is mostly quite bad, although genetic epidemiology has improved dramatically with the advent of whole-genome association studies and the imposition of rigorous statistical techniques.

The upshot is that recent scientific results should mostly be ignored. Nevertheless, even with all of this noise (wasteful and annoying as it is), science still accumulates knowledge. GPS really does tell you where you are, NASA really can get probes to Mars, HIV drugs really do work. Neither credulity nor nihilism are warranted.

 

[Zosimus]

And I respect that. I think an important thing to take from the discussion is that breakdowns in the process do occur but they are not the norm and generally get corrected.

Speculation.

Once published, it is out there for the entire scientific community to review.

Relevance?

If you ever search for papers through a scientific search engine you will notice with the returned search results are also citations attributed to those papers. Few to no citations generally indicates a work of little or no significance. Also pay attention to who is citing. When the majority of citations are by the actual author citing his own work from another paper, that's a red flag. That of course doesn't mean that citing ones self is improper, it just shows that if little or no citations are by other scientists, generally indicates little or no acceptance of the research findings.

We are discussing not whether the paper is accepted by the scientific community but whether the peer-review process adequately improves the probability of published findings being free from egregious errors.

http://retractionwatch.com/2014/03/...-corrupt-and-simply-a-regression-to-the-mean/

Nobel Prize winner calls peer review “very distorted,” “completely corrupt,” and “simply a regression to the mean”

...in a new interview, Brenner doesn’t hold back, saying that publishers hire “a lot of failed scientists, editors who are just like the people at Homeland Security, little power grabbers in their own sphere.”

"I think peer review is hindering science. In fact, I think it has become a completely corrupt system. It’s corrupt in many ways, in that scientists and academics have handed over to the editors of these journals the ability to make judgment on science and scientists."

 

[Zosimus]

The ironic thing is that the author of that New Yorker piece was subsequently fired for fabricating things in his writing.

Unless you are alleging that the author fabricated some of that article, I don't see the relevance.

There is indeed a serious problem with peer reviewed research, and quite a lot of all published research is simply wrong. In some fields, the fraction is probably more than half.

http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.0020124

"Most Research Findings Are False for Most Research Designs and for Most Fields"

Particle physics is very careful, at least these days, and they rarely claim to have observed something that doesn't hold up. Psychology seems to to really bad. Biomedical research is mostly quite bad, although genetic epidemiology has improved dramatically with the advent of whole-genome association studies and the imposition of rigorous statistical techniques.

The upshot is that recent scientific results should mostly be ignored. Nevertheless, even with all of this noise (wasteful and annoying as it is), science still accumulates knowledge. GPS really does tell you where you are, NASA really can get probes to Mars, HIV drugs really do work. Neither credulity nor nihilism are warranted.

There is no reason to believe that science accumulates knowledge.

 

[Loudmouth]

The ironic thing is that the author of that New Yorker piece was subsequently fired for fabricating things in his writing.

There is indeed a serious problem with peer reviewed research, and quite a lot of all published research is simply wrong. In some fields, the fraction is probably more than half. Particle physics is very careful, at least these days, and they rarely claim to have observed something that doesn't hold up. Psychology seems to to really bad. Biomedical research is mostly quite bad, although genetic epidemiology has improved dramatically with the advent of whole-genome association studies and the imposition of rigorous statistical techniques.

The upshot is that recent scientific results should mostly be ignored. Nevertheless, even with all of this noise (wasteful and annoying as it is), science still accumulates knowledge. GPS really does tell you where you are, NASA really can get probes to Mars, HIV drugs really do work. Neither credulity nor nihilism are warranted.

I guess I view it differently. From what I have seen, authors are faithfully reporting their data and they are being honest with the experiments that they are running. Their conclusions are always tentative. There is no expectation that the conclusions must be true. It is only after many papers are published on a specific subject that we can sit back and separate the wheat from the chaff.

If we sat back and waited until we were 100% sure of our conclusions, then no papers would be published and we wouldn't be able to draw off the knowledge from other research groups.

 

[Zosimus]

I guess I view it differently. From what I have seen, authors are faithfully reporting their data and they are being honest with the experiments that they are running. Their conclusions are always tentative. There is no expectation that the conclusions must be true. It is only after many papers are published on a specific subject that we can sit back and separate the wheat from the chaff.

If we sat back and waited until we were 100% sure of our conclusions, then no papers would be published and we wouldn't be able to draw off the knowledge from other research groups.

That's the first thing you've ever said that I've agreed with.

There is no reason to believe that published research findings are true.

 

[Loudmouth]

http://retractionwatch.com/2014/08/01/another-nature-stem-cell-paper-is-retracted/

Another stem cell paper has been retracted from Nature, this one a highly cited 2008 study that had already been the subject of what the journal’s news section called a "furore" in 2010....

This is the seventh retraction in Nature this year.

This is science in action. This is how it works.

In peer review, the reviewers do not replicate the experiments to make sure the data is correct. They aren't responsible for making sure scientists do the experiments right. What they do look for is the proper controls and experimental design.

Peer review and publication is just the first step. The important steps is when other scientists put those conclusions to the test in their own labs.

 

[lifepsyop]

The upshot is that recent scientific results should mostly be ignored. Nevertheless, even with all of this noise (wasteful and annoying as it is), science still accumulates knowledge. GPS really does tell you where you are, NASA really can get probes to Mars, HIV drugs really do work. Neither credulity nor nihilism are warranted.

An important distinction is that if engineering parameters are even slightly off than things blow up.

There is really nothing like that in terms of a theory of universal common ancestry.

Or in the case of the Big Bang as attested to in the OP:
"The successes claimed by the theory's supporters consist of its ability to retrospectively fit observations with a steadily increasing array of adjustable parameters"

These are soft, very pliable theories. They can barely be considered theories because of how useless they are to predict or quantify anything, and how open they are to ad-hoc adjusting. There is a consensus, not because Evolution theory has passed any rigorous tests or is particularly persuasive, but because it is the only way to attempt to model life in a purely materialistic framework.

And there's nothing wrong with that really. But it's the constant lies and myths and general ignorance that is spread that universal common ancestry is such a well proven fact borne out by all the evidence... which is not even remotely true.

 

[Loudmouth]

An important distinction is that if engineering parameters are even slightly off than things blow up.

There is really nothing like that in terms of a theory of universal common ancestry.

If you were ever able to show widespread and obvious violations of the accepted phylogenies, that would certainly blow it up. As it is, you can only find small discrepancies where we would expect to see them.

Or in the case of the Big Bang as attested to in the OP:
"The successes claimed by the theory's supporters consist of its ability to retrospectively fit observations with a steadily increasing array of adjustable parameters"

These are soft, very pliable theories. They can barely be considered theories because of how useless they are to predict or quantify anything, and how open they are to ad-hoc adjusting.

The Big Bang theory predicts that type Ia supernova luminosity should correlate with redshift, and that can be tested every time there is a new type Ia SN.

There is a consensus, not because Evolution theory has passed any rigorous tests or is particularly persuasive, but because it is the only way to attempt to model life in a purely materialistic framework.

It has been tested extensively by genetics.

 

[sfs]

Unless you are alleging that the author fabricated some of that article, I don't see the relevance.

It's relevance is that it is an amusing irony. Nothing more.

http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.0020124

"Most Research Findings Are False for Most Research Designs and for Most Fields"

That paper considered only fields within biomedical research.

There is no reason to believe that science accumulates knowledge.

I think there are good reasons for believing that science accumulates knowledge, for fairly unremarkable definitions of "knowledge". Very few scientists and few philosophers of science are pure instrumentalists.

 

[lifepsyop]

If you were ever able to show widespread and obvious violations of the accepted phylogenies, that would certainly blow it up. As it is, you can only find small discrepancies where we would expect to see them.

Nope, not true. As discussed previously, birds could be assigned to a completely different animal group than theropods if necessary, etc. etc. Also in general with any taxa, any number of traits could be labeled convergent (there is no strict limit because evolutionists can't even assign a limit in principle) to shift phylogenies around. Fossils can be found at least tens of "millions of years" out of sequence and be accommodated.

You're just repeating the same old myths and mantras. Phylogeny is not even remotely as objective as you'd like it to be. What's sad is that someone who doesn't know any better would probably believe you.

 

[sfs]

I guess I view it differently. From what I have seen, authors are faithfully reporting their data and they are being honest with the experiments that they are running. Their conclusions are always tentative. There is no expectation that the conclusions must be true. It is only after many papers are published on a specific subject that we can sit back and separate the wheat from the chaff.

I disagree strongly. Researchers are reporting results as if they actually demonstrate the existence of phenomena, often leading others to pursue that line of research and sometimes leading to clinical trials. They're doing so based on underpowered studies and statistical procedures that are guaranteed to produce lots of false positives. They don't have to be doing that.

If we sat back and waited until we were 100% sure of our conclusions, then no papers would be published and we wouldn't be able to draw off the knowledge from other research groups.

We don't have to wait until we're 100% sure; physicists don't. But they don't get two thirds of their results wrong, either. I'd be a lot happier if only a quarter as many papers were published in biomedical research, but with a quarter of the false discovery rate. Fewer studies with more power would be much better for science.