July 13, 2011

Genes that mediate breast cancer metastasis to lungs

by Jennifer Eve Appleton

The paper that I was given to analyze was:

Genes that mediate breast cancer metastasis to lungs.

It was published in Nature on 12/5/2005

July 13, 2011

The negatives

by Jennifer Eve Appleton

In contrast to my previous post, here is a run down of a few of the negatives that have become apparent whilst digging into the world of peer review…

1) There are instances where accusations have been made that the reputation of the author is more influential in the judging of a paper than its scientific quality. A good paper by a young inexperienced author may not make the cut however a substandard paper by a well known academic may make it through.

2) Peer review is extremely time consuming and expensive in particular for the top. Journals. The process can take months with back logs af papers requiring reviews, this can in turn hamper researchers plans for future work projects.

3) The final say comes down to the editors, the connection between author and referee. Cases have arisen where the authority has been exploited with some mauscripts being rejected before being viewed by peers.

4) There is evidence that decisions are often judged by country: a US based journal is much more likely to reject non-US papers, whatever the quality.

5) Conflicts of interest cannot be detected easily by the reviewers, such as sources of the research’s funding, ultimately all the peer reviewer can detect is whether the protocols where followed correctly.

6) Whilst and obvious blunders can be detected, determined fraud cannot be detected without reproducing the study.

7) There are no strict ranking systems in place about the worth of the peer review. Journals each have their own unique standard of grading, the level of skill of the individuals involved cannot be measured. In the past, less reputable journals generally had a smaller readership, but the internet has made them just as likely to be accessed and used.

July 13, 2011

The positives

by Jennifer Eve Appleton

Peer review is definitely not flawless as previous posts can demonstrate; it does however enable future readers to make a judgment on the quality and virtue of the research. Other positives are outlined below:

1) A variety of opinions can be brought to light during peer review, abandoning any personal biases and withstanding ideas from the equation.

2) Peer review prevents inferior science from gaining a place in journals with experts in corresponding fields generally being the reviewer. Experts that will be familiar with current research making the rejection of duplicate and plagiarized work easier to spot.

3) With the rejection of poor work from the publishing pipeline money and time is saved, particularly in the case of plagiarism.

“Without referees, a journal would have to employ a team of editors with expertise in every field, and this would make the cost of the production prohibitive.” Marin Shuttleworth

4) The journals which request the expertise of peer reviewers are generally well established in scientific publishing with influential reputations, this encourages the top academics to submit their work.

5) The reviewers are leading academics and scientists in their field, peer review brings current research into the limelight

6) In the academic world peer review is used for applications of grants, and University textbooks. Peer reviewing is not only used for journals but for grant applications and University textbooks. This guarantees that money is allocated to just the viable proposals for research.

July 13, 2011

Ethics and peer review

by Jennifer Eve Appleton

When a paper has been submitted and the ethics surrounding the peer review process come under scrutiny what happens? Where do the authors and reviewers battle it out?

The answer is COPE.

A registered charity, COPE (committee on publication ethics) is run by a group of editors. They smooth out problems of an ethical nature providing advice to editors and publishers on all areas of ethics and how to cope with cases of research and publication misconduct. Created in 1977 due to the occurrence of a number of high profile scandals COPE has a number of aims:

1) To advise on cases brought by editors
2) Publish an annual report
3) Publish guidance on the ethics of publishing
3) Promote research into publication ethics
4) Offer teaching an training

One such example of a case that COPE has to deal with is named “An unbelievable surgical series”

A surgeon has sutured the superficial temporal artery of 1200 patients that suffer from migraines. The surgery miraculously cured them all.
The problem was the was that there was:

“No ethics committee approval. No clear diagnostic criteria. No controls. No evidence of consent”

A Complaint was made to the hospital however no action was taken. COPE was then informed in order to resolve the dispute.

The process that a reader takes if they suspect undisclosed conflict of interest (Col) in a published article….

An archive of the cases dealt with over the years are easily accessed on the committees website, http://publicationethics.org/ naming and shaming scientists that stray away from the code of conduct they should adhere to when publishing work!

July 13, 2011

Public peer review

by Jennifer Eve Appleton

The world of science blogging was taken over with an almost instantaneous critiquing frenzy with the publication of a paper claiming the finding of extraterrestrial life. Four days before the publication of an online paper in Science magazine, NASA sent out a media advisory that it was going to hold a press briefing to discuss an extraordinary finding in the search for extra terrestrial life. This led to wild speculations on the web, even more so when the paper was published in Science on 2 December 2010. The media headlines to follow were of an ‘alien nature’.

Californian scientist Fellisa Wolfe- Simon, who had a NASA fellowship in astrobiology, published a paper about the discovery of bacteria which used the usually poisonous element of arsenic and other molecules instead of phosphorous in its DNA. These bacteria were found in Lake Mono, a lake full of arsenic rich water in a volcanic valley southeast of Yosemite national park. They suggested it as an alternative scheme to life as we know it; later growing the bacteria in the laboratory on a diet of arsenic they were surprised to find that the microbes eventually fully incorporated it into their cells. A chemical analysis with radioactive tracers showed that the GFAJ-1 strain bacteria were in fact using arsenic in its metabolism.

NASA staff found that some bacteria (GFAJ-1) thrived when they had access to phosphorus followed by exposure to a highly toxic culture rich in arsenate. Their results suggested that the bacteria replaced the element vital for life – phosphorus – with arsenic, which has similar chemical properties. They suggested the bacteria were replacing the phosphorus with arsenic in their DNA. If correct, it meant that they had found a new form of life on Earth, which also showed the essential requirements for life to live elsewhere.
Media hype soon followed, with the Daily Mail brandishing headlines such as ‘Alien life may have been discovered on earth lurking deep in Californian lake’. A corresponding picture of ET was duly attached.

of an alien nature..

When the paper was published it was criticised immediately in a blog by Professor Rosie Redfield who runs a microbiology research lab in British Columbia. She argued: “There was phosphorus in the culture and the authors did not calculate whether the amount of growth they saw in the arsenate only medium could be supported by the amount of phosphate present.”

Critics such as Ed Yong- who writes the popular blog Not Exactly Rocket Science- also blogged that the paper showed there was a small amount of phosphorus in the testing medium used, and also that the bacteria originally lived in Lake Mono. The lake itself contains a particularly high concentration of phosphorus than anywhere else on Earth, therefore there would be no selective pressure for a life based on arsenic to evolve.

The scientist Fellisa Wolfe-Simon and her colleagues came under attack by journalists when they declined to respond to media calls for clarifying answers to questions. They were shocked by the reaction to the press conference arranged by NASA and at the overall response to the papers publication, thinking that their findings would interest the general public and simply generate a discussion for further research amongst their peers. The hype was huge, demonstrating that whatever the Internet gives voice to spirals onwards and upwards.

The researchers needed to continue consolidating work and to produce supplemental online material and data for others to use. The attention gained due to the media and the ensuing criticisms from fellow scientists offered them access to expensive tools which would easily test whether or not the DNA contained arsenic in place of phosphorous. Such equipment the NASA scientists claimed they did not have the budget to provide; the authors further admitted they wanted the results published quickly.

However, in defense of NASA they did not say in their publication – as the media reported – they had found bacteria that naturally used arsenic to live; instead, they clearly stated that although the bacteria were naturally occurring in a high arsenic environment they used phosphorous to live.

Although generating a good story and encouraging debate in the form of a public peer review, the paper did not show proof of extra terrestrial life. Nevertheless, as Simon Conway Morris of Cambridge University said, “It did show the underappreciated versatility of life.” This in itself must warrant further examination…

July 13, 2011

Academic Peer review according to Michelle Lamont: The findings

by Jennifer Eve Appleton

Lamont wanted to “open the Black Box of peer review” giving authors of the work being evaluated a better understanding of what happens when the fruits of their labour are being scrutinized. She says, “I also want the older, established scholars — the gate keepers — to think hard and think again about the limits of what they are doing, particularly when they define ‘what is exciting’ as ‘what most looks like me (or my work).’ ”

During her study she also tried to discover whether “excellence” is defined in the same way by different academics, the quality that peer review theoretically should promote. Ultimately in her book Lamont states that she is not convinced it exists.

“I think excellence means nothing,I think you have to give the criteria. Typically it’s originality, feasibility, and also the social and intellectual significance. There is nothing wrong with those definitions per se, but people shouldn’t pretend they equate with some scientific measure of excellence, as other criteria could be used as well.”

The results of Lamonts study showed that the most frequent flaw that was encountered was that of professors being slightly biased in that they favoured work that has elements which they are personally interested in. Lamont says, ‘“People define what is exciting as what speaks to their own personal interest, and their own research.”

The book depicts scholarly peer review with academic panels looking to review a stack of papers and decide for example which authors will get their funding proposals granted. ‘How Professors Think: Inside the Curious World of Academic Judgment’ could shine shine light on the way a scientists mind works when reading their peers work and what inspires them to cite different papers.