Nobody is perfect

Bruce sent me this and points out that it is noteworthy for (a) science not being perfect, (b)
brevity and (c) Cesare Emiliani was a REALLY big name in Paleooceanography.

It is also worth noting that the mistake (in the calculated values in a table) did not alter the main conclusion of the original paper.

Ockham’s razor

An interesting article on William of Ockham (of Ockham’s razor fame) on BoingBoing today.

Here's the conventional translation:


“plurality should not be posited without necessity,"

Wikipedia defines Ockham's razor as:

“Among competing hypotheses, the one that makes the fewest assumptions should be selected.”

Except that's not what Ockham actually said. He's been the victim of selective editing. What he really said is:

“Nothing ought to be posited without a reason given, unless it is self-evident or known by experience or proved by the authority of Sacred Scripture.”

Hmmm

Arsenic Life Redux

Nov. 29, 2010. NASA announces a news conference "to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life."

If you don't remember this then read the story as it unfolded here: The Arsenic Chronicles
A humble arsenic-friendly microbe from Mono Lake, Calif., has recently stirred a tempest in the science world's teapot. Here's the story as it played out over the last two weeks in tweets, blogs and news conferences, of course.

Now, with that background, you may enjoy this article from USA Today a few days ago:
Glowing reviews on 'arseniclife' spurred NASA's embrace
USA Today reporters got hold of Science's reviews of the original article via a Freedom of Information Request.

Pace says there was "poor judgment at multiple levels" in the arseniclife case, from an "overly exuberant" interpretation of the study results by the authors to the peer reviewers missing "the big crux of the results: the claim of absence of phosphorus," to NASA repeating some of the mistakes that caused the agency trouble in 1996, when it publicized results suggesting a Martian meteorite contained microscopic signs of life. 

'Duh' Science

In the LA Times today - 'Duh' science: Why researchers spend so much time proving the obvious
Alcohol increases reaction time; obese men have lower odds of getting married. A waste of research money? Not necessarily, scientists say.

It's actually not a bad little article and it does make some interesting points.

Scientific Publishing from the Inside Out

Tomorrow (Friday, May 6, 2011) 11.30-12.30 p.m. in Bren Hall.
Sacha Vignieri, PhD, Associate Editor of SCIENCE
Scientific Publishing from the Inside Out


From the outside, publication in high-impact general-science journals can seem like a mysterious process. A general understanding of the procedures and practices at Science can help unravel the mystery a bit, and contribute to an understanding of what makes a good (or even great) paper a high-impact-journal paper. In particular, while many researchers strive to publish in these journals because of their high impacts, they are fundamentally general-science journals, and understanding this can help authors assess which aspects of their own work will be most successful in such outlets. I’ll discuss some of the inner workings of Science and provide insight for helping authors prepare and assess their own work for consideration in high-impact general-science publications.

Research Ethics Talk

And now for something completely different.

*Date and location*: Mon, March 7, 4-6pm, Girvetz 1004

*Speaker*: Prof. Herbert Kroemer

*Abstract*: In early 2002, Bell Labs physicist Hendrick Schoen was considered a rising star in the field of molecular electronics. A little older than 30, Schoen had already authored 90 publications and received a series of prestigious awards. In April 2002, he was being considered for the directorship of the Max Planck Institute for Solid State Research in Stuttgart. In September 2002, he was fired by the Bell Labs and his most prominent papers were withdrawn from publication. What happened? In this talk, Prof. Kroemer will tell us about his role in the investigation on scientific misconduct and discuss issues and repercussions of unethical conduct in research.


To whet your appetite for this talk check out The Rise and Fall of a Physics Fraudster in Physics World. Although this example is from the world of physics the implications for scientific research are very general.

I used to joke with my friends in the physics community that if you want to cleanse your discipline of the worst scientists in it, every three or four years, you should have someone publish a bogus paper claiming to make some remarkable new discovery — infinite free energy or ESP, or something suitably cosmic like that. Then you have it published in a legitimate journal ; it shows up on the front page of the New York Times, and within two months, every bad scientist in the field will be working on it.  Gary Taubes.

Monday funnies

I don't know what made me think of Tim Minchin, I must have seen a reference to him somewhere, but I thought you might enjoy these. Phrases like 'I don't think you're special, I mean you're special but you fall within a bell-curve' probably explain why so many scientists marry other scientists.

Weekend Wildcard

I try to make posts here roughly correspond to what we are covering in class (you don't have to feel quite as restricted) but because I have a life and because it gets hard posting every day I've decided to embrace a concept I dabbled with before - the weekend wildcard. Weekends are open to any posting on any topic of some relevance to the course.

Today is a great example because it pertains to science, the scientific method, how science is done and cards (wild or otherwise). All good fodder for an intro bio class. As some of you may have heard a leading psychology journal is about to publish an article providing evidence for ESP. Even the New York Times is writing about it:
Journal’s Paper on ESP Expected to Prompt Outrage
Some of the experiments are a little odd to say the least:
In another experiment, Dr. Bem had subjects choose which of two curtains on a computer screen hid a photograph; the other curtain hid nothing but a blank screen.
A software program randomly posted a picture behind one curtain or the other — but only after the participant made a choice. Still, the participants beat chance, by 53 percent to 50 percent, at least when the photos being posted were erotic ones. They did not do better than chance on negative or neutral photos.

You can read the actual paper here and a critique here.

The paper was reviewed by 4 referees before being accepted for publication. Should the extraordinary claims have required extraordinary evidence before publication? Should different papers have to meet different standards depending how well they fit our current paradigms? Is the publication of this paper helping or hindering the public perception of science? Is that even an issue scientists should be concerned with?

(I actually lied about having a life, posting here at 11:30 on a Saturday night kind of gives that away, but it does get tricky thinking of something to post every day, especially at the start of the class when we haven't covered very much.)

I don’t know what to believe…

Thanksgiving and Christmas are times where we traditionally meet with family, eat too much and have awkward conversations with relatives we barely know and realize we have very little in common with.

If they find out you are a biologist chances are you'll get asked about topics ranging from global warming to this week's cancer scare. Here's a handy dandy resource for putting people straight about why they shouldn't necessarily believe it when they hear that cell phone towers are killing plants, will cure/cause cancer, or how scientists are all faking global warming. 

Have a safe Thanksgiving.

Denialism

Vaccine-autism claims, "Frankenfood" bans, the herbal cure craze: All point to the public's growing fear (and, often, outright denial) of science and reason, says Michael Specter. He warns the trend spells disaster for human progress.

Another of the TED talks. This one raises interesting point about scientific literacy. The time machine question in the first few moments is really rather intriguing. I'd like to see the results from a large sample of people especially if the answers were broken down by age and sex. Actually I'd like to see them broken down by political affiliation too. Oh, and maybe by religious beliefs.

Anciently asexual

Spore-bearing fungal parasites emerge from the digested corpses of three bdelloid rotifers.

Wow, I was just looking around for something to post on and there it is right on the cover of Science this week. Great story and highly relevant to class.

Anciently Asexual Bdelloid Rotifers Escape Lethal Fungal Parasites by Drying Up and Blowing Away

Asexuality has major theoretical advantages over sexual reproduction. An important evolutionary puzzle, therefore, is why exclusively asexual metazoan lineages rarely endure. The Red Queen hypothesis posits that asexuality is rapidly extinguished by relentlessly coevolving parasites and pathogens. If so, any long-lasting asexual lineage must have unusual alternative mechanisms to deal with these biotic enemies. Bdelloid rotifers are freshwater invertebrates that abandoned sexual reproduction millions of years ago. Here, we show that cultured populations of bdelloids can rid themselves of a deadly fungal parasite through complete desiccation (anhydrobiosis) and disperse by wind to establish new populations in its absence. In Red Queen models, spatiotemporal escape can decouple and protect asexuals from coevolving enemies. Thus, our results may help to explain the persistence of the anciently asexual Bdelloidea.

The Neuroscience of Screwing Up

I mentioned this briefly on Tuesday and I may add this as reading for the Biology Colloquium next year but I thought some of you might like to read it. A fascinating discussion of how science is done, how and why we make mistakes and how we interpret them.

Accept Defeat: the Neuroscience of Screwing Up

While the scientific process is typically seen as a lonely pursuit — researchers solve problems by themselves — Dunbar found that most new scientific ideas emerged from lab meetings, those weekly sessions in which people publicly present their data. Interestingly, the most important element of the lab meeting wasn’t the presentation — it was the debate that followed. Dunbar observed that the skeptical (and sometimes heated) questions asked during a group session frequently triggered breakthroughs, as the scientists were forced to reconsider data they’d previously ignored. The new theory was a product of spontaneous conversation, not solitude; a single bracing query was enough to turn scientists into temporary outsiders, able to look anew at their own work.

But not every lab meeting was equally effective. Dunbar tells the story of two labs that both ran into the same experimental problem: The proteins they were trying to measure were sticking to a filter, making it impossible to analyze the data. “One of the labs was full of people from different backgrounds,” Dunbar says. “They had biochemists and molecular biologists and geneticists and students in medical school.” The other lab, in contrast, was made up of E. coli experts. “They knew more about E. coli than anyone else, but that was what they knew,” he says. Dunbar watched how each of these labs dealt with their protein problem. The E. coli group took a brute-force approach, spending several weeks methodically testing various fixes. “It was extremely inefficient,” Dunbar says. “They eventually solved it, but they wasted a lot of valuable time.”

The diverse lab, in contrast, mulled the problem at a group meeting. None of the scientists were protein experts, so they began a wide-ranging discussion of possible solutions. At first, the conversation seemed rather useless. But then, as the chemists traded ideas with the biologists and the biologists bounced ideas off the med students, potential answers began to emerge. “After another 10 minutes of talking, the protein problem was solved,” Dunbar says. “They made it look easy.”

Writing, Reading, and Reviewing Scientific Articles

This coming week in the bio colloquium we're reading an article from the primary literature. To provide general background on the elements of a scientific paper we also handed out "guidelines for writing a scientific paper". To help you think about it from the other end (reviewer vs. writer) you may want to see what guidelines the scientific journals provide their reviewers, that is, what helps us decide whether a paper is "publishable" by a given journal. This is useful in writing (and reading) a paper to see what the "critics" are looking for.

Here is the link for reviewers for the journal, Ecology:
http://esapubs.org/esapubs/reviewers.htm

Also informative is the "Reviewers Information Pack" (http://www.nxtbook.com/nxteu/elsevier/reviewersinfopack/) for everything you might want to know about the review process for journal articles. This is provided by Elsevier, which publishes Developmental Biology, and hundreds of other journals (http://www.elsevier.com/wps/find/journal_browse.cws_home)

Here's their reviewers' home page:
http://www.elsevier.com/wps/find/reviewershome.reviewers

Monkey-Man

Kathy pointed me to an interesting editorial in Nature today about the recent fossil primate discovery I mentioned here last week.

The article, entitled Media Frenzy, has the subhead:

A hyped-up fossil find highlights the potential dangers of publicity machines.

Take a look at the original paper in PLoS ONE, Nature's original report and today's editorial.

Do you agree with Nature's assertion that:
In principle, there is no reason why science should not be accompanied by highly proactive publicity machines. But in practice, such arrangements introduce conflicting incentives that can all too easily undermine the process of the assessment and communication of science.

Do you think the authors of the original paper did anything wrong?
Do you think the journalists who covered the story have been accurate in their reporting?

(The image above, which is from Nature's original report, is called 'monkey-man.jpg'. This is exactly the sort of misleading hype that Nature is railing against!)

Robot Scientist

If you've been in a research lab you can't have failed to notice not only how much expensive looking equipment there often is, but how much of it is linked together these days. Lots of machinery either comes with a computer or is later linked to one in the lab to automate data entry.

It's only a couple of steps from there to linking together all your equipment, adding in some simple algorithms for how the scientific process works, and you can go hang out on a beach whilst your lab equipment does its own experiments.

Sounds a bit futuristic? Nope, a recent paper in Science entitled 'The Automation of Science' describes just such a scenario. Scientists in England developed a robot named Adam to identify genes involved in yeast metabolism. Adam formulates hypotheses about the origins of enzymes for which scientists have been unable to identify the encoding genes. The robot then plans and executes experiments to test its hypotheses--selecting yeast mutants from a collection, incubating cells, and measuring their growth rates. Adam came up with 20 hypotheses about genes encoding 13 enzymes, 12 of which it confirmed.

There's a commentary on the paper in Science, the story was picked up by the media, but the best comment is in a New Scientist report:

'Will Bridewell, an artificial intelligence researcher at Stanford University in Palo Alto, California, says Adam is operating only at the level of a graduate student. '

The hype of science

Kathy sent me a link to this article at TheScientist.com - The hype of science Leading journals including Science and Nature are exaggerating research novelty. You will need to register to read the article but there's no cost.

When original and interesting research is distorted to garner additional attention, both the work in question and previous studies can be shortchanged. Here, I will describe a recent and notable case from the journal Science in which the perceived novelty and importance of a study were significantly enhanced.

Florigen - found and not found

From Science magazine's list of the 'Breakthrough's of the year' in 2005:

In August three groups of plant molecular biologists finally pinned down the identity of florigen, a signal that initiates the seasonal development of flowers. The signal is the messenger RNA of a gene called FT. When days get long enough, this RNA moves from leaves to the growth tip, where the FT protein interacts with a growth tip-specific transcription factor, FD.

However if you click on the original article then you may notice the sentence 'This article has been retracted.'

After the first author (T.H.) left the Umeå Plant Science Centre for another position, analysis of his original data revealed several anomalies. It is apparent from these files that data from the real-time RT-PCR were analyzed incorrectly. Certain data points were removed, while other data points were given increased weight in the statistical analysis. When all the primary real-time RT-PCR data are subjected to correct statistical analysis, most of the reported significant differences between time points disappear. Because of this, we are retracting the paper in its entirety.

In new experiments, we have reproduced the floral induction caused by a heat-shock induction of FT in a single leaf, but we have failed to detect movement of the transgenic FT mRNA from leaf to shoot apex. We therefore retract the conclusion that FT mRNA is part of the floral inductive signal moving from leaf to shoot apex.

Curious. After 70 years of elusivity (is that a word?) Florigen is not ready to give in yet.

PhD Comics

If a picture is worth a thousand words than a well crafted cartoon is probably worth, oh about five or six hundred. Here, from PhD comics, are some gems on the scientific paper and the publishing process. Enjoy.

• Deciphering Academese
• Author list
• Paper review worksheet
• Addressing reviewer comments