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Reviewing “Meet Science: What is Peer Review?” Part One

I have awesome friends, some in the scientific community and some not.  Recently one of them posted this Boing Boing article on What is Peer Review by Maggie Koerth-Baker on my Facebook page and suggested it would be right up Tiny Science’s alley.  And it is indeed.*

I only slapped myself in the forehead with frustration a couple of times during the article, so it must not be that bad.  In fact, I’d say the Koerth-Baker article is a good summary of peer review, written from the point of view of someone outside science for others in the same situation.  Clearly scientists were interviewed for the piece, and clearly none of those scientists was me, so I’m taking the opportunity to respond here on the blog.  If you want, you can read the original article and then come back and join the discussion.

Part One, in which the topic “what is a scientific journal article” is discussed.  Quotes from the article and comments section are pulled out in italics:

“Journal articles are like book reports. . . ”

Sigh.  When the meat of the article begins with these words, it’s almost enough to stop a girl from reading the whole thing.  Book reports?  Seriously?  Comparing the papers of Einstein’s miracle year and the article detailing the discovery of the structure of DNA to something done by fourth graders after skimming the Cliff’s Notes of Across Five Aprils??  Scientific discoveries written up in formal reports have saved millions of lives and changed the way we see the world and ourselves.  Let’s just forget that those words even happened and move on to the rest of the first sentence.

“. . . usually written to document the methodology and results of a single scientific experiment, or to provide evidence supporting a single theory.”

Oh how I wish that a single successful experiment was enough to get me a journal article!  I would have so many publications I would not know what to do with myself.#  The second part of the sentence is actually closer to reality.  An article provides evidence supporting a single hypothesis.  Hypothesis.  Not theory.  Please, for the love of all that is good and right in the world, STOP MIXING UP THEORY AND HYPOTHESIS.  The scientific community is all out of bubble gum^ on this topic. 

Journal articles are the story of a scientific idea.  A good scientific report starts with a description of the problem the authors are trying to address, put into the context of work that they (and other groups in their field) have already published.  Then it describes the series of experiments the authors did and the evidence they gathered from those experiments.  In the end, the authors try to explain how they interpret all the data related to the idea under examination (the results of their experiments and analysis as well as other evidence and analysis published by other groups) and why they think their interpretation has merit as a solution to the problem they set for themselves.  Peer review looks at all aspects of the report, including:

  • The validity of the original question.  Has this question been asked before? Does this article provide a unique perspective on the problem?
  • The reasonableness and reliability of the experiments done.  Do the authors provide proper controls? Do the experiments address the problem?  Are there other experiments that should have been done to address the problem from a different angle?
  • The authors’ interpretation of their data.  Are the results of the experiments conclusive, or are there other interpretations that the authors do not address?  How should those interpretations be handled?  Should more experiments be done, or can some wording be put in that discusses the limitations of the current work?
  • The authors presentation of the current knowledge in their field and how their work fits into that context.

If the reviewers think the article failed to achieve a certain (unwritten) standard in each of these categories, they can either reject the article for publication outright, or suggest ways that the article can be improved before publication.  Addressing reviewer comments in the first three categories can take a couple of months’ worth of experiments and data analysis, but usually makes the article stronger.  Comments in the last category are mostly an opportunity for reviewers to complain that their work was not cited, or that the authors are making their work out to be more important to the field than it really is.  A brief snort and a change in the wording of the article is usually all that is necessary here.  Hey, even the best scientists can get petty.  We’re humans, after all.  More on that later.

“No single journal article is meant to be the definitive last word on anything.”

Well thank goodness someone finally said it out loud.  Although if science journalists know this, why do they continue to do reports on single articles where the only indication that the article being discussed is not the be all and end all on a topic is the phrase “more research needs to be done.”?  If “peer reviewed journal article” is meaningless to laypeople, what does that trite little phrase mean?

I’ll tell you what I think it says to most laypeople.  If they agree with and like the conclusions presented in the report about the article, then “more research” means the conclusions will be supported by other people and “science” will have discovered a “truth.”  If they don’t agree with or don’t like what the report says, “more research” means, “don’t listen to a word we just said about this discovery, because when we do more research, it will just turn out to be wrong and everyone will go back to not worrying about it.”  Honestly, I think that is what “more research” means to most laypeople.  Laypeople, please, please write in and tell me that I’m cynical and wrong.  Tell me what you are thinking as you hear that phrase.  I genuinely want to know.

Now that the first part of the article detailing what a scientific journal article is has been given the Tiny Science treatment, I’m going to take a break and start a new post.  In Part Two, we’ll discuss the rest of the article, which is a nice summary of peer review with emphasis on who reviewers are, what they are supposed to do (vs. what they really do) and the pros and cons of the current peer review system.

If you’d like to discuss Part One, let’s dialogue in the comments section.  Remember that I’m a biologist, so my take on all this is from the biomedical sciences perspective.  I would love for people from other disciplines to weigh in with their take on the peer review process, and for laypeople to get into the discussion as well.

———-Notes———

Yes, I footnote certain blog articles.  It lets me add snark without interrupting the flow of the article.

* I have written an article on peer review, and a couple of articles about science journalists’ take on scientific culture (see them here, here, a funny take by someone else linked to here, and my personal favorite here).

# As it is I’m only listed as an author on ten papers.  This averages out to one a year for the twelve years I’ve considered science my full-time job.

^ B-grade horror flicks have awesome catchphrases.  Haven’t seen the John Carpenter movie “They Live”?  You’re not missing anything, except for this one line, which through the magic of YouTube you can see without waiting for Halloween on AMC.

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A Brief History of Earth Day

Happy Earth Day!

This week we celebrate the 41st anniversary of the first Earth Day, a day for environmental awareness and green living.  This week also marks the first anniversary of the BP oil spill in the Gulf of Mexico and the 25th anniversary of the Chernobyl nuclear disaster in the Ukraine; so we have a long way to go before we have a perfect record of living in harmony with our planet.

Earth Day was the brain child of Gaylord Nelson, then a US Senator from Wisconsin.*  Throughout his tenure as Wisconsin’s governor in the 1950’s and then as a senator in the 60’s, Nelson pushed for environmental causes such as natural resource management, wildlife conservation and the creation of green jobs.

But by 1969 he was frustrated with the lack of passion for such issues in Washington DC and his inability to pass legislation dealing with environmental issues.  So, inspired by the Vietnam War protests, he imagined a national “teach-in” on environmental issues.  He recruited then-Congressman Pete McCloskey and Denis Hayes to help popularize the movement, but mainly depended on local college campuses and community centers to organize and host activities.  The grass-roots “earth day” movement was a huge success, with 20 million people in 1,000 communities across the US participating in events on April 22, 1970.

The first Earth Day galvanized environmental groups and proved that there was popular support for environmental legislation.  This lead to the founding of the Federal Environmental Protection Agency in December 1970 and the passage of several landmark federal environmental protection bills, including the Clean Air Acts, the Clean Water Act, the Environmental Education Act, the Federal Pesticides Act, and the Endangered Species Act.

However, with the beginning of the Regan Era in 1980, priorities in Washington shifted and Senator Nelson lost his re-election bid.  He left the Senate in 1981, but continued his work as an environmentalist, working for organizations such as the Wilderness Society.  Earth Day activitsm was largely dormant until a revival in 1990.  For the 20th anniversary Earth Day, Denis Hayes agreed to coordinate a global day of environmental awareness.  April 22, 1990 saw 200 million participants in 141 countries around the world.  In 1995, Gaylord Nelson was awarded the United States’ highest civilian honor, the Presidential Medal of Freedom.

Today Earth Day is a global event, but the focus is still on locally organized events and individual commitment / participation.  The centerpiece of this year’s happenings is the Earth Day Network’s Billion Acts of Green program.  Organizations large and small from around the world can register and promote their events, from tree planting to recycling drives to massive water conservation projects.  The goal is to increase participation in green activities to one billion individual events in advance of the 2012 Conference on Sustainable Development in Rio de Janeiro, Brazil.  For more on Earth Day events in your area, visit the US EPA’s website or Google “Earth Day 2011 + your city.”  For tips on small things you can do to help the environment (and your budget) see this post from last year’s Earth Day.

Sources:

Earth Day Network

Gaylord Nelson and the history of Earth Day 

The Wilderness Society via Envirolink

Direct from the Wilderness Society 

Footnotes:

* Not to be confused with Lord Horatio Nelson.  Totally. Different. Dude.  I know, I’m a sad person that in my mind I get these two great men confused.  I’m odd, what can I say?

Answer to the Friday Whatsit for April 1, 2011

Shark egg cases

Congratulations to Uncle Michael, who guessed his first Whatsit (on Facebook) this week.  These are shark egg cases, sometimes called mermaid’s purses. Certain shark species, as well as their cousins the skates and rays, lay eggs inside these protective cases.  Empty egg cases often wash up on beaches and are found dried out and leathery from the sun.

I snapped this photo during a visit to Chicago’s Shedd Aquarium, where we learned that shark pups can develop in one of three ways, depending on the species.  These egg cases came from a species that was oviparous, or egg-laying (ovi denoting “egg”).  The egg is fertilized inside the mother’s body, and then the embryo and its food source, the yolk, are encapsulated in the egg case in the nidamental gland and then laid.

Shark

A shark at the Monterey Bay Aquarium

Other shark species keep their fertilized eggs in the mother’s body until they hatch, giving birth to live young.  These types of sharks are called viviparous sharks (vivi meaning “live”).  These species can be further divided into sharks that use the yolk as the primary food source for the growing embryo and those that make a placenta to provide food directly from mother to young.  But no matter how they develop, as soon as the pups are born they are on their own.  Unlike marine mammals like dolphins and whales, shark mothers provide little care for their young beyond development.

So there you have it, shark egg cases being raised at an aquarium.

Science is All Around You

This holiday Friday, in addition to our usual Whatsit, I’d like to issue a bonus post.  I know, right?  How lucky can you get?

This post highlights an important part of every budding scientist’s education: the science video.  Second only to learning to embrace failure, being able to watch an entire science video without falling asleep is the most important step on the road to becoming a successful scientist.

I personally love these things, especially if they have British narrators.  The Look Around You series is an all time favorite.  If you didn’t get to watch them in school, get our your workbooks and prepare to be educated!

Special thanks to BioChemical Brother for his Freshly Pressed post featuring the Look Around You module on water.

Friday Whatsit for April 1, 2011

Alright everyone.  Since EVERYBODY who wrote in on the Whatsit last week was right, I’ve decided not only to I have an exceptionally smart readership, maybe perhaps I’m also giving too many hints.  Just a thought.  This makes things totally no fun, at least for me.  How am I supposed to get ideas for future posts if everyone keeps getting the right answer!

What are these?

So, awesome readers, turn your minds to these cool things.  You could hold one in your hand, but don’t squeeze it!  There’s precious cargo inside.  What are they?  Leave your guesses in the comments section, the answer will be posted on Monday.

Answer to the Friday Whatsit for March 25, 2011

A late posting, but since EVERYBODY that guessed got it right I guess it doesn’t really matter.  Yes, this is a very highly magnified bit of common dandelion (Taraxacum sp.) fluff, the parachute that carries the dandelion seed away from its parent plant to flower in someone else’s lawn.

Whatsit

Dandelion, highly magnified

Most dandelions in our yard don’t get to the seed head stage.  My husband has spent years popping them out of the lawn with a pronged dandelion popper. Others prefer to spray weed killer on the little buggers, but we find that also kills the lawn (see this article on how Roundup works for why).

Final fun fact of the day: “dandelion” comes from the French dent-de-lion or lion’s tooth.  How the French decided the little yellow pests looked like lion’s teeth I don’t know.

And. . . if you have five minutes to waste, check out this YouTube video called, appropriately, Dandelion.  It features fractals and some atmospheric music.  With fractals being the subject for another post!

Earth Hour 2011 Tonight!

Help celebrate the fifth annual Earth Hour by turning off your lights for an hour tonight, starting at 8:30pm local time!

Earth Hour started in 2007 in Sydney, Australia.  Organized by the World Wildlife Fund, it was a way to raise awareness of Global Climate Change and the simple things that each person can do to help preserve the natural resources of our planet.  Each year the celebration has grown to include more people in more countries, and this year it is expected to include 1.3 billion people in 138 different countries worldwide.

There are many reasons to celebrate Earth Hour and this video from earthhour.org highlights my favorite.  Use it as a time to slow down, to simplify, to reconnect with what is really important in your life.  Too often we are caught up in a fast-paced global panic cycle.  Everything is a crisis of global proportion and we are overwhelmed.  It makes us just want to give up.  But if we slow down, gather our resources and act locally — within our communities, our homes and our families — we can make a difference AND keep our sanity.

When it’s over, let’s keep with this year’s theme and go Beyond the Hour.  Let’s think of ways we can change our lives and our communities for our own good AND the good of the planet.  It doesn’t have to be huge, it just has to be something.  Maybe we can walk or bike somewhere instead of driving.  Maybe just once a week.  To work, to school, to the store, to the park.  Maybe we can turn off the TV and read, play card games, or share music with our family or friends.  By connecting with what we have as a community, we recognize that its worth saving what we share as a planet.

Friday Whatsit for March 25, 2011

Whatsit

What is this part of?

This week’s Whatsit is a sure sign that warmer weather has arrived.  Even though we may not always want them around.

What is this thing part of, and how soon does my lawn turn green with yellow polka dots?  OK, the second part is not a serious question, mostly because my husband spends all summer in battle with these things keeping them out of the yard.

Guesses in the comments section, answer on Monday!

Explosion at Nuclear Power Plant Follows Sendai Earthquake

The BBC has just posted video footage of a large explosion at the Fukushima-Daiichi nuclear power plant.  The explosion happened at 6pm local time today, Saturday March 12, 2011.

Three of the six reactors at the plant were running yesterday, and all of the nuclear reactors at the plant automatically shut down during the powerful magnitude 8.9 earthquake.  But the diesel-fuel powered cooling system put in place to keep the reactor cool appears to have shut down due to tsunami flooding.  This caused the temperature and pressure levels in the plant to rise to dangerous levels.

Right now it is unclear exactly where the explosion occurred.  Early reports say the concrete building surrounding one of the Fukushima reactors has collapsed, but the metal housing of the reactor itself is still intact.  Seawater is apparently being pumped into the reactor to keep it cool and prevent further pressure buildup and another explosion.

If early reports from Japanese officials are correct and the radioactive core is still contained, this reduces the possibility of a major radioactive leak on the scale of the Chernobyl disaster of 1986.  Both the plant and the surrounding area were evacuated well before the explosion, but early reports indicate that at least four plant workers may have been injured.

Massive Earthquake Rocks Japan, Devastating Tsunami Follows

USGS Earthquake map

March 11, 2011 Sendai earthquake and aftershocks. Click to go to the real time map

News reports coming out of Japan are bleak after a massive 8.9 earthquake hit the country at 2:46pm local time on Friday, March 11, 2011.  The epicenter of the earthquake was offshore, about 80 miles (130km) east of the city of Sendai and 231 mi (373km) northeast of Tokyo.  The earthquake was followed by a devastating tsunami which rushed inland in the Fukushima prefecture, causing almost more damage than the earthquake itself in some parts of the country.  For scary footage of the tsunami washing ashore and smart commentary from a scientist at the Pacific Tsunami Early Warning Center, see this report from the BBC.

The earthquake occurred in what the US Geological Survey (USGS) calls the Japan Trench subduction zone, where the North American plate and the Pacific plate meet and the Pacific plate moves west, slipping under the North American and Eurasian plates near Japan.  Having trouble wrapping your head around that geography?  Click here for the USGS map of the world’s tectonic plates.  You’ll see that the North American plate wraps over the top of the Pacific plate, underlying not only North America all the way up through Alaska, but also the Bering Straight and a significant part of Eastern Russia.  Japan sits partially over a small finger of the North American plate and partially over the Eurasian Plate, near the boundaries of those plates and the Pacific and Philippine plates.  As you can imagine, that makes Japan particularly earthquake-prone, and the Japanese well aware of the dangers of earthquakes.

Even so, this earthquake was massive.  It is the largest earthquake to hit Japan in recorded history, and one of the largest ever recorded on earth.  Reports are now that at least a thousand people have been killed, possibly as many as ten thousand.  Thousands more are injured or still missing, particularly in areas hit by the tsunami.  Economically it is unclear what this means for Japan, a country hit hard by the world economic crisis.  A re-building boom could spur recovery in some parts of the economy, but with damages expected to reach the tens to hundreds of millions of dollars, it may take an international effort to rebuild the country.

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