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Exercise #1: Scienfic Literature Due Sep 14 at 11:59pm

Points 100

Questions 5

Available Aug 31 at 12am - Sep 14 at 11:59pm 15 days

Time Limit None

Instrucons No human brain, no matter how educated, can carry around even a tiny fraction of the available information in the world. Much of your job as an educated person is to carry enough information in your head so you can do useful things, fit new information into the big picture, and know where to find good information that isn’t lodged in your brain. Some people find new information by calling others, or by surfing the Web. But, how do you know that the information from your friends or from the web is reliable? If you wanted to learn about the history of the idea that the Earth is flat, and you searched on “Flat Earth”, what would you find? In March 2009, the first few hits in a Google search on that topic produced: 1 and 2) two Wikipedia articles, one telling the history of the idea but noting that it is now widely dismissed, and the second telling the history of the Flat Earth Society devoted to promoting the idea; 3) an advertisement for snack foods; 4) the home page for the Flat Earth Society, “deprogramming the masses since 1547”; and 5) an advertisement for a brewery. If you managed to click down to number 4, you might get a very strange view of the world! Numbers 3 and 5 might be enjoyable to some people (beer and chips!) but hardly answer the question. One excellent source of information is the library. But in the sciences, books are typically secondary sources of information. Like Wikipedia, they are useful at times but are not to be trusted completely. Instead, scientists (and wise nonscientists) rely on the refereed scientific literature, and on assessments of that literature by scientists acting in public for the public good. The refereed scientific literature is where scientists report their main discoveries. Suppose one of your professors discovers something new, such as Dr. Anandakrishnan’s discovery that the tiny rise and then fall of the tides, pushing back more and then less on the Antarctic ice sheet, slows and then speeds the flow of the ice almost 100 miles inland. (This is worrisome; if warming removes the ice shelf now “damming” the flow, Dr. A’s discovery shows that the flow into the sea will speed up a lot, which will raise sea level.) When Dr. A discovered this, he wrote it up in a scientific paper, with help from a colleague who went to the field with him, and another colleague who helped analyze the data. The paper reports where he went, how he measured the tide, how he measured the speed of flow, how he knows that they are related, why he is confident that the changes in ice flow were caused by the push from the sea and not the weaker tides on land, and so on. He provided pointers to other scientific papers that document the techniques used, and to similar behavior elsewhere (Dr. A actually discovered the effects of tides even earlier, in a slightly different part of Antarctica.) In this case, Dr. A asked a friend (Dr. Alley) to help him in building a mathematical model of the process, showing what it tells about the ice sheet. Dr. A

provided a list of the sources he used at the end of the paper, a note thanking other collaborators and various funding sources, details on how you could contact Dr. A and a short “abstract” in case you were interested in the study but not interested enough to read the whole thing. After having done this, Dr. A. submitted the paper to a learned journal—Geophysical Research Letters— which promptly sent the paper to several referees. These are world-class experts who did not work with Dr. A, who do not owe him money, and who otherwise are able to judge the paper. If there were anything wrong such as the methods weren’t described clearly enough so you could reproduce them, the mathematical model had an error, previous discoveries weren’t properly acknowledged, or anything else —these referees would complain, and Dr. A would be forced to change the paper to satisfy the referees and the journal editor before publication. Almost every paper is judged to have shortcomings, and most papers are changed a lot before being published. Eventually, Dr. A’s paper was published (this one with very few changes). You can find it as Anandakrishnan, S., D.E. Voigt, R.B. Alley and M.A. King, 2003, Ice stream D flow speed is strongly modulated by the tide beneath the Ross Ice Shelf, Geophysical Research Letters, volume 30, number 7, with a unique digital object identifier (doi) 10.1029/2002GL016329. This particular journal doesn’t include page numbers anymore, which drives some of us crazy, but that’s life. Papers such as Dr. A’s are the heart of science and provide highly reliable, useful information. They are refereed—he is not allowed to publish until he has satisfied world experts. They are public and open— you know who paid for them, and you can go find the scientists and discuss the work if need be. They are in it for the long haul—the journal is published by a non-profit professional society that was founded in 1919 and intends to be around for a very long time, and Dr. A is staking his reputation on the paper when he puts it out. Now, this does not mean that the refereed scientific literature is perfect. Even Dr. A might make a mistake, and you can be sure that there are mistakes in the literature as well as healthy controversies in science. Someone looking in from outside may not be very good at telling what is solid, speculative or silly, although most scientists have a pretty good idea. Governments have found ways to sort this out. Back during the Civil War, Congress and President Lincoln got together and authorized the US National Academy of Sciences. They asked the best scientists to come together, in full view of the public, typically at the expense of the scientists, to bring in a wide range of views present in the scientific literature, and to provide advice to the government on what was known or not known, silly or speculative. This is still the main path of advice for the US Government, and for the country as a whole. Similar national academies of science and bodies such as the United Nations Intergovernmental Panel on Climate Change function around the world. (The National Academy of Science assessment on climate change from 2001, and the American Geophysical Union statement on climate change from 2003, included among the authors, individuals often identified as climate-change "skeptics", and these individuals agreed with the science showing the high likelihood of humans changing the climate. It is always instructive to read the careful scientific statements made within the scientific assessment process.) On some politically charged topics, some groups have pretended to establish assessment mechanisms, but

a quick look at the way this was done, the participants, and the funding sources is usually sufficient to separate the real scientific assessments from the pretenders. So, with that very long introduction, here is an exercise to introduce you to the refereed scientific literature. When you’re out in the real world, doing a real job, working on things that matter to the life, health, and well-being of real people, do NOT rely on Wikipedia or the first five hits on Google for your information, or you are likely to be looking for a new job (or worse). Find the reliable assessments based on the refereed scientific literature, and learn enough to go into the refereed scientific literature yourself and sort it out. The computers in the Penn State library system are an obvious place to start. Databases are available through the Penn State Online Library System (http://www.libraries.psu.edu/psul.html) (http://www.libraries.psu.edu/psul/home.html). Our favorite is Web of Science (obtain by clicking on "Databases" which you will find in the “FIND" box on the Libraries homepage). Type "Web of Science" into the search box and select "Web of Science from the resulting page. (There may be a delay as the website loads.) Note that you have to work from a PSU computer or identify yourself as PSU when asked to log in. Parts of this exercise may seem a little tedious, but at the end, you’ll know how to use the Web of Science, among other things. You will only get one chance to submit this exercise so be sure to review your answers carefully before submission. You can, however, save your answers as long as you do not submit them first. Do not forget to hit the submit button when you are finished. This exercise will NOT automatically submit since there is no time limit (except to submit it by the due date shown on the calendar). This exercise will be graded automatically.

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Attempt 1

42 minutes

100 out of 100

Score for this quiz: 100 out of 100 Submitted Sep 10 at 1:07pm This attempt took 42 minutes.

Question 1

20 / 20 pts

Type "Alley RB" into the author space on the Web of Science. You will find lots of pages of refereed scientific literature that Dr. Alley has worked on.

What was he publishing on in 1991? (Hint: the older ones are near the back, so use the “page” box near the top in the center to go there.)

Correct! Deforming-bed origin of southern Laurentide till sheets, and changes in the West Antarctic ice sheet.

The Web of Science lists 5 papers that Dr. Alley helped write and that have 1991 publication dates. The great ice sheet the flowed down from the Laurentian Highlands of Canada is called the Laurentide Ice Sheet, and it gave Illinois and Iowa great soil by smearing special mud (called till) in a vast sheet across the landscape, sort of like smearing peanut butter on bread. The deformation during the smearing of the mud shows up in one of the 1991 papers. At the same time, worries were growing about the future of the West Antarctic Ice Sheet, so Dr. Alley helped review what was known about that big, unstable block of ice. (Dr. Alley also commented on the possibility of greenhouse warming affecting the ice sheet.) The other possibilities listed are all things that he studied, some rather closely related, but that were not published in 1986.

Question 2

20 / 20 pts

Scientists collaborate a lot. The Web of Science tells you who all the coauthors are. Search on Dr. A (Type “Anandakrishnan S” into the author box of the search page). Notice that many of the entries list a few authors followed by “et al.” (which stands for “et alia” and means “and others” in Latin). If you click on the blue title, you’ll see a list of all of the authors. So, who was Dr. A co-authoring with in 2001?

Correct!

P. Jung and R.B. Alley.

Dr. Anandakrishnan collaborated and coauthored with all of the people listed, and has worked with many other people; the key is finding the 2001 list. Stochastic resonance is an absolutely fascinating mechanism that sometimes amplifies small signals to make them big; if you like cool things with a little math, you might even enjoy reading the paper.

Question 3

20 / 20 pts

There may be more than one S. Anandakrishnan, or R. Alley, in the world. One way to tell them apart is to check the address, which is also listed in the Web of Science. The Web of Science actually tries to help you. If you make sure to click the tab near the upper left that says “Web of Science” rather than “All Databases” before you do the search, it provides a “View

Distinct Author Sets” option. In this case, don’t mess with that. Just search in the Web of Science on Alley R, and find the paper by T.B. Humensky, R. Alley, and others from 2004. Is this the same Dr. Alley who helps teach Geosc10 at Penn State? (If you find a Penn State address in the list below, you may assume that it is the same Dr. Alley you know, and if you don't find a Penn State address, you may assume that the author is a different Dr. Alley; we won't make you click through other Dr. Aley references to make sure)

Correct!

No

R. Alley in this case has no tie to Penn State. Whether there is any relation to Penn State’s Dr. Alley, we don’t know, but we do know that they are different people.

Question 4

20 / 20 pts

As described in the introduction to this exercise, citations are very important in the scientific literature. They show where ideas or techniques came from, who has done similar work, and more. The Web of Science used to be called the Science Citation Index, and started out keeping track of citations in scientific papers. This allows you to work forward and back. For example, search on Alley RB, and find the paper from 2004 first-authored by then-graduate-student (now professor) Byron R. Parizek, published in Quaternary Science Reviews. This is an important paper on the future of ice sheets and sea level. If you click on the blue title of the paper, you will see “Times Cited:” in black, followed by a number in blue (that number increases over time), and “References: 67” with “67” in blue. Clicking on the blue “67” will tell you all of the papers that Byron Parizek relied on in preparing his paper. Clicking on the blue number after “Times Cited” will tell you all of the papers who have cited Byron Parizek’s paper, and thus are relying on it. Click on the “Times Cited” number. There are a

few pages of papers citing the Parizek and Alley paper. In 2005, who was the first author of the Journal of Glaciology paper about the 2004 heatwave in Alaska, that cited the Parizek and Alley paper? Note: The Web of Science lists papers in the order received at the office, not in the order of the dates given in the publications. You may need to look up among papers published in 2006 to find this 2005 paper.

Correct!

Truffer M

Martin Truffer and coworkers are distinguished glaciologists, and (among other things) have been documenting rapid melting of Alaskan glaciers. The easiest way to have missed this question is by clicking on the wrong paper by Parizek and Alley; these authors worked together on a few projects, but only one of those was in 2004 in Quaternary Science Reviews.

Question 5

20 / 20 pts

As discussed in the introduction, refereed sources are very important in science. Refereed sources often are identified by names such as Journal of... or Annals of... or Transactions of.... They usually have a statement somewhere in the journal describing their standards for review and publication. A paper in a refereed journal usually starts with an abstract and ends with a list of references cited, and usually with an acknowledgement of funding sources and other sources of help. In between, there usually are sections such as Introduction, Methods, and Discussion/Conclusion (different papers have somewhat different

sections). Refereed journals usually do not have advertising, although a few do, so don’t rely on this one—look for the title, the abstract, the references, etc. Two journals that occasionally cause trouble are Nature and Science—both start with newsy, non-refereed parts with advertising, but this is followed by refereed scientific parts without advertising but with abstracts, references and acknowledgements of funding sources. Time and Newsweek are not refereed scientific journals (Dr. Alley once had an interesting exchange with a US Senator, who initially insisted that Newsweek speaks for the scientists of the world, but changed his stance when shown that Newsweek was contradicting the National Academy of Sciences.) National Geographic, Natural History, American Scientist and Scientific American are not refereed and are not acceptable--they are interested in whether something is newsworthy and can be reported legally, not necessarily whether it is true. If an important person says something stupid, it may be newsworthy and appear in Newsweek, even if the statement is not correct and would not appear in a refereed scientific journal. (The Web of Science actually includes Scientific American and American Scientist, because the Web figures that their users know the difference.) About Web Sites: Some scientific journals are now on the Web, so some Web sites (a VERY small percentage of the total) are now refereed and part of the scientific literature, but almost all Web sites are not. Wikipedia may be a nice shortcut to learn a lot of things, but it is NOT refereed in the ordinary sense; it (like this textbook) is no better than a secondary source. As a general observation, much of what is published in books is fiction, including much of what is published in supposedly non-fiction books. Books are typically not reviewed and so are not as reliable as the scientific literature. Because publication of a book is expensive, some quality control is used by publishers, although typically not enough. Because Web sites are so incredibly cheap, they experience much less quality control and all should be suspected of propagating nonsense. The Web is a great way to transmit words, pictures, and numbers, but much or even most of the transmitted material is misleading or wrong. Be wary of all Web sites! Make them prove reliability to you before you believe them. Click on the link to download the two articles. Which one is refereed? Paper #1

Paper #2

Correct! Paper #1, "Variations in the oceanic vertical carbon isotope gradient and their implications for the Paleocene-Eocene biological pump"

You could follow our description—Paper 1 has an abstract, an introduction and a boring title, and paper 2 doesn’t. Or, you could note that paper 2 is from Scientific American, and we told you explicitly in the instructions that Scientific American is not refereed.

Quiz Score: 100 out of 100...