| BNFO 301 |
Course at a Glance: How to Find Articles... and Why |
Spring 2012
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Finding research articles
"Calculating the global warming catastrophe: Scientists agree that we're hurtling toward disaster..." "The threat of catastrophic global warming is the greatest hoax ever perpetrated on the American people" People yell and scream at each other, pointing out unsavory motives. If this were a debate as to whether Star Wars is better than Star Trek, OK, fine. But we're talking about emperical truth, things that can measured. The dicussion is important because the observations inform projections as to what may be -- not emperical truth, except in retrospect, but nonetheless statements that can be couched in what is verifiably known and limited by what is not. If rants remain the general level of discourse, then we're doomed, one way or another. How do you find out what is true? I submit that what is verifiably true is not to be found in either The National Review nor the Huffington Post. There you'll find interpretations, conclusions, and of course rants. Not the truth. Not the raw observation shorn of interpretation. I presume that you are already quite familiar with finding information through the internet -- Google, Wikipedia, etc -- and there's nothing wrong with these resources. I use them many times a day. But they only get you so far. In general, you get a synopsis of what is known, as you would from a mini-textbook. The overview is a good starting place, but don't mistake it for the truth. At their best, web pages give you links to research articles from which you can understand the limitations of the generalization that appear on the pages. Wikipedia is sometimes good at doing this (here's an example). Usually, however, you just get bald statements (here's an example). It really doesn't matter who wrote the bald statement (the previous example is on the National Institutes of Health web page), they're still bald. One thing you'll learn from your first tour, What is a Gene, is that text books and web pages are quite limited. There's no replacement for doing experiments or reading about the experiments done by others. In general, you will need to be satisfied with the latter: how do you find accounts of experiments? Some of you have read research articles, and some have not. Of those who have, some have found the articles themselves, and some have had the articles given to them. For the latter, the days when people give you useful articles to read will soon be over, and if you don't know how to find scientific information on your own, you'll soon be helpless, victim to whatever anyone wants to feed you on the web. This must not be allowed to happen. You need to learn how to find research articles on your own. It doesn't matter that you may never do bioinformatics again.
Before we talk about how to find research articles, we have to agree on what we're looking for. We're looking for scientific truth. Where does that reside? How can you tell? High school teachers delight in giving lists of things to look for when deciding whether information is trustworthy. Near the top of the list is invariably "credentials": You're told to believe someone who has authority. Oh? Try this article: A proposed structure for the nucleic acidsThe journal is amongst the most prestigious in scientific literature. Both authors were highly respected and worked in a high profile university (Cal Tech). Pauling won the Nobel prize in chemistry. But while their observations are true (based on too crude Xray diffraction images of DNA), their conclusion -- that biological DNA exists as a single-stranded helix -- is mistaken. This is actually quite common at the edge of what's known. And just as geniuses can sometimes be wrong, idiots can sometimes be right (and no, I won't give an example). So if you can't rely on credentials, what can you rely on? Credentials are a matter of opinion (and of little use in any case). So it doesn't matter that a boatload of PhD's subscribe to global warming, just as it makes no difference that other PhD's disagree. What is true beyond the vagaries of human judgment is an experiment and its result. No matter who did it, if you understand what they did and what they observed, you have grasped immutable truth. Of course, their interpretations may be wholly fanciful -- that's something else. You might argue that even reported observations are not examples of the truth. After all, authors may lie about what they did. While you occasionally hear about cases of this sort, they are very, very rare. If the experiment is important and well described, then it will be repeated and the fraud will be discovered. If it is neither important nor well described, then it probably isn't worth your while. What is common and warrants your constant consideration is the inescapable habit of authors (all humans) to draw conclusions that go beyond what their results will support. It is generally conclusions that are reported on web pages, and that, not lack of credentials, is why web pages, while useful, cannot be trusted. A research article is one that provides the results of experiments and a description of how the experiments were performed, in sufficient detail that someone else might replicate them. You will recognize them by the detail paid to the methods on which the results were based. Strategies to find research articles Google is not a good way (too low a signal-to-noise ratio). Google Scholar is much better, but I haven't used it enough to be able to compare it to other sites, such as PubMed and Web of Sciences. There are two major strategies to find research articles (plus one general fallback strategy):
If your interest is mycobacteriophage, then definitely check out the huge collection of articles provided by Mycobacteriophage DataBase (click the Publications tab and use the search box). Logistics of how to find research articles The trick is to do the search so that when you find a reference to an interesting article, you are able to open it up as full text. Many journals restrict access to those having subscriptions, so you want to make sure that the journals realize that you are at VCU (which has many subscriptions). You can do this either by using a computer on campus (your affiliation is recognized by your IP address) or by accessing the site from off campus through the VCU library. At the moment that a subscription becomes necessary, you'll be asked for your VCU eID and password. Here's how to do it:
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