| BNFO 300 |
How to Find Articles... and Why |
Fall 2013
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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 discussion 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? [BEGIN RANT] 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 triple-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. [END RANT] Scientific truth resides in research articles. 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. A news report of a scientific finding is not a research article. It doesn't describe how to do the experiment. A review article is not a research article. It combines lessons learned from multiple research articles but, again, does not describe how to do the experiments it covers. Strategies to find research articles Unless you know something specific about the article you're looking for (e.g. title, authors, journal reference), Google is not the optimal search tool (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 (but if you do know the exact title, Google may be the fastest route). There are two major strategies to use these indexes to find research articles (plus one general fallback strategy):
And here are some alternate strategies:
Most article search facilities offer a (slightly) more complicated interface that gives you considerably more power. Using PubMed, for example, clicking Advanced just under the main entry box brings you to an interface where you can:
Logistics of how to find full-text research articles References are nice and abstracts sometimes helpful, but inevitably the time will come when you need the actual article. Sometimes simply googling the title of an article will get you there, but often this route fails. 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 some point, you'll be asked for your VCU eID and password. Here's one way to do it:
Another strategy is to use the excellent VCU Library general search facility. Just enter the title of the article. If the library thinks that online access to the full text of an article is possible, it will give you a link. Still another strategy is to go to the journal's web page. There are some journals (Journal of Molecular Biology comes to mind!) whose old articles are not listed in PubMed or the library database. Going into the journal archives might get you to the full length article. If all fails, contact someone, perhaps your friendly neighborhood librarian (see contacts above). |