scientific method
milhayser | December 13, 2011
Like addicts, we would love to stick to what is easy, familiar, and dependable. The withering consequences of our actions, abstracted to an intangible future, are easy to deny. Prominent politicians say that global warming is a fantasy, that we can keep doing what we're doing, that everything will be okay. Meanwhile their speech is paid for by the same corporations we enrich with our emissions. These corporations are addicted to our money like we to their energy and plastic, but corporations are not people, and unlike us, will never have the will to quit. Recently a number of groups…
revere | May 9, 2010I just started reading an interesting book, "How Mathematicians Think," written (naturally enough) by a mathematician (William Byers). It got me thinking not only about mathematics but also science, what it is and why I do it. Here's the paragraph that triggered it:
The most pervasive myth about mathematics is that the logical structure of mathematics is definitive--that logic captures the essence of the subject. This is the fallback position of many mathematicians when they are asked to justify what it is that they do: "I just prove theorems." That is, when pressed, many mathematicians…
revere | April 29, 2010I'm all for scientific -- and statistical -- literacy, but sometimes the calls for it exasperate me. Just a little. Not significantly. If you know what I mean. Or you think you know what I mean. Anyway.
Yesterday Wired carried a piece by Clive Thompson, Why We Should Learn the Language of Data. It's a bit presumptuous to say that statistics is "the" language of data (data speak many languages and there are dialects within each), but I'll let that go. And I'm sympathetic when someone has to keep answering charges that if global warming was happening, why was there so much snow? This question…
revere | April 9, 2010This week Canadian public health researchers published the long awaited paper on possible association between vaccination for seasonal influenza the previous flu season and risk of having a medically diagnosed infection with pandemic influenza during the first wave of infections (April to July) just as that season was ending. When preliminary results were first announced there was only vaccine against seasonal flu, which was still being given, and the results were contrary to what we thought we knew about flu biology and the immune system. Inevitably it became caught up in the wider anti-…
revere | March 25, 2010The Robby in the title refers to Robby the Robot in the 1956 movie, Forbidden Planet, and what follows was a tag line in an ad for Grant's whiskey: "While you're up, get me a Grant's." That's in case you've forgotten or never knew.
I'm still working on the grant, doing things it feels like a robot could do. Writing pieces on the facilities, lists of Key Personnel, charts of graduate students trained, budgets, budget justifications, etc., etc. I have lots of help from great staff and colleagues, but it is the kind of necessary but tough slogging that doesn't feel very creative. I don't mind…
revere | March 11, 2010The latest study on flu vaccine effectiveness in children has been well discussed in the MSM and the flu blogs, so I'll point you to those excellent pieces (Branswell, crof, Mike Coston at Avian Flu Diary) and just add some things not covered elsewhere. The full text of the article is available for free at JAMA and it's a pretty good read, so if you want to see for yourself what is involved I urge you to read it, too. First, let me back up a bit and connect this to the controversy about observational and randomized clinical trials we've been discussing here of late (before my grant writing…
revere | February 10, 2010I'm a scientist and my research is supported by NIH, i.e., by American taxpayers. More importantly, the science I do is for anyone to use. I claim no proprietary rights. That's what science is all about. We make our computer code publicly available, not just by request, but posted on the internet, and it is usable code: commented and documented. We ask the scientists in our program to do the same with the reagents they develop. Reagents are things like genetic probes or antibodies directed against specific targets mentioned in the articles they publish. There is an list of the reagents on the…
revere | January 26, 2010[Previous installments: here, here, here, here, here, here]
Last installment was the first examination of what "randomized" means in a randomized controlled trial (RCT). We finish up here by calling attention to what randomization does and doesn't do and under what circumstances. The notion of probability here is the conventional frequentist one, since that's how most RCTs are interpreted by users. Before we launch into the details, let's stop for a minute to see where we've been and why.
We began with a challenge to you, our readers. In the first post of this series we described an…
revere | January 16, 2010[Previous installments: here, here, here, here, here]
After a detour through the meaning of causation and the need to find a substitute for what can't, in principle, be observed (the counterfactual), we are now ready to consider what many of you might have thought would be the starting point, randomization. It's a surprisingly difficult topic and this post will probably be more challenging for non statisticians, but I feel confident you don't need to be an expert to understand it.
First a quick recap. If you want to know if mammography screening will prolong the life of a woman under the age…
revere | January 12, 2010[Previous installments: here, here, here, here]
We'd like to continue this series on randomized versus observational studies by discussing randomization, but upon reviewing comments and our previous post we decided to come at it from a slightly different direction. So we want to circle back and discuss counterfactuals a little more, clarifying and adapting some of what we said for the coming randomization discussion.
Let me change the example to a more recent controversy, screening mammography for breast cancer. Should women under 40 get routine screening given that there is said (on the…
revere | January 9, 2010Continuing our discussion of causation and what it might mean (this is still a controverted question in philosophy and should be in science), let me address an issue brought up by David Rind in his discussion of our challenge. He discussed three cases where a rational person wouldn't wait for an RCT before taking action, even though there remained uncertainty. The first was a single case report of rabies survival after applying an ad hoc protocol. The next was use of parachutes while sky diving. The third was the first reports of antiretroviral therapy for AIDS. Here's what Rind said in his…
revere | January 8, 2010Let me start with an apology. This post is again fairly long (for a blog post). Blog readers don't like long posts (at least I don't). But once I started writing about this I was unable to stop at some intermediary point, although I might have made it more concise and less conversational. I haven't done either. Even worse, I didn't quite finish with the single point I wanted to make, so it will be continued in the next post. Hence the apology. Now to recap a bit and then get down to business.
My "challenge" from 10 days ago has drawn quite a response: over 40 quite substantive comments on the…
revere | January 5, 2010Just a day into the New Year I was feeling feisty and issued a challenge to readers and the Evidence Based Medicine (EBM) blogosphere in general. I asked for a critique of a fictitious uncontrolled, non-randomized non-blinded small scale clinical study. It was truly a fictitious study. I made it up. But I had a template in mind and I intended to go somewhere with the example and I still do. But it will take longer to get there than I anticipated because it has raised a lot of things worth thinking and talking about in the meantime. I was going to wait a week to give people a chance to read…
revere | January 2, 2010I've noticed that whenever I have the temerity to suggest (e.g., here and here) that maybe the word of the Cochrane Collaboration isn't quite the "last word" on the subject and indeed might be seriously flowed, I hear from commenters and see on other sites quelle horreur reactions and implications this blogger doesn't believe in the scientific method. Why? Because "everyone knows" that a randomized controlled trial (RCT) automatically beats out any other kind of medical evidence and any Cochrane review that systematically summarizes extant RCTs on a subject like flu vaccines is therefore a…
grrlscientist | October 25, 2009tags: intelligent design, scientific process, science classroom, rational thinking, AtheistBusCA, streaming video
Kenneth Miller provides a brief explanation as to why "intelligent design" is not admissible in a science classroom.
sciencewoman | October 5, 2009Remember this summer when I was working on the course design for my new prep on Experimental Design and Data Analysis? We're now a month into the class, and while it has had its rough moments, I think it will ultimately be quite useful to the students enrolled in it.
I'm currently avoiding grading, so I thought I'd take a moment to show the results of an exercise we did the first week. I gave groups of students two sheets of paper. On one I asked them to diagram the scientific method as they understood it. On the other, I asked them to diagram their experience with how scientific research is…
rallain | April 16, 2009I have been meaning to write about this for quite some time. Really, I wanted to reply to Chad's article on science at Uncertain Principles, but you know how things go. So, here are my key and interesting points about science in random order.
Science is all about models (not ball bearings)
Science is about making models. What is a model? A model can be lots of things. It can be a mathematical relationship, a conceptual model, or even a physical model. One model I like to use is static friction. For many cases, the frictional force can be modeled as:
This model says the frictional…
esiegel | April 18, 2008Bret Underwood, a friend of mine from my time in Madison, WI, saw my post on String Theory, and took issue with my statement that it wasn't testable. I'm still standing behind what I said, but let's address what Bret has to say.
I donât understand your argument above for why string theory is untestable. In fact, it seems to me you just outlined the best possible case for string theory! What you said above is that if I have a string theory construction of a phenomenon (say, the Standard Model or Inflation), which uses a set of parameters X, and makes some predictions, then I can find another…