- The p-value doesn't tell scientists what they want (it is the probability of the data given that H0 is true, and scientists would like the probability of H0 or H1 given the data)
- H0 is often known to be false
- P-values are widely misunderstood
- Leads to binary yes/no thinking
- Prior information is never taken into account (Bayesian argument)
- A small p-value could reflect a very large sample size rather than a meaningful difference
- Leads to publication bias, because significant results (i.e. p < 0.05) are more likely to be published
July 2011 Archives
There's no biology there! Well, almost no biology. There is one flower. We have four beakers, four test tubes, two, atoms, a couple of radio waves, and something in the top left corner that I can't identify, but only one flower to represent biology. No DNA, no chromosomes, no animals. That's what's wrong with this picture. (And don't get me started on why there's no geology.)
I'm part of the team collecting samples and measuring traits of Protea and Pelargonium as part of our Dimensions of Biodiversity project (see also the project wiki for more information). The community ecology team has been "in country" (at Baviaanskloof) since early July.
For most of the time we're in South Africa, we'll be staying in self-catering cottages. I haven't checked, but I doubt that any of them have Internet access. I will have my Blackberry, but I can't make blog posts from it. I will post an occasional tweet, which you can either find by following me (@keholsinger) or by searching for the hastag #dimensionsSA.
If I have time when I find an Internet cafe, you may find one or two posts here between now and when I return to the U.S. on August 16th. But don't count on it.
Image via Wikipedia
In case you don't know, JSTOR is a non-profit organization that provides online access to scholarly journal articles in a wide variety of fields, everything from African-American studies (17 titles) to zoology (65 titles). It is an invaluable resource, and I use it frequently.1
Aaron Swartz, a 24-year-old programmer and online political activist, has been indicted in Boston on charges that he stole more than four million documents from the Massachusetts Institute of Technology and JSTOR, an archive of scientific journals and academic papers. (Read the full indictment below.)
Mr. Swartz was indicted last Thursday by the United States Attorney for the District of Massachusetts, Carmen M. Ortiz, and the indictment was unsealed Tuesday. The charges could result in up to 35 years in prison and a $1 million fine. ("Internet activist charged in M.I.T. data theft," by Nick Bilton, The New York Times, 19 July 2011).
But it isn't free.
I don't know how much UConn or other institutions pay for access, but the fees they pay are how JSTOR is able to scan old titles, run them through OCR, post them and new articles on servers, and maintain the servers. It costs money to provide those services, and subscriptions provide that money.
I wish it were possible for all scholarly literature to be freely available without charge.2 But until someone figures out how to provide the funds necessary to make that possible, subscriptions will be necessary. And make no mistake. If Swartz did what he is accused of doing, he clearly broke the terms and conditions for use of JSTOR. I'll leave it to lawyers to determine whether his actions fit the legal definition of stealing, but if he did download more than four million articles from JSTOR, I will regard him as a crook.
I do have one complaint.The title should have been Plants are cool!, not Plants are cool too!Adding the word "too" makes it sounds as if plants are playing catchup with animals, which is wrong. Plants are much cooler than animals.
There are more videos from Botany 2011 on the BotanyConference video channel at YouTube, including Peter Raven's plenary address.
Image by pmarkham via Flickr
One Caribbean species, the Blue Iguana of Grand Cayman island, found nowhere else in the world, is looking like that rarest of things, a threatened species roaring back from the brink. Once down to perhaps fewer than a dozen animals, the long-tailed lizards, some growing to 5 feet and weighing 30 pounds, now number about 500, suggests a tally from a weeklong health screening that ended July 3.Read the whole story at USA Today.
Photo by Sean Flynn from UConn Today
Next week Nikisha leaves with a group of us for fieldwork in South Africa associated with our Dimensions of Biodiversity project on Protea, Pelargonium, and plant community diversity in the Cape Floristic Region.
You can read more about Nikisha in an article from UConn Today, and you can see the full list of Young Botanists at the BSA website.
As future scientists and educators, we, the undersigned students, encourage Congress and the President to make sustained investments in the nation's scientific research, education, and training programs. The extramural, competitive, peer-reviewed grant programs administered by federal agencies are critical to our nation's scientific enterprise and future.As of June, nearly 2800 students had signed the letter. If you are a student and you have not yet signed the letter, I encourage you to visit the AIBS website, read the letter, and sign it.
Addressing the nation's current budget challenges is essential, but we must not sacrifice investments in our future. One way to grow our economy is through scientific innovation. Science, however, cannot move forward in an environment where one year brings a rapid budget increase and the next year a precipitous budget cut. Research and development require people, facilities, and equipment - recruiting, retaining, and building this infrastructure requires a sustained and predictable investment.
UNITED STATES FISH AND WILDLIFE SERVICE RESOURCE MANAGEMENTIf you're like me, you won't have a clue what that means until someone explains it to you. Ken points out that this would have the effect of providing FWS with funds only to delist species, not to list them.
For necessary expenses of the United States Fish and Wildlife Service, as authorized by law, and for scientific and economic studies, general administration, and the performance of other authorized functions related to such resources, $1,099,055,000, to remain available until September 30, 2013 except as otherwise provided herein: Provided, That none of the funds shall be used for implementing subsections (a), (b), (c), and (e) of section 4 of the Endangered Species Act, (except for processing petitions, developing and issuing proposed and final regulations, and taking any other steps to implement actions described in subsection (c)(2)(A), (c)(2)(B)(i), or (c)(2)(B)(ii) of such section):
Here's a brief outline of what sections (a), (b), (c), and (e) of Section 4 provide for. Remember, I am not a lawyer. This a layperson's reading, but here goes.
(a) Gives the Secretaries of Interior and Commerce authority to determine whether species are threatened or endangered.Anyone who supports this bill cannot claim they are concerned about loss of biodiversity.
(b) Describes the basis for determining whether species are threatened or endangered and for designation of critical habitat.
(c) Provides for changes in the list of threatened and endangered species. The only part funded under the House Interior-Environment appropriations bill are those that would allow species to be removed from the list or to have their status changed from endangered to threatened.
(e) Provides for protection in "similarity of appearance" cases, i.e., where a threatened or endangered species might be confused with one that is not listed.
Image via Wikipedia
In late May, Coburn returned and upped the ante. He released a report accusing NSF of mishandling nearly $3 billion. Of course, he was wrong. I can't link to all of the posts explaining why, but you'll find some a few of the more relevant links at the bottom of this post.
In Friday's New York Times, David Brooks does a good job of explaining why "[t]his is exactly how budgets should not be balanced -- by cutting cheap things that produce enormous future benefits." You should go read the whole thing for yourself, but here's how it starts:
Over the past 50 years, we've seen a number of gigantic policies produce disappointing results -- policies to reduce poverty, homelessness, dropout rates, single-parenting and drug addiction. Many of these policies failed because they were based on an overly simplistic view of human nature. They assumed that people responded in straightforward ways to incentives. Often, they assumed that money could cure behavior problems.Scientific research often sounds funny because the technical detail needed for full understanding requires years of training. Coburn1 doesn't provide the context for the funny-sounding research he describes. When you know the context, it sounds a lot less funny. In fact, it sounds pretty important, and you can often imagine real-world applications quite easily.
Fortunately, today we are in the middle of a golden age of behavioral research. Thousands of researchers are studying the way actual behavior differs from the way we assume people behave. They are coming up with more accurate theories of who we are, and scores of real-world applications. (emphasis added)
Interestingly, in his first complaint he cites Garner's Modern American Usage as support for his advice that a comma should separate introductory phrases of more than three words from the main clause of a sentence. I say "interestingly", because if you go to the accompanying FAQs on Style and scroll down to the question "Where's the comma?", this is what you'll find.
Many readers complain about what they view as a missing comma in a sentence like this: He bought apples, pears and bananas.Those complaining readers are the same ones who rose up in arms on Twitter when it was (wrongly) reported that Oxford was giving up its comma. And Garner would be one of those readers. Quoting from my copy of Garner:
Style guides for book and academic publishing generally would insist on another comma after "pears," the so-called serial comma. But news writing has traditionally omitted the serial comma -- perhaps seeking a more rapid feeling in the prose, or perhaps to save time and effort in the old days of manual typesetting.
We do use the additional comma in cases where a sentence would be awkward or confusing without it: Choices for breakfast included oatmeal, muffins, and bacon and eggs.
Whether to include the serial comma has sparked many arguments. But it's easily answered in favor of inclusion because omitting the final comma may cause ambiguity, where as including it never will.Mr. Corbett, I suggest that you, the New York Times, the Washington Post, the Associated Press, and all of your fellows follow Mr. Garner's advice.
There isn't an "official" Twitter hashtag for Botany 2011. The BSA staff will be posting using @Botany_ . I'll try to tweet at least once or twice a day using the #botany2011 hashtag, and I'll try to recruit a few people to join me.
Update: In case it's not obvious. The video illustrates an iPhone app that uses the built in camera to "see" where it is and paste in the "appropriate" scene from a movie.
The review in the New Scientist confuses Bayes' Theorem1 and Bayesian inference In a way that I presume the book doesn't, but it concludes:
[T]o have crafted a page-turner out of the history of statistics is an impressive feat.Indeed. I can imagine it being a page-turner for a stats geek like me, but David Robson doesn't sound like a stats geek. If Sharon Bertsch McGrayne really turned a history of Bayesian inference into something that more normal people find interesting, she's accomplished a task many of us would envy.
If you're wondering what the review (I hope not the book) got wrong about Bayes' Theorem versus Bayesian inference, read on.
With her severely injured eyes covered by dark glasses and her dreams brutally derailed, Rumana Monzur returned on Tuesday to Vancouver, where she wept as she spoke of her hopes for the future.
"It's so different - but it feels great to be here among all you beautiful people," Ms. Monzur said, speaking through tears as her father gripped the handles of her wheelchair. "And I want to see you beautiful people again. I really do." ("UBC student maimed in Bangladesh attack returns to Vancouver", by Wendy Stueck, The Globe and Mail, 6 July 2011)
Image via CrunchBase
A visit to the miniature forest: Insights into the biology and evolution of bryophytes in northeastern Connecticut
It was written by Jon Swanson (a teacher at E.O. Smith High School in Mansfield), Jessica Budke (a graduate student in my department), and Bernard Goffinet. You can download the PDF for free and print it yourself or contact Bernard Goffinet to order a printed copy for a small fee.
Graphic from the New York Times
In last week's Nature, Hania Zlotnik, Director of the Population Division, responds to Pearce's criticism. She disputes Pearce's claim that differences are due to revisions in fertility estimates.
I am not an expert, and I'm more than willing to be corrected, but I find Zlotnik's response persuasive. But the most important point is the one she makes in her concluding paragraph:
The medium variant of the 2010 revision produces a 2050 world population that is, as Pearce notes, 156 million higher than that projected in the 2008 revision. This 1.7% difference is comparable to that between earlier revisions produced during this decade.Two things are important about that paragraph:
- Pearce and Zlotnik agree that the projection for 2050 is 156 million higher than in the 2008 revision.
- That difference amounts to only 1.7 percent of the total expected (roughly 9 billion).
Since the projections don't diverge until after 2050, it may not make much of a difference to policy makers in any context. Even long-term projections for social insurance programs like Medicare and Medicaid in the U.S. don't go out beyond 2050. By the time we need accurate projections for 2100, we'll be a lot closer to it, and small differences in fertility rates will have far less of an impact on those projections.We need to focus now on how we'll deal with 9 billion people in 2050, not on whether there will be 10 billion in 2100
A judge threw out the suit. But that's not the end of it.
In January, the American Tradition Institute Environmental Law Center filed a Freedom of Information Act request "documents, including e-mails Mann exchanged with other scientists while employed at the university". Since the University of Virginia is a public institution, it must comply with the request, and it will provide the material by mid-August.
Here's part of what the Washington Post's editorial board has to say about the FOIA request:
Going after Mr. Mann only discourages the sort of scientific inquiry that, over time, sorts out fact from speculation, good science from bad. Academics must feel comfortable sharing research, disagreeing with colleagues and proposing conclusions -- not all of which will be correct -- without fear that those who dislike their findings will conduct invasive fishing expeditions in search of a pretext to discredit them. That give-and-take should be unhindered by how popular a professor's ideas are or whose ideological convictions might be hurt.The board of AAAS agrees:
Scientific progress depends on transparency, the Board said, but "the sharing of research data is vastly different from unreasonable, excessive Freedom of Information Act requests for personal information and voluminous data that are then used to harass and intimidate scientists."Let me repeat that last phrase. It captures my feelings precisely:
The sharing of research data is vastly different from unreasonable, excessive Freedom of Information Act requests for personal information and voluminous data that are then used to harass and intimidate scientists.
This sentence uses it.
For teaching me that the Oxford comma resolves ambiguity, I'd like to thank my parents, Sinead O'Connor, and the Pope.This sentence doesn't.
For teaching me that the Oxford comma resolves ambiguity, I'd like to thank my parents, Sinead O'Connor and the Pope.See the difference? I didn't learn it from Hart's. I learned it from Strunk & White and had it reinforced by Fowler.
Why do I bring this up? Because there was a report on Twitter that Oxford had ditched its comma. As far as I can tell the Twitter explosion stemmed from a tweet by @ktheory that used deleted the Oxford comma and referred to a post on kottke.org. The Twitter explosion was enough to prompt an official response from Oxford making it clear that they will continue "to retain or impose this last comma consistently".
I am very pleased.
Update (5 July): I should have mentioned that the second sentence above is the tweet from @ktheory that appears to have started the Twitter explosion.
C++ code can be assigned to an object in R and called as a function, receiving arguments from R and returning them. I'm not sure what magic happens under the hood, but it sounds very promising and powerful.
There's an example of its use over at Life in Code. Pretty cool, if you're a code geek like me.