Phylogenetic fallacies

T. Ryan Gregory has a pair of “must read” articles over at Genomicron

• Phylogenetic fallacies: “early branching equals primitive”
• Phylogenetic fallacies: “branching from a main line”

If you aren’t too sure about how to read phylogenetic trees, then these articles are for you. If you understand them, they’re still well worth reading.

And here’s a third that fits nicely with with the other two

• Primitive versus [blank]

Science communication and framing

The “framing science” debate raised its ugly head again recently. By the time I came along, the battle lines had been drawn and hardened, and everyone cared enough about the issue that I didn’t have to. At this stage, I rather doubt there’s anything I could say that would change anyone’s minds. Fundamentally, I’m lukewarm on an issue that requires passion. But a question I was asked today made me think about the difference between communicating an issue and framing an issue.

I was asked a question something along the lines of: “You’re teaching an advanced ecology course, and you are asked by a pre-med student why they should care about this stuff. How do you answer them?” There are a couple ways to approach this question. One answer stems from what a friend of mine told a pre-dental student when asked the same question – dentistry, when it comes down to it, is oral ecosystem management. More importantly, ecology is an exercise in complexity, one of the few places that you will be exposed to that level of complexity in living systems. And the human body is a complex system (and a complex ecosystem).

There are other valid reasons for making students take biological classes that they believe they will never need…the “informed citizenry” argument. Issues like climate change, GMOs and stem cells are fairly complex issues that the general public needs to know about. But they don’t work equally well for all audiences…”stem cells” isn’t going to get much traction with a pre-med student complaining about having to take a botany class. So, you say…framing matters. Right? Well…no. There really are a number of different reasons why students should take a biology class. But these are real reasons. Sometimes the correct answer is “I don’t see any reason why you should be required to take this class, and maybe you should take this up with whomever it is makes these rules.”

There are a number of good reasons why some people find evolution so challenging to their world view. Some aren’t able to cope with “dethroning” humans. Some are afraid of modernity and a world that moves at a pace they can’t relate to. (“Having been led astray by creationist lies” is, in my opinion, a reason devoid of any redeeming qualities.) You can argue that someone like PZ or Dawkins isn’t going to reach them. That’s a plausible argument, and I’d be interested in seeing the data behind such an argument. But I suspect that you are going to reach far fewer people if you don’t want to take anyone outside of their comfort zone.

The creationists have successfully framed science as atheistic and amoral. More importantly, they have communicated atheistic to mean “anti-religious” and amoral to mean immoral.*  It would be great if we could separate atheistic from anti-religious and amoral from immoral.  But if you’re arguing semantics, you’ve lost already.  The counterargument is to accept the creationist equation of atheistic with anti-religious and trot out people like Ken Miller to prove that they’re false.  While that might sway a few people, it’s fairly easy to say “but they’re not real Christians” (making, of course, “Christian” the antonym of atheistic”).  Mind you, this is different from saying “religion and science are not incompatible”.  This is unrelated to religious scientists speaking of the universe in terms of God.  The problem with saying “science is not atheistic” is that (a) it doesn’t change the playing field, and (b) it’s not true, unless you accept the other side’s redefinition of the terminology.

You change people’s minds and perceptions when you take them outside of their comfort zone.  You don’t change the way people think if you start by accepting their world view and then tinkering.  “Love the sinner” hasn’t made religious homophobes more accepting of gays.  And people who use the bible to justify homophobia aren’t convinced when you try to present the idea in the broader context.  What has worked is getting people out of the closet and into the everyday lives of the general public.  I strongly suspect that, in order to change people’s minds, you need to take them out of their comfort zones.

Tangled Bank #102

Welcome to the latest issue of The Tangled Bank, the blog carnival dedicated to the world of biology, medicine, natural history…and Sarah Silverman.

We’re all getting older. And as we get older, we lose the ability to hear some frequencies. Diane Kelly of Science Made Cool offers Is That…A Dog Whistle? – a tale of a test that lets you know just how much damage you did to your hearing back in your clubbing days…or will do when you finally finish grad school and are able to emerge onto the social scene.

Ed Yong at Not Exactly Rocket Science has a two part post: Punishing slackers and do-gooders and Winners don’t punish: “Punishing slackers Part 2”. And, quite honestly, these are a compelling read. Ed is one of the best writers in the world of science blogging, and this pair of stories doesn’t disappoint. But even if they were badly written, they would still be fascinating.

PalMD recently joined the Brothers Hoofnagle at the denialism blog. He has a post entitled Malawi to curb fake AIDS healers. It’s a positive move by the government of Malawi all the more given the truly horrible cures that these fake AIDS healers are prescribing.

In a post that ties together Sarah Silverman, PZ’s octopus babies and gender differences between men and women in comedy, neuromotor control of smiling, and psychology with Japanese culture (and far more impressively, does so in a way that actually makes sense), Podblack Cat of PodBlack Blog: talks about what it’s like to be the Sarah Silverman Of Skepticism.

Take a moment and head over to the Agricultural Biodiversity Weblog. The entries for The First Great Agro.biodiver.se Competition are in, and your votes are needed to help pick the best video related to agricultural biodiversity. So head over to Clash of Titans — You Pick The Winner (the finalists are pretty cool).

Since every movie needs a prequel these days, Russell Seitz of ADAMANT supplies one for everyone’s favourite creationist propaganda flick in: Expelled: The Prequel. And onto an equally pleasant (though more easily correctable problem) Archaeozoology has an informative post entitled Know Your Pathology: Cleft Palate.

[That reminds me – I need to interrupt at this point with a public service announcement: the following posts consist of sharp brains – brain-eating zombies beware: they will do horrible things to the roof of your mouth]

Gregory Kellett at Sharp Brains talks about Relaxing for your Brain’s Sake. Apparently, experiencing excessive chronic, long-term stress is bad for the brain. Just great – now when I’m stressed I’ll have something else to stress about – the fact that the stress is bad for my brain. Also at Sharp Brains, Shannon Moffett talks about Sleep, Tetris, Memory and the Brain. Apparently, after playing Tetris all night, you’re supposed to get some sleep. That way, you’ll be better able to learn from your experience. (Apparently it applies to other skills as well…go read the post, it’s actually a lot more interesting that reading my inane rambling.)

Continuing at Sharp Brains, Pascale Michelon gives you Brain Teaser: Boost your visuospatial skills. Not only can you an exercise to boost your visuospatial skills, you can also learn what visuospatial skills are. And to round off all things sharp and brainy, John Medina gives you Brain Rules: science and practice, which introduces you to 12 things we know about how the brain works.

[And now continuing with the zombie-safe posts]

Mike at 10,000 birds delves into Striped Basilisk Lizard Lore; the Stripes Basilisk is one of the four Basilisk Lizards commonly known as the ‘Jesus Lizard’ because of the habit of turning water into wine umm, feeding the multitudes, no, overturning the money lenders tables in the temple…well, something like that. Scott Sherrill-Mix of Dammit Jim! addresses the question: When Do Leatherback Turtles Migrate South? (No one told me that you were allowed to blog about your own publications!)

Transitioning from organismal biology to gene stuff Barn Owl at Guadalupe Storm-Petrel has a post entitled Cream, No Sugar: Taking AIM at Pigment Dilution in Horses which talks about genes that affect colour in fish, mice and horses. Very cool stuff. Joe Dunckley at cotch.net is dissects a claim that epigenetics poses a problem for the “neo-Darwinian” view of evolution in Evelyn Fox Keller on genes, evolution, and epigenetics.

Finally, Andre of Biocurious has a post entitled Fluorescence Nanoscopy Just Keeps Getting Better. He starts off by saying “If you’ve been following the development of optical microscopy at all…” Developments? You mean there’s more to microscopy than choosing between the 4x, 10x and 40x objective lenses? Turns out that there is. So if you’re like me and have major deficiencies in your knowledge of light microscopy, this article is a must read…after all, you need to be able to come up with more than just a blank look the next time the subject of fluorescence nanonscopy comes up at a cocktail party.

Thanks for dropping by. The next edition of the Tangled Bank will be at rENNISance woman on April 16. Be sure to send your next round of submissions to host@tangledbank.net.

Climate Debate Daily

Climate Debate Daily is a website which claims to offer “a new way to understand disputes about global warming”:

Climate Debate Daily is intended to deepen our understanding of disputes over climate change and the human contribution to it. The site links to scientific articles, news stories, economic studies, polemics, historical articles, PR releases, editorials, feature commentaries, and blog entries. The main column on the left includes arguments and evidence generally in support of the IPCC position on the reality of signficant [sic] anthropogenic global warming. The right-hand column includes material skeptical of the IPCC position and the notion that anthropogenic global warming represents a genuine threat to humanity.

On the surface of it, it sounds promising. Present all the evidence to people and let them make up their own minds. Isn’t that what informed democracy is all about? Sadly, no. Science isn’t a democracy. Good science is separated from bad based on the weight of evidence. In order to evaluate the evidence, you need to understand the field as a whole. Context is everything – and if you don’t understand the context, it’s almost impossible to gauge the significance of any one paper.

The site is run by two philosophers – Douglas Campbell a doctoral student in philosophy at the University of Arizona (who is impressed by the breadth and depth of the scientific evidence supporting the theory of anthropogenic global warming) and Denis Dutton, an associate professo at the University of Canterbury (who is skeptical about the degree to which human activity has contributed to the general warming trend). Therein lies the first problem – philosophers have a bad habit of weighing arguments instead of weighing evidence. I’ve seen that approach among philosophers and historians of science in the evolution-creation debate – some of them seem almost naive in their willingness to suspend judgment.

Looking a little deeper at the site, more red flags pop up. It pits a graduate student against an associate professor. Hardly a battle of equals. It is funded by Peter Farrell, who is skeptical of the threat of anthropogenic global warming. That shifts the balance of power even more.

Farrell is quoted as saying “Let the best argument win”. Sadly, that is the problem that’s at the heart of the issue. Science isn’t a battle of rhetoric – it’s a battle of evidence. And whatever its public policy implications, climate change is a scientific issue.

A quick search on Google turns up quite a few links to this site. Most simply document its existence, or broadly fall for its spin. A few sites call it for what it is – a website playing the Fox News game of deception “we report, you decide”. And then there’s a wealth of libertarian/Objectivist sites which, unsurprisingly, are almost giddy over the site. Perhaps that the most telling bit – the people who are praising the site are all “skeptics”. No one pro-science seems to have anything positive to say about the site. Only the “skeptics”. Curious, isn’t it?

David Brin pays tribute to Arthur C. Clarke

Writing at Daily Kos, David Brin paid tribute to Arthur C. Clarke.

Arthur has long and deservedly been called one of the finest “hard” science fiction authors, for good reason.  From the beginning of his career as a writer, he explored frontiers of human knowledge, pondering the implications of everything from cetacean intelligence to planetology.  From the logic of John Von Neuman’s universal self-replicator to the possible motives of beings far in advance of ourselves.

And yet, what most intrigues me about Arthur’s work is something else — his ongoing fascination with human destiny — a term seemingly at-odds with the scientific worldview.

Read the rest of it.

What surprised me most was that David Brin is a contributor at dKos, and has been a regular contributor since January 2007.  As Markos said: “It’s things like this that make this site so darn cool”.

Farewell, Arthur C. Clarke

I just heard that Arthur C. Clarke had died. He was just 90. It’s a very sad loss. Farewell.

Update: Read what Phil Plait says about Clarke and why he was important; it was not just 2001 A Space Oddyssy, it was not just that he came up with the idea of geostationary orbit…it was also that he inspired generations of “rocket scientists, engineers, astronomers, and more”.

Burmese pythons invading California?

This is a great article from the San Francisco Chronicle – according to USGS predictions, exotic Burmese pythons (which have established in the Florida Everglades and can move as much as 20 miles a month) could make it to California as soon as 2020.  Californians – run for the hills!

The top map shows current suitable habitat for Burmese pythons in the US, while the lower one is a projection for 2100.

While I hoping that the article is intentionally funny, it does touch on some interesting things.  A large population of Burmese pythons has become established in the Florida Everglades.

People tend to think of south Florida’s problems with exotic tropical wildlife as unique, but as the USGS maps show, there’s an awful lot of suitable habitat for pythons all across the US.  No one is expecting a rapid spread, but it isn’t a lack of suitable habitat that’s stopping them from spreading.  More to the point though is the fact that anywhere within the green area, there’s a potential for escaped or abandoned pets to become established.  It’s a problem that will only become worse as the climate warms.

H/T Pharyngula.

Other coverage at ScienceDaily, and press releases from the USGS Newsroom and Fort Collins Science Center.

Update: R. Alexander Pyron and colleagues at the City University of New York disagree with the predictions of the USGS models.  Using niche modelling, they predict a far smaller distribution for Burmese pythons – southern Florida and the southern tip of Texas at present, and southern Florida and parts of the Pacific Northwest in the future.

Ants

When I was a child I read a book about ants – about one ant in particular, who was born in a colony, tends to one of her sisters before her nuptial flight, gets swept away from the colony is a flood, and finds herself alone.  She discovers a new colony, but the ants reject her because she doesn’t have the smell of the colony.  She finds a nearby abandoned tunnel and lives there, just to be near other ants.  And then one day, she runs into an ant from the colony and is welcomed – living nearby for so long, she has picked up the scent of the colony.  She is happy, and joins the colony where she eventually meets the queen, who it turns out is the sister she tended to just before her nuptial flight.

I learned so much about ants from that book – about their colony organisation, about the fact that workers are all female, about the existence of male and female alates who are winged and go on one nuptial flight were they mate before shedding their wings (in the case of females) or dying (in the case of males).  I learned that ants recognise colony members by smell.  What I learned from a children’s book was enough to make me better informed about ants than many a zoology gradate student.

I wish I had any idea what that book was or who wrote it.

Florida science standards

The Florida Board of Education eventually adopted the science standards with “evolution” in them (details here, here and here). Their compromise to the creationists was to preface the word “evolution” with “scientific theory of”; the good thing about that was the decision to preface evolution and other concepts with the phrasing “scientific theory”. As PZ says, the creationist may have scored an own goal. He writes

Well, the word is out that the creationists screwed up big time, and their own ignorance has turned around and bit them on the ass. They really did think inserting the word “theory” would help discredit evolution (it may still do so, as they try to frantically spin it in their church newsletters, but it’s only going to work among their true believers), but it’s going to have the opposite effect in the public schools.

Creationists love to spit the epithet it’s just a theory at evolution. Obviously evolution is both fact and theory, but it’s the theory that’s the interesting bit, because a theory allows you to make non-trivial predictions in a way that observations (“facts”) do not. There’s no slur in calling evolution a theory in a scientific context – a scientific theory is a very well supported hypothesis. The creationists’ point, of course, isn’t to call evolution a scientific theory, it’s to call evolution an unsupported conjecture. It amounts to playing games with language.

Florida Board of Education

Mike O’Risal has more on today’s vote by the Florida Board of Education on whether to accept the new science standards.  He has links to live webcasts of the meeting and a discussion of editorials that “get it” and that don’t.