How R you at statistics?

[Disclaimer] This post is little more than an exclamation of science-geek joy at some media attention for the stats program I use. Non-geeks are free to stop reading now, lest you be contaminated. Also, I must apologize that it is a little dated now, the original news item that sparked it having come out 3 weeks ago.

esearch in science invariably includes running statistical tests. The more complicated the experiment, the more complicated the test to determine whether my results are significant. I am delighted that the research community has a tool like R, which in addition to being fully-featured, extensible, and producing pretty figures, is free software (as in free beer, but also as in free speech). There are other tools out there that have comparable features (so I hear, anyway), but as a student I could not have afforded to put them on my personal computer.

So I'm a big fan of R, and am delighted to report that it is gaining headway in my local linguistics department against the old commercial packages.

Imagine my glee, then, to learn that the New York Times published an article earlier this week on the merits of R for data analysis!

Of course, the R discussion lists are all abuzz with the news. People are pleased that it's getting some wider attention, but also (of course) noting the apparent inaccuracies of the piece. None of them are catastrophic, and the writer of the article addresses some of them in his blog follow-up. Which has itself been responded to.

More on R and other free software projects in future posts - for now I'm just enjoying the glow of almost-fame for my little corner of geekdom. Ahhh.

Mooning over creationists (sequel)

In a post last year, I noted an intriguing question asked on the website of the local Edinburgh Creation Group (ECG).

They asked how the moon got into orbit.


The standard answer emerging from science is that some large object about the size of Mars (sometimes called “Theia”) hit the Earth very early on in the formation of the Solar System. That impact threw up debris which coalesced into the Moon. This hypothesis explains many otherwise-odd facts about the Earth-Moon system, such as their relative composition and their angular momentum.

However, the ECG folks claim to have found a problem. It’s very simply and persuasively illustrated by this simulation of orbital mechanics, which was linked from the ECG's website*. Play with it a bit yourself, to get a feel for the principle involved. Basically, once other forces (rocket thrust, planetary impact, atmospheric friction, etc) have stopped acting, only gravity is left. And when two objects (say, a fragment of debris and the Earth) are interacting only by gravity and are not substantially affected by external forces, there are three possible outcomes:

1. The smaller object already orbits the larger (or they orbit each other), and will continue to do so indefinitely.
2. They are on a collision course, and will impact (probably not parting again).
3. The smaller object meets or exceeds escape velocity, and leaves.

There is no trickery here – the simulation linked to is a faithful representation of two bodies interacting gravitationally. Now, I am not a creationist. I tend to distrust claims from people with a vested interest, unless they can demonstrate that they've tried to set aside their own bias (for example, by doing actual science). I therefore put more trust in the scientists who report in a peer-reviewed forum, suggesting they've worked out the bugs in their hypothesis. But I do like to understand things. The creationist question is a valid one, a question I wanted to know the answer to. So in my earlier post, I asked my readers to help me out and let me know what the simulation is missing. One of them pointed to a researcher who has some animations on her website. However, the details of exactly how the creationist argument falls down were not obvious there. So (after a thesis-induced hiatus) I finally decided to look it up myself. Here is what I found.



First, I learned that scientists occasionally call it the Giant Splash rather than the Giant Impact, because at that scale even bodies of solid rock behaves more like a liquid when thumped together.

Second, when a bunch of debris is flying through space above the Earth's surface after such an impact, there is a very obvious force present that is adjusting the orbit of the fragments: the other fragments! Collisions and gravitational interaction between the bits of debris (which, remember, must together have massed at least as much as the moon) caused some of the fragments to settle into a stable orbit, where over time they accumulated into the single satellite we know today.

All this is a very abstract description of the answer. The details take massive computing power for simulations of all the particles thrown up by a big splash. Researchers have simulated many different types of impact, with different impactor sizes, different angles of impact (from head-on to glancing blow), and so on. Not all of the questions are resolved, but the problem highlighted by the ECG is certainly a non-issue.

If all that is too cerebral for you, I'll repeat something I said in the earlier post: I love games that use orbital mechanics. KSpaceDuel is one that models only a single centre of gravity, so if you don't use thrust you'll just stay in your initial orbit (until your opponent blows you up, anyway). [Note that it's a Linux-only game - yet another reason to start shedding that Windows or Mac addiction.] And for those of you who haven't yet converted to Linux, Orbit is an online flash game that very neatly illustrates how complex the gravitation effects become when you’re dealing with more than a couple of objects.

References:
Notes for an undergraduate course at UCL (detailed)
New Scientist, 2006 (summary)

* I am currently unable to find the link - they seem to have redesigned their site and left it out. I therefore cannot be certain whether or not the claim is supported by the members of the ECG.

Truth about dyslexia

Gentle and thoughtful Cath is on the warpath - and justifiably so.

Some loon (Graham Stringer, MP for Blackley) is trying to deny the existence of dyslexia, a well-evidenced and widespread disorder, using false claims, fallacious reasoning, and other tactics familiar to rational people.

I cannot add anything to her very lucid demolition of his article. I'll just give a couple of potentially useful links for further reading.

Here's an international list of Dyslexia research and support organizations that a quick search brought up, in case anyone wants to read further: Dyslexia Parents Resource.

And if you're from the Blackley area, check out Stringer's contact info, voting record, etc. on this page.

Primo Levi - quote

From Primo Levi's afterword to the combined volume of If This is a Man and The Truce, which relate the author's experiences as a prisoner at Auschwitz and on his journey home.

It is, therefore, necessary to be suspicious of those who seek to convince us with means other than reason, and of charismatic leaders; we must be cautious about delegating to others our judgment and our will. Since it is difficult to distinguish true prophets from false, it is as well to regard all prophets with suspicion. It is better to renounce revealed truths, even if they exalt us by their splendor or if we find them convenient because we can acquire them gratis. It is better to content oneself with other more modest and less exciting truths, those one acquires painfully, little by little and without shortcuts, with study, discussion, and reasoning, those that can be verified and demonstrated.

One step closer

I have submitted my PhD dissertation. It is right now in the hands of my examiners, who are reading it and deciding whether I'm worthy of three more letters after my name. I'm one step closer to being a fully-credentialed scientist. Pretty cool.

This also means I'll have time to get back to a somewhat more regular blog schedule, and to participating in the online humanist community a bit more. But I do still have a viva coming sometime soon, for which I need to prepare; I do still have a post-doc jam-packed with paper-writing for the next year; and I do still have a gregarious daughter and a patient wife who I want to spend the bulk of my free time with.

So please bear with me as I look for the right balance between family, work, and you. And, if you have any particular hopes or aspirations for this blog, let me know in the comments for this post.

Confessions of a Recovering Meat Eater

Humanitie, the quarterly publication of the Humanist Society of Scotland, is out now. In it is my second column, included below. Visit the Not Quite So Friendly Humanist for the twin column. (Confession: I cadged my title from his. It was too good not to.)

I'm a vegetarian. I don't eat meat because I don't want to cause the deaths of sentient beings. I cannot justify killing them (or paying someone else to kill them) just for my pleasure or convenience. It is a decision based on deeply-held values, and one I try to stick to despite frequent temptations. It is also, I think, a natural consequence of humanist philosophy - indeed, an essay by humanist philosopher A.C. Grayling was the catalyst for my shift to vegetarianism this past February.*

Having grown up omnivorous, it has been difficult to become vegetarian. Despite the strong rational and compassionate argument for vegetarianism, the habits and tastes of thirty years cannot easily be set aside. I miss the taste of meat: steaks, fish suppers, roast beef sandwiches. It is against this non-rational urging that my ethical decision always fights. I am happy to say that my daughter will not have that struggle: deciding between a vegetarian or an omnivorous diet, she will not be distracted by the irrational influence of habit and custom.

I've had a wide range of reactions since becoming vegetarian: indifference, curiosity, even encouragement and support. Mostly indifference, though. It's no more an issue to most people than declaring a taste for Thai food. But for some people, my vegetarianism is not so easy to accept.

For example, my parents have told me that, by calling my choice an "ethical" one, I imply that their choice is an unethical one. Not only that, my dad raises beef cattle - so my choice also implicitly condemns his work.

I want to be clear: I do not condemn people who choose to include meat in their diet. Eating meat does not mean they are less ethical. Am I being hypocritical, holding myself to one standard and others to a different one?

No. Humanist ethics need not polarize the world of choice into right and wrong, good and bad. Human understanding is imperfect and provisional; this inherent humility of humanism means that I do not set up every personal choice as absolute and universal.

We are a somewhat smarter type of ape, using our ape senses and our ape reasoning to construct meaning and purpose in a confusing and ambiguous world. This ambiguity requires us to be flexible and accommodating of the various ways that people infuse the world with value.

I encourage everyone to think about our kinship with other animals. Consider carefully whether the value of their lives is so small as to be outweighed by the comfort of our habits, or by the slightly greater convenience of constructing an adequate diet with meat.

Think about it, and try to be true to your convictions. Whatever they are. That's all I ask.

* "Speciesism", from The Meaning of Things

I am ...

The fall equinox occurs today at 15:44. As the sun sits in balance, straight above the equator, I give you a post about balance, about thinking of the other side. About including others with you and including yourself with others.

Derek at Disonanz Cognitif has a post that just begs to become a blog meme. (Thanks to Mike Clawson at Friendly Atheist for pointing me to Derek's post.) Here are three of his "I am" statements (go read his blog for the rest):

I live in a world of people, animals, places, things, ideas, time, space, matter, energy, forces, galaxies, quasars, mesons, and bosons. I live in a universe that seems self-sustaining and acts a whole lot like there's no God in it. I am an Atheist.

I believe I have not yet sufficiently investigated the myriad of religious, spiritual experiences others claim to have had, and that there are too many well-educated, intelligent people who claim religious belief without a hint of shame, to discount the existence of an otherworld completely. I am an Agnostic.

I believe the teachings of Christ regarding positive social change and mercy to the oppressed are just a bit too clear a message of the gospel to be swept up as a minor sub-plot to securing an eternal country club membership for oneself. I am a Christian.

Derek explicitly avoids labelling himself in general (at the end of his post, he says "I am a person who has made a conscious choice to make no overt profession of faith or disbelief"), so it's quite a bold thing for him to make such a list as this. If you read through the comments on the Friendly Atheist post, you can see that some people don't even try to take the statements in the spirit they're intended. It seems obvious to me that Derek is trying to point out bridges. Some commenters just want to nitpick and try to impose their own definitions of terms on Derek.

Going through his list, I could echo "me too" to every one of his declarations. More importantly, I think this is a great way to crack through some of the divisive oppositions in our society, if people can bother to listen.

And I think I could add a couple of entries to the list myself. Here goes ...

---

I delight in solving puzzles and probing mysteries. I love to discover things which can be discovered and to know things which can be known. I am determined to learn about the reality that lies beyond my subjective, biased human perceptions. I am a scientist.

I savour the taste of a good, unsolved mystery. I enjoy the potential that lies in the unknown. I could lie for hours looking up at the sky, contemplating the fact that I will never know most of what there is to be known in the universe. I am a mystic.

I refuse to let people's reproductive anatomy dictate how I treat them, except when I expect to interact directly with their reproductive anatomy. I resist sexist behaviour in myself and in others. I am a feminist.

I value the lives of all sentient animals, and cause them as little suffering as possible. I enjoy a variety of foods, but do my best to eat things whose production does not involve the deaths of feeling beings. I am a vegetarian.

I think the best hope for human well-being and betterment lies in treating one another with compassion and reason in this life, the only one we can be sure we have. I value human life above non-human life. I am a humanist.

---

So there it is. I invite you to add your own items, either in the comments here or, of course, on your own blog.

I know that many people will disagree with the connections I'm making between characteristics and labels. But remember, this is an exercise in seeking connections. There may be an element of exaggeration in some or all of the items, but there is also an element of truth. It is that truth, that seed of inclusiveness, of universality, that is (in my mind) the point of the whole exercise.

I think I'll close this post as Derek closes his, with a line of hope and openness.

"And yet, the spiritual journey continues."