Friday, November 30, 2007

The argument from extra belief

I find this particular argument amusing, even astonishing, but it's the way some believers (not just religious ones, but woos of many stripes) think. I have encountered it numerous times in different contexts.

"I believe X"
"Well, okay, but believing something doesn't make it true. We can be fooled. What evidence is there to believe it?"
"But I really, really believe it!"

For some reason, really, really belief is supposed to be more convincing.

I used to be completely unable to understand how this kind of reasoning came about. Lately I suspect it has something to do with the privileged position faith is supposed to be accorded, because faith is supposed to be admirable. More faith is supposedly more admirable, and hence, more privileged. We actually are expected to find that really, really more convincing in some way, or at least to stop thinking about it!.

I originally posted thinking there was no need to refute this, but I guess the fact that I see this argument sometimes indicates that some people at least can't see just how pathetic it is. So for posterity, here's one such argument. Believing something doesn't make it true - you can be wrong, you can be deceived. Believing it more doesn't remove that.

Saturday, November 24, 2007

A blog I read


To quote the first post:
My plan for this blog is to critique (and perhaps occasionally praise) the statistical methods used in current research articles. Sort of a post-publication statistical peer-review. Unfortunately, too few journals engage in quality pre-publication statistical review, so there should be no shortage of material. I'm going to be focusing on debunking research that seems implausible, poorly conducted, or just silly, especially research into so-called complementary and alternative medicine (CAM). But anything is fair game!

My hope is that this format will provide some really good case studies for introducing or clarifying statistical concepts and methods. So, we'll have some fun, and maybe we'll learn a lesson or two along the way.

An admirable aim. The standard of the discussion seems to be of a level that will keep me reading.

Friday, November 23, 2007

The problem with debunking bad science...

... is you need to not fuck it up.

If you're going to flame science papers for bad mathematics, you better not do it yourself!

Junkfood Science quotes Dr John Ioannidis as follows:
"the probability that the research finding is true is only 1.5".

Sandy seems unimpressed by this figure she quotes.

[No, I didn't quote-mine there and leave off an important word like "percent"... the quote continues " — hardly any higher...".]

I don't know about you, but I'm very impressed by a probability larger than 1.

Having something occur more than 100% of the time seems quite dramatic enough to me.

Exactly how much more often than "occurs 150% of the time" would it take to make you guys think the effect was strong?

Maybe Junk Food Science should check the quote, because statisticians tend to get a bit skeptical when probabilities don't come between 0 and 1.

In normal circumstances, I wouldn't post something like that here, I'd put it in comments on the original blog, but junkfoodscience doesn't seem to allow comments. Doesn't even give an email address. Since I can't say it to them quietly, I will say it to everyone loudly.

Wednesday, November 21, 2007

More evidence of dumb design?

If cdesign proponentsists had an intelligent designer
    they'd be smart enough to understand evolution.

The amazing power of faith

A rant. You have been warned. (Edited to be less of a rant. Still pretty strong.)

Faith can have the power to change lives. This is often held to be a good thing. I think that in fact, it is a very, very dangerous thing. And, quite often, a terrible thing.

My reasons range from the mundane to le monde. These are merely examples; there are many more.

The mundane: I know a boy. A very nice, intelligent boy. A likeable lad. His brain is, unfortunately, completely infected with the faith meme. He takes ridiculous risks with his life. If you warn him of danger, his reply is that he believes in God and God will protect him from harm (and he will yell this over his shoulder as he plummets full-tilt down concrete stairs or heads toward traffic, in spite of the added danger not looking poses). The faith that his parents have inflicted him with, or have allowed others to inflict on him, places him directly in harms way.

If a parent deliberately and with forethought chose to deny their child some essential nutrient that substantially increased the risk of the child dying, the media would trumpet it to the world as evil child abuse. But instill blind faith in God’s providence, and the faithful treat it as admirable. This child is being denied an essential nutrient. The lack of it affects brain development and as a result, this child’s risk of death has gone up dramatically. One can cross one's fingers and hope he will come out of the worst of it before he is too badly harmed, but it’s rather like seeing a teenager taking up petrol sniffing – they might stop before the permanent harm becomes tragically too great, but you don’t necessarily believe they will.

The larger problem is, this increased risk in not limited to this boy. His faith rubs off on those around him (and, worse, he’s far from the most faith-meme-infected child I know). The fuckers that are playing with that child’s life are also playing with the lives of many children. Including my children. And, if experience is any guide, pleased with themselves. Like it's a good thing.

Perhaps slightly less mundane: Teenagers have sex. Many of them get pregnant. They always have. They always will. Getting pregnant when you’re not ready for it can be a bad thing. Further, having sex before you're mature enough to deal with it and everything that goes with it can be a bad thing. Some people of faith feel that the appropriate way to deal with it is to tell kids simply not to have sex. This is known as abstinence-only sex education.

The problem is, it does not work. Study after study show that it doesn't. Kids whose sex education consists of abstinence-only programs have sex younger and more often than kids who get full on sex-education, including explanations of how contraception works. Millions of dollars are being spent, especially in the US, on programs that, in effect, lead to more teenage sex and pregnancy. Older kids who take a pledge not to have sex until they are married have sex almost as often as kids who don't, but they're much more likely to engage in unsafe sex, and less likely to seek treatment for sexually transmitted disease. (And they feel guilty about it, for all the good that does them.)

The solution of the faithful is to spend more money on abstinence-only programs. You see, the problem is, faith cannot be in error, because it is faith - you have to believe it works, no matter what the evidence. To even examine if the results of a faith based program works is to doubt your faith, and that, apparently, is a bad thing. If, somehow, they cannot avoid noticing that it doesn't work, we must have done it wrong, so we all have to pray harder and do it more, and no matter how much harm it does, we have to force people to go along with it.

Le monde: Faith is, to a great extent, what got Bush elected. Faith is what convinces him that reason and evidence are trumped by the voice in his head. Faith (well, that and money, I guess) is what has convinced Bush and his cronies that trillions of dollars and hundreds of thousands of human lives must not only be spent, but must continue to be spent in a war that has made the world a far more dangerous place - and they were plainly told this in all manner of ways before it was too late. Faith trumps reason. Faith trumps evidence. Faith trumps truth.

Faith tells priests in Africa to tell people not to use condoms, that they're an evil Western plot. I see people say "that's no longer church policy". Well, they don't seem to have gotten the message in a lot of places. Go tell them, or stop whining that it's not fair to bring it up. If you're not doing anything about it, stop trying to interfere with those of us who want to give it some attention.

Faith is, to a large extent, why the world cannot currently deal with the greatest threat to my great-great-grandchildren, and my neighbors great-great-grandchildren, and dammit, all great-great-grandchildren everywhere – runaway global warming. Faith blinds people to truth, and makes them condemn the people who tell it.

Faith makes for very bad decisions, both large and small.

As a result, faith, in short, because it encourages bad decisions, harms, even kills children. It ruins lives, brings death, poverty, waste, ruin, tragedy. Don’t expect me to sugar coat this, because it's not a matter about which decent people should be polite.

Many theists, individually, might not agree with the bad decisions I’m talking about, but faith, and the belief that faith is somehow inherently good, is at the root of the problem of many bad decisions. Every major problem that keeps me awake at night, I see people of faith using that faith as a reason to stand in the way of solutions. Standing beside them I see people of less strident faith, people who hold “liberal” “sophisticated” beliefs, good decent people, not condemning them and everything they stand for, not fighting them. Instead, they praise their faith. They treat the misguided faith as admirable.

Pardon me if I don't join you in admiring it.

Tuesday, November 20, 2007

Greta Christina on truth vs helpfulness and how they are related

Greta Christina writes about the tendency to conflate arguments about the truth of religious claims with arguments about the possible benefits of religious belief - a mistake that is often made. However, she then goes on to discuss why false beliefs are inherently harmful. The two arguments can never be entirely separate.

She makes some excellent points. Go take a look.

Friday, November 16, 2007

Human makes Influence roll; God saves vs existence

A lot of people pray to ask for something they want to happen.

Sometimes they get what they want and sometimes they don’t.

People who pray a lot get what they want at about the same rate as those that pray hardly at all

People who don’t pray get what they want just about as often.

People who pray earnestly get what they want at about the same rate as those that pray half-heartedly.

People who behave well get what they want at about the same rate as people who don’t.

People who badly need help get what they need at, if anything, a slower rate than people who don't need anything at all get more of what they don't need (the rich get richer while thousands starve and die of preventable disease).

God not only answers prayers quite at random, he answers the complete absence of prayers just as much.

He’s a crafty old fellow, that God.

Apparently, God does play dice

Adding information about adding information

A number of posts back I was trying to make a point about the fact that even with a straw-man version of biology (and, incidentally, a very narrow definition of information), evolution could add information to the genome, most obviously by duplication followed by mutation. I figured that out for myself (it took me all of about 30 seconds of rumination), but it turns out that cdk007 was there before me - he gives exactly the same example (in a much funnier way) in his video "How Evolution Causes an Increase in Information".

I can only assume many other people have thought of the same thing (if someone as ignorant as me can come up with the example, obviously it's not that hard, unless you're a biochemist or something).

Anyway, I don't think I'll polish the argument I was trying to work on in that earlier post, since cdk makes the point much more succinctly, in the middle of a much more educational work.

Featured at Austin Cline's blog

Austin Cline at featured a comment of mine.


Thursday, November 15, 2007

His Noodly Appendage

... is such a wonderful, delightful phrase.

I cannot say it - I cannot even read it - without a smile growing into a barely held in snort of laughter. I'm grinning like an idiot right now as I type, trying like hell not to just burst out in joyous laughter.

It's not like I've just heard it for the first time - I've been aware of the FSM for ages, but it still amuses me no end.

What made me blog

(This comes from a comment I made to Greta Christina on her blog)

I have a confession to make.

You are the reason I have an atheist blog.
(I do have another, older blog elsewhere that's just sort of a "chatting with friends" thing, about my hobbies and interests and family. It's not really an attempt to communicate with the wider world, but with some people that share some of my interests and in many cases, some common experiences.)

My atheism blog has many parents, but you're both parent and midwife.

Because of Wil Wheaton I found that a blog could be personal and the same time real, inspiring and fun. Because of Wil Wheaton, I started using a blog aggregator (Bloglines). Because of Wil Wheaton, I started to read more than a couple of blogs. I have been reading Wil's blog for years now. Wil also directed me to the Bad Astronomy blog.

Without Richard Dawkins, I'd never have thought to look for other atheists on the web, nor gotten "fired up" enough about it to try to read what other atheists had to say. I started to think about my own experiences in the broader context of what's going on in society. I've been reading his books at least since I read The Selfish Gene around 1985, but The God Delusion got me to really think hard about my atheism. Because of Richard Dawkins, I realized I had to find a way do more. The first thing I had to do was read more. And because of his website, I read Bad Astronomy some more, and I found Pharyngula. That would have been just after mid-year I guess.

Because of Pharyngula, I realized a good blog could be snarky, and entertaining and right, all at the same time. And because of Pharyngula, I found your blog. (It may have been the link back in August, unless there was one a little earlier.)

And I kept coming back. Soon, I put you in my feeds, then moved you up into my couple of "special blogs".

Because of you, I realized I had things to say, and I had to start saying them, not one day, not soon, but right away. I don't think it was any single post, but the cumulative effect over several weeks. However, I think your two posts on September 30 were the final straw, and a few days later, I had a blog ready to go. Because of you, I actually began to write.

I don't know if my writing will ever be inspiring and moving and funny the way yours is. I certainly don't have enough time to really polish my posts, and what I write often comes out pretty raw and unfocused. But there are things in me that I am finally saying, and that means a lot to me.

You gave me a voice. Thank you.

Wednesday, November 14, 2007

Joining the Atheist Blogroll

Been meaning to do this for weeks. I asked to join mojoeys atheist blogroll. (won't be up yet) I'm up now!

The Atheist Blogroll is a service provide to the Atheist and Agnostic blogging community. The blogroll currently maintains over 350 blogs. Membership is limited to Atheist and Agnostic bloggers. To join, follow the instructions there.

Added the A

Finally got around to adding the Scarlet A. Yay. Take a look at their campaign.

[Edit 21 Nov]
Well it's been a long while, and they still don't seem to have added me to their list. I wonder if I should poke them again.
[Edit 24 Nov]
On the Out Campaign blogroll now!

Seen at Pharyngula

In the comment thread on P-Zed's liveblog of the NOVA Judgement Day program:

Posted by: Ex-drone | November 13, 2007 9:33 PM

cdesign proponentist n. a transitional evolutionary form between creationist and IDist

[By way of explanation - it comes out of a stuffed-up global edit of the creationist book Of Pandas and People, when they converted it to an ID textbook by attempting to replace "creationists" with "design proponents" and a variety of similar label substitutions, without changing the actual content, and cdesign proponentsists remained in the text as evidence of the mangled substitution.]

Why is your blog so plain?

You've probably seen Powerpoint presentations with lots of bits whizzing in, fancy wipes, flashy background colours. In fact, anything to distract from the lack of content.

Some websites are the same way.

I have an aversion to glossy presentation with no content.

Now I have nothing against a well-presented website or blog that also has content, as long as it's not distracting.

My wish is that the content I present stand or fall on its own merit (I guess I'm not much into the whole "framing" and marketing thing).

If I post good content, it's good, even if it has a vanilla presentation. If it's bad content, I want nothing to stand in the way of that assessment. You should immediately be able to see if my stuff is contentless, and rightly reject it.

I'm wary of going too far in terms of gussying up my blog. I'd prefer plain to distracting.

On top of that, I have a lack of time. If I spend 10 hours playing about making a fancy logo, that's a whole lot of posts I don't have time for. Frankly, I'd rather make the posts.

That said, I may dress it up a little as I go (I've only been doing this blog for six weeks), piece by piece, but it will always be spartan.

Behe's rudeness

Behe's response to Musgrave's open letter (which is in itself a response to Behe's reaction to ERV's demolition of Behe's HIV arguments) is, as was his response to ERV, totally inadequate.

As always, Behe does not deal with the actual substance of the arguments he is presented with. I have seen only the following kinds of argument from him:
(i) unsubstantiated claims (see his books. Not promoting them here.)
(ii) arguments from authority
(iii) ad hominem attacks/ reference to peoples age, gender or qualifications
(iv) reference to the form rather than the substance of the arguments
(v) dismissing an argument as "weak" or "irrelevant" without dealing properly with its content
(vi) lies

Musgrave: "in science... we pay attention to the evidence and logic of an argument" Behe makes not a single reply about content, evidence or logic. He has the gall to lecture Musgrave on what's appropriate argument, yet fails to see that he only appears to use inappropriate arguments himself.

Most ludicrous of all is his reference to ERV's tone. If you read back through all of ERV's posts, her tone definitely gets stronger... for an obvious reason. Again, and again, ERV's opponents totally fail to deal with the substance of the arguments, and instead rely on references to ERV's age/gender/qualifications/tone or simply dismiss the arguments as weak or irrelevant.

He also won't allow comments on his blog, and wont comment on ERVs. Or on Panda's thumb, where Musgrave posts. That allows him to pick his ground, to shift his ground, and avoid addressing the actual substance of his opponents' argument.

Indeed, the disgusting tactics are common to all IDists - they're so unsure of their ground that they prevent real argument on their own forums, while their opponents allow for dissent and opposing views as part of the open debate. But the IDists refuse to engage them there either.

It's Behe and his cronies that are being rude by refusing to engage ERV. ERV's response is a reasonable reaction in the face of their awful behaviour. Claims of "polite tones" don't excuse them (I don't see them as polite, but it's perfectly possible to hide a disgusting argument behind a polite tone). They're appalling. Either deal with the actual science content or shut up.

Tuesday, November 13, 2007

Three second argument: Is God good?

(click to enlarge)

This is the first of what will hopefully be a series of arguments distilled down to some single basic point.

The idea for this grew out of frustration with theist ground-shifting:
[It rains. Or thousands of people die in an earthquake but a 5 year old survives. Or a football team wins.]
Believer: "God is good! Praise the Lord!"
Nonbeliever: "What about all these bad things?"
Believer: "You can't make moral judgements about God's actions!"

I suspect the problem is that the your average god-praising theist doesn't actually have an explicit belief about whether we can make judgements or not (even though the theist will make them all the time). What's going on is we always start in one of the arms, and the believer jumps from one to the other at will - apprently without recognising that they're doing it. I think the inability to follow through with even the most basic of reasoning (reasoning that my six-year-old displays daily) is a consequence of starting with a conclusion based on an emotional response - it's NOT about being right, or making sense, or truth, or ideas. It's about avoiding cognitive dissonance. The belief meme must be protected at all costs, even if it's false.

By making the arms an explicit choice, the ground is established. The commitment to an arm at the beginning makes it harder to keep changing the claim, and the argument from there becomes more straightforward.

I want to expand both the terminal nodes into fuller arguments (particularly the left one, so I can give a few examples), but the original point was to keep it short.

I have a few more of these vaguely swimming around at he back of my head that I will probably bring out as the mood takes me, but if you have a believer's argument involving ground-shifting or circular reasoning (leave it in the comments), I'll see if I can break it down.

Pushed into a church wedding?

(via friendlyatheist ) On Oz Atheist, a reader, JP, asks:


i found this blog through a google - like you i am not religious but that hasnt stopped a big problem - i am due to be married and both families are pushing for a full trad church wedding (and trad dress etc) and i dont like it - i feel cornered and trapped and not sure what to do. Do you have any advice you can give me?

If you have some good advice, maybe you could drop in on the thread there and pass it on.

Friday, November 9, 2007

What goes up

A scientist, an actuary, a woo and a fundamentalist play the stockmarket.

Scientist: "About half the ones I predicted would increase went down, and about half the ones I predicted would go down went up. My model for predicting movements in the stock market is apparently not very good. Time for a new conjecture."

Actuary: "Last week, I predicted these ten stocks would rise and those ten would fall. Next week, I predict *these* 6 here will go up, and *those* 7 will fall. The week after that..."

Woo: "Those two /would/ have gone up, but the scientists are fiddling the numbers. This one did go up, but the government covered it up. Anyway, look! Three months ago I correctly predicted which direction *this* would go! And it did! See! Proof!"

Fundamentalist: "No, I didn't get the predictions wrong. In fact, they weren't predictions at all. No true Christian would claim that *those* stocks would go up, and that's not what I said. And you're using far too literal a sense of the word "up". Oh wait, see this stock we didn't discuss last week? It went up. That's perfectly in accordance with Ecclesiastes 3:5. The Bible correctly predicted it! Of course the text says that it would go up, you're reading it wrong - anyone with true faith can see that's what it really means. Of course we can use the word "up" literally! It's the plain meaning of the word! Why are you always so angry?"

Thursday, November 8, 2007

Adding information

[This is a work in progress {now a junk meme, which may one day get duplicated and evolve new functionality}. I need to go back and actually read more of the arguments I am arguing against here (rather than the bits and pieces I have read), so that my points are better aimed - views like those of Egnor and Luskin. So this post will probably change {or not...}. If I had readers, I wouldn't do this, but apart from the occasional person who drops by and is kind enough to give me some comment love, I don't think I have any readers. If I'm having a conversation with myself, I can afford to think out loud here since there's nobody to annoy. If you are a regular reader and you think this is bad form, drop a comment.]

Here I'm going to show you just how unutterably dumb ID/creationist arguments against genetic change adding information can be.

Oh, one thing to keep in mind. Genes are not "always on". Sometimes they're doing stuff, but for most of them they're only on some of the time. Some only for a very short time. The activity of genes are controlled by other genes (and sometimes by epigenetics). Most of the time, a lot of your genome isn't actually doing anything.

IDist claim 1) "You can't add information, only delete it"

So the point being, presumably, that you can (say) alter a gene, but the genome can't acquire new functionality without destroying the old - presumably the idea is you can change a base pair or delete base pairs, but you can't add base pairs.

This is false. It's demonstrably false (just right off the top of my head I know counterexamples, and I'm no biologist). But I'm not going to give a link for this - other people (like, say ERV) are better placed than me to do that (and people have done so). You can add DNA that does something without necessarily harming the organism. But I'm not going to talk about reality - I'm just going to apply a little logic to the IDists own arguments.

So anyway, one of the things that's easy to point out is that gene duplication happens. So you can have two copies of a gene where there was one. This has happened many times and it's a bit hard to dispute. So there's a shifting of the goalposts:

IDist claim 2) "Okay, gene duplication exists, but having two copies of a gene doesn't add information - you have two copies of the same thing"

Well, actually, that's false as well. In some circumstances, that actually is new information. For example, it's now possible to have 0, 1 or 2 copies of the gene expressing at a time, instead of 0 or 1. The genome can do things it couldnt before, without losing the ability to do what it could.

But let's ignore that. Let's jump right into the denialist tent and agree for a moment that you will consider if duplication were the only way the genome could get longer - any other changes will change an existing function or remove it, and either way you don't add information.

So under dumb IDist logic I'm allowed these transformations, with a tiny piece of pretend genome from a simple organism:

1) [Gene A ]....[ Gene B ] => [Gene A']....[ Gene B ]
(a base pair, or maybe a few base pairs get lost or changed)

2) [Gene A ]....[ Gene B ] => [Gene A ]..
(a whole gene gets lost)

3) [Gene A ]....[ Gene B ] => [Gene A ].[Gene A ]....[ Gene B ]

and the claim seems to be none of those three can add information. The additional claim is that (1) and (2) are almost always deleterious. Well, that may be usually true. But sometimes a somewhat different version of a gene will still work okay at what it used to do and can nevertheless do a bit of something else. An IDist will argue that that doesn't get you anywhere.

(Well, some IDists might agree that you can have some of the other change that are observed, like inversion, but then they'll claim that they're always going to be bad and don't add information. Also wrong, but lets leave it aside for now. We don't need it.)

Now watch. Imagine for simplicity we're just looking at something with asexual reproduction, to make things nice and simple. Remember we're totally ignoring a whole pile of nifty stuff that actually happens. Doesn't matter. The IDist's fake genetics will do fine.

Anyway, here's the argument with our pretend genome:

Original genome:
[Gene A]....[ Gene B ]

Apply IDist transformation 3:
[Gene A ].[Gene A ]....[ Gene B ]

(imagine copy 2 of gene A is always switched off, or only switched on
briefly at some point in development and doesn't do a whole lot. Whether it's advantageous or disadvantageous to have a second copy, imagine for a moment it's not doing enough to be selected for or against. Its pretty much just sitting there, generation after generation. "No real information has been added!" comes the cry.)

Now apply legal transformation 1:
[Gene A ].[Gene A']....[ Gene B ]

That's all. Note this A' is a different locus. A' is not an allele for A. It's a whole entire copy of A, which has then altered.

We now have *all* the information of the old genome, plus an entirely new gene. We have NEW information, and the genes or epigenetics that control its expression can now either express it more or less. New information. End of story.

Well, end of that story.

Now, lets say that most of the time, a change like this is middling bad. No problem, since if the organism isn't sick or dead, it's because the gene is off (or at least nearly always off). If it's Really bad, copies that are "off" more will be selected for, because the organism that happens in is around longer to reproduce. So we have a gene it doesn't use hanging around. Sooner or later it will mutate again, to gene A'', say. That might be bad, too. Some offspring might express it for longer and die, or maybe just reproduce less. Others will express it less and stick around.

But once in a while, a sequence like that will produce a gene that does something that helps a bit in some circumstance. It might be gene A' that does something just a little bit nifty. It might be A''. It might be A'''. One of the descendants expresses that gene a bit longer, and maybe it can metabolize a slightly different food source, or it can remove a particular toxin from its cell or any of a thousand other things.

That change hangs around. A whole lot of other such changes accumulate. Some of these "sort of" helpful changes interact - they can do things together that they didn't do apart. Now, if they could be made to work together better, that would be nifty, but the IDist will say, if you change that, you don't add information - in fact you could harm the sort-of-nifty stuff that you were getting. Here's the thing - if that's true, we can do exactly what we did above - duplication followed by a change, and lose nothing, while having the new interaction free to adapt to work better.

Evolution doesn't really work exactly like all of this. This is fake IDist genetics, remember. Evolution has much more to work with. But even fake IDist genetics can add NEW information.