Tuesday, January 10, 2012

How Science Works, Part 1: What We "Know"

Hello. Where have I been? Hiding, that's where!

Not really. I've just been busy, doing research, pulling together manuscripts, doing illustrations, and being homeless and poor. Now I am more or less stationary in Salt Lake City for a while, I feel for the first time in a year like I have something resembling a routine, so I want to start writing again.

One of the big motivators for me going back to blogging was a message I received from a fellow (we'll call him "Martin") involved in a long-term debate over evolution with his parents, who believe that the Bible is a historically accurate account of the history of the world. At one point, he and his mother engaged in a three-hour discussion with a creationist with a PhD who is a faculty member at a university (I don't want to say who), and I've been asked to provide an alternate perspective based on actual evidence and reason. I received quite a lengthy transcript of the original discussion, and have been crawling through it. The creationist in question has backgrounds in both biology and geology, and draws a lot of Biblical scripture into it, so it makes for pretty interesting reading. As I started writing up my responses to Martin, I realized that it was good stuff to blog on. Some of of this material is probably better being discussed over at "Flying Blind," the blog I created specifically for discussing the specific claims and reasoning of creationists. However, there is a lot of material on the more general nature of science and faith that are suitable to talk about here.

One subject I've been addressing in my responses deals with what science is actually trying to do, and what scientists mean when they talk about "proof." From the creationist transcript:
"anytime you hear a scientist say that something is true or proven, you know he is talking philosophy, which is the same as religion in that context. Only in logic and mathematics can you really say something is 'proof'. And even there that can be challenged.”

The argument that science in general or evolutionary science in particular is a type of religion is a common one, but since it wasn't elaborated on, I won't get into it here; AronRa has a perfectly good dissection of it anyway. I want instead to focus on the statement that science doesn't "prove" things. I've talked before about how science is fundamentally based on the recognition of human fallibility, and want to elaborate a bit about what this means for knowledge, and what we can actually "know."

Science certainly does not “prove” things beyond any doubt, and there is always the provision in science that ideas, even well-accepted ideas, can change. The most extreme version of this philosophy, advocated by Karl Popper, is that a single piece of falsifying evidence can destroy and entire theory, no matter how many tests that theory has previously survived. This is an oft-repeated bit of bullshit which deserves an entire post, so I won't get into what I call "the Myth of Single Bullet Falsification" here. Sufficient to say, the more general claim that any idea can be shown to be wrong is correct.

However, the same thing is true of real life. That doesn’t stop us from forming opinions, and being reasonably certain about them. I’m pretty sure my mother isn’t a robot. She looks and acts human, and everything I know about modern technology and artificial intelligence indicates that building a robot as human-like as my mother is impossible. That’s the evidence I have at my disposal, so that is what I base my opinion on. And I am pretty confident about it, so confident that I would stake my life on it if I really had too.

Of course, I STILL could be wrong. There might be some secret lab somewhere that can make super realistic robots that no one knows about. And if I saw a reputable news story about such a lab, or caught my mother changing her batteries, I would revise my opinion. However, I have not been presented with that evidence. Right now, it exists only in my imagination. The real world evidence I can point to is what I listed in the paragraph above. So for the time being, I’m sticking with that. This is what scientists usually mean when they use the word “proof”; not absolute certainty, just certain enough that they don’t have any real doubts about it (for now).

There are different levels of certainty of course. I’m pretty sure (though not as sure as I am about my mother not being a robot) that my car will run tomorrow, that I will not be diagnosed with cancer tomorrow, or that a comet will not hit the Earth tomorrow. My current plans revolve around these things being true…but I could be wrong. Indeed, I'm much more likely to be wrong about these things than I am about the existence of lifelike androids. That doesn’t stop me from making plans. It doesn’t stop MOST people from making plans, most of the time, and when it does we tend to throw around terms like "mental illness." Part of being a sane, reasonable, and functional human being is whether or not you can distinguish between probabilities, possibilities, and pure imagination. The same thing is very much true of science, where there are also many levels of certainty. The basic difference between speculation, hypotheses, and theories has to do with how much evidence they have supporting them (speculation has the least, theories the most), and how certain we can therefore be about them.

Anyway, the point is that being really sure about something doesn’t mean that you can’t change your mind, and accepting that you can change your mind doesn’t mean that you can’t be really certain. We all juggle this conundrum in our day-to-day lives, and seem to do just fine. I’m really sure Mom isn’t a robot. I’m also really sure I could change my mind if the right evidence was presented. This may seem like a contradiction, but it doesn’t keep me from having an opinion or making specific plans about whether to take to a doctor or a mechanic if she is feeling poorly. The same thing is true of science. We can’t really “prove”, but we can be certain enough. I’m about as certain that evolution is a real thing, and that the Earth is more than 6,000 years old, as I am that my Mom isn’t a robot.

Saturday, April 2, 2011

Paleo Errata Retires.

I began Paleo Errata during a time when I was in bad need of constructive distractions, and had a variety of science and religion-related things to talk and think about that I didn't really have another available forum for. I really enjoyed the creative process of blogging, and I have produced a few posts over the past two and a half years that may actually be worth reading. However, over time, my focus wavered quite a bit. There was no real core theme to Paleo Errata, and a result, I tended to ramble quite a bit. I had a lot of fun posting random shit which amused me, but that is really the domain of Facebook.

When I was invited to participate over at Labspaces.net, I initially had no idea what I was going to blog about. I named the blog House of Bones because it sounded cool. I eventually decided I wanted to do a post about transitional fossils in the archosaur family tree, but I quickly realized that I was going to have to give a lot of geology and biology background to get non-paleontological readers to the point where they could understand it. At that point, the blogs pretty much started writing themselves. The structure provided by House of Bones as a blog with a theme was invaluable for me finding a point in blogging again. As a result, I have made two decisions regarding my blogging.

The first is that I'm starting up a new one called "Flying Blind", which will deal with specifically with my self-education on antievolutionism, something I've wanted to get serious about for a while now. The other is that it is time for Paleo Errata to retire. I have two main focuses for my blogging now, and any other biographical posts on my traveling or whatnot can get thrown into Flying Blind. The only subjects that I might post on Paleo Errata from time to time are commentaries on particular paleontology papers and subjects which are a little too technical for House of Bones; in this case, the name "Paleo Errata" will actually reflect something on the content.

I have provided an organized list of my favorite posts and links over the past two and a half years below. Scattered amongst the bullshit are a handful of posts which have actual content and that I am actually a bit proud of, and a few things I wrote which made me laugh; I honestly couldn't give too much of a shit if anyone else finds the same things funny that I do, but if you did, I'm glad. It's been a lot of fun, but time to move on.
(p.s.: This is not an April Fool's Day joke)
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Advice for Aspiring Researchers in Vertebrate Paleontology
Part 1
Part 2
Part 3
Part 4
Part 5
Part 6
Part 7
Part 8

Science and Religion
What Science Is.
What Does "Supernatural" Mean?
Open Letter To Supporters of Teaching Intelligent Design
Why is God Better Than Evolution?
The Reality Fish
Darwin Worship
The Limits of Science
Agnostic Secular Humanist Morality
Thoughts on 9/11
The "WTC Mosque"
The Difference Between Persistent Rationality And Dogma
Talking To Creationists
Being An Atheist Is Easy
Answering Michael Ruse
Why It Matters.

Jeff Reads Genesis!
Part 1: Introduction
Part 2: Genesis Synopsis
Part 3: The Creation Story
Part 4: The Old Testament God
Part 5: Sex! (originally a two-parter, but I accidentally deleted part 2; that still pisses me off).

Actual Stuff About Paleontology
The Future of Upper Triassic Biostratigraphy and Biochronology
William Smith's Bitchin' Map
Red Canyon
Phytosaurs and Evolution
Late Triassic Dispersal And Endemism
The JVP Typothorax Paper
Don't Impose Personal Style When Reviewing A Paper
My Interview on Dave Hone's Blog
My Dinosaur Origins Lecture at 21st Floor
Stereopairs Are Cool
The Curse Of Big Picture Study Bias

Hee Hee
We Like Janet
Spencer Was Like An Angel
Our Official Disclaimer
Heh.

Miscellaneous
Today is the Day That Music Dies
The Food Was Good In the Faraway Land of Connecticut
How I Spent My Summer Vacation
Bristol Has Been Fun (The England Trip Part 1)
We Are Now In London (The England Trip Part 2)
More On London And Bristol (The England Trip Part 3)
Why I Am Basically An Optimist
Don McLeroy Is (A Little Bit) Right
The Science And Art Of Banagma
Too Many Stars
The True Story Of How Jurassic Park Made Everything O.K.
And oh yeah, remember this?

Other People's Shit That Amused, Astonished, or Touched Me
Tim Minchin's "Storm" and "White Wine In The Sun"
Holy shit, did you know that bats can screw and fellate at the same time? And Walruses can fellate themselves. Biology fascinates me.
Ian Murphy Visits the Creation Museum
Peer Review Circa 1945
The Evolution of Homer Simpson
Sumerians Look On In Confusion As Christian God Creates World (Onion)
Dinosaurs Sadly Extinct Before Invention of the Bazooka (Onion)
Dog Hates Me On The Power of Prayer
Dog Hates Me On Drugs and Alchohol
The Known Universe
The OK-Go Video With The Treadmills
The OK-Go Video With The Rube Goldberg Machine
The OK-Go Video With The Dogs
BRING ME THE LAST DODO BIRD!
Jon Stewart On The WTC Mosque
George Carlin On America
Dr. Tran!
The Furious Little Cinnamin Bun
DA NA NA NA DA NA NA NA NA NA!
Conan O'Brien Drives an Explosive-Packed Car Off A Cliff

Two Things So Awesome That They Need Their Own Section
A Universe Not Made For Us (Carl Sagan)
Science Save My Soul (Philhellenes)

Sunday, February 27, 2011

Letters!

Dear Ray Comfort,

God, if He/She/It exists, is probably pretty smart and might have opinions. However, God didn't tell me that he created life using magic instead of chemistry and evolution. You did, and you aren't God. You are a fallible, flesh and blood human being, and therefore potentially delusional. If I say that life evolved and probably originated through abiogenesis, I'm not questioning God. I'm just questioning you.

Dear James Ussher

God, if He/She/It exists, is probably pretty smart and might have opinions. However, God didn't tell me that the world was created on October 23rd, 4004 B.C. In fact, the Bible didn't either. You calculated that date using a lot of guesswork, and no one has checked your math. If I say that the world was probably not created in 4004 B.C., I'm not questioning God or the Bible. I'm just questioning you.

Dear Bible,

God, if He/She/It exists, is probably pretty smart and might have opinions. However, God didn't tell me that slavery (Exodus 21:2-21; Leviticus 25:44-46), having drunken sex with one's daughters (Genesis 19:31-35), and genocide (e.g. 1 Samuel 1:1-3), were morally right (or at least permissible under certain circumstances), that homosexuality and getting tattoos (Leviticus 18:22, 19:28)was wrong, or that the world was created in six days (Gensis 1). You did, and you are just a book, written and assembled by fallible flesh and blood human beings. And yes, I know that at several points you say this clearly yourself and never even claim to be written by God, but a lot of people say that you were. Perhaps the next edition could include a disclaimer.

Dear Jesus,

God, if He/She/It exists, is probably pretty smart and might have opinions. However, God didn't tell me that you are the son of God and could do magic. The Bible did, and the Bible is a book written and assembled by fallible, flesh and blood human beings. If I say that you were probably not the son of God, I'm not questioning God, I'm just questioning a book. I already wrote the Bible a letter explaining this.

The Gospels don't really present you as being some kind of ingenious moral philosopher anyway. You seem to have spent half your time getting pissed off at your followers for not understanding your parables, and your moral theory seems to have mostly consisted of "give your money to the poor and follow me around, or else". However, you do seem to enjoy eating; you let your followers eat of the Sabbath, and in fact would make so much fish and bread for them to eat that they had leftovers. I like eating too! The Bible also never says anything about you being abstinent, and you seem to have really liked that Mary Magdalene chick more than your other followers, so hey ;). I picture you as an impoverished, overweight, egotistical, and slightly ill-tempered Jewish teacher who at least appreciates food and women, so we have some things in common (hey, I'm even circumcised!) But you were no deep moral philosopher, buddy.

Dear God,

(If You really exist), You can really be a fucking asshole, do you know that? Do you really have any kind of plan at all, or are you just fucking around? It gets a little stressful sometimes not knowing what your game is. I mean, a lot of people talk about how everything that happens is part of God's plan for us, but what if the plan involves getting raped, dying of a painful childhood disease, or having one's burning body fall from the top floor of the World Trade Center? I'm sorry, but that plan sucks, God. I would not feel comforted by being a domino just because I was part of a plan.

Don't get me wrong, I'm grateful for my life and all; even in the worst times, it's better to be alive than dead because I know you will throw me some more good times sooner or later (at least, until you kill me). But SHIT dude, you couldn't give me one measly pair of functional wings?

Dear Science,

I am pretty smart, and I have opinions. However, I am a fallible flesh and blood human being, and therefore potentially delusional. If you say that everything that I think is complete bullshit, you aren't questioning God. You're just questioning me.

LNJ

p.s. Dear Reverend Storms: Stay classy. I'm sure you and Ted Haggard have a lot to talk about.

Wednesday, February 23, 2011

Why It Matters.

I’ve stated in this blog that evolution is not a particular problem for religion. Although I think that a careful analysis of how science operates completely falsifies the argument that science cannot comment on the supernatural, religious scientists are certainly capable of practicing their particular disciplines as competently as non-believers.

I am also not bothered by religious people in general, even if I do not accept what they believe, unless their behavior compels them to treat other human beings badly...and the vast majority of them don’t. I am not offended by religious practice and ritual (unless, again, it involves treating people like shit). Far from it. I’ve gone into churches, mosques, and synagogues, and attended Christian and Jewish services and rituals, and thoroughly enjoyed the atmosphere and vibe, even if it changed nothing about my thoughts on what is real. Why then do I insist on publicly being a pain in the ass about God and the supernatural? Why can’t I be a nice, quiet atheist who keeps his opinions to himself?

Because I don’t like being lied about. And more importantly, I don’t like it being taken for granted by most of the American public that lying about me is normal.

Conservative politics rely heavily on accusing secularists of “persecuting” them. This is a grotesque misuse of the word. “Persecution” means that you are legally prevented from practicing your religion and/or risking violent reprisals by doing so. Any Jew living in medieval Europe, or Christian living in first century Rome, would laugh uproariously at the notion that secularists and atheists in this country are a practicing a form of “persecution” against religious people.

All religious denominations in this country have the right to practice their religion. The have the right to attend whatever church they choose. They have the right to publicly advertise their religious beliefs (even by coming up to my front door). They even have the right to raise their children in an intellectually stifling atmosphere, if they are so inclined (while they are limited in their abilities to enforce their children’s obedience to their religion with physical violence, psychological abuse is still perfectly legal). They are not being pursued down the street by mobs of atheists with torches and pitchforks, although they may imagine that they are. It is legally prohibited to pay them less, deny them employment, or give them fewer legal freedoms than non-believers.

What then do conservatives actually mean when they talk about “persecution”?

Quite simply, they use the word “persecution” when they are not allowed to force non-believers to pay lip service to their religion. The classic example is gay marriage. Conservatives, who have the legal right to marry consenting adults of the same sex (if they are so inclined), are going out of their way to keep other consenting adults from making the same decision for themselves. What possible excuse could they have? Because it undermines their heterosexual marriage. That’s right. Heterosexual marriages and nuclear families aren’t fucked up because spouses are insensitive, philandering, and/or physically abusive bastards, or insensitive, philandering, and/or emotionally abusive bitches. No, it’s the fault of some gay couple living thousands of miles away. They don’t actually want to get married because they love each other, they are just doing it to fuck up the life of straight people. They are persecuting conservatives by not letting them tell them who they can marry.

To a certain extent, this is also the same impulse behind opposition to teaching evolution in schools. We can’t teach evolution in biology classes just because it is the cornerstone of modern biology, oh no. It isn’t even enough for conservatives to be able to take their kids out of schools that teach real biology and hom skool them. No, they have to fuck up the education of everyone else’s kids by teaching something in biology classrooms which is not actually biology but that they personally wish was biology…and if the courts don’t let them, they are being persecuted.

It gets even more infuriating when conservatives lie directly (or at least, repeat bullshit that they might actually believe) about atheistic secularism and evolution. Nazi Germany was an atheistic and Darwinian regime? Evolution is accepted only by a scientific minority? Atheists have no basis for morality? These statements are not matters of opinion or belief; they are flat out bullshit. Hitler was explicitly anti-Darwin, and Nazi Germany was steeped in Christian propaganda. Evolution is apparently accepted by the overwhelming majority of scientists, and certainly by nearly every biologist and paleontologists I've ever spoken to on the subject. Every atheist I’ve ever discussed morality with most certainly has a clear opinion of what is right and wrong, and why. These are facts, not opinions or beliefs.

Insecurity is the only plausible explanation for this behavior on the part of conservative apologists and politicians. Why else would anyone feel persecuted for simply not being allowed to fuck with someone else’s life? Why would someone feel the need to lie about what other people think and do to justify their own beliefs? Is it simply that their own belief system is so fragile that denying the reality of what other people say and think is the only way to preserve it?

That can't possibly be the reason, of course. I'm just being silly, ha ha!

This attitude, this impulse to stifle facts and opinions and lie about what secular atheists think and do, is not restricted to the far right. Left-leaning apologists and non-believers pull the same shit, accusing Dawkins and Meyers of being as “dogmatic” and “militant” as religious extremists, simply because they won’t say something along the lines of “well, your position is devoid of reason and unsupported by evidence, but still on equal par with what I think.” P.Z. Meyers (one of the most “militant” atheists in America) supports of the right of Muslims to build a community center in downtown Manhattan, something that no extremist Christian would ever do. Richard Dawkins was criticized by a Catholic liberal for claiming that child rape is wrong, and should be punished. Having an opinion based on reason, evidence, and a concern for human welfare, and (horror of horrors) explaining that opinion publicly...this is what even left-leaning apologists and politically sensitive non-believers mean by “militancy.”

Fucking serious?

Philhellenes (who also posted one of the most exceptional defenses of science and atheism I've ever seen) also had an eye-opening post on reactions to an atheist billboard proclaiming: “Don’t believe in God? You aren’t alone.”

The billboard is simply saying that atheists exist. We exist. And people freaked the fuck out.

In that same upload, Philhellenes stated a very clear and reasonable goal of openly advertising and discussing secular atheism. It is not to eradicate religion and turn everyone in the world into an atheist. It is simply to get atheism to the point where people can acknowledge its existence, and where making patronizing and blatantly false statements about atheism and its supposed lack of morals, reason, or intelligence is not taken for granted. That is enough. Why should that be problem for religious apologists?...unless of course, allowing larger numbers of people to hear our views honestly explained would cause them to flock from stifling and close-minded religious denominations in large numbers. And that couldn't possibly happen, ha ha.

If you are an atheist or an agnostic who has any manner of self-respect, please pay attention. The next time you hear someone talking about how atheism and agnosticism is a “religion” or a “belief”, or that atheists simply explaining their opinions publicly is “persecution” or “dogmatism”, please don’t stand there bobbing your head like a fucking retard. If you actually agreed with that, you probably wouldn’t be an atheist or agnostic to begin with.

You are being dissed. You are being misrepresented. You are being lied about. And you are letting them get away with it. Stand up for yourself. Don’t let some insecure douchebag feel comfortable about their position by lying about you, and above all, don’t let them tell you that it is an offense for you to exist.

Wednesday, February 2, 2011

Sunday, January 23, 2011

The Curse Of "Big Picture Study" Bias

Vertebrate paleontology is one of the most broad-based, interdisciplinary branches of the natural sciences. Even though it is usually considered a branch of geology (and most university-based vertebrate paleontologists belong to Geology departments), it straddles the line between geology and biology. While it may be concerned with the lives of once living organisms, nearly all information about these organisms comes ultimately from the rock record. This occurs most notably in the form of the fossils themselves, but also as information about the environments these organisms inhabited (depositional systems, paleoclimate), the ways in which taxa and faunas changed over time (biostratigraphy/biochronology), and possible causes for faunal change (many of which, such as the identification of bolide impacts, rely heavily on geochemistry). The biological aspects of paleontology also loom large of course; systematics (including both alpha taxonomy and phylogenetics), functional morphology, and ontogenetic development studied through histology (especially what it may tell us about metabolism) perhaps being the most prominent. It’s a lot to process, but combined these various lines of evidence have the ability to tell us a great deal about the history of life on Earth.

A modest example of this is my own work with Bill here at Petrified Forest, where we have spent the last couple years collecting a great deal of geologic and morphological data to tell us about faunal change over time, and its relationship to environmental change, within this particular little corner of Arizona during a particular little segment of time. However, in mostly confining its gaze to one particular geographic unit, our work is not what might be considered a “big picture” study. “Big picture” studies tend to look at global issues, especially over long periods of time. They synthesize large quantities of data compiled by (mostly other) scientists, and they get a lot of attention. And money. What is sometimes under appreciated is that these big picture studies are only as solid as the multiple lines of evidence on which they are drawn.

The fact is that detailed small picture studies and big picture studies need each other. Small scale studies need big picture studies to give them ultimate relevance…but big picture studies need detailed small scale studies to give them validity. A small-scale study that isn’t incorporated into an overall picture of the grand scheme of things is an irrelevancy, and isolated novelty with no context. A big picture study can’t exist without small picture studies, and if the small picture studies are poorly done, the big picture study is bullshit. Garbage in, garbage out as they say.

In light of this co-dependence between small picture and big picture studies, I never fail to get pissed off when universities, grants, and journals consider big picture studies to be more important and worthy than small picture studies. Back in 2005, when the first preliminary paper on the Revueltosaurus material from PEFO which demonstrated that Revueltosaurus was not an ornithischian dinosaur was being prepared, we (well, Bill Randy, and Sterling; I had almost nothing to do with it) initially submitted it to JVP. However, the initial JVP paper was rejected for being of “too provincial” in its scope, or something along those lines.

One problem with this criticism is its inherent ridiculousness…ALL papers published in ANY journal are of provincial interest to some degree. I have never received an issue of JVP where I was particularly interested in all of the papers, or even most of them. While I recognize that bovid phylogeny or trace element geochemical analysis of vertebrate bones are as important and valid (to someone) as my own studies are to me, I couldn’t personally give a flying fuck about them. Even bigger picture studies, such as the impact of statistical tests or coding methods on phylogeny, are not so pressing to more geology-oriented workers like me.

But there is a deeper and more fundamental problem to this bias: it discourages detailed small-picture studies. This bias is ultimately destructive to science. If careful and detailed work to really nail down a limited problem is discouraged so that such studies are neglected, then what becomes of the larger, big picture syntheses based on these studies? For vertebrate paleontology to flourish as a rigorous science, detailed small-picture studies need to be supported and encouraged. They must be put an equal footing with broader-based big picture studies in terms of respect and funding. If we can reward scientists for playing with other people’s data, why can’t we reward the people who did the work to produce that data in the first place?