Thursday, June 25, 2009

My Afternoon Teaching Evolution on Townhall: Part II

Chris said: 'Science Avenger, if you can say "matter has always been", then I can say "God has always been" with equal certainty.'

Uh, no you can't, for the simple reason that you can't say with certainty that God has been just now, where I can do so for matter. You've got an epistemological burden I lack, and a big one.

"Where did the original pre-big bang matter come from? For that matter where did space-time come from? These questions are un-knowable."

Unknown perhaps, but unknowable? I'm not sure how that can be known, especially with questions so poorly defined (through no fault of yours). For instance, how do you even know any of these things came from anywhere? What does that even mean? It borders on gibberish.

"Evolution, on the other hand, requires unlikely things to happen routinely - and THAT violates the laws of statistics."

No, it does not. In the first place, there are no laws of statistics to violate. Second, there has never been a rigorous peer-reviewed mathematical proof of this claim, and indeed, the vast majority of those known (ie Hoyle's junkyard 747) make fundamental errors that would have made my intro-to-statistics prof cringe, like presuming all events are independent, or simply wallow in meaningless sciency-looking jargon (Dembski's CSI). None gained any traction with those experts, and for good reason.

And step back a moment. Mathematicians and physicists are smarter than biologists (just ask them). If there were a problem with evolution in their fields, no force on earth could shut them up about it. Yet no physics or math journal has ever come out against the theory of evolution. In short, all those arguments are bunk.

I rarely bother responding to anything Fabius Cunctator writes because he is obviously living in an alternate universe, but I thought this comment was worth examining:

FC: "The flaw of Evolution theory is that it cannot explain the origin of atoms or matter."

This is like saying the Pythagorean theorem is flawed because it cannot explain particle physics. It reveals a profound lack of understanding of the limitations of scientific theories, and how we much evaluate them within those limitations. Of course evolution can't explain the origin of atoms or matter. It was never intended to. Neither can the theories of relativity, Keynesian economics, or euclidean geometry. So what? For someone to condemn a theory for failing to explain everything is a daftness beyond redemption.

His other posts are loaded with similar, gargantuan mistakes. Read them only as a lesson for how out of touch with modern scientific thought a person can get.

Joel-de said: "DNA in humans is similar to DNA in animals because they serve a similar purpose. Once The Creator had designed the code for hair, would he re-do the code for each new creation?"

But "he" did redo it, many times, for many traits. Human eyes are not designed like octopus eyes, and in fact are inferior in some ways. Wings are designed differently in bats and birds. Worse yet, there are mistakes that were used in more than one place. Most mammals have a gene that synthesizes vitamin C, but in chimps and humans it is broken. Not different, not used for something else, busted, no bueno. Countless other examples abound. Further, as Ken Miller demonstrates here:

Humans have a gene that is the fusion of two ape genes. There is no way to describe this as anything but a natural screw up, not the work of a divine designer.

Your logic is sound Joel. IF we found every design of all parts in nature across all species to be the same, your argument would be plausible. But the facts betray you. There is nothing remotely resembling the common design you assert.

JD: "The objection is this: That the THEORY of evolution is taught as SCIENTIFIC FACT, and that there can be NO debate on the matter. If a child asks questions about the mathematical probability of life occurring because lightning zapped some chemicals in a puddle, he is told to shut up. If he tries to question the gaps in the 'evolutionary chain' he is told to shut up."

This sounds like urban myth to me. Show me a documented case of a child asking these questions being told to "shut up". If they were, the teacher ought to be fired, because the questions are legitimate and fairly easy to answer:

1) Evolution is a scientific theory, which means a great deal more than "theory" as you and your friends use it. It means it has been subjected to many falsifiable tests without failure and explains many facts. Theories stay theories. They never graduate to be called "facts".

2) No one is able to make very good estimates of the probability of life arising on ancient earth because we lack the necessary knowledge of the exact conditions on the planet at the time to do so. Anyone who claims they can is making claims beyond the facts and evidence, and are probably making many mistakes.

3) The notion that leading scientists think life began by lightning striking chemicals in a puddle is urban myth at best and an outright lie at worst. We really don't know how it all began, and you should be skeptical of anyone who pretends they do.

4) From what we know of the history of life, with it's slow genetic motion, motion of landmasses and water, changes in the environment, and the extraordinarily rare circumstances necessary for fossilization to occur, we can expect large gaps in what we are able to find. This is not a game where some giant adult placed all the puzzle pieces for us to find. Science is not that easy.

JD said: "If evolution was taught as a THEORY, and the teacher and textbook would be honest, and admit that it cannot be proven, and does not have answers for all questions, few if any parents would have an issue with it. We object to the INDOCTRINATION of our children into the false religion of Darwinism, which requires AT LEAST as much faith to believe in as Christianity."

Then none of you have any business ranting as you seem to be doing. Every textbook on the subject I've ever seen or heard about from a reliable source says all those things you demand. Evolution is a scientific theory. It cannot be proven because science does not deal in proofs. That's for the mathematicians and philosophers to worry about. Science deals in evidence, and evolution is the best explanation we've found for the evidence of biology. It does not have all the answers for all the questions and, in fact, as some of us are more than willing to show, it is downright silly to expect it to. It explains what it explains, nothing more. There is no such thing as a religion of Darwinism (if there is I'm a little pissed, cause I never get invited to the meetings), nor does evolutionary theory require any faith, certainly not on par with believing that the supreme being of the universe had himself killed to absolve us of a punishment he himself created (don't get me started).

It sounds to me like you've all been whipped into a frenzy over a myth, and no, I don't mean the gods. No textbook that I've ever seen says anything about evolution being "proven", nor that it is anything but scientific theory

JD said: "Life did not come from non life. Life has ALWAYS existed, and will always exist. The universes have always existed, and always will."

That is an article of faith, not science. The best scientific evidence suggests the universe is ~14 billion years old, the earth ~4.5 BYO and life ~2-3 BYO, and that is what should be taught in science class.

JD said: "God did not create this world 'out of nothing'. He organized the raw, chaotic matter that was in this part of the galaxy into our solar system. He then transplanted plants, animals, and Adam and Eve from another world onto this one."

Interesting religious faiths, and ones you have every right to believe. But you do not have the right to expect a public school teaching children of various (and no) faiths to teach such a thing, nor to alter their science curriculum because it runs afoul of it.

JD said: "Humans should not be classified as 'primates'. The various types of apes are one 'kind'. Humans are unique. We are not part of any other 'kind'."

This is rhetoric with no science to back it, and as such does not belong in a public school science class. Humans are 99% chimp, we are not unique.

Chris said: "Sorry - I meant the laws of probability (LOP)."

I knew what you meant, I'm not keen on semantic games, but the answer is the same - there is no such thing as "the law of probability". It's just a fiction made up by someone looking for a sciency-sounding word to attack science with. Nonetheless, I'll try to address your comments that contain it.

Chris said: "The junkyard 747 is a good analogy for abiogenesis, but not evolution afterwards."

You have no way of knowing that. No one has nearly enough information to do so. And given that we already know about self-replicating nonorganics like crystals, I'd say it's a worse than 50/50 bet.

Chris said: "What DOES violate the LOP is when multiple unlikely things have to happen at the same time to cause a major re-design of an already fit system...

The odds of that many mutations, together with all the expression controls, all happening at the same time in the same animal are astronomically small."

But you have no way of knowing that such is required! Evolution doesn't occur by several major things happening all at once. It happens by gradual multiple changes over long periods of time. Your argument is just a more sophisticated version of "why doesn't a dog give birth to a cat?". No one said it should.

All the details you posed, and all the examples you, or anyone else gives, makes assumptions you can't possibly know, about function, time, cooption, everything. Evolution is not a unidirectional, step by step, constant function process. Parts are routinely coopted for different functions, some parts serve multiple purposes, amd a whole host of other possibilities I couldn't begin to list in such a small space. Pretending you can somehow retrace the exact path it took and make a probability calculation is sheer fantasy.

All you've done (at best) is pose a problem for evolutionary scientists to solve. At worst, you've composed a nonproblem that's already been solved in a way you never began to imagine (have you even looked at the scientific literature on the subject? My bet is you haven't).

I know it is frustrating to go to all that trouble typing all that out only to have me brush it aside, but I do not do so whimsically. I do so because this is the crucial problem most people doubting evolution have. Such problems, regardless of how they are presented, merely fall into the category of "what we don't know yet". And as I've mentioned previously, there are such questions in all sciences, not just evolution. That doesn't give anyone intellectual warrant to dismiss the theory, any more than it would give someone warrant to dismiss mathematics because for so long no one could solve Fermat's proof.

Now if you could show something in nature that is impossible to evolve, then your argument would have some mettle. Creationists have been trying this for years, the bombardier beetle, the bacterial flagellum, the clotting system, the human eye (which is a real laugh given how poorly designed our eyes truly are). All have failed to withstand the scrutiny of science, and the proof is out there for all to see.

Chris: "And that's just one example. I could give you thousands."

And they'd be just as impotent in saying anything about the reality of evolution.

AndifNot said: "No, [a documented case of a child asking these questions being told to shut up] IS true...a district judge [in Cobb County Georgia] prohibited ... a sticker on science textbooks which stated: "Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully, and critically considered."

My goodness, you think that's the same as telling a kid who asks a question to shut up? That's a reach Yao Ming would have a hard time making.

AIN said: "Why the fight by evolutionists to keep the sticker off the book?"

As Ken Miller (Biology instructor at Brown and devout Catholic) explains here:

Those stickers singled out evolution for special treatment for religious reasons. No such sticker was required for any other science. This also gave students the false impression that other sciences didn't require critical examination.

Miller's suggestion was for a sticker to be put on all books that said:

"This book contains information about science. Science is built around theories which are strongly supported by evidence. EVERYTHING in science should be approached with an open mind, studied carefully, and critically considered."

The creationists of course, didn't like that one bit.

AIN said: "Opposition or criticism to evolution is still silenced elsewhere in selected localities around the country."

I'm still waiting for evidence one that your claim is anything more than an urban myth

"BTW- Interesting handle. Why does science need an AVENGER?"

Because it is under attack by people who either don't understand it, or who desire its demise because it offends their religious sensibilities, and I figured scientists had enough to do without having to fight those battles we layman are capable of fighting. This thread is a perfect example.

20 comments:

parakeet said...

"Humans are 99% chimp, we are not unique."

That figure might be old.

http://www.sciencemag.org/cgi/content/
summary/316/5833/1836
"Relative Differences: The Myth of 1%"

"But truth be told, Wilson and King also noted that the 1% difference wasn’t the whole story. They predicted that there must be profound differences outside genes—they focused on gene regulation—to account for the anatomical and behavioral disparities between our knuckle-dragging cousins and us. Several recent studies have proven them perspicacious again, raising the question of whether the 1% truism should be retired.
“For many, many years, the 1% difference served us well because it was underappreciated how similar we were,” says Pascal Gagneux, a zoologist at UC San Diego. “Now it’s totally clear that it’s more a hindrance for understanding than a help.” "

contrarian said...

"No textbook that I've ever seen says anything about evolution being "proven", nor that it is anything but scientific theory"

Is that the same as saying "proven beyond a shadow of a doubt"? I bet the science textbooks have no qualms about saying that.

chris said...

On behalf of the serious science teachers, I thank you. What you say about scientists needing an advocate holds as well for those of us who teach it. I've been following this blog for a while now, and while I don't agree with everything you support (I have doubts about the gun thing, e.g.), your position on science advocacy is spot-on. This thread should be pasted into the endpapers of every biology book in the country.

ScienceAvenger said...

Contrarian conjectures thusly:

"Is that the same as saying 'proven beyond a shadow of a doubt'? I bet the science textbooks have no qualms about saying that."

What you would be willing to bet has no bearing on the matter. That's what those of us in the reality-based community call "making shit up". Speculations are not evidence.

Besides, in layman's terms, evolution HAS been proven beyond a shadow of a doubt, which is why the resistence to it has such a potent evangelical flavor. So even if a book said that, I'd consider it poor pedagogy, but othewise unworthy of note. I've seen far worse errors in schoolbooks, such as an algebra book dividing by zero in an example. In other words, you're grasping at straws.

ScienceAvenger said...

Chris,

Wow, thanks. I try to give the side of sound science good ammunition, and it seems sometimes the professional scientists just don't have the time or inclination to translate their concepts into conversational English, or worse, learn what the bogus arguments are so they can be effectively combatted. I do what I can to help, and it's nice to be appreciated.

ScienceAvenger said...

Parakeet, or Alex, or whoever you are:

Apparently this is old news:

Sequence divergence between humans and apes
The draft sequence of the common chimpanzee genome published in the summer 2005 showed the regions that are similar enough to be aligned with one another account for 2400 million of the human genome’s 3164.7 million bases[3] – that is, 75.8% of the genome. This 75.8% of the human genome is 1.23% different from the chimpanzee genome in single nucleotide polymorphisms[3] (changes of single DNA “letters” in the genome). Another type of difference, called indels (insertions/deletions) account for another ~3 % difference between the alignable sequences.[3] In addition, variation in copy number of large segments (> 20 kb) of similar DNA sequence provides a further 2.7% difference between the two species.[4] Hence the total similarity of the genomes could be as low as about 70%.

The figures above do not take into account differences in the organization of the alignable sequences within the genomes of humans and chimps. Short stretches of alignable sequence may be in very different orders and locations within the two genomes. At present we cannot fully assess the difference in structure of the two genomes, because the human genome was used as a scaffold when the chimpanzee draft genome was assembled. When genomes are sequenced, relatively short sequences of DNA are produced, and these sequences have to be fitted together like a jigsaw puzzle. This requires multiple overlapping reads to accurately assemble the overall sequence. The human genome sequence is relatively accurate, with 8 to 9-fold coverage, but the chimpanzee draft genome only has 3.6-fold coverage.[3] The human genome was sequenced using a hierarchical shotgun method which can deal with duplications and difficult-to-assemble sequences better than the whole genome shotgun method that was used for the chimpanzee draft genome. The human genome was used as a template for the assembly of the draft chimpanzee genome, on the assumption that the two genomes would be similar.

Almost half of that 1.23% SNP change belongs to the human at 0.53%, whose genetic variance is lower than a chimp, and just over half to the chimp at 0.7%. If we also take into account that random "genetic drift" takes up the bulk of the 0.54% difference, then that percentage difference where SNPs have a potential positive impact on human abilities, is between 0.01% and 0.02%. The bonobo is a sibling species of common chimpanzee and is genetically about as different from humans as are common chimps."

There's a complete table there of the differences, depending on the measure.

You can also go see (join) a conversation of the subject here.

alex said...

Thanks for the detailed response. One comment though: Anyone who has eyes, whether he lived three thousand years ago, 200 years ago, or today, can look at a chimp and a human side by side and conclude that they are related. So what additional ammunition is there knowing that their DNA is so similar? It's icing, but not much else.

ScienceAvenger said...

Oh come on Alex, you've got to be kidding? Anyone who has eyes can look at a shark and a whale and conclude they are closely related, and he'd be dead wrong. You've illustrated the problem with casual observation as science. Its one of the fundamental problems with evolution-deniers, and with denialism in general - a lack of understanding of what constitutes evidence and an appreciation of what it means.

Scientifically, when you or I, based on casual observation, conclude that chimpanzees and humans are related, or that sharks and whales are, we've just gotten started We've done no science yet. All we've done is form a hypothesis. Without some falsifiable testing, it's nothing better than a guess. Indeed, that's as far as ID gets, and why as science goes its useless crap.

Science demands we one go further. From our hypothesis of close relationship, we'd need to make a falsifiable prediction, something that could give us a variety of answers, many of which would clearly indicate a flaw in our theory. (!) Let's check the DNA. If they are closely related (we'd reason), their DNA should be pretty similar.

So them we open them up, and lo and behold, the shark and the whale don't have DNA nearly as similar as we'd expect. In that case our hypothesis is disproven. But with the chimp and the human, the match is nearly total (95-99% depending on how you want to count it). This would be a confirmation of our theory. It doesn't prove it, but it gives it a huge leg up on any theory that hasn't passed such a test.

Empirical, falsifiable, repeatable testing of a theory, and adjustments to account for those results when they differ from prediction, is what makes science different from other epistemologies. The the rate at which mankind's knowledge grew once science became the standard is why it is held in so high a regard today, and why even those who criticize it with their words crave its stamp of approval with their actions. It doesn't get any better.

As long as you see THE thing that makes science the power it is as mere icing, you'll never understand science or the perspective of those whom practice and appreciate it.

ScienceAvenger said...

Finally, it pays to remember that we knew nothing of DNA in Darwin's time. Some of the most enjoyable parts of "The Origin of the Species" were watching struggle to understand how traits were passed from one generation to the next. His theory demanded a mechnism, but he had none.

When DNA was discovered Darwin was vindicated in a huge way. There was simply no reason that such a thing had to exist outside his theory. Gods could easily have created without it. When it was ultimately mapped out so we could compare one creature to the next, the scientific battle over evolution was over for anyone with access to the information and the education to understand it. There was (and is) simply no way to explain, with any sensibility, why it looks like it does one creature to the next except through evolution via common descent.

Creationists take advantage of the ignorant and confuse them as to just how certainly Darwin's theory, with many modifications through subsequent discovery, won its scientific war. But win it it did, and those who recognize it will continue to grow as they have over these last 150 years until this debate is as quaint a memory as those about the existence of germs.

alex said...

Ugh, if I had thought of the shark and the whale, I would've made a different argument. Y' got me there.

Troublesome Frog said...

Alex,

It stands to reason that things that look similar will have similar DNA in many ways, since obviously their morphology is governed by their DNA. The really interesting part is that regions of DNA that don't code for anything are also similar or identical. Without common ancestry, there's no good explanation for the types of similarities we see.

Think of it this way: Exams with the same set of correct answers are not very good evidence of collusion between students. Exams with identical sets of wrong answers strongly suggest a common source. DNA is full of these sorts of artifacts, which is a fascinating result.

ScienceAvenger said...

That is an excellent point TF. What evolution gets wrong in some ways is more powerful evidence for it than what it gets right.

alex said...

Well, the pool of so-called Junk DNA is getting smaller and smaller.

Troublesome Frog said...

"Well, the pool of so-called Junk DNA is getting smaller and smaller."

For these purposes, I don't think I agree with that statement. Most of the cases in which people say, "See, non-coding DNA is used!" are cases in which, given a mutation, that non-coding DNA becomes active again in some useful way. That still doesn't invalidate that non-coding DNA as a useful genetic time marker.

More importantly, there are still genes that are just plain broken. It's clear what they were when they were working, and that they've been damaged through mutation. It's highly improbable for two species to have the same type of breakage without them getting that DNA from a common source *after* the breakage occurred.

It's still very compelling, unless the position is that the creator said, "I'd like to give both humans and chimps a broken vitamin C production gene because that's more efficient than breaking both of their vitamin C synthesis capabilities separately."

alex said...

Lets be careful calling a broken gene simply broken. In 2003, a group of Japanese geneticists led by Shinji Hirotsune of the Saitama Medical School reported their discovery of a functional pseudogene. It's in dispute, but still...
http://en.wikipedia.org/wiki/
Pseudogene#Functional_pseudogenes.3F

ScienceAvenger said...

Let's be even more careful that we don't play the "scientists were wrong once, so therefore they are wrong now" canard, especially when the scientists and subjects are different. The historical record of scientists vs outside-their-field deniers favors the scientists heavily.

alex said...

"Chris said: "What DOES violate the LOP is when multiple unlikely things have to happen at the same time to cause a major re-design of an already fit system...

The odds of that many mutations, together with all the expression controls, all happening at the same time in the same animal are astronomically small."

But you have no way of knowing that such is required! Evolution doesn't occur by several major things happening all at once. It happens by gradual multiple changes over long periods of time. Your argument is just a more sophisticated version of "why doesn't a dog give birth to a cat?". No one said it should."

The answer is in between your two positions. If we take the number of years needed for human beings to come into existence from a certain lifeform, and divide that by the number of "parts" that needed to involve (include each type of enzyme, hormone, cell types, ligaments, blood vessels, various neurotransmitters, etc), and take into account the appropriate mutation rate, I think we'll find that it is very likely that over our history, there have been many times when "several" changes had to have occurred simultaneously. I'm not sure what that number is, but it's not insignificant.

ScienceAvenger said...

Once again Alex, you reveal your lack of understanding of what evidence is, and how mathematical arguments work. Speculation is not evidence. "I think" means no more and no less than "I guess" in that context, which makes it worth exactly squat.

As for your mathematical arguments, they require, you know, actual math. Otherwise, they're just hot air. If you can't do the math, your mathematical conclusions are baseless.

But don't feel bad. There's a reason you could peruse the mathematical journals closely and find no mathematical arguments against evolution, just like all the other fields creationists try to co opt for their purposes. The evidence just isn't there.

alex said...

Can you find any mathematical arguments FOR evolution in these journals?

Troublesome Frog said...

"If we take the number of years needed for human beings to come into existence from a certain lifeform, and divide that by the number of "parts" that needed to involve (include each type of enzyme, hormone, cell types, ligaments, blood vessels, various neurotransmitters, etc), and take into account the appropriate mutation rate, I think we'll find that it is very likely that over our history, there have been many times when "several" changes had to have occurred simultaneously."

As convincing as unsupported speculation is, you'll have to be more specific. Let's start with what that "certain lifeform" is and look at the estimated timescales involved. The next step would probably be to define terms like, "several," "changes," and "simultaneously."

As for arguments in the mathematical journals in favor evolution, I would be surprised if there were any. There aren't a lot of them in favor of the germ theory of disease or any number of other well supported theories. The reason the absence of articles against evolution is notable is that the creationist movement spends an inordinate amount of time producing scary looking math to support their groundbreaking position. Why has none of it gotten through peer review?