Tuesday, May 26, 2009


See, because evolution provides solutions, but creationists think the very idea is evil...see, ha ha, I'm so clever.

That is, solutions to adaptive problems, not trying to imply right off that evolution must be true...and evil as opposed to true, not true-yet-evil. Yeah. So clever.

That plus the Zerg. A case of evilsolution if ever there was one. But anyway.

This debate is wrong. Just...wrong.

I'm going to start, however, with something that isn't. From La Wik,
"In biology, evolution is the process of change in the inherited traits of a population of organisms from one generation to the next."
As has been noted before, the idea of evolution predates Darwin. Darwin, as noted below, just came up with the mechanism - natural selection. Indeed, the idea of evolution is kind of obvious. See animal husbandry.

"Evolutionary biology documents the fact that evolution occurs"
Actually, until very recently, only paleo-documentation was possible, which as you know is not very convincing to creationists...which means you should stop trying to use it. Gaah.

Similarly, if:

"Studies of the fossil record and the diversity of living organisms had convinced most scientists by the mid-nineteenth century that species changed over time. However, the mechanism driving these changes remained unclear until the 1859 publication of Charles Darwin's On the Origin of Species, detailing the theory of evolution by natural selection."

Then why do I keep hearing stories about evolution getting the Galileo treatment? Pick one or the other. You don't get to claim Galilean ethics when all your peers agree with you.

The stories are not matching up. Did Darwin come up with evolution by looking at Galapagos finches, or just natural selection? (Turns out, just natural selection; New Scientist) Was it broadly accepted, or not? It seems to depend on what the speaker is trying to prove. A classic symptom of politicized science.

"This powerful explanatory and predictive theory"
Um, predictive, eh? So these would be the kinds of predictions that I see brought up in evolution debates all the time. You know, the prediction that creationists are feebleminded idiots clinging to a security blanket, or the one about how creationists are evil bastards who are going to be responsible for an Inquisition?

Actually, I kid. In my mind, I make a distinction between predictions about the future and other predictions, which is not how the word is used by scientists. And indeed, evolutionary theory has made many predictions about what we'll find in the fossil record, and predictions about the similarities we'll find between mammal genomes. However, evolution does not, and basically cannot, make anything I'd actually call a prediction.

In fact, the predictions are about the patterns that shared genes conform to. Which as I just linked, turns out to be mostly wrong. Evolution is, right now, an explanatory theory. (Of course, the theory supported by that link won't be any more palatable to creationists.)

"Organisms will adapt to their environment." Okay. Using what strategy? Changing which genes? How likely? Which adaptive pressures are lethal? Which are not? You can bring up experiments on bacteria, but that's just animal husbandry, known since antiquity. This is the basis of the claim I will make that there is no technical context in which you need to know evolutionary theory. It explains things that have already happened. And that is all.
"it has become the central organizing principle of modern biology, providing a unifying explanation for the diversity of life on Earth."
Thankfully, they said something that's actually true. It's quite the relief. Hopefully they don't screw up too much further down.
"Simple organisms have therefore been the dominant form of life on Earth throughout its history and continue to be the main form of life up to the present day, with complex life only appearing more diverse because it is more noticeable."
An excellent example of poor thinking. What does 'dominant' mean? Hah, trick question - they're equivocating. They're trying to imply that humans are not dominant simply because they are less numerous. However, to most people, dominance is about power, and dominance due to overwhelming numbers is called 'dominating counts' not just 'dominating.' (New Scientist says 'dominating counts.') This is an intentional (if possibly not conscious) obfuscation of the facts. When questioned, of course they will say they always meant that single-celled life 'dominates biomass counts.' However, they know their target audience and they know or should know that 'dominant' is about power to them. They are intentionally implying that humans are puny.

Further, they are intentionally implying that the 'fact' that humans are puny is inherent in the data. It is not. Puniness or lack thereof is entirely an aesthetic call. Putting on the lens that scientists like to 'prove' humans are puny will quickly show how common it is.

The idea we are some people on a generally unremarkable planet orbiting a unremarkable sun during an unremarkable time in history...is completely aesthetic. According to whose perspective is our sun 'unremarkable?' Ours. The sun really doesn't give a damn.

So. Scientists enjoy 'tearing down the illusions' by sustaining other illusions. They really need to stop that. As an example...

There is one unremarkable planet of an unremarkable sun in the middle of nowhere...except for the fact that this planet is entirely unique, as is by extension the sun. This apparently random planet is the only planet with consciousness ever observed in the entire universe. This apparently random weird ape thing - the one with only very fine body hair - dominates the entire planet, and by extension, is the most powerful consciousness in the universe. In a fight between a human's goals and basically any other goal - the humans win.

That's a pretty incredible height. Despite living for a tiny amount of geological time, with flaw-riddled bodies and pathetic muscles and making up a tiny fraction of biomass, human beings are the only species who hold the destiny of the planet in their hands, are the only species that may have an entire geological age named after them. That's some pretty incredible power multipliers over some scummy unicelled stuff. It's the vast majority and yet which of us can irradiate the entire planet? Which of us could, in theory, affect the climate at will? (Not talking about AGW. Am talking about solar mirrors.)

So. The data supports either opinion as that's all it is - an aesthetic opinion.
"They are produced by a combination of the continuous production of small, random changes in traits, followed by natural selection of the variants best-suited for their environment."
Actually, no. We don't know that at all. The small, random changes, when calculated out, do not accurately reproduce observed (and obviously necessary) rates of change. In fact, actual evolution can proceed extremely quickly compared to this standard. (Case in point; human brain size increase.) Further, phenotypes follow the punctuated equilibrium model, although genes tend to change continuously - the phenotypes only change significantly at tipping points, with long buffered stretches in between.

Similarly, there is at least one feedback that increases mutation during times of adaptive stress and decreases it during times of adaptive success. Considered a priori, this should be expected. If there is any way for genes to affect their own evolution, they will create the mechanisms to do so to their benefit. Some finches recently immigrated (ctrl-f 'real time') to a Galapagos island, causing significant beak size change in another species in one generation, coinciding with a gene-stressing drought.
"A substantial part of the variation in phenotypes in a population is caused by the differences between their genotypes."
Note that for the purposes of pure philosophy, this is not strictly true. All phenotypes are caused by the genetic code. Which particular phenotype is selected is determined by the interaction between genes and environment. The environment, alone, causes nothing, except in the sense that given an Earth, life arises spontaneously, or so it is thought.

So, rather, all possible phenotypes are almost entirely dictated by differences in the genes. To predict one in particular requires the calculation to involve the environment as well.

Consider the opposite. "Phenotypes would vary continuously over everything, except sometimes they're restricted by genes." Phenotypes are not somehow their own phenomenon, but rather and effect of genetics.
"For example, the human eye uses four genes to make structures that sense light: three for color vision and one for night vision; all four arose from a single ancestral gene."
Also strictly untrue. While rods are used for night vision now, the ancestral gene they're talking about was the rods, which were used for all vision. Similarly, what do you suppose colourblind people see with? It's not like red or green things are invisible to them.
"Another effect of these mobile DNA sequences is that when they move within a genome, they can mutate or delete existing genes and thereby produce genetic diversity."
I like this. "They can delete existing genes, and thereby produce genetic diversity." I'm not sure why exactly they give a crap about the exact mechanisms of mutation; for this debate, all you need to know is thermo #2. However, you certainly don't get new features by deleting genes, which means it always reduces genetic diversity, although if you're lucky it can make a new species. (More likely it deletes something important before the two variants cannot breed.)
"In asexual organisms, genes are inherited together, or linked, as they cannot mix with genes in other organisms during reproduction."
They do not, not can not. Sexual reproduction is the only known way to scramble the genome, not the only way possible. Frankly, unless this is wildly unrepresentative of the quality of evolutionist thought...well, it's not surprising they're failing to convince their opponents.

"Natural selection is the process by which genetic mutations that enhance reproduction become, and remain, more common in successive generations of a population. It has often been called a "self-evident" mechanism because it necessarily follows from three simple facts:
  • Heritable variation exists within populations of organisms.
  • Organisms produce more offspring than can survive.
  • These offspring vary in their ability to survive and reproduce."

They missed thermo #2.
  • Heredity. Something has to tell the next generation how to grow.
  • Variation. This instruction can't be perfectly followed or copied. Thermo #2.
  • Selection. Some imperfections will suck, but others will be awesome. This is feedback.
These reasons may be contained in theirs, but it's just too much work to look - especially if you're bent on proving them wrong. I guess if I'm saying that, I shouldn't use vague terms.
  • Selection. Some imperfections will hamper the ability of the inherited instructions to execute, and some will improve this ability. Since we're talking about something that has generations, one of the instructions is to create the next generation - that is, the concept of 'reproduction' is contained within the first so-called 'simple' idea.
I feel better now.

Evolutionists often confuse Creationists' objections to evolution with the rejection of the idea of natural selection. This is only exacerbated by the fact that stupid people can be Creationists too, and these people will sometimes reject the idea, because they don't have the cognitive resources to parse all the sub-modules of evolution. If they've decided to reject evolution overall, this means, as it does in children, that they reject everything within evolution. As long as they aren't committing any crimes, it's pointless to try to improve their granularity. Also, it's a bit cruel to debate people significantly stupider than you are, especially on TV. Honourable people don't do that kind of thing. (You're welcome to decide to be dishonourable, if that's what you really want. However, you can't make me decide that I really want to respond positively to the behaviour.)


So, if you want to know about evolution, for the sake of whatever you hold dear...don't go anywhere near an evolution-creation debate. Do not pass Dawkins, do not collect 200 soundbites.

Overall, these people are deceptive, self-righteously vindictive, and not even that good at debate. They think evolution is obvious and that most people agree with them. If it is so obvious, then I guess Darwin wasn't all that great, eh? Second, the fact is, rightly or wrongly, most people do not agree. Evolution is a highly contentious subject for people outside the field of biology, something you'd never learn of you spend all your time in the echo-chamber of Dawkins and people who don't realize he's a jerk; they use these prejudices to justify all kind of slander and villany directed against people who disagree with them.

Good lord, as if disagreement was grounds for anything but greater efforts at civility.

So, what's a good reason for believing in evolution?

First, let's talk about the system under which we take evolution as true. Then I will talk about how it is true.

Evolution is an empirical theory which is used to explain observations. At present, we cannot apply biological evolution directly, unless you count animal husbandry, which predates Darwin...just a tad. (Again, natural selection as artificial selection, the idea that if you have a random set of components you should save and develop the ones that work better, is a pretty obvious idea and while it's often linked to Darwin, it has been used since before history. Incidentally, if you know a good historian of philosophy, please direct me. I'm working very indirectly here, lacking the expertise I might wish.)

That is, evolution is not True, it simply Works. (Good example; see references to Newton in the New Scientist article.) If there is a second theory that can explain everything that evolution can, then there is no particular reason you have to choose evolution over it. Second, as there is exactly one technology which depends on evolution,* knowledge of it is almost completely unnecessary. If you want, you can completely ignore this idea in any technical context. (Talking to evolutionary biologists, without begging the question, isn't a technical context, but rather a social one. Trying to publish a paper which ignores evolution in one of their journals would be a pretty dense move.)

*(Specifically computer-aided design routines using reproduction and selection, but this could have been inspired by animal husbandry instead. Wasn't, but could have been.)

Because of this, talking about the metaphysical consequences of Evolution is also a pretty dense move. Certainly you can speculate, but only out of idle curiosity and entertainment, because Evolution is just a set of data. While it happens to be explained one way now, there is not one single guarantee that it will be explained the same way in the future, in which case you'd have to throw out every single metaphysical conclusion and start again.

Plus, of course, it is metaphysics. You can't build anything out of metaphysics.

As a result of these two facts, evolution is the absolute last thing you should hang an atheist crusade on.

But anyway, given that this is an empirical theory, what does it work to explain? Notably, not all of this was lacking from La Wik, but it was mixed with so much shit that I feel the need to filter it out.

My primary source is this, via this here. I found it a wonderfully detailed and clear article, including many bits of info I had never seen before, most of which I have yet to see again.

First and foremost; every single organism on the planet uses a nearly identical genetic code. (With handy chart.) We know which sequences of letters correspond to which amino acids. We can go out looking for organisms that use transcription factors that violate this code, and what we find is that they're incredibly rare. For me, this is the primary reason to believe in a universal common ancestor, and in addition to use evolution to explain the diversity of forms which use this basic, fundamental code. Which, again, is all of them. (Horizontal gene transfer would be impossible, otherwise.)

There's also, at that link, innumerable things like how you can tell reptiles and mammals are related because you can go into the fossil record and watch reptile jaw bones move and morph into mammalian inner ear bones.

Since this is the case,

Evolution does polish Her products. While it is difficult to disentangle genetic instincts from pure appreciation of beauty, most mammals have several universal-seeming traits of beauty and good design, including simplicity, elegance (solving problems efficiently and ingeniously) and sensory richness. Especially, the elegant

Nevertheless, we also expect many kludges, especially in recently-formed species, or during and immediately after rapid evolution, a condition humans fit extremely well. While I'm not convinced that we haven't just overlooked the function of the appendix....

The coccyx. Body hair, especially on women. Conflicting urges; jealousy and promiscuity. The desire to be accepted versus the desire to excel. The urge to relax and be lazy versus the need to procure food and reproduce.

(The reason our wisdom teeth don't work is because if you work your jaw as a kid, it gets bigger. Cooking and more complex food processing has made chewing easier, resulting in smaller jaws at maturity.)

All these things are easily explained by evolution. Either they are effective now, or they are the remnants of things that were effective in the past. Evolution, of course, has no overriding goal, and so logical consistency of drives is accidental at best. It's simply that organisms that are good at surviving are stable and thus continue to exist.

If any of the ancient divine hypotheses were true, I would expect to find urges that were adaptively neutral or negative, but clearly served some kind of religious or spiritual end. I find nothing but the exact opposite - it is easy, even trivial, to at least construct an argument showing any 'spiritual' or 'religious' urge to be in fact utterly self-serving.

There being one exception - psychologists repeatedly find that children and adults are psychologically healthier with what they call a 'spiritual' life. What, exactly, they mean I don't know, but it seems odd to me. (I would be very happy to find I cannot explain this urge in terms of self-servitude.)

Despite all this, I have some questions in case a biologist randomly stumbles on this article.

How does the cell know not to produce copies of broken genes, or to attempt to transcribe parts of junk DNA? Or, do cells end up producing a lot of useless protein strings? Shouldn't there be at least one genetic disease caused by treating a part of junk DNA as a gene?

If life arose spontaneously, then considering the size of Earth, it's extremely likely that it arose more than once. What happened? Why aren't there at least two cell lines?

Could a virus or bacteria with an alien genetic code really attack our cells? Wouldn't their proteins and ours just break?

Are the 22 amino acids the only possible amino acids, or should we expect aliens to use a different set entirely? If so, wouldn't this mean that we would be unable to digest their food, and they would be unable to digest ours?

I should first ask; I know that we higher organisms construct ourselves not out of elementary molecules, but out of pre-existing bits like amino acids and sugars and fatty acids. We cannot manufacture these ourselves; we rely on bacteria and plants to do it for us, then eat them. Doesn't this mean that any alien life, even one from our own planet using a radically different DNA code, would be inedible at best and, more likely, chaotically poisonous?

Now onto the more difficult problems.

What are the mechanics of sexual recombination? How does the cell manage to not snip genes a monomer or two off of where it should be, and break genes? How does it manage the inevitable typos? Speaking of which...
"Sexual reproduction helps to remove harmful mutations and retain beneficial mutations."
People say this all the time, but always expect you to take it on faith; nobody ever explains how. So, er, how?

How does DNA compute? In a computer, encoding is completely arbitrary. But DNA's transcription factors don't seem like they can have this flexibility. So, how does it work? Second, given this answer, is it really true that there are "1.4 x 1070 informationally equivalent genetic codes"? Wouldn't at least some of these be nonviable because the required transcription factors cannot be built out of our amino acids, or indeed violate physical law?

Of similar criticality is how, exactly, by what mechanism, genes code for proteins, especially considering that this is recursive - the decoding protein is itself encoded into the genome...how on Earth did this start up?

I hunger for knowledge.

Logical basis
Given 1000 processes, most of them will reduce the chance they will occur again, usually by using up reactants. However, if one of them increases the chance, no matter how small that increase is, eventually it will occur enough times to become perpetual. Let there be a hypothetical equilibrium-like situation where processes will have a 0.2% chance of occurring, all things equal. But what if one, when it occurred, increased the chance by 0.04%? Most processes have a 0.2% squared chance (0.0004%) of occurring twice in a row, while this process has (0.00048%). This seems small, but after only 2495 repetitions it becomes perpetual; the process's probability hits one.

...okay that's rather a lot. The probability of this happening is indeed miniscule. (It's a 2495-term product...if YOU want to calculate it... Graphing the log and using it to estimate order of magnitude, I got well over 1000 decimal places. There are only about 1080 atoms in the universe, and most of those are hydrogen.)

Right. So from this, plus the fact that life leapt at the chance during the formation of Earth, I can conclude either that the process is way way more likely that 1/1000 or that the increase is something on the order of 20%. The chances of RNA arranging itself by chance...miniscule. Hence, it must really really like to replicate itself.

The real estimate calculation is even nastier to do by hand, because in reality the process will never actually reach 100% chance of surviving, plus to actually spawn life it has to replicate. So every success actually spawns two chances to survive again, but eventually the chance to die stabilizes against the chance to live...if the population manages to survive that long. The odds will still be (something enormous) to one. Sure growth is exponential, but it's still probable growth; the death rate of proto-life is going to be enormous.

And...uh...no there. Adding complexity is going to make it worse. In reality, the chain of events starts with that one really rare reaction, but leads to different reactions which have different optimum environments, which are going to become more stringent as the complexity grows, just as simultaneously the delicacy and thus half-life of the reactants decreases.

I can be sure they've basically exhausted any simple reaction that can do this, and probably pairs as well. (http://www.talkorigins.org/faqs/abioprob/abioprob.html) Okay, so put all that shit in a test tube at massive concentration and see what happens! ... Oh wait, they already did. Several teams have tried and failed.
I can be sure, however, that they haven't tried to cook up the necessary probabilities on the processes, from which I can conclude that biologists, as a whole, are terrible at logic. (How can I be sure? Because it would have been widely reported. "Probability of life starting calculated to be X%, with Y% chance of surviving to form stable cellular life." Even journalists can understand that.)

The only solution is that it's not any of the known chemical possibilities.

But anyway, given a self-perpetuating process, any tiny error will suddenly cause a different process to self-perpetuate. Basically it will be molecular speciation. I would expect such a self-perpetuating process to be robust, simply because an error-tolerant process is more likely to survive, and indeed complexity, especially randomly sourced complexity, usually leads to redundancy.

And so, the fact that life leapt at the chance on Earth is actually a serious problem for Evolution, unless panspermia is true. While it could have just been a fluke - we hardly know anything about biogenesis - we at least have to consider that it was not. It's not a serious problem for universal common ancestor, because after the first serious go at life, bacteria are going to eat every other biogenesis event. However, if it's so easy, we should have figured it out by now, or at least found something similar in nature.

The other serious possibility is actually also problematic. Panspermia requires that life emerged and then a serious asteroid impact spread rocks across the galaxy or even intergalactically. While it's actually quite plausible to think of bacteria surviving in space like this, it once again puts the probability of biogenesis at 'high' because instead of leaping for the chance on Earth, it had to leap at the chance within rock-striking distance of Earth, which goes pretty far back in time very quickly. (It's similar to working out the size of the impactor in the impactor theory of moon formation. It has to be a certain size and a certain speed to reach Earth and not pulverize itself.) And, again, considering how fast Earth got life, the neighbourhood would have had to have been crawling with crawlies, and we should be finding more Earth-style life forms in places like the asteroid belt.

So go have a look, y'all.

I think biogenesis is a very elegant theory. It connects the elementary particles and the highest form of consciousness into a continuous, integrated process. Unfortunately it's also, given the evidence we have, very very unlikely.

Nevertheless, life did somehow occur on Earth. Given this, evolution is logically inevitable.

There has to be some way to pass on instructions on how to grow to the next generation, because where else are they going to come from? Since perfection doesn't exist, these instructions will randomly get corrupted, but part of the instruction is how the next generation should grow...and thus, evolution is inevitable given the second law of thermodynamics. Given this, what are now called mutations will sometimes improve survival to the next generation, and sometimes not, a feedback that will automatically cause organisms that 'fit' their attempted goals better, to survive better, causing Nature to equip Her creatures with the tools they need, and also causing changes in those tools over time, a process now called natural selection. So that is inter-species evolution, microevolution.

Now, the definition of species is an arbitrary concept, but however you define the boundaries, the mutational shifts will eventually cause a species or part of a species to cross the boundary.

The only way for microevolution to not imply macroevolution would be to dethrone genetics. Not all the information about the animal would be encoded by the genes; specifically, the information encoding which species the thing is. The genes would just be details about the organism, which would in turn imply that the genetic code isn't universal; the details would all be a function of the underlying species code. This species code would basically have to be stored off-platform; neither in the genes or anywhere in the organism, because otherwise it will also be subject to mutation, and thus selection.

If you want a concrete analogue to this hypothetical, go look at machine language codes on different chipsets. Many of the instructions are the same, (they look like 5BE1, which may do something simple like flip a bit or increment a memory address) but many of them are different as well. The machine itself would correspond to the species code, while the genes would correspond to the machine instructions.

But none of the evidence supports this; embryo growth appears to be entirely controlled by fragile, non-error checked* genes transcribed from the genome.

*(Indeed, as there's no 'right' or 'true' genome, you can't even coherently define error.)

I hate writing conclusions. You should draw your own, anyway. So here's some random biological tidbits instead.


Organisms often suffer catastrophic failures. Either many or most embryos self-abort. That isn't the mother rejecting the embryo (which also happens) - that's the embryo failing to divide, just dying in the womb or in the egg.


Two things. First, while for the vast majority of subjects evolution is just an explanatory theory...there is that one application. You can use random mutation plus selection to design circuits, antennas, and so on, and further these prove that evolution is smarter than you. The circuits had apparently independent loops with no apparent computation link whatsoever...yet failed to work when they were removed. The mutation+selection process was taking advantage of the physical quirks of the chip itself - it was no longer digital, but analogue-digital hybrid.


Seth said...

Before and including the God Delusion, Dawkins was writing some pretty interesting books on science. He's a scientist after all. Of the four horsemen of the new atheism: Hitchens, Harris, Dennet, and Dawkins, in my opinion Hitchens is the disagreeable one. But in spite of that, I ran across some of your posts on ethics of ignorance which I thought were insightful. So I thought I'd point out in my opinion writing a book isn't the same as forcing an opinion. Because the book doesn't necessarily even have relevance and people choose the reading. Also, with the fame and the lectures and the Youtube broadcast, all of those things are self-service. And being self-service, I don't think they fall into a previously asserted type that you disapproved on in that ethics post Accepting Ignorance... May 16, 2008. That strikes me as blaming the leader for the follower. And I'm pretty sure you just meant Dawkins as a metaphor. So I'm just saying, he's rather thoughtful and the worst that can be said of him is his books tend to have rather sensational titles.

Alrenous said...

Ah, I see your point.

I must accept that Dawkins often does not fall afoul of the ethics of ignorance.

And yes, I'm using Dawkins as a poster boy. The debate in which he is one of the so-called thought leaders is usually guilty of such.

For example do you think Dawkins would condemn this behaviour? I have to predict that he's applaud it.

"That's just not cool. That's just not acceptable." I call BS. If you care that deeply about what complete strangers think, there's something wrong with you.

However, I must argue that Dawkins can indeed be accused of worse. If you really want to go all the way, Google Mencius Moldbug's open letter to Dawkins, although only the first few parts are directly about him, I'd say. (I assume you don't care that much, though.)

Erik said...

"If life arose spontaneously, then considering the size of Earth, it's extremely likely that it arose more than once. What happened? Why aren't there at least two cell lines?"

It's extremely unlikely that they happened at the same time, so I'd guess earlier one would have been developed enough to eat the later one for lunch.

Alrenous said...

That's my guess as well.