Comments: Species Demarcation.

Kay asks:
Explain this for me if you will. The other day I saw a post from a creationist stating that the Theory of Evolution has to have some fault in it because there is no interbreeding of species. How in layman's terms did the first humans evolve from apes and then proceed to separate themselves from the apes? At what point did breeding with apes stop by humans?

That's not the theory of evolution. That's a question of taxonomy and demarcation. It's a real problem, but mostly with the way we typically think about such things, as oppose to the reality of evolution. Evolution doesn't directly deal with speciation, or how far is far enough to say that one species stops and another species starts. That's like asking where childhood ends and adulthood begins. There's just not a clear point.

Evolution says that the struggle for existence and nature selecting such that the most advantaged individuals have the most children who are similarly advantaged. This ensures that species tend to adapt better to whatever niche (way of living, food etc) they occupy. Evolution says that species adapt to changing conditions of life, and can result in amazing adaptations and solutions to environmental problems. This is all evolution says. Things go forward. But since they go forward in different ways, they also tend to drift apart.

Where the species fork, and part irrevocably is a matter of happenstance and saying how far is far enough, and what a species is, turns out to be a harder problem than one would suppose because gene pools in populations do not adhere to the sort of Platonic ideals. There is no perfect human. There's no absolute ape. There's no abstract rabbit to which all rabbitness is to be compared. That's just not the way it works.

If you go child, to mother, to grandmother, to great grandmother, and so forth and go back 350,000 generations, you'll never hit a point where a child was a different species than it's mother. It just doesn't happen. However, if you do this, with me and you do this with Oliver the Chimpanzee you'll end up at the same critter. My 350,000th grandmother is likely the same as his 350,000th grandmother. And at no point were any of my ancestors a different species than their direct offspring. And at no point were any of his ancestors a different species than their direct offspring. But, at some point, at some time, you could draw a line and say that these distant cousins are now two different species. But, that line would always be arbitrary.

We think there's some absolute human, that somehow adheres to a Platonic ideal of humanness. But, really that's not how things work. I mean, would one consider Neandertals a different species than human beings? They broke off the main human lines some 600,000 years ago. But, it turns out that modern humans interbred with them, and anybody with European ancestry is like 3% Neandertal. So are they really human? Were they always human? The Denisova hominims broke off of the Neandertal stock, and share a common ancestry with homo sapiens some 600,000 years ago too. But, they too interbred with humans in modern Melanesians (people in Oceania, like Vanatu where you get black-skinned kids with blond hair likely due to such influence). And apparently Denisova also from time to time (if a newly found toe bone is to be believed) bred with their closer cousins the Neandertals. So were any of these really different species? Under different definitions there are different answers, because the term species is absolute and evolution is gradual and progressive.

Species in some sense are a sort of hind sight thing. It is certain that at one time all of the rodents and all of the lagomorphs (rabbits, hares, pikas) had a last common ancestor (which DNA analysis suggests lived ~90.1 million years ago). This last common ancestor had at least two offspring. One of which gave rise to all the mice, rats, capybara, beavers, squirrels, porcupines, etc, and the other which gave rise to every rabbit, hare, and pika. Somewhere along the line, you can draw a line, but it would an arbitrary line. And is somewhat irrelevant to the actual history that actually happened with regard to their populations. And more and more this is what we're finding. Taxonomy is largely what we tend to call things, we give populations names. But they aren't that exact thing, there is no exact thing. They gradually change all the time.

This is largely why more and more we're trying to move away from such things. Replacing the typical system of taxonomy with a nested hierarchy so we can say that this last common ancestor of rodents and lagomorphs was a glires and so are all of its offspring. But, this ancestor doesn't necessarily fit into any of the subgroups of it's progeny.

So if for example in the distant future, many animals have died off, and bats have diversified to take over their now open niches. Let's say there are bats that swarm during the day, bats that swim under the ocean, bats the size of mosquitoes that suck blood from bats that that graze in the fields. All of these bats would be different species, but they would never stop being bats. There would be more groups inside the old groups, but the old groups, which would be the species we currently know, wouldn't stop being real. Perhaps the bats under the ocean and the bats that graze in the fields, and the ones that burrow into trees to hunt for insects, would all be fruit bats. So fruit bats wouldn't be a species but rather a group of distinct species (to some extent they are as there's many species of fruit bats), just as the glires are a group that gave rise to every rabbit and rodent on the planet.

Which is a long way around to the question you initially asked. Largely this creationist is confused as to what evolution says and what problems are really problems for the theory. The problem here is with our old ideas of taxonomy and what species are. This isn't a problem for evolution. Reality is what reality is. Our taxonomy needs to fit with reality rather than our general beliefs about names and putting things in boxes (Platonic ideals). It's all gradual, and there are no absolute lines, and we know this because we know evolution. It isn't that there's flaws in evolution, it's that there are flaws in the way we think about biology and evolution lays these errors out for us.

How in layman's terms did the first humans evolve from apes and then proceed to separate themselves from the apes?

It doesn't work like that. We didn't separate ourselves from the apes.  At some point some of our ancestors took different paths than their siblings. One brother went one way, and the other brother went the other way, and they never got back together. And these ancestors of ours were apes, so we are apes. We don't ever stop being apes. Populations split and divide. The group that gave rise to the orangutans went one way and the group that gave rise to the gorillas/humans/chimps/bonobos went another and didn't get back together. Then the group that gave rise to the mountain and lowland gorillas went one way and the group that gave rise to the humans/chimps/bonobos went the other, and didn't get back together. And the group that gave rise to humans went one way and chimps/bonobos went the other. And then the chimps went one way and the bonobos went the other. There isn't some set in stone principle that says this is X and it perfectly exemplifies Xness. There are populations and they divide. Sometimes they get back together and sometimes they don't. When things started, they were no different than one brother is from another brother, in fact, necessarily you could find a set of siblings that gave rise to every divided group. You could find a pair of siblings where one gave rise to all the reptiles, dinosaurs, and birds, and the other to all the mammals.

At what point did breeding with apes stop by humans?

 There's no absolute lines there. Humans are apes. And humans breed with humans. So in a very real sense humans still breed with apes (namely humans). But, looking back to our last common ancestor with chimpanzees (our closest relatives), and it may well be that humans might still be able to breed with them! It's not impossible for lions and tigers to breed or horses and donkeys. They produce offspring, and it might well be possible to have human-chimp hybrids. We just don't try it. So at one point did the ancestors of all humans and the ancestors of all chimpanzees stop breeding? -- They stopped breeding when they stopped. Seemingly about 7.8 million years ago or so.

There are some humans in some distant parts of the rain forest who do not know civilization. The large interbreeding population of humans haven't bred with them since we stopped breeding with them. If for some reason we never started back up, eventually we couldn't and we may well end up with two species of humans, such as the Morlocks and the Eloy (from H.G. Well's the Time Machine). It all depends on when the populations stop and happen to stay stopped.

So how did we separate from the other groups of apes. We went one way, and the other group went another. At what point did we stop breeding with them? We didn't breed with them anymore, when we didn't breed with them anymore.

The actual answers seem sort of anticlimactic, and they are. But, mostly because the problems are with our understanding and not evolutionary theory. We tend to see species as these distinct things which fit into these specific boxes. But, that's not what they are. They are siblings and a few million years of isolation. If you want to draw a line, at some point and say your 30,000th cousin is no longer the same species, you can, but realize that it's an arbitrary line, and our 30,000ths cousins the Neandertals bred with us just fine.
You could go further back, but it's still all just where you draw the line and that has nothing to do with evolution, that has to do with you and your line.

" The other day I saw a post from a creationist stating that the Theory of Evolution has to have some fault in it because there is no interbreeding of species."

No. There's a problem there but it's our idea of species that has the fault, not the theory of evolution.

The invisible hand of the market and God.

Apparently every third-order emergent property is God at work. There's apparently a belief gaining some steam that the invisible hand of the market is God at work.We see this same thing in various other places too, in Evolution by natural selection we see that it's God at work, and within the human brain we see that that too is mysteriously God.

a third-order emergent structure is a consequence of shape, time, and heritable instructions. For example, an organism's genetic code sets boundary conditions on the interaction of biological systems in space and time.

Well, sometimes things like markets, intelligence, science, and evolution which all rely on evolutionary algorithms are easy to confuse. Early on we develop a theory of minds, and are often keen to assign minds where they don't belong and end up painting with a broad brush to catch all human minds and any other third-order emergent structures, so we see the products of nature as the products of minds. And the invisible hand of the market as God's hand. And the amazingness of our own minds. We see minds in every third order emergent structure, because realizing something is/has too much design to be the result of first or second order emergent structures typically in our lives means it's the result of a mind. Though, it could similarly be the result of anything implementing the evolutionary algorithm, which basically is just the non-random selection of randomly occurring differences.

I don't know which is sadder.

http://thisiscolossal.com/2011/07/world-record-connect-the-dots-mona-lisa-in-6239-dots/

I'm not sure which is sadder, the fact that in instantly recognized that collection of dots as the Mona Lisa or that I instantly knew what it was and that I could do significantly better.

The case against Corbett was finally thrown out.

Apparently as a teacher, you can say creationism is superstitious nonsense, not because it's absolutely true but because teachers have qualified immunity and should get a bit of leeway rather than the hard boot.

http://www.csmonitor.com/USA/Justice/2011/0819/US-judges-rule-for-teacher-who-called-creationism-superstitious-nonsense

Also the court finally reversed their decision on some math teacher who was hanging up religious posters. When the initially decision came down I thought it was amazingly stupid. It's not about the teacher's freedom of speech but rather about the teacher in his role as an agent of the government. He doesn't get first amendment protected because the first amendment is specific to restrict what he can do.

http://www.csmonitor.com/USA/Justice/2011/0913/God-Bless-America-Not-in-high-school-math-class-US-judges-rule

How to MacGyver a knife sharpener.

I tried it. It actually works.

The typical Weighted Euclidean color distance values are wrong.

There's a rather common set of weights for Euclidean Color Distance, to better approximate the human eye.

(30*(r1-r2))**2 + (59*(g1-g2))**2 + (11*(b1-b2))**2

30, 59, and 11 for RGB weights.

Well, they seemed rather pulled out of one's ass. And I'm not the first to notice. But, I did bother to code up a routine to compare CIELab to color distance weights and find out, by brute forcing each and every color distance to find out where the weights there should be.

22.216091748149788, 42.88860259783791, 34.895305654012304

Or 22, 43, 35 since we're very likely going with integer math. This is just brute force average best approximation of weighted Euclidean to CIELab.

From the cited Color metric article:

• Several individuals suggested a weighted Euclidean distance in R'G'B', according to the formula:
  ∥ΔC∥=3×ΔR′2+4×ΔG′2+2×ΔB′2−−−−−−−−−−−−−−−−−−−−−−−−−−√
  This function has practically the same result as YUV. Its simplicity and speed of calculation make it a better choice than YUV.
• As explained in the section "gamma correction" below, the perception of brightness by the human eye is non-linear. From the experiments it appears that the curve for this non-linearity is not the same for each colour. The weighted Euclidean distance presented works quite well for the subset of colours where the "red" signal is 128 or more (on a scale of 0-255). For the other half of the full R'G'B' cube, this different weighting produced better results:
  ∥ΔC∥=2×ΔR′2+4×ΔG′2+3×ΔB′2−−−−−−−−−−−−−−−−−−−−−−−−−−√

 2, 4, 3, are pretty close to my values (they are weights and thus need to be proportional to each other not similar in absolute magnitude). 2/9, 4/9, 3/9 or 22.22, 44.44, 33.33 when you bring the weights up to how many parts I have. So 22.22 vs 22.21...  44.4 vs 42.8 ... 33.3 vs 34.9.

Update:
I also ran the colors for CIELuv.

R G B weights:
0.2753667361197665, 0.3846815980739518, 0.3399516658062818

28, 38, 34

Evangelist says things in response to atheist.

So part of Google+'s features is something called sparks. It's actually pretty cool for finding relevant bits of fun things. Like this interesting article which vaguely consists of an Evangelist saying things in response to an unlinked Atheist in some state somewhere.

There is a lot of really pathethic bits, once again highlighting the difference between answering or countering something and simply responding.

“The greatest leap of faith is assuming that order evolves out of complete chaos,” -- This statement particularly stuck in my maw. That's not a leap of faith, that's actually demonstratively true. From Benard Cells, to hexagon's on Saturn, snowflakes, round planets, orderly solar systems. The fact is you can mix a crap ton of whatever in a blender, and leave it for a few days on a table and it will get very orderly. It turns out that chaos is actually rather unstable and things tend to get orderly. While it is true that the second law of thermodynamics insures that higher energy and greater entropic points will necessarily equalize out, that's actually making things more uniform over time. There was a lot of chaos in the early solar system with rocks and debris flying every which direction, but over time, order evolved and the Earth is the only big rock in this very close to perfect circle we orbit in. This is especially true for higher degree emergent phenomenon like evolution, which as a natural consequence of heredity and natural selection creates organisms which bias towards the preservation of better genes and better adapted bodies coded by those genes.

And as for the balanced ecosystems and perfect design of nature, he's just wrong. Everything in nature is poised on a knife's edge, being eaten by parasites and killed by predators, and often starving to death. Most animals suffer through most of their lives with the smallest amount of bad luck separating one from suffering through another week or dying what must be a very painful death. If a loving God designed such a system, that God's only love is for suffering and pain, because nature is red in tooth and claw. And the life of animals is solitary, poor, nasty, brutish, and short. The only thing such a system manages is to make the smallest genetic advantage thrive within that population's gene pool and thereby selectively bias the future generations towards having rather than lacking that advantage.

And then there's his other really terrible bit of claiming:

“Nothing in life is free. The more valuable the object, the higher the price. Nothing is more valuable to God than the human race, which is why such a high price had to be paid, and in this case with a divine human life.” --- Paid to whom?

Really, to whom?

While it's certainly the case that propitiation by blood is a common theme throughout religion and religious views, it's not something that actually would be fundamentally important in our 13.75 billion year old universe. The idea that that the oxygen carry molecules of some species, on this tiny little planet, around this tiny star, in this large galaxy, which is simply one of billions, is obviously absurd to anybody who really questions the core bit of Christian dogma, that Blood Sacrifice of God to God makes any real sense.

And the thing is, it does make sense. This is exactly what we should expect to find if a culture obsessed with primitive blood magic were to make a religion. Because if we give blood for blood for criminal offenses, it's rather quick to give blood for sin in religious ones. And then the better the blood, the more it will atone for, so how great and powerful must be the blood of God? This argument is found wholecloth here by Jason Frenn as well as in Hebrews 9. Christianity is exactly what we should expect to find coming out of a culture rife in belief in blood magic, but not what we should expect to find being true. And lo and behold, we find Christianity first coming out of exactly a place and region and people obsessed with exactly that. So it really does make sense, as long as Christianity is false.

Flat adverbs always seem sketchy.

The evolution of lines. That's clever.

I'm a huge fan of evolutionary algorithms and some general crowd sourcing stuff.

There's stuff we haven't seen! Save the world.

So if there's a bunch of critters that we know everything about is it okay to kill them all?

It likely is about time to explain basic climate science to people.

Hopefully in the simplest terms possible.

http://scienceblogs.com/startswithabang/2011/08/if_you_believe_that_blankets_k.php

CO2 works like a blanket. It traps heat. We're making it thicker. That'll have consequences.

On design, of birds and beaches.

My response to a person who acted hostile after I told him that there really is design in nature. I think denying such is bizarre and wrong, and really just a terrible line of argument. The truth is a far better argument for reality anyhow.

--

Let a beach exist for a billion years. It will stay a beach. It will change a bit and the shore will move. But, there's nothing really designing it. Let some reproducing creatures exist for a billion years and they will develop new designs and adaptations and forms that one could never imagine.

Evolution is a process of self-design, and beaches do not evolve in that sense. They are not designed. They are not improved.

There really is a difference which calls an explanation and evolution is that explanation. There is a very real difference between beaches and birds.

It's certainly true that evolution is the answer, but the question is why is there so much design in nature. Birds have insanely adapted well adapted form, hollow bones, light feathers, amazing lungs, huge pectoral muscles, and that can't have just happened or happened by chance. And it didn't they evolved. The design is the result of the system of reproduction and death.

Some of the oldest rocks in the world have some of the oldest signs of life.

Oldest fossils of life going back 3.5 billion years ago. It's cool and all but I was thinking and went off on a tangent. I think it's really cool that we have 3.5 billion year old rocks. Australia is about the only place with them because it's been a pretty consistent land mass over the history of Earth. With the amount of shifting and moving and subduction zones, it seems like sitting there unchanged for 3.5 billion years ~ 3,500,000,000 years is quite a feat. If anybody could do it, rocks could do it. Go rocks! Way to exist.

While really old fossils are cool, my suddenly being impressed by the feats of rocks warranted a blog post.

Rape and Pillage

I so love David Michell. He's always awesome.

A tale of two Michelles.

I so totally wish that more things on television were this good.

The worst part of Kalam

I think the worst part of the Kalam Cosmological Argument is the presumptive nature of the whole thing. While the Bible answers the question of cosmology with "God did it", the cosmology in the Bible that "God did" isn't starting the inflationary expansion of the universe or causing the big bang. But rather painstakingly and skillfully (Psalms 19:1 The heavens declare the glory of God; and the firmament sheweth his handywork.) created a large metal-like dome held up by strong pillars to keep the cosmic ocean divided and the waters above the heavens and below the Earth apart.

In the Bible, we live under a large metal like dome of heaven, with little twinkly lights stuck into it and above the heavens there's the waters and below the earth the other waters which God so helpfully divided up in Genesis. The Bible's answer to this is "God did it".

-- That's fine, but you don't get to copypasta that answer onto a modern cosmological framework and suppose that the authors of the Bible had any freaking clue what the universe was like.  "God did it" is the answer the Bible gives to the metal-like dome protecting us from the cosmic ocean, you don't get just re-appropriate that answer to new cosmologies that are less horribly wrong. It's like saying Jesus cured diseases. No, he shooed out demons that caused diseases. You don't get to use the modern understanding and the answer "God did it", because the "God did it" was to answer in the context of the primitive understanding. The Bible says God is the reason the sun revolves around the Earth, sorry Bitches, no backsies!

The fluxuations of science.

Science use to say the universe was infinitely old, then 2 billion years, 3 billion years, 10 billion years, 8 billion years, 9.5 billion years, 10 billion years, 8-12 billion years, 12 billion years, 13-14 billion years, 12.5 billion years, 14.8 billion years, 13 billion years,  13.7 billion years, 13.72 billion years, 13.73 billion years, 13.75 billion years.! Science can't make up it's mind. It could be anything tomorrow, and then something different the next day! -- Anybody who supposes things along this line of reasoning, really didn't pay enough attention to that sequence of numbers to notice the underlying pattern.

Genesis 1:2 and the Christian Delusion.

I read the Christian Delusion a while back, having gotten a copy in Riverside signed by Richard Carrier. The chapters are all pretty fantastic and it's hugely informative, and I'm already rather encyclopedic so learning new things is rarer than it should be on such subjects. But, Babinski's chapter on Biblical Cosmology has been hugely influential on me. My views were pretty shattershot.

I understood that parts of the Bible talked about the vault of heaven and that the sky was a hardened dome. But, I never really understood the entire picture. I figured that people thought the sky was water because it was blue. It turns out that within Semitic cosmology that's just the color of the bottom of heaven of the firmament which is held up by the mountains. But, I never understood why the dome was spread-out like hard metal or resting on firm foundations, or the other bits that relate to cosmology. And it has a lot to do with how the world was created in the myth and what existed before and the picture people had of the universe.

Genesis starts out with basically a preamble, in the beginning, the gods created the heavens and the Earth. And then describes how they came to be. What's interesting is how the second line of the creation myth is just glossed over, and largely ignored. The first line we get, the third line is understandable, but what the hell is that second line saying?

1:2 And the earth was without form, and void; and darkness was upon the face of the deep. And the Spirit of God moved upon the face of the waters.

Sure, formless earth, nothing there, darkness are all understandable. But, what is the "face of the deep"? And the spirit of God moved upon the face of the waters? What waters? When did waters get created? If you read through the genesis account, water is never created. There's a lot of sections about dividing the waters by making the firmament and keeping  it apart from the waters of the Earth. And allowing land to be exist, and gathering waters into seas, but never actually making the water. The reason for this is that at the core of the cosmology it isn't a creation ex nilho.

The universe was created out of a cosmic ocean. The firmament and the Earth divide the waters because its all waters. And cosmic ocean underlay all the cosmologies of the Semitic regions. The universe according to the Bible wasn't made out of nothing, it was made out of a formless ocean that was divided up. The reason for professing repeatedly in the Bible as to how strong and secure the firmament, how it's made of strong metal, and upon solid foundations and expertly crafted, is because it was a very real fear that the ocean might crush you. That Noah's Flood might very well happen and the waters will flow out of the vault of heaven and out from under the Earth, and our precarious little bubble might not exist.

7:11 In the six hundredth year of Noah's life, in the second month, the seventeenth day of the month, the same day were all the fountains of the great deep broken up, and the windows of heaven were opened.

8:2 The fountains also of the deep and the windows of heaven were stopped, and the rain from heaven was restrained;

And given the myth of the flood it was absolutely vital to assure people that such a thing would never ever happen again, with God's regrets, and pinky-promises and rainbows.

9:11 And I will establish my covenant with you, neither shall all flesh be cut off any more by the waters of a flood; neither shall there any more be a flood to destroy the earth.
9:12 And God said, This is the token of the covenant which I make between me and you and every living creature that is with you, for perpetual generations:
9:13 I do set my bow in the cloud, and it shall be for a token of a covenant between me and the earth.

It was a very real worry that the cosmic ocean would kill everybody., and much of the Bible goes to dissuade our fears of this. And in fact, because the sky is hard and metal and protects us, it's clear evidence for God.

Psalms 19:1 The heavens declare the glory of God; and the firmament sheweth his handywork.

And really, understanding this is rather devastating  to Biblical cosmology and a lot of apologetics. There's a lot of stuff with like the Kalam Cosmological Argument that largely says that the universe was created ex nilho and science can't explain this, but God fully explains how this happened. But, the Bible never actually said that, it starts out with a cosmic ocean and a sky made of hard material on solid foundations, which attest to the handiwork of God. Far be it for Christianity to explain the Big Bang with a divine fallacy, they need to explain rather where that original cosmic ocean came from. The gods created the heavens and the Earth to divide up the waters, but that's doesn't explain the origins of the cosmic ocean.

The Bible doesn't actually fit that paradigm at all, it not even trying to answer to the question of what caused the initial expansion/existence of spacetime. It's answering very specifically  how did the strong firmament of heaven and dry land get formed out of a cosmic ocean. The answer is "God did it", in fact God spent a solid 1/6th of the time he spent making stuff to make that firmament, that majestic roof fretted with golden fire (as Shakespeare put it). Spending the entire second day on it. Dry land was part of the third day. Then in day four God spends a lot of time adding bling to the firmament. Putting stars in it, and really big balls of light to travel across the firmament. The little tiny spots of light (which according to Revelations will fall to the ground during the end times) and the giant greater and lesser lights of the sun and moon, just to deck it out and give us signs for seasons and such. A lot of the OT is depended on this view of the universe, and really by coming to understand that, you really see how hollow various claims about how God explains the universe actually are. If you read the Bible, the authors have no clue what the universe is really like and spend a considerable amount of time explaining how why the cosmic ocean doesn't kill us, how the sky is hard as metal, and how awesome God is for making said firmament.

So the general theist argument that atheists can't explain the origins of the universe but God does, is even hollower, not just because the answers we have are really good and anything is better than the always wrong answer theists try to shove into every gap, but because the Christian God explains the origins of the metal dome protecting us from the cosmic ocean..

Kalam and Cosmology

There were some bits towards the beginning that irked me a bit, but after understanding there was no advocacy here but rather a presentation of the possible with the arguments of the apologists I got into the groove.

Sir Galahad, Josh Ritter

Pretty awesome.