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Evolution: the Facts.

cyborg said:
EVOLUTION IS NOT GOAL BASED.
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http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_54
Especially this drawing.
laddervstree.gif
 
The Atheist said:
It occurs to me, seeing yet more fundies explaining why evolution is bunkum, that they come from the same pod as "No plane" CTists - lacking facts, behaving irrationally and refusing to accept evidence.

Now, there are lots of places where scientific evolutionary theory is available on the net, but I wondered if maybe a few of the excellent scientists involved in JREF could make up a thread containing factual analysis of evolution from several different angles - much as Gravy has with his outstanding series on 9/11 and WTC.

If there's support for the idea, let's kick it off and have the thread as a lasting monument to science's triumph over BS/ID and any other stupid acronym you like. If good enough, we could get it put in spotlight so it doesn't get lost in the dross. I won't be posting any data since I'm not a scientist, but I envisage lots of data such as the stuff dr Adequate and others were recently posting in one troll or another's thread. I'll just keep things on topic, then take all the credit for everyone else's brains! (In business, we call that management.)

These are the type of issues:

Age of the earth - how can we be sure it's not 6011 years old?

How did life arise? What were conditions really like at the dawn of life?

How do species evolve? When does one species "break away" from the other?

What are some examples of intermediate species?

Any algorithms and their connection to methods of proof.

Debunking popular ID myths. Questions to ask IDiots.

I find the best place to start is at the start, so let's have the data about age of the earth. Just copy it from elsewhere if it's handy already as i know lots of age-related posts were made in rittjc's thread.

Any takers? If there's support, I'll see if we can get it stickied.
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Seems like a good idea, though it does seem a big project and I think it should include critiques of evolutionary theory.
 
"We are apes."
"We are fish."

UnrepentantSinner said:
* We also need to clarify claudistics and taxonomy in terms of some other phrases I see tossed around "humans are apes" and "humans are fish". Both are true claudistically, but ring hollow to the uninitiated.
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I see the assertions above tossed out by evolution supporters in response to Creationists who ask various forms of "how did we come from fish" or "if we came from apes, why are there still apes", etc. The responses, while technically correct are insufficient when dealing with someone who, upon hearing this, thinks you're telling them humans and tuna are exactly the same. We're not. We've been seperated since our last common ancestor maybe 475,000,000 years ago. But we are both fish, and with some explanation they might not then ask where are our gills.

This was a post I made back in March regarding classification and I think it's content would work here in demonstrating a way to further clarify a "we are fish" response to evolution deniers. I'm going to edit some of it, but will leave some stuff in you might want to check the original thread for context.

UnrepentantSinner said:
Something this is won't produce something that isn't, but it will produce something different. I realize at first this seems contradictory, but if you look at a phylogenetic tree you can probably deduce the answer to your question about pelicans on your own.

Lets start with Vertebrata. All species in this classification will have these characteristics.


Within Vertebrata are Gnathostomata or jawed vertebrates. And within Gnathostomata are ray finned fishes or Actinopterygii and lobe finned fishes or Sarcopterygii

Now here is where it gets important. You know the old stumper, "did humans come from fish?" The answer isn't as easy as yes or no. Humans are under the clade Sarcopterygii, and thus are classified with lobe finned fishes, but evolution has changed our form many times since sharing a common ancestor with the ancient root species.

So then humans are Homo sapiens
and also Hominidae
and also Catarrhini
and also Primates
and also Eutherians
and also Mammals
and also Therapsids
and also Synapsids
and also Amniotes
and also Terrestrial Vertebrates
as well as being Sarcopterygii.

We, nor any other species will ever stop being a part of the groups we are now, we only further divide below what we currently call a species to branches within it that can no longer interbreed. Ex. Homo sapiens terra and Homo sapiens luna.

Similarly the pelican will never stop being a pelican, a bird, a reptile, an amniote, a terrestrial vertebrate or a Sarcopterygii either, the species will just branch.
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If any of you have any questions about the Chimpanzee Genome Project, I am on friendly terms with one of the authors on the paper. He posts infrequently and lurks quite often at CF.

Here's an example of his work

I am going to describe here a small part of the genetic evidence for common ancestry of humans and chimpanzees, which is one tiny piece of the overall evolutionary picture of life. I hope it will give some idea of what geneticists see when they compare species, and why they rely on evolution for interpreting their observations. The data come two sources: first, the comparison of the human and chimpanzee genomes (in whole or in part), which gives detailed information about huma-chimpanzee genetic divergence, and second, the study of genetic variation between humans, which gives information about human genetic diversity.

First, some background. Humans and chimpanzees are thought to have diverged from a common ancestral species about five to seven million years ago. This means that if you compare a human chromosome with the corresponding chimpanzee chromosome, the two pieces of DNA were originally identical, because they were once the same chromosome. (Note: the last common ancestor of the two chromosomes is actually somewhat further back in time than the species split, by a million years or so. This is because you also have to include the time to get back to the common ancestor of two chromosomes within the ancestral species. So I will use seven million years as the time to the last common ancestral chromosome.) Of course, this assumes that the evolutionary picture is true.

Humans and chimpanzees differ genetically because during those seven million years, mutations have been accumulating in both species' genomes. The great majority, perhaps 95%, of these can be treated as being selectively neutral, neither helping nor hurting the organism; mostly, in fact, they do nothing at all. These are the mutations I am interested in. Since they do not have any effect on survival, these mutations accumulate steadily, with a new crop being added every generation. Similarly, all genetic differences between individual humans are the result of mutations accumulated over the last several hundred thousand years. Presumably this is very different from most creationist scenarios, in which the human and chimpanzee genomes were indidually created with whatever characteristics and genes the creator desired, while human variants are either the result of a short period of mutation or were created in Adam and Eve. (I say presumably because there are not many detailed creationist models of genetics.)

What are these mutations? They are any change in genetic information that can be passed to offspring. The genome can be thought of as a string of letters (called nucleotides, or bases), some of which spell out words (genes). (In this alphabet, though, there are only four letters, A, C, G and T). In the human or chimpanzee genome there are three billion of these letters, grouped into a couple of dozen chromosomes. A mutation can be a change from one letter to another (an A to a T, for example), or it can be the deletion of a group of nucleotides, or the addition or inversion of a group, or the fusion or splitting of whole chromosomes. The first of these, the single-base substitution (the replacement of a single nucleotide by another) is the most common kind of mutation and the best studied, so that is what I will focus on.

The scientific question then is this: Do genetic differences between humans and chimpanzees look like they are the result of lots of accumulated mutations? What predictions about the differences can one make, based on the hypothesis that they are all the result of mutation?

Total divergence

For starters, we should be able to predict how different the genomes should be. The seven million years of evolution in each lineage represents about 350,000 generations in each (assuming 20 years per generation). How many mutations happen per generation? Estimating mutation rates is not easy (at least without assuming common descent): it is hard to find a few changed nucleotides out of 3 billion that have not changed. By studying new cases of genetic diseases, individuals whose parents' do not have the disease, however, it is possible to identify and count new mutations, at least in a small number of genes. Using this technique, it has been estimated[1] that the single-base substitution rate for humans is approximately 1.7 x 10^-8 substitutions/nucleotide/generation, that is, 17 changes per billion nucleotides. That translates into ~100 new mutations for every human birth. (17 x 3, for the 3 billion nucleotides in the genome, x 2 for the two genome copies we each carry). At that rate, in 350,000 generations a copy of the human genome should have accumulated about 18 million mutations, while the chimpanzee genome should have accumulated a similar number.

The evolutionary prediction, then, is that there should be roughly 36 million single-base differences between humans and chimpanzees. The actual number could be determined when both the chimpanzee and human genomes had been completely sequenced. When the two genomes were compared[2], thirty-five million substitutions were found, in remarkably good agreement with the evolutionary expectation. Fortuitously good agreement, in fact: the uncertainty on most of the numbers used in the estimate is large enough that it took luck to come that close.

Types of mutation

Next, we can analyze different types of substitution. This is worth doing because not all sites in the genome mutate at the same rate, which means that we should expect to find different levels of divergence at different kinds of site. One important consideration is simply which nucleotide is doing the mutating. The bases A and G are chemically similar to one another, as are C and T. A nucleotide is more likely to be replaced by a similar one; as a result, rates for mutations between similar nucleotides (called transitions) are higher than for mutations between dissimilar ones (called transversions). Another important effect is that one particular combination of nucleotides is unusually prone to mutation: a C followed by a G (called a "CpG") is chemically unstable under some circumstances, and is known to mutate at very high rates. Thus, in the disease study mentioned above, the mutation rate at CpG sites was 11 times higher than the non-CpG rate. The rate for transitions was also found to be higher than the transversion rate, by more than a factor of three.

The prediction from common descent is that human-chimpanzee differences should show the same pattern. They do. In a human-chimpanzee comparison[3], transition differences were 2.4 times
as common as transversions, and substitutions at CpG sites were 17 times as common as at non-CpG sites; the agreement with the mutation rate estimates is quite good, considering the large uncertainties on the latter. In other words, we see the same pattern in new mutations occurring in humans today as in the genetic differences between humans and chimpanzees. This is to be expected if the same process, random mutation, is driving both phenomena; it doesn't seem to make a lot of sense in other models.

It is also possible to make a better test than the crude mutation rate estimates permit. We can do this by looking at the genetic differences between individual humans, since these differences are also (according to standard evolutionary thinking) the result of accumulated mutations. The test is to see whether patterns in genetic diversity within humans match those already described for human-chimpanzee divergence. This comparison has been done[3]. Here are the results:
mutclassA.png

mutclassB.png


The first plot shows the pattern for the human-chimpanzee comparison, while the second shows the pattern for human diversity. Differences are broken down into CpG and non-CpG, and into transitions ("Ti") and the three kinds of transversion (G<->C, A<->T, and A<->C/G<->T). The similarity of the two patterns is striking. It is difficult to escape the conclusion that genetic diversity among humans and genetic divergence between humans and chimpanzees have both been produced by accumulated mutations.

Local mutation rate

We can use the same technique, comparing human diversity with human-chimpanzee divergence, to look at various regions of the genome, rather than at different kinds of sites. It is well known that the mutation rate varies somewhat from place to place on the chromosomes. If the hypothesis of common descent is correct, parts of the genome with higher mutation rates should show both a larger divergence between species and more variation within a single species. It is a simple matter to compare the two and see if there really is this kind of correlation. Here is the comparison:

div_pi.gif


For the figure, I divided the genome into 1 million nucleotide windows and calculated divergence and diversity within each window. Each point on the plot represents one window, with the human diversity along the x axis and the human-chimpanzee divergence along the y axis. As expected, there is a strong correlation between the two: spots with large divergence are very likely to have large diversity as well. Again, this is a simple prediction from common descent, and I cannot think of any reason why it should be true in a creationist model.

Mutation on the sex chromosomes

Yet another way that mutation rates vary is by the sex of the parent. For many mutations, it is known that males have a higher rate of mutation than females, at least in part because it takes many more cycles of cell division to generate sperm than eggs. One implication of this is that the X and Y chromosomes should accumulate mutations at different rates from the rest of the chromosomes (the autosomes), since the Y chromosome is only found in males, while the X chromosome spends two/thirds of its evolutionary life in females. The prediction from common descent, therefore, is that human-chimpanzee divergence should be higher on the Y and lower on the X than on the autosomes. In this case a quantitative prediction is hard to make, since the size of the effect can only be measured by assuming common ancestry. The qualitative prediction, however, has been confirmed very nicely by observation[2]: divergence on the X chromosome, the Y chromosome and the autosomes is, respectively, 0.94%, 1.90% and 1.23%.

Conclusion

Consistently, the hypothesis of common ancestry makes accurate predictions about the comparative genetics of humans and chimpanzees. No other hypothesis has been offered that provides any kind of useful prediction. Not surprisingly, geneticists overwhelming use evolution, because that is what works.

References

[1] Kondrashov AS. Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Human Mutation 21:12-27 (2003).

[2] The Chimpanzee Sequencing and Analysis Consortium. Initial sequencing of the chimpanzee genome and comparison with the human genome. Nature 437:69-87 (2005).

[3] Ingo Ebersberger, Dirk Metzler, Carsten Schwarz, and Svante Paabo. Genomewide Comparison of DNA Sequences between Humans and Chimpanzees. Am. J. Hum. Genet. 70:1490-1497 (2002).
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And back to the age of the earth, there was a lot of great stuff in rittjc's How old is the Earth thread but unfortunately he was nothing but a Creationist troll. I'll try and seperate the wheat from the chaff in that thread and post links to messages which we can cut/cull/distill down to the most usable information.
 
John Hewitt said:
Seems like a good idea, though it does seem a big project and I think it should include critiques of evolutionary theory.
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Sure, and as long as the critique is fair and balanced, I think that's a good thing.

Glad you're here, I was going to drop you a PM, because of your interest in the field.

UnrepentantSinner said:
If any of you have any questions about the Chimpanzee Genome Project, I am on friendly terms with one of the authors on the paper. He posts infrequently and lurks quite often at CF.
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I need one of those salaaming smilies!

UnrepentantSinner said:
And back to the age of the earth, there was a lot of great stuff in rittjc's How old is the Earth thread but unfortunately he was nothing but a Creationist troll. I'll try and seperate the wheat from the chaff in that thread and post links to messages which we can cut/cull/distill down to the most usable information.
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Yes indeed, there are some excellent posts in the dross in that thread. You're doing all my work for me, which is a trait I admire! I may even let you share [a very small part of] the credit.
 
I think TalkOrigins is the place to go. No need to rewrite all their marvelous articles.

However, I also think a 1- or 2-page succinct summary of the main evolution debate points would be a great idea. For example, a paragraph titled "Evolution is not goal-directed" could then explain, in simple terms, exactly what that means.

~~ Paul
 
That Dawkins youtube simulation of clock parts ending up as functional clocks was the best visual interpretation of the process I've ever seen. Now, where's the bloody link gone?
 
Take a look at the SkepticWiki sections on Biology and on Creationist Arguments.

So far, so good, but there are still lots of issues not covered.

I'll be happy to stick any good stuff on the SW for those who lack the necessary skillz --- or you can register and learn to do it yourself.

---

NB: some of these articles are much better than TalkOrigins, there I said it.
 
Paul C. Anagnostopoulos said:
I think TalkOrigins is the place to go. No need to rewrite all their marvelous articles.
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I agree, but that doesn't take into about the fact that... I'm sorry - please turn off your irony meters before I continue - Creationists have a knee-jerk reaction to the bias* on TO to the point where they won't even look, much less consider and try and counter the information there. Look at rittjc's responses or a million others on the 'Net. With that in mind I think having alternate sources for, well, what is essentially the same evidence, at least we can nip the knee-jerk reaction in the bud.

Paul C. Anagnostopoulos said:
However, I also think a 1- or 2-page succinct summary of the main evolution debate points would be a great idea. For example, a paragraph titled "Evolution is not goal-directed" could then explain, in simple terms, exactly what that means.
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Great idea, the links to alternate sources can be a resource, while those summaries can serve as talking points. "Goal-directed" and "We are fish" are two to start us with.

* yeah yeah, it is biased, towards science and reality and... well, you get the idea.
 
Probably the most contentious point about evolution, as far as ID proponents are concerned, is how it relates to hominids (and thus humankind). Here's a site that gives a multitude of further sources with lots of nutritious detail:

http://www.antiquityofman.com/hominin_evolution.html

(Apologies if someone else has already posted it.)

'Luthon64
 
I think there is possibly no better place to start by suggesting they actually read Darwin's acutal words and his actual thinking as he tries to work it all out. The Origin of Species by means of Natural Selection, 6th Edition is downloadable from http://www.gutenberg.org/etext/2009 (and it is also avaible there in various "talking book" audio formats for those that can't read).

I have had a hard cover copy for many years. It's not an easy read (because Charles says things that are so damn obvious :D ) but can be dipped into almost anywhere.

I've read most of the Bible. How many ID supporters have read Darwin? Most get their input from the lying ID quote miners.
 
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Can we make a separate FAQ solely aimed at helping Ray Comfort understand evolution? I'll start:

1. Isn't the fact that a banana fits in my hand a sign that God created both of us?

2. Why is there no such animal as the crocoduck?
 
UnrepentantSinner said:
This is my pet on-line debate topic. It's less work per se, than a labor of love.
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Oh, well that's an even better reason - you feel satisfied about having done a great job and I take all the kudos. Symbiotic.

Egad! This is a thread where almost everyone can agree with each other for once!

We're winning on the questions and the expertise, so far.

Paul C. Anagnostopoulos said:
I think TalkOrigins is the place to go. No need to rewrite all their marvelous articles.

However, I also think a 1- or 2-page succinct summary of the main evolution debate points would be a great idea. For example, a paragraph titled "Evolution is not goal-directed" could then explain, in simple terms, exactly what that means.

~~ Paul
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Great idea. You know how it goes, now that you've suggested it, you have to do it.

1-2 page overview of evolution. That's a great place to start.

Thanks for volunteering to do that - tomorrow lunchtime will be fine.

:bgrin:

Oh, two days then.

Dr Adequate said:
Take a look at the SkepticWiki sections on Biology and on Creationist Arguments.

So far, so good, but there are still lots of issues not covered.

I'll be happy to stick any good stuff on the SW for those who lack the necessary skillz --- or you can register and learn to do it yourself.

---

NB: some of these articles are much better than TalkOrigins, there I said it.
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Thanks!

Excellent pay rates will be negotiated for you, circa $0.00000/hr.

Anacoluthon64 said:
Probably the most contentious point about evolution, as far as ID proponents are concerned, is how it relates to hominids (and thus humankind). Here's a site that gives a multitude of further sources with lots of nutritious detail:

http://www.antiquityofman.com/hominin_evolution.html

(Apologies if someone else has already posted it.)

'Luthon64
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Thanks very much!

Juustin said:
2. Why is there no such animal as the crocoduck?
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But, but, there is! Damien Evans has one as his avatar. Native to Australia, proper name the drucodile. That's all the problem was. A "crocoduck" would be a crocodile father, a most unlikely prospect, the drucodile has a duck father.

Bleeding obvious.
 
UnrepentantSinner said:
This is one of those phrases that gets bandied about as if its self explanitory, but really should have a paragraph or so to go along with it.
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Yeah, to respond to this Creationist canard, we need to look at the ideological underpinnings of Creationism. Creationism shares a great deal with Platonism. I don't know how much is them just coming to the same conclusions, how much from Creationists being cultural descendents, and how much from them getting idea from the same source, but looking at the idea of Platonic Forms gives great insight into Creationist thinking. To a Creationist, each animal is an instantiation of a metaphysical Form. For instance, there is a concept of a Dog Form which exists independently of any actual dog. Each dog has all the characteristics of that Form, as well as variation not prescribed by that Form. Having four legs is part of the Form, so all dogs have four legs. Well, there are some that don't, but they're "deformed", or perhaps I should say "deFormed". The Form has some restrictions on color (no blue dogs), but for the most part, color is unspecified, so dogs can come in all sorts of colors.

There are then types withing the Form, such as terriers and poodles. All of these types are contained within the Form, and it's possible for one type to evolve into another type; creationists refer to this as "microevolution". The Form comprises all possible variations of dogs. It's possible to evolve a "new" type in the sense that hasn't been instantiated before, but the type won't be "new" in the sense of being added to the Form; the form already included the type, even if no one had seen it before.

Creationists consider the transition from one Form to another to be "macroevolution", and contend that it is not possible. In support of this, they demand "transitional" animals. By this, they mean an animal that instantiates two different Forms. Now, it's important to note, at this point, that they are closing off the debate. They are asking for something that, according their ideology, is impossible. They assume from the very beginning that these Forms exist, and from that they "prove" that evolution is impossible. This is the logical fallacy of "begging the question": they assume the conclusion from the beginning, and base their proof of assuming that they are right.

From the Creationist point of view, there are two types of species. There are "real species", such as crocodiles and ducks, which fit into this Form framework. Through their transcendent Forms, they have an existence independent of anything else. Then there are "transitional" species, such as the crocoduck, which have no Forms of their own. The are defined simply in terms of other Forms (in this case, the crocodile Form and the duck Form), and thus have no existence separate from those other species.

So, yes, you and arthwollipot are getting at the same point: on one hand, every species is transitional in that it has no eternal Form which it follows; every species is constantly evolving, and any permanence is due to environmental equilibrium, not some supernatural “Form” keeping the species in line. On the other hand, no species is transitional, in that each species exists on its own accord, and no species exists merely in relation to other species.

The apparent contradiction comes from the fact that when Creationists talk of “transitional” species, they are speaking of something defined in terms of Forms, a fictitious concept.

Perhaps a good analogy would be to compare it to history: in each moment in history, the world is changing from one state to another, but if you look at any moment in time, the world exists in the present, not as merely a transitional state from one state to another.
 
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