The evidence for evolution., Since it comes up... over and over...

[TheDreadedAtheist]

This is a topic from another forum, created entirely by someone that goes by the name of Reformentia. It is rather long, but conclusive. This will include many posts, so I would apreciate it if they were uninterupted, no posting untill I am dont please. From this sentence on, it is only his words.

This topic is not "evolution vs. creationism". This is "Here's the evidence for evolution, discuss". If you think it's incorrect or insufficient, feel free to share why. I am constantly seeing claims that there isn't any evidence for evolution occuring... like for example in the current "evolution vs. creationism" topic. This is a response to those claims.

This is a series of posts I made on the General forums of the game that shall not be named back about a year or so ago. It's my best shot at putting together a relatively comprehensive overview of the kind of evidence we're dealing with when we talk about evolution occuring and presenting it in a way which is hopefully fairly clear even to those who don't have much familiarity with the subject. Some visitors to the Legion offsites may have seen these there as well.

If anyone notices any broken links I'd appreciate having them pointed out. I think I've verified them all but I might have missed something.

Post 1: Dating Methods

Carbon (C14) Dating:

C14 dating is used to date the remains of organic, air breathing organisms up to approximately 50,000 years old. While living these organisms breathe the atmosphere, which contains trace amounts of the radioactive isotope Carbon 14 that is constantly being produced in the upper atmosphere through neutron bombardment. So long as they are alive the C14 content of their bodies will remain in equilibrium with the C14 content of the atmosphere. When they die respiration ceases, along with the intake of any new quantities of C14. Over time the C14 decays with a half-life of 5568 years into N14. By measuring how much C14 remains un-decayed the time elapsed since the death of the organism can be determined.

A common misperception of C14 dating is that it relies on the assumption that atmospheric C14 levels remained constant in the past so that we can know how much C14 an organism started off with. While this was an assumption made when the technique was first developed about half a century ago it has not been the case for several decades. Historical atmospheric C14 concentrations have been charted and calibrated using both dendochronology and lake varves which incorporate organic sediment in their annual deposition layers. One particularly good example of this is Lake Suigetsu in Japan where cores have been drilled to a depth of 45,000 annual layers. Because of the layering process we have an independent count of exactly how old every layer is… and because the layers incorporate organic material (the remains of a surface algae which dies off every year and sinks to the bottom of the lake) each layer can be C14 dated as well, and using these two data points the atmospheric C14 content can be charted all the way back for the entire time span encompassed by the varve core. This data (cross-checked against multiple other sites and methods) then allows us to apply C14 dating to other sites already knowing how fluctuations in atmospheric C14 concentrations in the past will effect the results… and allowing us to calibrate out error that would otherwise be introduced due to those past fluctuations.

Just one more note on C14 dating... once this calibration scale was applied it was discovered that previous C14 dates had been underestimating ages. By a few percent. There are also the occasional examples of C14 dates which have supposedly been wildly inaccurate. Many of these examples are the result of grossly improper applications of the method. For example, one I have encountered quite often is the "C14 dating of a living snail shell" that came back as thousands of years old... I believe this is one of Hovind's pet illustrations. The mollusks in question were extremely inappropriate subjects for C14 dating, which anyone familiar with the method would know. They form shells which are in equilibrium with the carbon content of the water sources in which they live... NOT the atmosphere. No C14 lab worth it's salt would ever date such an organism without warning the person requesting the test of the reservoir effect that would most likely render the test results invalid.

 

[TheDreadedAtheist]

Longer Ranged Radiometric Dating:

There are a great many longer ranged radiometric dating methods using radioactive isotopes with longer half-lives than C14. I’ll quickly review a couple of them.

1. Argon-Argon (Ar40-Ar39) dating. Argon-Argon is a method closely related to Potassium-Argon, where the age of a sample is determined by measurement of how much of the potassium-40 in the rock has decayed into Argon-40. However, with the Argon-Argon method it is also possible to tell if there is any Argon-40 present which is NOT a product of the decay of the potassium in the sample. This is done by placing the sample to be dated in close proximity to a nuclear reactor for several hours. The resulting neutron bombardment from the reactor causes potassium-39 in the sample to be transformed into Argon-39. Argon-39 has a half-life of only 269 years, and is not found in nature… so any subsequently detected argon-39 is known to be a product of the decay of the potassium-39 in the sample. After this is done the sample is then put through an incremental heating process and the released argon-40/argon-39 ratios are measured at every stage. A sample that contains only argon-40 that is a product of the decay of the potassium-40 in that sample will release argon-39 and argon-40 in the same proportion at EVERY heating step. If there is parentless argon-40 in the sample that is not a product of the decay of that sample’s potassium-40 however the ratios will change at different heating stages. This eliminates the popular claim that excess parentless argon in a sample can cause that sample to date as older than it really is.
2. Rubidium-Strontium (Rb-Sr) dating. Very useful for dating igneous rocks in particular. There are many different isotopes of Strontium (Sr-87, Sr-86, etc&#8230. Rubidium-87 decays into Strontium-87. When magma first cools into an igneous rock formation all parts of the rock will have the same ratio of strontium-87/strontium-86 because the isotopes are freely dispersing through the molten rock prior to that time. However, once the rock hardens different parts of the rock will have different rubidium/strontium ratios than others since the atomic make-up of rubidium is larger than that of all the strontium isotopes and it will be incorporated into the structure of some minerals more or less easily than that of others. From that point on the rubidium will continue decaying into strontium-87… and the areas of the rock with higher initial ratios of rubidium/strontium will have their concentrations of strontium-87 increase at a higher rate than those with a lower ratio of rubidium-strontium. By taking multiple measurements from different sections of a sample and plotting their final ratios of strontium-87 to other strontium isotopes which, not being byproducts of the radioactive decay of other elements, have remained stable since the formation of the rock… the initial ratios of those isotopes throughout the sample can be determined and the elapsed time since the samples formation is established. Again, this method is highly resistant to any objections that we have to assume the concentrations of the isotopes in the samples being dated in order to date them. That is simply not the case. The initial concentrations are experimentally determined.

For further info on the various radiometric dating methods, and since (I believe) all the other participants in this discussion are Christians, I would highly recommend this page:

http://www.asa3.org/ASA/resources/Wiens.html#page%206

Dr. Wiens goes into considerably greater detail than I have, there’s the added advantage of several visual aids, and he’s not a godless atheist like me for those that tend to distrust us as a matter of principle… just in case there are any of those reading along.

 

[TheDreadedAtheist]

Constancy of Decay Rates

For my last point in this post I’ll address one more often-encountered claim. That we just assume that decay rates have remained constant over time. This is not true. The constancy of decay rates over time has been independently established by multiple tests. Among them the isotopic analysis of the byproducts of the Oklo Natural Fission Reactor at Gabon which establish that decay rates have undergone absolutely no detectable change for a minimum of the past 1.8 billion years. There is also an entire battery of interstellar observations that can be made that would detect a past alteration of decay rates since that would require a change of the fine structure constant of the universe… with quite readily observable effects. Effects which are never observed no matter how far away (and thus how old) the object is we are looking at.

And that is a summary of the “evolutionary” position on dating methods. The dates arrived at are accepted and used in establishing ancient evolutionary timelines, ages of fossils, etc... because there is extremely solid evidentiary support for the reliability of those methods.

 

[TheDreadedAtheist]

Post 2

When the geologic column was first being mapped out by geologists they could only establish relative dates of the position of formation of a given layer in the column based on the premise that 'layers buried further down' = 'older than newly formed surface layers'… with care being taken to ensure you weren’t analyzing something like an overthrust where one section of plate has pushed up on top of another one. Then came radiometric dating which allowed them not only to independently test that hypothesis but to assign specific age values to each of those layers… resulting in the modern understanding of the geologic column. For example, in Glenn Morton’s article on the geologic column at Talk.Origins (http://www.talkorigins.org/faqs/geocolumn/) one of the references used is a well dug in North Dakota to a depth of over 15 thousand feet. The following layers were encountered at the respective depths: (Fm = Formation, Lm = Limestone, Grp = Group)

Tertiary Ft. Union Fm ...............................100 feet
Cretaceous Greenhorn Fm .......................4910 feet
Cretaceous Mowry Fm............................ 5370 feet
Cretaceous Inyan Kara Fm.......................5790 feet
Jurassic Rierdon Fm................................6690 feet
Triassic Spearfish Fm..............................7325 feet
Permian Opeche Fm................................7740 feet
Pennsylvanian Amsden Fm.......................7990 feet
Pennsylvanian Tyler Fm...........................8245 feet
Mississippian Otter Fm.............................8440 feet
Mississippian Kibbey Lm...........................8780 feet
Mississippian Charles Fm..........................8945 feet
Mississippian Mission Canyon Fm................9775 feet
Mississippian Lodgepole Fm.....................10255 feet
Devonian Bakken Fm.............................11085 feet
Devonian Birdbear Fm............................11340 feet
Devonian Duperow Fm...........................11422 feet
Devonian Souris River Fm.......................11832 feet
Devonian Dawson Bay Fm.......................12089 feet
Devonian Prairie Fm...............................12180 feet
Devonian Winnipegosis Grp.....................12310 feet
Silurian Interlake Fm..............................12539 feet
Ordovician Stonewall Fm........................13250 feet
Ordovician Red River Dolomite.................13630 feet
Ordovician Winnipeg Grp........................14210 feet
Ordovician Black Island Fm.....................14355 feet
Cambrian Deadwood Fm.........................14445 feet
Precambrian.........................................14945 feet

The article also includes 25 other sites where the entire column has been observed.

The span of ages since associated with each of those eras since the advent of radiometric dating are:

Tertiary –------------------ 1.8 million -> 65 million years old
Cretaceous --------------– 65 million -> 145 million years old
Jurassic ----------------– 145 million -> 205 million years old
Triassic ----------------–205 million -> 250 million years old
Permian –---------------- 250 million -> 290 million years old
Pennsylvanian –---------- 290 million -> 325 million years old
Mississippian –------------ 325 million to 355 million years old
Devonian –--------------- 355 million -> 420 million years old
Silurian –----------------- 420 million -> 445 million years old
Ordovician –-------------- 445 million -> 490 million years old
Cambrian Deadwood Fm –- 490 million -> 545 million years old
Precambrian –------------------------ 545+ million years old

So, the further down we go, the older the dates we see. Exactly as predicted. But that isn’t the only indicator to consider, there is also the fossil composition of the geologic column. I’ll do a quick overview of which fossils are found in which layers for now... starting with what are dated as the oldest layers and progressing through to the youngest. Note that the precise locations of many of these "earliest known fossil" finds are constantly being adjusted to some degree as more and more fossil finds come in and the body of what is known is added to.... for example, not too many years ago the earliest known multicellular fossils were early Cambrian (540 million years old) but then someone found some in layers about 20 million years older than that and the date of the earliest known multicellular fossils got shifted back a few percent into the late Precambrian. This is to be expected... and will certainly continue to happen in the future.

 

[TheDreadedAtheist]

Precambrian
--In the oldest dated layers of rock in the Precambrian there has never been a fossil found. Of anything. Ever.
--As we move to newer layers in the Precambrian we start finding fossils of single celled organisms at about the 3.5 billion year mark. They appear to be prokaryotes. We find fossils of nothing else.
--In still newer layers we begin finding fossils of what seem to be eukaryotic single celled organisms. (Prokaryotes have cell structures that lack mitochondria and nuclei, eukaryotes incorporate mitochondria and nuclei).
--In the late Precambrian layers leading up to the Cambrian, we begin finding fossils of small, simple, multicellular organisms (for example: the Ediacaran fauna) and also fossils of what appear to be simple chloroplasts.

Cambrian
--Once we reach the Cambrian we have the “Cambrian Explosion”. Keep in mind that this “explosion” takes tens of millions of years… some people have the unfortunate tendency to think this means that: *poof*… a bunch of different animals just all showed up simultaneously.
--By the end of the Cambrian we see the emergence of the earliest representatives of most existent phyla. Note that for the most part they look absolutely nothing like modern representatives of those phyla… another point on which people have an unfortunate tendency to become confused. They think that (for example) because we have brachiopods today, and brachiopods showed up in the Cambrian, therefore modern brachiopods have been around since the Cambrian. This is just plain wrong.
--Among the organisms first appearing in the Cambrian are: Arthropods (trilobites!), Molluscs, Chordates (near the end of the Cambrian), Brachiopods, etc…

Ordovician
--The first fossil Bryozoans show up in the Ordovician, little colonies of interconnected aquatic organisms that ten to inhabit rock surfaces, etc…
--The first coral fossils.
--Earliest jawless fish, although there is some evidence they may have shown up in the late Cambrian.

Silurian
--Fossils of jawless fish are abundant and diverse. Earliest fossils of fish with jaws are found.
--The first fossil evidence of any land organisms. Fungi, and also cooksonia, the earliest known plant with a vascular network.
--By the late Silurian we also find primitive fossil arachnids and centipedes.
--Note that we have four and a half billion years of rock layers and find no evidence of anything non-aquatic until the latest ten percent of them.

Devonian
--Earliest fossils of tetrapods (amphibians).
--Towards the end of the Devonian we find the earliest fossils of seed bearing plants.

 

[TheDreadedAtheist]

Mississippian and Pennsylvanian (Combined = Carboniferous)
--Earliest amniote fossils.
--Tetrapod fossils become increasingly diverse.
--Land based plant fossils also diversify.
--Towards the end of the Pennsylvanian the earliest diapsid fossils are found (animals with two fenestrae. Ie: reptiles)

Permian
--For most of the Permian increasingly diverse examples of the previously mentioned groups are found…
--At the end of the Permian there appears to be a large scale mass extinction event. A massive number of species found in the fossil record prior to this time cease to be found at any point later (goodbye trilobites… you had a good run&#8230.

Triassic
--The emergence of the dinosaurs in the fossil record. The popular giant versions are not found at this point in the fossil record… Triassic dinosaur fossils consist of smaller representatives of that group.
--Towards the very end of the Triassic we find the first fossils of small mammals.

Jurassic
--Dinosaur fossils get bigger and more diverse.
--Crocodiles show up.
--By this point in the fossil record aquatic life is extremely diversified. Sharks, rays, fish, squid, ammonites, all kinds of aquatic plants…
--Land plants also become increasingly diverse, as well as mammals.
--Near the end of the Jurassic, we have Archeopteryx. Clearly reptilian… but feathered.

Cretaceous
--Fossils of flowering plants (angiosperms) appear.
--Fossils of modern looking versions of some mammals and insects.
--Dinosaur fossils continue to diversify. A crowd favorite, T-rex, makes it’s appearance in the cretaceous layers. Unfortunately for it:
--At the very end of the Cretaceous there is another apparent mass extinction event, the K-T event. No further fossil evidence of dinosaurs and many other species found previous to this point in the fossil record are found in later layers. The K-T boundary marks the end of the Cretaceous period in the geologic column, a thin layer in the column with heavy iridium concentrations, found worldwide, leading to the hypothesis that there was a massive meteor/asteroid strike at this time which kicked up enough impact debris to lay down a coating over the entire surface of the planet. This event is more well known than the Permian mass extinction, even though it appears to have wiped out a smaller percentage of the extant species than did the Permian event.

Tertiary
--Within the Tertiary layers we find fossils of modern animal forms. Modern angiosperm plants, mammals, ray-finned fish, birds, etc…
--We begin finding the first primate fossils right near the KT boundary. They’re small… in appearance they resembled something like a squirrel. The first prosimian fossils (for example: Smilodectes) show up in the early Tertiary layers. The first ape and monkey fossils begin appearing in the mid-Tertiary layers. ( Apidium, Aegyptopithecus, etc…). Ape and monkey fossils continue to diversify throughout the later layers of the Tertiary. Approaching the end of the Tertiary the first Hominid fossils are found, dating back approximately 5-6 million years. It bears thinking on that hominid fossils occupy only the upper approximate 1% of the geologic column. Fossils of homo sapiens are not found in Tertiary layers.

 

[TheDreadedAtheist]

Note that the well mentioned earlier was dug in a basin, beginning below the very upper layers (the Quaternary layers which are dated at 1.8 million years to present) which are populated with modern looking animal and plant fossils. Hominids of varying morphological similarity to homo sapiens are found throughout these layers, with fossils classified as archaic and then modern homo sapiens found in the most recent layers, dating as far back as several hundred thousand years... a fraction of a percent of the span represented by the column.

We never find mammal fossils embedded in pre-Carboniferous layers. We never find bird fossils in Permian layers. We never find primate fossils in Jurassic layers. We never find angiosperm fossils in the PreCambrian. We never find reptile fossils in the Ordovician layers. Etc.

This kind of distribution presents quite a distinctive pattern... which will be elaborated on as the discussion continues.

 

[TheDreadedAtheist]

Having covered why radiometric dating is considered reliable, how the geologic column appears, and how the cross correlation of radiometric dates, fossil composition, and layer depth in the column all converge on expectations it’s time to take a closer look at some of the transitional sequences in the fossil record. I could just list some series of transitional fossils, but quite frankly there’s no way I could summarize that info in a manageable sized post and do it near as well or as comprehensively as the Transitional Vertbrate Fossils FAQ at talk.origins does so so I’ll leave the listing to them:
http://www.talkorigins.org/faqs/faq-transitional.html
Instead, here I’ll focus on just a few example transitions with some detailed discussion.
Reptiles to Mammals
The list provided at the link above for this particular transition is extensive, covering a sequence of 30 fossil species… the early quite reptilian, then reptilian but with some somewhat mammalian features… then reptilian with some more than somewhat mammalian features… then a solid mix of reptilian and mammalian features… then decidedly mammalian with reptilian features… then mammalian with some somewhat reptilian features, and finally mammalian with few if any reptilian features.
One particularly well illustrated example of what was occurring during this process is the development of the mammalian ear from reptile jaw structures… illustrated here:

Starting at the far left side of the image we have the timescale of which periods each of the fossils are found from. As we move forward from the Carboniferous to the Jurassic we see the clear gradual change in the shape of the skeletal structure in each consecutive example. The left hand column of images if the view of the jaw from the inside. The right hand column is the view of the same jaw from the outside. The bone highlighted in yellow is the articular reptilian jaw bone, which eventually becomes the mammalian malleus (the “hammer” in the ear). The bone hignlighted in pink is the reptilian angular jaw bone, which eventually becomes the tympanic annulus in mammals. The bone highlighted in light blue is the reptilian quadrate jaw bone, which eventually becomes the mammalian incus (the “anvil” in the ear).

 

[TheDreadedAtheist]

This particular sequence is also an excellent illustration of the gaping flaw in claims of “Irreducible Complexity”. Such arguments simply don’t understand how evolution progresses. Someone who held to the IC line of argument would look at something like the ear and say “Well, what good is an ear without the hammer? Huh? What good is half an ear? All those interconnecting bones would have to evolve all at the same time! That’s just silly... so the ear is Irreducibly Complex”. (And if you don’t believe me, read it for yourself. A group of people proclaiming themselves to be “responding to evolutionist propaganda in the media” wrote a whole big long article on how the human ear is irreducibly complex because if you take away one of it’s parts right now it’ll stop working.: http://www.darwinism-watch.com/bbc_evolutionarytales_02.php)
On the surface of it, if you don’t really understand how evolution operates, that article has a certain compelling appeal to common sense. People who haven’t been exposed to the full weight of the evidence for evolution and how it operates think that is a perfectly reasonable statement. It is however dead wrong, as we can clearly see. They look at a modern human ear, which is the product of millions of years of refinement to optimize it for operating with the structures available to it… and then just because after all that fine tuning if you suddenly come along and yank a gear out of the mechanism it stops working it couldn’t have developed gradually? Nonsense. Nobody with any knowledge of evolution would ever say that at some point in the past there was some animal with an ear that was completely missing a malleus… but otherwise was an ear exactly like a modern human with all the same bones in the same shape for no apparent reason whatsoever… just waiting around for a fluke mutation to pop that bone right in there out of nowhere. That is an absurd representation of evolutionary progression and does not remotely resemble what is encompassed by evolutionary theory. It is nothing but a flimsy strawman.
On to the next example:
Reptiles to Birds
Another of the big ones, and also another of the favorites of the Irreducible complexity crowd. “What good is half a wing?” is a question you’ll see asked quite often in Evo/Creo discussions.
Well, let’s just see about that:

Here we have four images of different forelimbs.
At the top we have Ornitholestes. A bipedal dinosaur found in the late Jurassic.
Below that we have the rather well known Archeopteryx, found at the very end of the Jurassic. Notice the forelimb skeletal structure is practically identical… the claws are a little more hooked, the second and third digits seem to have fused, the bones are just a slightly different shape… but Archaeopteryx is feathered. Apart from that it is clearly more reptilian than bird and there’s almost no chance it was capable of flight. At best it’s modified forelimbs provided it with some extra lift while leaping.
Below that we have Sinoris. An archaic bird from the Cretaceous. It had everything it needed anatomically to be fully flight capable. That’s right… that forelimb is a an early version of a wing…. which still has the claws from when it used to be a forelimb on the end of it. I don’t exactly see a useless “half a wing” stage between those first three forms.

Below that is a modern chicken wing… which serves to demonstrate just how much a wing can change given 60 million years of evolutionary adaptation... but that’s a change between wing and wing so there’s hardly a need for a “half a wing” stage between those two. Unless of course, considering the rather unimpressive flight capabilities of the chicken, you consider them to have "half a wing".

 

[TheDreadedAtheist]

Hominid Evolution
And for the final example… us.

Entries are:
A) Pan troglodytes, chimpanzee, modern
B) Australopithecus africanus, STS 5, 2.6 My
C) Australopithecus africanus, STS 71, 2.5 My
D) Homo habilis, KNM-ER 1813, 1.9 My
E) Homo habilis, OH24, 1.8 My
F) Homo rudolfensis, KNM-ER 1470, 1.8 My
G) Homo erectus, Dmanisi cranium D2700, 1.75 My
H) Homo ergaster (early H. erectus), KNM-ER 3733, 1.75 My
I) Homo heidelbergensis, "Rhodesia man," 300,000 - 125,000 y
J) Homo sapiens neanderthalensis, La Ferrassie 1, 70,000 y
K) Homo sapiens neanderthalensis, La Chappelle-aux-Saints, 60,000 y
L) Homo sapiens neanderthalensis, Le Moustier, 45,000 y
M) Homo sapiens sapiens, Cro-Magnon I, 30,000 y
N) Homo sapiens sapiens, modern
With the exception of the first skull, a modern chimpanzee for comparison purposes, all the skulls are arranged in chronological order. The blue pieces in the skulls are reconstructions, everything else is original fossil material. The progression should be obvious. Decreasing upper jaw protrusion, increasing brain cavity size, the changing brow ridges… on some other skulls (examples below) where dental records are more intact changing size of the canines is also evident.
I should also mention that the consensus view today I that the Neanderthal were not direct ancestors to modern humans but more like cousins. A very recent branch off of the hominid line which subsequently went extinct.
Now, if we were only to display B and N directly next to each other I doubt that there’s an anti-evolutionist on the planet who wouldn’t immediately declare something very like “Well, one’s an ape and one’s a human. They’re obviously different. Don’t tell me you think we could have come from THAT”
But just put B and C next to each other and ask them if “microevolution” could change one into the other. I doubt they could deny it. And thus they would declare they were the same “kind” and this was only minor variation within kinds.
Only put C and D next to each other and ask.
Only put D and E next to each other and ask.
Etc…
This is clearly a transitional sequence between a modern human form and an early primate form… exactly the thing it is constantly being claimed doesn’t exist.
For a better of view of some of these fossils click this link then follow the instructions below it:
http://www.anth.ucsb.edu/projects/human/#
-Click on “Enter the Gallery”. Don’t have pop-ups disabled.
-Along the bottom of the window that opens click on the seconf last image that looks like a gorilla (it’s actually a chimp).
-If you click and drag on the skull that comes up you can rotate it through a full 360 degrees. This lets you get a much better look at the overall shape of the skull. Also, if you hold down the shift key then click and drag you can measure the skull since they aren’t displayed to scale
-After that move on and click on the picture of the human, the bottom sequence will zoom in to show a progression of fossil hominids. You can click on each of them and manipulate them the same way. They are also arranged in chronological order as they are dated and found in the column.
To sum up... the claim that "there are no transitional fossils" has been around for a very long time... and it has been completely wrong for a very long time. Unfortunately I don't expect to stop hearing it any time soon. These fossils provide clear indication not only that gradual change of species occurs over time, but in what manner it has done so. [/QUOTE]

 

[TheDreadedAtheist]

Post 4

The Nested Hierarchy.

This is one of the most fundamental concepts which needs to be properly understood if you want to properly grasp the evidence for evolution. It describes the structure of the pattern of biological diversity produced by an evolutionary process. Evolution is the only process which predicts and explains such a pattern.

The nested hierarchy is a consequence of the way in which genetically heritable traits are transmitted from generation to generation. For an illustration, see the following (animated gif):

http://img267.echo.cx/my.php?image=phyloanimated0in.gif

“NGT” represents a point at which a new genetic trait is introduced to a population which through natural selection comes to be spread throughout that population to the point where it reaches fixation in the genome. From that point on it will be heritable by all the future generations of that population. Such an event can occur at any time, in any group, but due to the nature of biological reproduction and genetic heritability it can be propagated only “downstream” of the point at which it is introduced. So, the earlier in the process a new trait is acquired, the wider a cross-section of the final population it will be present in. Any traits acquired after that point will be found grouped into smaller and smaller cross-sections of the population and always completely contained within the groupings of earlier acquired traits. For example, in an evolutionary scenario we never expect to see something like this:

http://img278.echo.cx/my.php?image=phylozoomednever0gf.gif

There is no way an “ABCF” combination could coexist with the other final products listed there. There is no evolutionary pathway for producing both that combination and the others shown. (That red dotted line does not happen in an evolutionary framework)

To contrast, if we were examining the products of a common design process we not only could, but would expect to see such outcomes all the time. If while working it’s way along those branching design paths a designer came up at some point with the “C” trait and noticed… “hey, this works better than anything I’m using over on that “AF” development line” then of course any designer would utilize that knowledge in his other designs. For example: The human eye vs. the octopus eye. The eyes on an octopus are far superior in design to our eyes. Their optic nerves attach in a manner which does not produce a blind spot in their vision, that same attachment anchors their retinas, and because all the nerve connections come in through the rear of the eye they do not degrade visual acuity. In our eyes the optics nerve pokes through the back of the eye causing a blind spot which our brains must constantly correct for, because our retinas are not anchored by the nerve attachments a sharp blow to the head can detach them, and because the nerve attachments are in the front they get in the way of incoming light screwing up our visual acuity. Any designer who knew how to build an octopus eye would know there was a better way to design an eye than that. The evidence indicates however that the octopus evolutionary path simply experienced optical development which was superior to anything that occurred in human ancestry after the two branched off from each other… and after that branching occurred there was no way in which to share the advances experienced on one line with the other. Not within an evolutionary framework.

Now, what do we see when we look at the pattern of biological diversity present today? Here’s an example using 30 major examples (animated gif, modified from the universal phylogenetic tree diagram in Doug Theobald’s “29 evidences for macroevolution”. Takes a little while to cycle through.)

http://i82.photobucket.com/albums/j243/gco...al_Animated.gif

http://i82.photobucket.com/albums/j243/gco...l_Animated2.gif

As you can see, a distinctive nested hierarchical pattern, precisely what is predicted and explained by an evolutionary development process. No other process has ever been proposed that would produce that particular distinctive pattern. I am quite aware that someone can now come along and say “well a designer could have designed it so that it made that pattern on purpose” but the point is that it doesn’t matter what pattern was found you could always say the same thing. It’s an unfalsifiable hypothesis... which is another way of saying a completely useless answer. It tells us nothing. At all. It’s the same as saying “I hereby predict we will find… something!” and then when we do find “something” pointing out how the findings are completely consistent with your “theory”.

Evolution on the other hand makes a very specific prediction which is a necessary consequence of the mechanisms it describes… a prediction which, if the theory were wrong, could very easily be disproven. That prediction is however specifically confirmed by the data. That’s considered very powerful evidence that a theory has it right.

What is considered even more powerful evidence is that the fossil record overlays the nested hierarchical pattern created by the phylogenetic groupings of modern species which is shown above to an extremely high degree of accuracy. The innermost (and therefore within an evolutionary framework, latest to be introduced) groupings of genetic characteristics are the latest to have representation within the fossil record… etc…

This excellent cross-correlation of data between modern biological diversity and the fossil record is known as the twin nested hierarchy.

 

[TheDreadedAtheist]

Post 5

Alright… so we’ve covered radiometric dating and why it’s considered reliable, the geologic column and the fossil record conforming to overall evolutionary expectations, the existence of transitional sequences within the fossil record showing evidence of past evolutionary events, and the distribution of genetic characteristics among modern life that conforms to the pattern produced by a biological evolutionary process in which traits are inherited from common ancestry. We’ve covered that the fossil record also overlays that distribution to a high degree of accuracy with characteristics in inner groups having their first representations later in the fossil record.

Next piece of evidence. Vestigial and other non-coding genetic characteristics.

Vestigial genetic sequences.

Looking at the nested hierarchy shown in the previous post we can see humans and chimps (along with the rest of the primates) are grouped inside a larger group of animals. Their grouping also indicates a recent evolutionary divergence from that group. This is corroborated by the fossil record. Now… the members of this larger group of animals are capable of synthesizing ascorbic acid, also known as vitamin C. Humans and primates are not. As our little evolutionary branch of the tree only recently diverged from the rest of the group, and since large scale gene deletions are extremely rare (usually a gene is disable because of a disabling mutation… it is not deleted from the genetic code), if evolutionary theory is correct we should expect to still be able to find clear evidence of the genetic sequence responsible for the synthesis of ascorbic acid in humans and primates (even though we are not capable of such synthesis) and subsequently compare it to the functional sequence in other animals and determine what alteration made to it caused it to become non-functional. This is a prediction unique to evolution, relying entirely on the premise that we inherited our genetic material from an ancestral source we share in common with those other animals in the larger group.

This prediction was confirmed in the early 1990s with the identification of the L-gulano-gamma-lactone oxidase genetic code in humans and primates. Subsequent analysis showed it had experienced a frame shift mutation that had caused it to become non-coding.

Let me summarize this again to ensure it is fully understood.

1. Humans and primates do not produce their own ascorbic acid. From simple direct observation there is NO reason to think they would have the genetic code required to do so.
2. The nested hierarchical structure humans and primates fit into within an evolutionary framework however indicates that they diverged from a wider group at a time when ascorbic acid synthesis was already present in the genome of the group, and thus that genetic information should have been inherited.
3. Since we do not produce ascorbic acid, and since it would be unusual to have an entire gene simply deleted in entirety from the genome, evolutionary theory and evolutionary theory alone predicts we should find vestigial genetic code for the production of ascorbic acid which was inherited from an earlier common ancestor in the human and primate genomes… and which has since been deactivated by mutation.
4. They looked for it. They found it. Deactivated by a frame shift mutation that wiped out the end of the sequence on that gene. Prediction confirmed.

Once again… I can’t stop someone from looking at this clear example of evidence of common evolutionary descent and declaring “it just looks that way because it was designed that way” but at this point, whether it’s impossible to disprove that statement or not, it would be beginning to get silly… proposing that the same non functional section of genetic code would be designed into humans and primates… and in such a way that it looked just like a functional piece of code in other animals that had undergone a mutation. If you want to design an organism that doesn’t synthesize its own ascorbic acid you sure as heck don’t need to give it most of the genetic code to do so only to make it not do so!

And this is hardly the only example of a vestigial genetic sequence that fit this pattern…. Olfactory receptor genes, RT6 protein genes, etc… the genetic code of all kind of organisms is packed with pseudogenes that used to code for something in an ancestor… still codes for that same function in related organisms, but has been disabled in one particular group by a crippling mutation while the bulk of the genetic code remains present.

Continuing on that line, there is also the matter of endogenous retroviral insertions... some of you may recognize the next section. I’ve posted most of it previously in another thread.

 

[TheDreadedAtheist]

Endogenous Retroviral Insertions

Retroviruses contain viral RNA, as opposed to the DNA in humans and other animals and plants… and they also contain a reverse transcriptase. What this means is that they have the ability to insert the complimentary DNA sequence of their own RNA genetic code into the genetic code of the host organism they infect. It’s how they reproduce. Example of a retrovirus: HIV.

Here’s how it works in a little more detail.

The virus infects a cell. It then releases the reverse transcriptase. The reverse transcriptase makes a copy of viral DNA from the viral RNA. The viral DNA then gets spliced into the DNA of the infected host cell, at a random location… so from now on every time that cell’s DNA is replicated the viral DNA gets replicated right along with it. In the meantime the viral DNA in the cell serves as the template for producing new copies of viral RNA. Now, while the initial insertion point of the viral DNA is random, in any subsequent copies made when the cell reproduces the exact same location of the viral DNA will be copied as well.

(Side note: The random nature of the retroviral insertion is one well known hurdle faced by researchers of genetic therapies, since if they attempt to engineer a retrovirus to deliver their developed therapy to their patient a random insertion could place it in the middle of DNA that was already coding for something else that was fairly important)

When a retrovirus infects a host’s reproductive system - and thus the copies of the host’s DNA which will be passed on to it’s offspring - it becomes heritable by the host organism’s offspring, passed onto them just like any gene would be. And again, the location of the viral DNA within the genetic code will be the same as in the parent organism the DNA was inherited from.

The human genetic code is huge. It’s over 3 billion base pairs long. The genetic codes of the other primates (chimps, gorillas, orangutans, gibbons, etc&#8230 are similarly massive. The odds of a single retrovirus infecting two of these individual species independently and just happening through pure coincidence to randomly splice themselves into the exact same location in their DNA are, obviously, not good.

So if we were to find, for example, that an analysis of human and chimp DNA revealed a single identical retroviral genetic sequence at an identical location that would be extremely solid evidence that they had both inherited that genetic sequence from a common ancestor who was originally infected by the retrovirus… thus also inheriting it’s common location in their genome. Not only is this a similar type of evidence that is possible from analysis of other genetic information… but this information in particular is completely immune to being hand-waved away as being somehow due to “common design” of similar appearing animals or functions as IDers and creationists attempt (and I stress “attempt&#8221 to do with other findings. There is no rational way to argue that a viral infection was an element of the design of an organism.

So, in all of our studying of the genetic codes of humans, chimps, and other primates have we found a case of a retroviral insertion in an identical location in both humans and another primate? No…

We’ve found multiple cases.

The odds of finding a single example occurring by coincidence are mind bogglingly bad. The odds of finding multiple examples occurring by coincidence are exponentially worse. They defy description. And for the final nail in the coffin (as if we needed it), there’s the pattern we find these common insertions in:

So far (with the sequencing of the human and primate genomes still far from complete) the primate species we share the most common insertions with are chimps, which all other genetic evidence says are the most closely related primates to humans. We share the second most common insertions with gorillas… the second most closely related primates. Third and fourth most common insertions = orangutans and gibbons respectively… also the third and fourth most closely related according to the other genetic evidence. Fifth most = old world monkeys… sixth most = new world monkeys… fifth and sixth most closely related groups, respectively, according to the other genetic evidence.

A diagram of the pattern of insertions in question, courtesy of talk.origins:

http://www.talkorigins.org/faqs/comdesc/im.../retrovirus.gif

The arrows show where the evidence indicates the original retroviral infection occurred. Again, it’s impossible to prevent a claim that this is the case “just because God made it that way”… but again, it’s getting silly when the alternative hypothesis to what has been presented is that God deliberately designed identical remnants of past genetic infections into different species in a nested hierarchical structure in just such a way that it would really really look like they evolved from common ancestry.

 

[TheDreadedAtheist]

Post 6

Phylogenetic Analysis.

Previously we kind of skimmed over the creation of a phylogenetic tree with a very simplified example of how they are constructed using only some selected major genetic characteristics. In the last post we touched on how even much less obvious genetic characteristics can also be analyzed for phylogenetic relationships… like ERVs. As th discussion progresses the importance of the nested hierarchy and it’s very nontrivial nature will continue to become more apparent. Like in the case of ERVs it goes significantly beyond such superficially obvious observations as “we never expect to find snakes producing orange juice”. It applies right down to the molecular level even to genetic sequences which have absolutely no reason, from the standpoint of observing the “obvious” groupings of organisms, to display nested hierarchical patterns... except that evolutionary theory says they should because of their patterns of common ancestry.

When actually constructing a consensus phylogenetic tree such as the one shown at (http://tolweb.org/tree?group=life_on_earth ) not only are a great many genetic traits taken into account, but a rigorous mathematical analysis of the actual DNA sequences of the organisms in question (where such DNA is available) is done to create cladograms (the branching diagrams showing patterns of descent) with the highest possible percentage confidence. These techniques have been tested in situations where the correct evolutionary relationships are already independently known for an absolute certainty to verify that they do in fact not simply produce an evolutionary relationship but the correct evolutionary relationship to within a very low margin of error..

One example:

http://www.unifesp.br/dmip/Sanson-etal,2002.pdf

In the paper above the researchers started with an original sample of DNA from Trypanosoma cruzi. They bred it over successive generations and allowed it to continually mutate, and every 70 generations 2 of the resulting DNA sequences were isolated at random and then used to found new populations. This process was repeated 4 times until 16 different ancestral DNA sequences had been generated. A rough diagram illustrating the process is shown in Figure 1 on page 2 of the paper.

Now this might not sound like much… but the number of possible phylogenetic trees that can be generated for a group of N different related genetic sequences increases in a steeply exponential manner as N increases. That number is described by the equation: (2N-3)!/((2^(N-2)) (N-2)!).

For 2 organisms this gives us only 1 possible tree (which should be obvious).

For 3 organisms it gives us 3 possible trees.

For 5 it gives us 105.

For 10 it gives us over 34 million.

For 16 organisms that gives us a total of (29!)/((2^14)(14!)) = 29!/1.428x10^15 = 6.19028x10^15 possible phylogenetic tree diagrams that can be generated. Picking the correct one isn’t something you can do by luck... unless of course you can beat better than 6 quintillion to 1 odds. If you have mathematical routines that can, when applied to genetic sequences from those 16 organisms, subsequently generate the correct tree or even a very close approximation of it, it can safely be concluded that it’s because the routine works and works well.

 

[TheDreadedAtheist]

So, they subjected the 16 final (terminal) sequences to phylogenetic analysis to see what the calculated highest likelihood phylogenetic tree for the organisms was. The result is displayed in figure 3 on page 5 of the paper. The top tree is the actual observed branching pattern during the experiment. Each of the circles represent a point at which sample sequences were isolated to found new populations… ie: an evolutionary branching of the population into two separate groups. They are numbered to correspond to the illustrated points in figure 1. The numbers along each branching line along the diagram represent the “branch length”. A value that can be used to represent either time between nodes… or amount of genetic sequence changes between nodes. In this case, the latter. For example, between node 2.1 and 3.1 the sequence undergoes 5 changes… while between node 2.1 and 3.2 it undergoes 6. T1 through T16 are the final 16 sequences generated as the end result of the process.

Displayed below that is the highest probability tree returned by the phylogenetic analysis of the sequences. Note that not only is every single node and branch correctly placed but the predicted length of each branch is also found in 29 out of 30 cases to within the calculated margin of error (on the branch linking the 2.2 and 3.3 nodes it missed the branch length by 1 sequence change more than it’s calculated margin of error.)

The entire evolutionary history of all 16 terminal sequences back to their common ancestor… reconstructed completely starting only from the end product and working backwards. Just as we can do with any other living things we have DNA samples from.

In short, the method works. Very well.

As noted in discussion of the previous topic there are, occasionally, some grey areas where it is not clear where a species should be placed in the tree to within a node or so due, in most cases, to some small scale discrepancy between phylogenies based on morphological data and phylogenies based on molecular or genetic data. An example will follow further down the post.

Evolution critics will often point to these regions of uncertainty as some kind of indication that evolutionary theory is incapable of explaining the evolutionary origins of some species… that evolution is “stumped” by certain species and should therefore be rejected. This is ludicrous. Even in a cladogram of only 16 organisms if this had been true of one of them… and a single branch had been mis-located by one node… given the amount of possible trees that had to be eliminated to arrive at the correct location for each of those nodes and branches it amounts to the equivalent of a margin of error in the results of 1 part in roughly 3x10^15…. or a measurement inaccuracy once we reach the equivalent of the 14th decimal place. An incredibly tiny margin of error if ever there was one.

 

[TheDreadedAtheist]

To contrast … last I checked the charge of the electron has been measured reliably to 7 decimal places. G, the gravitational constant, to 3 decimal places. Nobody in their right mind suggests that this means we need to toss out physics and start from scratch because G and the charge of the electron “stumps” us through our inability to achieve a 100% perfect correlation between experimental results. 99.99% is pretty damn good too.

99.999999999...% is extraordinary. (They don’t say that evolutionary theory is one of the (if not the) most strongly evidentially supported scientific theories in the history of science just because they think it sounds good.)

Is it frustrating on those occasions when there is one branch on the tree with a positioning uncertainty of one branch... or maybe even two on sufficiently zoomed in scales? Yes. Ideally we would like to have absolutely every last detail right down to every single individual species nailed down with absolute certainty. It is why scientific research always continues to try to narrow those uncertainties... to add just that one more decimal place to that correlated value…

Is it somehow fatal to evolutionary theory that we still require some more data and better measurements to get that one branch position nailed down once and for all? Ridiculous.

Actual example of discrepancy between two phylogenetic analyses:

http://www.talkorigins.org/faqs/comdesc/images/croc.gif

These are two different phylogenies for species of crocodile. One based on the morphological data, one based on a molecular analysis of the c-myc proto-oncogene… taken from this study:

http://163.238.8.180/~fburbrink/Courses/Se...cs/gharials.pdf

Morhohological data will under almost any circumstances be considered secondary to molecular and genetic analysis... this being because the units of biological inheritance are the genes themselves. Analyzing morphology is observing a secondary characteristic of inheritance and thus has an expected slightly larger margin of error which can occasionally cause minor discrepancies in the two phylogenies like this one. If you scan down to the figure on page 8 of the linked paper you get a slightly better picture of the extent to which the sequences are analyzed to establish the tree in a genetic analysis. The chart shows the multiple mutations which were experienced along each branch to arrive at the final c-myc sequences.

The two charts created differ only on their placement of Gavialis. Based on the morphological data it was expected it would be less closely related to Tomistcoma than to other crocodiles… but the genetic analysis says they’re more closely related than other crocodiles. Notice that with the exception of the single Gavialis branch both trees are identical.

Note that even if we are to consider only these 8 species in isolation from the much larger tree into which they fit, and in which their position is well established, a difference of a single branch position for a single member of the group between one measurement and the other is miniscule. There are over one hundred and thirty five thousand possible phylogenetic trees for a group of 8 organisms… having the morphological and genetic sequence data correlate to this degree is an impressive level of agreement. Resolving that last branch position is the same as resolving a measurement out at the 4th or 5th decimal place. We still want to do it, but it’s not bringing the theory crashing down while we’re waiting for the call to be made. It’s not causing any difficulty to the theory at all.

 

[TheDreadedAtheist]

Post 7

Compilation of additional information.

Since topic 7 is looking like it will be the last official topic post in the thread I’ll try to cover a little wider range of additional points in this one.

Chromosome Fusions

A lot of animals have different numbers of chromosomes. An often raised objection to evolution is that this means at some point an organism would have been born with a different number of chromosomes from the rest of the population but it wouldn’t have had anything it could mate with that had the same number of chromosomes so the mutation wouldn’t have been preserved. This objection is based on the false idea that animals with different numbers of chromosomes are incapable of interbreeding.

If this was true the existence of modern domesticated horses would be something of a genetic miracle. Domestic horse populations have 64 chromosomes… wild horse populations have 66.

In reality chromosome fissions and fusions are hardly an unknown phenomenon.

One such fusion clearly occurred after the hominids branched off from the rest of the primates. Humans have 23 pairs of chromosomes, all the rest of the primates have 24. Evolutionary theory and the nested hierarchy then tells us this means there was a fusion event which reduced the number of chromosomes in humans to 23 after their ancestors split off from the wider population. If this prediction is true, we should be able to see clear evidence of it in a chromosomal analysis.

Lo and behold:

http://www.evolutionpages.com/chromosome_2.htm

There is overwhelming evidence that human chromosome 2 is the product of the fusion of two chromosomes which just happen to look basically identical to two chromosomes found in chimpamzees… as seen in the image included in the above link.

Note that this is not just evidence that human and chimp genetic sequences kind of look the same. The telomere and centromere sequences in the middle of human chromosome 2 are clear indication that that chromosome is the product of the combination of two different pre-existing independent chromosomes. If humans had been independently created in their modern form rather than having evolved into it from a common ancestor with other animals there is no reason to expect find something like this in the human genome… but there it is.

Biogeography and Paleobiogeography

Biogeography is the mapping of spatial patterns of biodiversity. Ie: which animals and types of animals are found in which geographic regions. Combined with paleobiogeography, which is the mapping of the same in the fossil record, this presents us with yet another piece of corroborating evidence for evolution. Fossil forms which are morphologically transitional stretching back from modern animals back to earlier ones are found in geographically contiguous locations throughout the record. Obviously this is something which is to be expected if all those transitional forms were to have evolved one from the other. If they were not transitional ancestral organisms but rather just completely independent separately created lineages of some kind there would be no reason to expect the geographical distributions we do observe that they fall into.

 

[TheDreadedAtheist]

Properties of DNA Replication

DNA is the genetic identity of an organism; it’s the primary factor in making an organism what it is biologically. The DNA changes - the organism changes.

It is a well established property of DNA that it undergoes mutation during replication on a fairly regular basis. Different nucleotides are substituted for each other, new nucleotides are inserted in or deleted from a sequence resulting in shifted reading frames, entire genes are occasionally duplicated and subsequently subjected to independent mutation events, chromosomes split and fuse… and over time those changes spread even as they continue to accumulate. There’s no avoiding that simple fact.

The genetic code of all living things is in a constant state of change and thus all living things are changing. Generation, after generation, after generation.

Another simple fact is that, unless under the influence of some restraining factor which places boundaries on the absolute range of change achievable, this fact presents us with a very simple equation:

Constant Change + Time = Greater Change.

And in dealing with the history of biological life on Earth we are considering a very, very great length of time indeed.

As for that “restraining factor”, this is one place you’ll see a great deal of anti-evolutionists try to take a stand… if you can call it that. You’ll see them say things like ”Oh sure, evolution can happen… but only microevolution that produces variation within species. Evolution doesn’t make new species.”

Of course they’re quickly forced to retreat from this claim as soon as the numerous examples of observed speciation events are called to their attention demonstrating quite unequivocally that evolution not only can but does produce new species.

The fallback position from that point is usually to say that evolution can’t produce new “kinds” of organisms. Even a cursory examination of this position topples it in short order as well. When asked to define how to recognize what a “kind” is so that this claim can be put to the test no answer ever seems to be forthcoming. When asked the nature of the genetic barrier somehow preventing genetic changes from crossing the threshold between “kinds” no answer ever seems to be forthcoming. When asked for an example of which genetic code would be preserved by this barrier they can’t describe no answer ever seems to be forthcoming. When asked on what possible other basis the claim that evolution doesn’t result in these new “kinds” is made no answer ever seems to be forthcoming. When asked how exactly a person can claim that “A” never happens when they can’t explain why it is that “A” never happens or even worse, define what “A” is in any detail whatsoever … well, just guess.

Rates of Genetic Change

Another claim you’ll see sometimes made against evolution is that there hasn’t been enough time for all the observed “microevolution” to produce the degree of biological diversity we see today. Again, a claim that is quickly debunked.

Multiple studies have been done measuring average rates of mutation within species, average genetic divergence between species, and amount of time since divergence of those species ancestral lines indicated by the fossil record in which that genetic divergence had to occur. Despite the vague claims against evolution in this respect every time an actual objective measurement is performed it somehow fails to turn up any kind of problems.

For example: the fossil record indicates the ancestors of chimps and humans diverged approximately 6 million years ago. Based on analysis of the regions of the human and chimp genomes with the highest divergences from each other today (worst case scenario from the evolutionary perspective) and using that as the basis for calculating how fast mutation would have had to occur to produce the differences between those sequences if starting from a common genome the required rate of mutation arrived at is approximately 2x10^-8 nucleotide substitutions per site per generation… taken from Futuyama’s ‘Evolutionary Biology’, Third Edition. Current measurements of the average rate of mutation of human and chimp genomes gives a figure somewhere between 1x10^-8 and 5x10^-8 nucleotide substitutions per site per generation… right where it should be.

Conclusion

Every way we can think of to look at the data it comes out supporting evolutionary theory. Geology... Biology and Molecular Biology... Paleontology... Genetics... every way we have of approaching this issue gives us the same answer. That evolutionary theory has it right.

 

[TheDreadedAtheist]

I am done posting it now. You can respond...

 

[TheDreadedAtheist]

Wow, no responses? Did I beat the CrEvo forums?