irreducible complexity takes a hit.

This is seven years old but it is important to note that when Dr Behe used the blood clotting system as an example of irreducible complexity, he was mostly depending on God of the Gaps. Step by Step evolution of blood coagulation.

As for vertebrates, although the jawless fish have genes for generating the thrombin-catalyzed conversion of fibrinogen to fibrin, they lack several clotting factors, including two thought to be essential for the activation of thrombin in mammals. Fish in general lack genes for the "contact factor" proteases, the predecessor forms of which make their first appearance in tetrapods. The full complement of factors known to be operating in humans does not occur until pouched marsupials (opossum), at least one key factor still absent in egg-laying mammals such as platypus.

Via Pharyngula, uh, via csicop.

Behe's other example, the flagellum of certain bacteria, has also taken a beating since the Dover Trial.

Darwinism Refuted tells us*:

The complicated structure of the bacterial flagellum is sufficient all by itself to demolish the theory of evolution, since the flagellum has an irreducibly complex structure. If one single molecule in this fabulously complex structure were to disappear, or become defective, the flagellum would neither work nor be of any use to the bacterium. The flagellum must have been working perfectly from the first moment of its existence. This fact again reveals the nonsense in the theory of evolution's assertion of "step by step development." In fact, not one evolutionary biologist has so far succeeded in explaining the origin of the bacterial flagellum although a few tried to do so.

DR is correct in that no one has described step-by-step evolution of the flagellum.  Molecules don't leave much in the way of fossils so there is no trail heading back.  If someone walks across a muddy field, we expect footprints and similar evidence.  If someone swims a similar distance, no one expects to evidence of such a thing.
DR is incorrect in stating, "If one single molecule in this fabulously complex structure were to disappear, or become defective, the flagellum would neither work nor be of any use to the bacterium."

Nick Matzke at Panda's Thumb shows that many molecules can be removed. A screenshot of only some of the proteins involved and how necessary they are:

He summarizes with:

Total number of proteins listed: 42
(this table excludes the chemotaxis proteins; there are ~10 chemotaxis proteins in standard E. coli, but the number can range from 0 to 10+ in various bacteria)
Total number thought to be indispensable in modern flagella: 23 (55%)

If you noted that 55% is still pretty high, I agree.  Still, 45% is plenty reducible.

More at Panda's Thumb:

The relevance to flagellum evolution? Variants of at least seven T3SS proteins are also found in the flagellum, within a subsystem called the protein export system. This sits within the basal body and funnels replacement flagellin subunits to the filament, using a mechanism remarkably similar to the T3SS. In fact, the two systems are so similar that the flagellar protein export system is now considered to be a subclass of the T3SS (Trends in Microbiology, vol 14, p 157).
Such similarities, or “homologies”, are strong evidence that the two systems evolved from a common ancestor - analogous to the way that the arrangement of bones in the limbs of horses, bats and whales reveal their common ancestry despite their very different outward appearance and function. Similar homologies can be seen in the DNA sequences of genes, and in the amino acid sequences and 3D structures of proteins - all are clear evidence of shared descent.

A good video of the evidence.

Ken Miller - quoted in the video above - discusses the subject at his website.

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* Defeating Darwinism also considers the eye an example of irreducible complexity:

For an eye to be able to see, the 40 or so basic components which make it up need to be present at the same time and work together perfectly. The lens is only one of these. If all the other components, such as the cornea, iris, pupil, retina, and eye muscles, are all present and functioning properly, but just the eyelid is missing, then the eye will shortly incur serious damage and cease to carry out its function.

DR seems unaware of all the animals that exist without eyelids.  Someone should tell them about fish, lizards and snakes.

Evidence for evolution, an overview

There is no proving in science. Below I am offering evidence or support for evolution.  No single point 'proves' the theory of evolution but they all support it.  At the end of this essay, I will offer an explanation for gaps in the evidence.

Evidence for evolution:

Linnaeus

 "In Linnaeus's original system, genera were grouped into orders, orders into classes, and classes into kingdoms. Thus the kingdom Animalia contained the class Vertebrata, which contained the order Primates, which contained the genus Homo with the species sapiens -- humanity. Later biologists added additional ranks between these to express additional levels of similarity."

Linnaeus was not an evolution proponent, having died eighty years before Darwin publicized his theory.  But his classification system offers great support for the theory of evolution and a universal common ancestor. A designer who made every species as one-offs, with no required connection to each other would not have included such similarities. Sure, in the smaller classification levels - Genus or maybe Family - two animals that live in similar ways can be expected to look similar.  This explanation falls apart at the higher levels,though.  Fish and cephalopods both live in the ocean, at a wide variety of depths. They are both cold-blooded although their bloods are very different.  Of interest here, we mammals, and all vertebrates all share the same kind of eye as fish while squid, which live in the same conditions as fish, have a different architecture for their eyes.
Some creationists want to see "Croco-ducks" or "Fronkeys" (frog-monkeys).  It is possible that a creator could have made such things but they would destroy the theory of evolution because attributes specific to different classifications would be mixed.

Recent additions and descriptions of the Tree of Life

"The tree of life is one of the most important organizing principles in biology," said Jill Banfield, a UC Berkeley professor of earth and planetary science and environmental science, policy and management. "The new depiction will be of use not only to biologists who study microbial ecology, but also biochemists searching for novel genes and researchers studying evolution and earth history."

As the Sensuous Curmudgeon says, 

But we can’t help wondering what people like ol’ Hambo [Ken Ham of AiG] make of this. Did all those species somehow appear in the 4,000 years since Noah’s Flood? Why does every species — including our own — fit into its proper place in this one hierarchy — as if they were all related? Why aren’t there any unique outliers that don’t fit anywhere?

The Daily Mail has a great slideshow. After finding the best images I could, I have -as usual- shrank them a little.  If you want to see them full size, follow the link.

 In the image above, you can see Animalia, which includes us, at the top right-hand side.  Note the whole tree above is the small, narrow set of branches on the bottom of the image below.  Animalia is not a large part of life's diversity - it includes us but it not therefore a prominent group.

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Fossils

Fossils offer two forms of support for evolution. First, various groups of fossils are always linked and found together and these groups always exclude other fossils.  Humans are never found with dinosaurs and rabbits are never found in the Cambrian.
Second, transitional fossils are only snapshots in time and have limited value, but they do show that a transition from fish to amphibian is at least possible.  When a creationist claims there is no way  fish could evolve into land animals "How would it walk? How would it breathe? It's impossible!" these transitions -and there are a great set of seven transitions from fish to amphibian - show it is at least possible.  They don't prove a universal ancestor but they do show it is possible.
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Bio-geography: As Pope John Paul II wrote, "The convergence, neither sought nor fabricated, of the results of work that was conducted independently is in itself a significant argument in favour of this theory."  The very distribution of animals on the Earth supports the Theory of evolution.  This is a convergence of age of the Earth, plate tectonics and evolution.  This support also specifcally argues against the view some creationists hold of a Global Flood and resettlement of the Earth originating from the Middle East or Turkey.
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Vestigial organs

"Charles Darwin was familiar with the concept of vestigial structures, though the term for them did not yet exist. He listed a number of them in The Descent of Man, including the muscles of the ear, wisdom teeth, the appendix, the tail bone, body hair, and the semilunar fold in the corner of the eye. Darwin also noted, in On the Origin of Species, that a vestigial structure could be useless for its primary function, but still retain secondary anatomical roles: "An organ serving for two purposes, may become rudimentary or utterly aborted for one, even the more important purpose, and remain perfectly efficient for the other.... [A]n organ may become rudimentary for its proper purpose, and be used for a distinct object."[8]"

Cave Fish are a great example - some are blind and appear to have no eyes, but in fact have eyes that are overgrown by flesh and skin.  This would seem to show they are a new species that originated from one that had functioning eyes.  It would be hugely difficult to suggest that the Designer accidentally included them in building this specific animal.  Again, this does not 'prove' there was no Designer or 'prove' evolution true, but evolution and the generation of new species has to be seen as the most reasonable explanation.

From AiG:
"The Definition of Vestigial Organs Has Been Changed
As the list of “functionless” organs has grown smaller and smaller with advancing knowledge, the definition of vestigial organs has been modified to include those whose functions are claimed to have “changed” to serve different functions. But such a definition removes the burden of proof that vestigial organs are a vestige of evolution. Thus, the evolutionist might concede that the human coccyx (“tail bone”) does indeed serve an important function in anchoring the pelvic diaphragm—but still insist, without evidence, that it was once used by our ancestors as a tail."
This has to be seen as dishonest as Darwin himself stated that secondary functions are possible.  If the originator of the theory specified this in his definition, it cannot be said to have changed.
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DNA

I have not dug into the arguments whether chimps and humans share 98% of our DNA.  Creationists seem to suggest that all English books use a lot of 'e's so stating that two separate books both have more 'e's than any other letter is silly. I would agree with this simple statement but I don't think geneticists use such a simple argument.  I haven't bothered to look.
However, we do share inserted viral DNA in ways that best support a common ancestor.  Also, we have 23 pairs of chromosomes and chimps have 24.  The thing is, we have a chromosome pair that shows two pairs got stuck together in historic times.  This does not mean that we share an ancestor with chimps, but offers support.
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Gaps in the evidence

We will never have the entire picture.  We will never have the original cell that evolved into all life as we see it today.  We do have hundreds or thousands of arrows all pointing to the same place so we don't need an 'X' to mark the spot.

Why are we lacking in evidence?
Fossils: There were 5 billion passenger pigeons alive at one time.  We have zero fossils of them.  There are a few hundred thousand chimpanzees alive now and probably more in times past.  We have fossils of fewer than ten individuals.  There are places near the border between Eastern Canada and the US where the tides are phenomenally fast.  Paleontologists go out at low tide and try to recover some fossils, working quickly because they know the next cycle of tide will wear them away to nothing -and display new ones.
As chimps and passenger pigeons show, few animals actually fossilize.  As the tidal rocks show, many fossils are destroyed before they are ever seen.
With organic chemicals, the traces or fossils are even less enduring.  We don't know how a bacterial flagellum evolved and don't know what every individual step would have looked like but we do have a halfway point.
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More than enough evidence points to the Theory of Evolution and none contradicts it.

Essay on Quora

I've been spending way too much time on Quora these days, but I think my writing has improved as a result.  I'm sure Quora has an official description but I think of it as a thoughtful Yahoo Answers! or the like.  In my writing there, I have tried to explain things clearly and sympathetically to the person asking the question and those with similar questions.

I wrote 'sympathetically' because I spent most of my time answering questions about evolution and i try to imagine the (entirely anonymous) questioner as seriously asking and willing to learn.  That is not always the case away from Quora and admit with embarrassment that my responses have gotten hot and sometimes even rude.

I am one of the top ten answerers, as voted by readers, in Evolution (process) and am quite proud of the fact.  Here is my top essay there:

Science:

Is evolutionary theory falsifiable?

Again, please stay on topic without mentioning theistic arguments or involving God in the discussion. Please answer scientifically or logically... Many failed to do so in previous similar questions...



Brian Dean, science enthusiast and evolution proponent
35.6k Views • Brian is a Most Viewed Writer in Evolution (process) with 30+ answers.


There are two major or popular ways to falsify the theory of evolution. First, the famous 'rabbit in the Precambrian' fossil and second, far less famous and more recently proposed, finding two but not three or four species with a common ancestor containing the same viral DNA at the same location. I will give more detail on these points, but first I want to offer sympathy with your question.

The Theory of Evolution has changed and adapted and itself evolved over the past 160 odd years that it sure seems that nothing can falsify or disprove it. Lack of fossil evidence? ... Well, uh, Punctuated Equilibrium. Natural Selection isn't enough on its own to allow evolution of all the diversity we see? ... Well, uh, Sexual selection, Genetic Drift and Founder Effect can be used to patch over the flaw. 

More specifically, the theory of evolution somehow explains the human reproduction strategy of having few offspring and caring for them nearly forever and the salmon strategy of having thousands of eggs and not caring for them at all. (Note these are termed K- and r- selected strategies are are well explained here: K and r reproductive strategies ) 

Here I will say remind readers that I am an evolution proponent and described the above difficulties with acceptance of the theory as examples. Punc Eek does explain the fossil record pretty well, for example. 

The problem for evolution is that there are so many different strategies for success. Just as the US Navy does not use aircraft carriers exclusively, but rather a wide variety of craft suited to different purposes, small, simple living things succeed in situations where larger, more complex living things do not, and vice versa. 

Further, the asteroid impact that killed the dinosaurs and made room for mammals to grow and diversify has no place in the theory. The diversity of life is a complex mess and further confusion is added by inorganic events. 

All that said, back to my two claims on how the theory of evolution could be falsified or proven wrong. 

The "Fossil rabbits in Precambrian deposits" suggestion was an offhand one made by J.B. Haldane (Wikipedia tells me this may be untrue: Precambrian rabbit ) and can be expanded to mean any mammalian fossil found in rock over 250 million years old. From that same link are some reasons why such fossils might not disprove evolution:
" The first question raised by the assertion of such a discovery would be whether thealleged "Precambrian rabbits" really were fossilized rabbits. Alternative interpretations might include incorrect identification of the "fossils", incorrect dating of the rocks, and a hoax such as the Piltdown Man was shown to be."
Still, something of this sort would cause great problems for the theory. 

The discovery that viruses can and do insert occasionally their own genetic material into Eukaryote chromosomes is relatively new. The image below is slide 17 of this lecture PPT set: Bio%201130 c%203 19%20lecture

If Chimps and Bonobos shared the same bit of viral DNA and we did not, that would be no problem for the theory but if Gorillas and chimps carried the same viral DNA and we did not, this would be a serious problem for the theory. Or, if humans and gorillas carried the viral DNA but chimps or bonobos or both did not, we would have the same problem. There is evidence -somewhere and I cannot find the link or citation - for gorillas and orangutans that share the DNA of a specific virus that we humans do not have. Further study (again, going from memory only) showed the viral DNA was on different chromosomes and although from the same type of virus were different segments (gorillas had section A of the viral DNA and orangutans has section G, while the shared ancestor DNA should be of the same section), implying that there were two separate viral DNA insertion events. 

I would suggest a third thing that would prove evolution false would be eyeless vertebrates.... wait, there's a catch. There exist eyeless fish but these cave-dwellers actually have eyes that are covered by flesh. If a mammalian species were found to have no eyes and no vestiges of ancestors with eyes or genes for eye development, this would be a huge problem for evolution. 

Finally, and I am brushing against your limit against mentioning religion here, if we ever found the creatures that some creationists think evolutionists need, that would disprove evolution hard! I am writing about the 'croco-duck' the 'Bird-dog' and the 'bull-frog' that were championed by Ray Comfort and Kirk Cameron. And also the 'frunkey', that one creationist felt should exist between frogs and monkeys. 

As a test to the asker:
"Please answer scientifically or logically... Many failed to do so in previous similar questions."
Can you link to such an example?