Carl Zimmer and fused chromosomes

Man, the lengths creationists, and ID is a form of creationism, will go to hide and protect their unsupported claims.

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.

Historic and Observational Science

From AIG:

[I]t is useful to divide science into two different areas: operational science and historical (origins) science. Operational science deals with testing and verifying ideas in the present and leads to the production of useful products like computers, cars, and satellites. Historical (origins) science involves interpreting evidence from the past and includes the models of evolution and special creation. Recognizing that everyone has presuppositions that shape the way they interpret the evidence is an important step in realizing that historical science is not equal to operational science. Because no one was there to witness the past (except God), we must interpret it based on a set of starting assumptions. Creationists and evolutionists have the same evidence; they just interpret it within a different framework. Evolution denies the role of God in the universe, and creation accepts His eyewitness account—the Bible—as the foundation for arriving at a correct understanding of the universe.

and:

IF AN IDEA IS NOT TESTABLE, REPEATABLE, OBSERVABLE, AND FALSIFIABLE, IT IS NOT CONSIDERED SCIENTIFIC.

and:

 The denial of supernatural events limits the depth of understanding that science can have and the types of questions science can ask. We may define naturalism and materialism as:
Naturalism: a belief denying that an event or object has a supernatural significance; specifically, the doctrine that scientific laws are adequate to account for all phenomena.
Materialism: a belief claiming that physical matter is the only or fundamental reality and that all organisms, processes, and phenomena can be explained as manifestations or interactions of matter.
The problem with the above definition of science is that, even though naturalistic science claims to be neutral and unbiased, it starts with a bias. The quote from Dr. Todd on page 19 demonstrates that bias: only matter and energy exist and all explanations and causes must be directly related to the laws that matter and energy follow. Even if the amazingly intricate structure of flagella in bacteria appears so complex that it must have a designer, naturalistic science cannot accept that idea because this idea falls outside the realm of naturalism/materialism. Many scientists have claimed that allowing supernatural explanations into our understanding of the universe would cause us to stop looking for answers and just declare, “God wanted to do it that way.” This is, of course, false.

The ability to study the world around us is only reasonable because there is a Lawgiver who established the laws of nature. Most people do not realize that modern science was founded by men who believed that nature can be studied because it follows the laws given to it by the Lawgiver. Johannes Kepler, one of the founders of astronomy, said that science was “thinking God’s thoughts after Him.” Many founders of scientific disciplines, such as Bacon, Newton, Kepler, Galileo, Pascal, Boyle, Dalton, Linnaeus, Mendel, Maxwell, and Kelvin were Bible-believing Christians.  

... In a biblical worldview, scientific observations are interpreted in light of the truth that is found in the Bible. If conclusions contradict the truth revealed in Scripture, the conclusions are rejected. The same thing happens in naturalistic science. Any conclusion that does not have a naturalistic explanation is rejected.

...Making a distinction between two types of scientific study helps us to understand the limitations of naturalistic presuppositions in science:Operational (Observational) Science: a systematic approach to understanding that uses observable, testable, repeatable, and falsifiable experimentation to understand how nature commonly behaves.
Operational science is the type of science that allows us to understand how DNA codes for proteins in cells. It is the type of science that has allowed us to cure and treat diseases, put a man on the moon, build satellites and telescopes, and make products that are useful to humans. Biblical creationists believe that God has created a universe that uses a set of natural laws that operate consistently in the universe. Understanding how those laws operate is the basis for scientific thinking.
Some events defy natural laws. Christians refer to these things as miracles, but naturalistic science must find a way to explain these occurrences naturally. This approach rejects miracles in the Bible because they cannot be explained using natural laws. Such scientists occasionally try to explain the miracles in the Bible as natural phenomena, but this ultimately undermines the authority of God and His Word.
Historical (Origins) Science: interpreting evidence from past events based on a presupposed philosophical point of view.
The past is not directly observable, testable, repeatable, or falsifiable; so interpretations of past events present greater challenges than interpretations involving operational science. Neither creation nor evolution is directly observable, testable, repeatable, or falsifiable. Each is based on certain philosophical assumptions about how the earth began. Naturalistic evolution assumes that there was no God, and biblical creation assumes that there was a God who created everything in the universe. Starting from two opposite presuppositions and looking at the same evidence, the explanations of the history of the universe are very different. The argument is not over the evidence—the evidence is the same—it is over the way the evidence should be interpreted.

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That's a long set of excerpts.  Read more -there is a lot more - at the link.

I feel there are two main themes in the post and in the excerpted above.  The (artificial) distinction between observational and historic science and the inclusion of the supernatural in science. I also want to look at the claim that natural laws require a lawgiver.

This all-in-caps quote demonstrates the perceived difference between observational and historic science."IF AN IDEA IS NOT TESTABLE, REPEATABLE, OBSERVABLE, AND FALSIFIABLE, IT IS NOT CONSIDERED SCIENTIFIC."

I agree with this wholeheartedly.  If only I could find an example of so-called historic science that failed these criteria.
Let's look at the Greenland Ice Cores.  Superficially, looking at the long, thin cylinders and counting backwards through the layers is problematic.  We have not seen the snow fall on that location for more than a few decades and as the layer pile up and squeeze those below, there might be changes in the way those layers look, confusing the observer.
However, there are ways to repeat the tests and falsify them.  Let's look at falsification first.  The original creationist argument mentions "isotopes" once in one sentence and never again.  The method of looking for differences in the isotope ratios is not explored and yet it is a way to test the results.  The article also leaves out the presence of identifiable volcanic dust and ash.  When researchers find dust at 200 years-before-present, they can look for records of volcanic eruptions and compare the dates.  This is the definition of falsification.

Is it repeatable?  Yes.  There is lots of ice out there and researchers can drill more than one core and compare the results of one to another.

The same thing happens when we look at the insertion of viral DNA and how if an this happened to an ancestor all the descendants should have the inserted DNA in the appropriate place.  Researchers in a variety of locations and labs can look at viral DNA and compare that to the DNA in humans and other apes and confirm to deny that the DNA is the same.  Exceptions can be looked for.  No such exceptions have been found.

The Sensuous Curmudgeon covered similar ground in 2012.

Now for whether the supernatural can tested in a scientific way.  No, it can't.  When I teach ESL to young children, I sometimes amuse them by appearing to push a piece of chalk into one ear and pulling it out the other.  If you accept the supernatural, then even if you see that the chalk is hidden in my hand in one performance, you have to accept that the next time I do the trick, real magic occurred.

In my opinion, the best response to the science-testing-the-supernatural claim comes from Richard Hoppe and his look at Behe's suggested bacterial flagellum experiment.  Behe had suggested that bacteria lacking a flagellum be exposed to condition that would favor the evolution of a flagellum to see if one actually evolved.

Hoppe thought about the results of such an experiment.  

But then Hoppe notes that Behe states we can know nothing about the Designer and Its abilities.  He then imagines the experiment runs its course and bacteria flagellum appear...

. Does that mean that evolution works and ID is “disproven”? Not at all. After all, since we know nothing about the skill set and intentions of the putative designer(s), it’s possible that the designer(s) somehow ‘watched’ our culture, and sometime during the course of the generations ‘reached’ in and poofed a flagellum into existence on one of the bacteria.

If a flagellum appears, it means that evolution occurred the bacteria gained the flagellum through evolutionary processes or that The Designer chose to give them a flagellum.  If no flagellum appears, it means evolution did not occur or that it did occur and the bacteria were about to sprout flagella but The Designer chose to remove it. 

 Adding the supernatural to the mix means nothing can be scientifically determined. The argument turns into the brain-in-a-jar-on-a-desk-in-a-lab hypothesis.  If the supernatural is accepted, then nothing is settled.  We see what The Designer wants us to see and nothing else.  I try to keep this a religion-neutral blog but the only rebuttal that I can see Christians make to this point is that the Christian God is always honest and never deceptive.  If that is the case, then we can accept what our senses inform us of and the supernatural is not relevant.

"The ability to study the world around us is only reasonable because there is a Lawgiver who established the laws of nature."
The laws are what is observed, not required.  The quote above makes the same conflation that allows the joke about the judge outlawing gravity to be funny.  The law of universal gravitation has nothing in common with the laws of your country against murder.  The former is a fact of the universe and the latter is a arbitrary rule made by humans.
Further, Ham et al require the 'lawgiver' to mess around with the laws of nature.  In addition to claiming that any change to the laws of nature would destroy us all, they need the speed of light to change so light from distant stars can reach the Earth in six thousand years or less.  They need ice layers in Greenland to pile up so they appear to show one hundred thousand years  after only four thousand years passed.
They simultaneously state that the laws of nature are unchanging and they may have been different in the past.
Henry Morris made this claim - link is to Talk Origins:

Radiometric dating assumes that radioisotope decay rates are constant, but this assumption is not supported. All processes in nature vary according to different factors, and we should not expect radioactivity to be different.Source:
Morris, Henry M. 1985. Scientific Creationism. Green Forest, AR: Master Books, p. 139.

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In his debate with Bill Nye, Ham stated that the current diversity of life evolved from the far-fewer animals on the ark, simultaneously arguing against evolution and requiring evolution to occur at far faster rates than ever observed.

Nye argued that there are some 16,000,000 species on the planet today, and that if there was a Flood only 4,000 years ago, and only 7,000 representative species on the Ark to start with, there would have to have been 11 new species evolving every day over the last 4,000 years since the Flood.

Why the theory of Intelligent Design is so hard to rebut.

It is because there is no clear theory of ID. John Pieret of Thought in a Haystack posted an interesting bit recently. Well, he posted more than a bit, but here is the bare minimum that I that describes his point.  I, on the other hand, am posting only a bit, so you can follow the link for more.

The many interesting examples that dominate the ID discussion—the little tail on the bacterium, our eyes or our blood-clotting mechanism, the explosion of new life-forms in the Cambrian period—are just snapshots of things in nature. They are not "evidence" for anything and won't be until the ID theorists develop a theory of how their "designer" works. Once they provide a well-articulated version of their central claim, we can decide whether or not our eyes—or our tails— support their theory.

Darwin knew this: 

About thirty years ago there was much talk that geologists ought only to observe and not theorise; and I well remember some one saying that at this rate a man might as well go into a gravel-pit and count the pebbles and describe the colours. How odd it is that anyone should not see that all observation must be for or against some view if it is to be of any service!

Pieret is quoting Karl Giberson who is describing a debate he had with Stephen Meyer.