This article is precisely what is wrong with evolutionary thinking by modern evolutionists. It is not science, nor even pretends to be. It is another one of those evolutionary just-so stories that is tailored to the imagination of the reader so that they may see the ‘evidence’ of evolution unawares that they were just deceived by masterful story-telling. These evolutionary just-so stories are fodder for the naive, for true believers, the gullible and naieve. As science, it does not wash. No doubt the writer of this argument is using the same technique that they themselves were sold on evolution.
I do not see the name of the author of the above article, so we do not know whose story this is. The author admits that some of the proteins required for the Flagellum are not present in the secondary system he references, then DECLARES this is no problem for evolution. And then he author adds his/her final piece of ?science? that supposedly proves Dembski wrong:
“It seems likely, then, that the evolutionary pathway that resulted in the flagellum also includes the type III secretory system. The flagellum, then, is not irreducibly complex.”
As I already stated, thie above statement is fodder for the naieve and ignorant, as science is does not wash. This is why I hate evolution theory, The arguments presented on its behalf are far far removed from hard science.
Science and math do have the ability to say ‘NO!’ to scientific hypothesis. Only a madman would disagree that Science has said ‘NO!’ to Abiogenesis, even though all the materials for making the proteins ‘exist on our planet’ (LOL).
For the same reason science says ‘NO!’ to abiogenesis, science also says ‘NO!’ to evolution, even if we assume the existence of the first self-replicating progenote, which not contain many if any of those 30 proteins necessary for the flagellum. However, I’m sure the author of the above article could confirm that this is no problem for evolution by declaring this is no problem for EVOLUTION by appealing to the ‘natural pathways of evolution’ which the reader is led to assume, does exist.
Hard science has revealed what appears to be the impossibility of mutations to exisitng Prokaryotes, or Eukaryotes for that matter, to produce new classes of proteins, and thus the new genes required for evolution. The Theoretical work of biological information specialist Hubert Yockey, confirmed by an MIT team led by Bio-Geneticist Robert Sauer, informs us that short proteins, consisting of 100 amino acids or less, have a 1 in 10^65 chance of being discovered by chance mutations to the amino acid chain choosing only from the 20 ‘left handed’ proteinous acids. For longer Proteins consisting of hundreds of amino acids the odds decrease astronomically. In short, the gap between the different classes of proteins are so astronomically huge that it is fair to conclude they could not have ‘evolved’ into existence from one to the other. It should also be noted that the known processes of making proteins in the cell has several precise checks and balances to assure faithful reproductions of all proteins being manufactured in the cell, including a few feedback loops that assure fidelity. And all the required functions must be present simultaneously or it does not work. Hox genes turn on or off entire sets of genetic functions. They are akin to our intelligently designed control panels used in buildings, be they electrical or pneumatic. Only recently has human intelligence been able to engineer and construct similarly complex specified machines, systems, and functions.
The problem with materialistic evolution is that it violates the 2nd Law of Thermodynamics. The 2nd Law requires that the flow of large masses of molecules, akin in number to those found on the tip of a needle, will always flow from states of low probability to states of ever increasing probability. And unfortunate for Darwinian or P.E. evolution, Chaotic meaningless arrangemeants astronomically outnumber the arrangemeants needed for life and for materialistic evolution.
In conclusion, real ‘HARD SCIENCE’ says loud and clearly ‘NO’ to evolution. OK, I’m finished, ye evolutionists may reply with your usual declarations and disbelief of my response to the current topic: ‘The Flagellum Unspun’.

Just for a bit of clarification on my above post, Yockey’s Theoretical calculation and the Hard Science results from Robert Sauer’s team at MIT, which confirmed Hubert Yockey’s Theoretical work, that out of every sequence of an proteinous amino acid arrangments that will function at least 5%, that 10^65 will will not, mostly due to the inability to fold.
Sauer’s Team stated that if two or more amino acids were randomly replaced, they expected the falure to function would rapidly increase enormously. They also reference Information specialists Hubert Yockey, stating their finding confirmed his theoretical calculation a decade ealier. The purpose of the test was to determine the true ambiguity of amino acid replacement in a protein.
It should be noted that yockeys Theoretical work displeased the pro-Evolution orthodoxy, They were not happy with Yockey’s resuts. Such a probability is certainly very damaging to any possibility of macro-evolution being at all plausible.
To counter this, a scientist with excellent mathematical skills, Ken Dill, using different assumptions than Yockey, arrived at a 1 in 10^15 probability of finding via an undirected search a protein molecule the size of cytochrome C, which under other reasonable assumptions may occur as frequently as once every 32 years.
However, Sauer and his MIT team proved Yockey to be correct and Ken Dill to have assumed wrongly.

Art…
If “The 2nd Law requires that the flow of large masses of molecules, akin in number to those found on the tip of a needle, will always flow from states of low probability to states of ever increasing probability” that would mean that skyscrapers, trees and basically anything with any sort of order would be impossible.
The “evolution violates the second law” argument is one of the easiest anti-evolution misconceptions to correct.

This post is based on an article by Ken Miller in my book, co-edited with Michael Ruse, titled DEBATING DESIGN (Cambridge University Press, 2004). The article by Miller came out a year or two before that (it was posted on his website) and I responded to it at http://www.designinference.com in an article titled “Still Spinning Just Fine” — you can find it there still. In any case, the field has moved on considerably since then. I encourage people to check out the work of the Evolutionary Informatics Lab (www.evoinfo.org).
–WmAD

“This post is based on an article by Ken Miller in my book, co-edited with Michael Ruse, titled DEBATING DESIGN (Cambridge University Press, 2004). The article by Miller came out a year or two before that (it was posted on his website) and I responded to it at http://www.designinference.com in an article titled “Still Spinning Just Fine” — you can find it there still. In any case, the field has moved on considerably since then. I encourage people to check out the work of the Evolutionary Informatics Lab (www.evoinfo.org).”

Why can’t you explain how the field has move on right here?

Not so Tm61, The 2nd Law of Thermodynamics applies to unfettered Nature, that is why it is called a Law of Nature!
It is quite obvious that humans can use their minds and know how to place boundary conditions on the laws of Physics and Chance to bring into existence specified complexity, such as computers and beautiful Mansions. This is the advantage that applied Intelligence has over nature. Keep in mind, left unattended by intelligent beings, Nature and the 2nd Law of Thermodynamics will take over and the Beautiful Mansion will decay as the molecules of its’ construction flow from the human-made states of low probability to natures states of higher probability, which is ongoing decay and disorder.

Art,
We are off topic again, but evolution does not violate the 2nd Law. You need to research trophic levels. Available energy decreases as you move down trophic levels (as the 2nd Law predicts), but complexity can certainly increase. Humans depend on sunlight for all our energy needs, but obviously a human is much more complex that sunlight, which in no way violates the 2nd Law. In relation to biology, basically the 2nd Law is just saying that less energy becomes available for work as you go down trophic levels, but it does NOT say that complexity must decrease.
I used to use the 2nd Law argument often when I was a young earth creationist. Now I see I only used it because I did not understand evolution, physics, or ecology.
I found my ecology textbook helpful in explaining trophic levels, and physics textbooks will explain the 2nd Law in a general way that I think would help you see the difference between free energy and complexity. So reading some college textbooks might help you out in understanding the 2nd Law and it’s relation to biology. They helped me a lot at least.

Dan
I never claimed there was a lack of energy for living things to survive, regardless of their trophic level.
I attended college for 5 years and earned degrees in Electrical Engineering, Math, History, and in my favorite subject in which I was an ‘A’ student, Physics. The earth abounds with energy, coming primarily from the sun.
But understand this, the principle of why the 2nd Law of thermodynamics works is due to the fact that large masses of molecules (e.g. the amount left by a pencil making a period)will continually flow from low probability states (i.e. arrangements) to ever higher probability states.
Physicist Richard P. Feynman explained entropy as the flow from order to disorder, from states of lower probability to states of higher probability. He gives the example of filming two gases, a gas of white particles and a gas of black particles, in a container separated by a boundary. He calls this state highly ordered as all the black particles in the container are all on one side and all the white particles are on the other side. When the boundary is removed, the particles will mix together, order decreases and disorder increases. This is considered an irreversible process. But Feynman has an objection, if you play the film backwards, the particles separate and all the white particles go to one side of the container and the black particles go to the other side of the container, and not only that, but careful observation shows that no physical laws are broken, all the particles are moving at just the right speed and are forming just the right collisions at just the right angle for this to happen. Thus the process is reversible and, Feynman adds, so are all the fundamental laws of physics. So what is it that makes the natural mixing of the two gases irreversible? Feynman’s answer is `probability’. The number of states (particle distribution) of disorder far outnumbers the number of states of order, so much so that it becomes unrealistic to expect reversibility. The gases are moving from states of very low probability to states of much higher probability, from order to disorder. Feynman considered it a mystery how the universe as a whole began (i.e. Big Bang) in such a low state of entropy.
If there were many more `orderly’ states that molecules can arrange themselves than there were `disorderly’ states for the molecules to arrange themselves into, then the natural flow would be from states of disorder to states of order. If this were true, and we also define “Orderly” as the molecular states needed for the origin of life and for the origin species, then Evolution could be possible.
For example of what Feynman is saying about the 2nd Law, when a large vase falls and smashes onto a stone floor, it could produce little tea cups if the probability of the molecules arranging themselves into cups was much higher as compared to any other possible configurations. But the laws of physics being what they are, the vase breaks up into many pieces of varying sizes and shapes that will be meaningless in terms of performing a useful function for human beings. The molecules of the vase have “naturally” undergone a change in arrangement from a specified complexity that performed a function for humans to a more probable disordered chaotic functionless arrangement.
Physicists are aware that Evolution is in need of a new natural law. A 1993 Time Magazine issue covered the astonishing explosion of diverse biological life that occured in a very narrow range of the Cambrian period. Nearly every known Phyla of life appeared at that time. Physicists have argued that Evolution will never make sense unless some new physical Law is discovered that will provide an ordering principle that can account for the natural organization of molecules into arrangements required for life.
e.g. A Phsyicist viewpoint
Physicist Henrik Lipson, an agnostic, examined evolution theory from the point of view of the 2nd law. His conclsuions was published in a science peer reviewed journal. The following are excepts of that aricle.
“I have always been slightly suspicious of the theory of evolution because of it’s ability to account for any property of living beings (the long neck of the giraffe, for example). I have therefore tried to see whether biological discoveries over the last thirty years or so fit in with Darwin’s theory. I do not think they do. … To my mind, the theory does not stand up at all.”
“Evolution became in a sense a scientific religion; almost all scientists have accepted it and many are prepared to ‘bend’ their observations to fit in with it.”
“I think, however, that we must go further than this and admit that the only acceptable explanation is creation. I know that this is anathema to physicists, as indeed it is to me, but we must not reject a theory that we do not like if the experimental evidence supports it.”
(Physics Bulletin, “A Physicist Looks at evolution,” Lipson, 1980, Vol. 31,p. 138.)
With Respect to Abiogenesis:
Nobel Laureate, Biologists Christian De Duve, in his 1995 book `Vital
Dust’, states that any and all scenarios for spontaneous generation
must be certain that each step of the process flows from lower
probability molecular states to higher probability molecular states so as not to violate the 2nd law.

Art,
You earned 4 bachelor degrees in 5 years? If you really earned 4 bachelors in five years you must be some kind of genius. I am seriously impressed, if that is the case. Or do you mean that you earned one degree with four majors?
Anyways, the 2nd Law does not mean that complexity cannot increase. Every explanation of the second law I have seen has said that it applies to closed systems, the earth is an open system. Also, the law is talking about NET entropy, not the entropy of each individual component of a system.
In ecology and evolution, the 2nd Law has to do with decreased energy available for work, NOT the inability for increased complexity. As I said earlier, if you take your view of the 2nd Law and apply it to trophic levels (a fundamental part of ecology) than even trophic levels violate the second law. A proper understanding should lead you to believe that trophic levels do not violate the second law, because energy to do work decreases over time, but complexity can still increase. The same is true for evolution.
According to your definition of the 2nd Law, not only does evolution violate the law, but so do trophic levels, embryologic development, the atom-creating Big Bang (a major foundation of your favorite subject in college), antibiotic resistant bacteria, and even micro-evolution of new traits within species.
If you accept antibiotic resistance, embryological development, trophic levels, or micro-evolution and admit that one or more do not violate the 2nd Law, then to be logically consistent you have to admit that evolution does not violate the 2nd Law. It is one or the other; you cannot use one definition of the 2nd Law to try to falsify evolution and another to justify trophic levels and embryological development.

Art,
The quotes you provided do not show that the physicist Henrik Lipson thought evolution violated the 2nd Law. His quotes only show that in his understanding of biology the evidence for evolution is not strong. That is a far cry from you saying he criticized evolution based on the 2nd Law. Maybe Lipson does think this, but your quotes certainly do not reflect this. Also, he is not a biologist and wrote 30 years ago before much was known about the overwhelming DNA evidence for evolution.
You said he is an agnostic, but if so Henrik Lipson is the strangest agnostic I have ever head of. I have never heard of a creationist-agnostic. Seems like an oxymoron to me.
I could not find much information on Lipson. The “peer-reviewed” journal is not listed as a peer-reviewed journal in my Universities historical journal database and “Physics Bulletin” does not have a website. A search for Lipson’s name in the databases Pubmed, Web of Science, google Scholar, JSTOR, and Academic Search Permier also showed no results for the physicist Henrik Lipson, so I can’t find any evidence that he published any other articles.
When I searched for his name in Google, I only found a few relevant hits. I actually only come up with a few posts on other blogs that are mostly copies of your above posts. I assume they are your posts, and not someone plagiarizing you. I guess you use this post often? I also find a reference to these quotes on TalkOrigins in the “quote-mine” section.
PS: It appears Lipson actually did accept evolution, he just did not accept Darwin’s mechanisms. Here is a quote that Lipson said to clarify his position on evolution (from Talk Origins):
“Several people have given clear indications that they do not understand Darwin’s theory. The Theory does not merely say that species have slowly evolved: that is obvious from the fossil record.” – H. J. Lipson, “A physicist looks at evolution – a rejoinder”, Physics Bulletin, December 1980, pg 337.
Anyways, whatever Lipson believed, he did not seem to argue that evolution violated the 2nd Law. From my quick research, Richard P. Feynman also seems to have accepted evolution, so obviously, contrary to your post, he did not think it violated the 2nd law.
Hope this helps.
- Dan