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Darwin definitely noticed something in the Finch beaks. However, the changes that Darwin saw were due to natural selection, not evolution.

What is natural selection? It is the preservation of the species, not the origin. Natural selection is all about the specialization of existing structures that helps a species to survive in an ever changing environment. In short, it’s simply a population shift.

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What about general purpose structures like the human hand? What’s it good for? Can you bury a bone with it? Not too well. At least not by itself. It’s much easier with a shovel. Can dogs dig? Yes they can. Are they better equipped to dig? Yes.
What about swimming? Can a hand help you swim? Yes. Well? Ah, so so. Fish are much better equipped. They have fins.
What about flying? Can a hand help you fly? Not so far. Birds have wings that are much better for flight.
So what’s a hand good for? Well, it’s a general purpose instrument.
How can natural selection that operates off of specialization produce a general purpose instrument like the human hand? It can’t. It never did. It never will.

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ORIGINAL: alex123
Natural selection is generally considered to be the major process by which evolution occurs, not the process of evolution itself.

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It is now more and more accepted that NS is inadequate to be the fundamental process of Darwinian evolution.

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NS selects for structures that are best adapted to the requirements of the organism within its environment.

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If the organism is in the process of developing an intellectual appreciation of and contol over its environment and an advanced tool-using capacity then the best adapted structure is going to be a limb that can control tools,

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NS selects for structures that are best adapted to the requirements of the organism within its environment.

The above statement is not supported based upon observable evidence. NS does not select for structures, it shifts the population favoring those who’s existing structures that are best suited for the current environment. In other words, NS works with existing information, it never starts form scratch.

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NS has only been observed to occur with existing structures that provide immediate survival benefits. And now you’re telling me it can produce a general purpose organ that learns(i.e. a Brain). Sorry, but that organ can never develop either. At least not by natural selection.

For your scenario to see the light of day, parallel changes would have to occur. That will never happen because natural selection is a blind unintelligent processes. Beneficial parallel changes require future knowledge and a preexisting intact storage and retrieval system that can differentiate between helpful and harmful changes. In other words, you are venturing off into the area of irreducible complexity.

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ORIGINAL: alex123

"More and more accepted"? Hardly.

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The best that can be said for modern observations of gene expression is that "genetics might be a bit more complex than we thought",

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...nothing in the discovery of DNA-based genetics has invalidated the basis of his theory

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- far from it, the identification of the nature of mutation provides a mechanism by which new heritable characteristics can arise.

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...basic 'descent-with-modification' idea

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(and even more unlikely that the mechanism for internal self-organisation so hoped for by the DI will emerge).

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ORIGINAL: alex123

You assume that complex structures cannot arise by stepwise mutation/selection process because the absence of any one part causes the entire structure to fail and the organism is not viable without that structure?

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This is the old 'what-use-is-half-a-wing' argument and it fails for the heart and hand in the same way as it does for the eye, the blood-clotting cascade, the bacterial flagellum and all the other irreducible structures that have proved to be not so irreducible after all. It fails in detail because every slight modification improves the structure by a small amount (look at the sequence of 'eye' structures from a simple light spot to a human eye)

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Wings appear to have been arms that developed gliding potential, perhaps as a result of the increased aerodynamic capacity conferred by the insulating feathers. Convergent parallel processes can be seen in bats and pterosaurs and in modern animals such as flying squirrels and gliding frogs.
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For if it is true, as the Darwinian model of evolution implies, that all the character traits of living things were gained in the first place as a result of a gradual random evolutionary process, then why should they have remained subsequently so fundamentally immune to that same process of change, especially considering that many diagnostic character traits are only of dubious adaptive significance? It was precisely this fundamental constancy of the unique character traits, or homologies, of every defined taxon which led nineteenth century biology to the theory of types!" (Denton M.J., "Evolution: A Theory in Crisis," Burnett Books: London, 1985, pp.134-135)

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Modern Darwinism is built on what I will be calling “The Primary Axiom”. The Primary Axiom is that man is merely the product of random mutations plus natural selection. Within our society’s academia, the Primary Axiom is universally taught, and almost universally accepted. ….

Late in my career, I did something which for a Cornell professor would seem unthinkable. I began to question the Primary Axiom. I did this with great fear and trepidation. By doing this, I knew I would be at odds with the most “sacred cow” of modern academia. Among other things, it might even result in my expulsion from the academic world.

Although I had achieved considerable success and notoriety within my own particular specialty (applied genetics), it would mean I would have to be stepping out of the safety of my own little niche. I would have to begin to explore some very big things, including aspects of theoretical genetics which I had always accepted by faith alone. I felt compelled to do all this – but I must confess I fully expected to simply hit a brick wall. To my own amazement, I gradually realized that the seemingly “great and unassailable fortress” which has been built up around the primary axiom is really a house of cards. The Primary Axiom is actually an extremely vulnerable theory – in fact it is essentially indefensible. Its apparent invincibility derives mostly from bluster, smoke, and mirrors. A large part of what keeps the Axiom standing is an almost mystical faith, which the true-believers have in the omnipotence of natural selection. Furthermore, I began to see that this deep-seated faith in natural selection was typically coupled with a degree of ideological commitment – which can only be described as religious. I started to realize (again with trepidation) that I might be offending a lot of people’s religion!

To question the Primary Axiom required me to re-examine virtually everything I thought I knew about genetics. This was probably the most difficult intellectual endeavor of my life. Deeply entrenched thought pattern only change very slowly (and I must add — painfully). What I eventually experienced was a complete overthrow of my previous understandings. Several years of personal struggle resulted in a new understanding, and a very strong conviction that the Primary Axiom was most definitely wrong. More importantly, I became convinced that the Axiom could be shown to be wrong to any reasonable and open-minded individual. This realization was exhilarating, but again – frightening. I realized that I had a moral obligation to openly challenge this most sacred of cows. In doing this, I realized I would earn for myself the most intense disdain of most of my colleagues in academia – not to mention very intense opposition and anger from other high places.

What should I do? It has become my conviction that the Primary Axiom is insidious on the highest level – having catastrophic impact on countless human lives. Furthermore, every form of objective analysis I have performed has convinced me that the Axiom is clearly false. So now, regardless of the consequences, I have to say it out loud: the Emperor has no clothes!

…To the extent that the Primary Axiom can be shown to be false, it should have a major impact on your own life – and on the world at large. For this reason, I have dared to write this humble little book – which some will receive as blasphemous treason, and others – revelation.

If the Primary Axiom is wrong, then there is a surprising and very practical consequence. When subjected only to natural forces, the human genome must irrevocably degenerate over time. Such a sober realization should have more than just intellectual or historical significance. It should rightfully cause us to personally reconsider where we should rationally be placing our hope for the future.

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NS is still the most coherent explanation for biodiversity and is supported by a huge mass of observational and experimental evidence.

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at the same time new varieties continually arise through the process of mutation. It is the combination of mutation and selection that generates diversity.

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You assume that complex structures cannot arise by stepwise mutation/selection process because the absence of any one part causes the entire structure to fail and the organism is not viable without that structure?

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It fails in detail because every slight modification improves the structure by a small amount

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This creationist does not see natural selection as important in the origin of species. After the Ark diversity was so quick that selection could not account for results. Therefore a innate trigger must be at work to bring important change.

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for example I know placental creatures became marsupial ones.

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Also land creatures became sea ones, like whales etc, all finished withiin a few centuries after the flood.

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The true nature of the post flood world was like the present amazon. Every acre having different kinds of the same thing.

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The fossil record also shows great diversity of everything at the earliest time and not later.

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"More and more accepted"? Hardly.

You didn't read it and/or are not aware of the upheaval going on over it.

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...nothing in the discovery of DNA-based genetics has invalidated the basis of his theory

Quite the contrary. The specified complexities within every living cell are being revealed more and more each day. These specified complexities cannot be accounted for through random mutations + NS. Indeed it has been estimated over and over that the probability for so much functional complexity arising naturally, without guidance, is less than 1 in 10^150 - a far greater number than 2^80 - the estimated number of elementary particles in the universe.

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No. Mutations are notoriously bad for the genome. All known diseases are caused by mutations.

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The very rare and very minor beneficial ones cannot account for the level of specified functional complexity observed.

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...basic 'descent-with-modification' idea

Under this definition even creationists are evolutionists.

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(and even more unlikely that the mechanism for internal self-organisation so hoped for by the DI will emerge).

Say what? I'jm afraid you don't understand ID at all. There is no "internal self-organisation" hoped for by the DI. On the contrary self-organization is a Darwinists greatest need and yet already proven impossible. ID postulates no such thing as self-organization!

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In the real world, nothing is going to create a functional flagellum because about 40 separate and required parts are needed.

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Where did these complex instructions come from? How is that when a correct flagellum is not achieved in the building process, it is immediately destroyed? How does the genome "know" when an incorrect flagellum is produced?

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This is the old 'what-use-is-half-a-wing' argument and it fails for the heart and hand in the same way as it does for the eye, the blood-clotting cascade, the bacterial flagellum and all the other irreducible structures that have proved to be not so irreducible after all. It fails in detail because every slight modification improves the structure by a small amount (look at the sequence of 'eye' structures from a simple light spot to a human eye)

Actually no. Irreducible structures such as the flagellum are still irreducible. The efforts by Darwinists to demonstrate the contrary have failed miserably.

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The bacteria is motionless and helpless without it and no partial means of producing it can be demonstrqated.

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Co-option also fails. Again where do the instructions for the assembly come from? By accident? The probability of those 40 parts coming together in the correct order and placement is astronomically low. Again, statistical mechanics tells us this.

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What you fail to see here is that an eye that does not see is useless and would be eliminated by NS like a tumor.

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Same with your "every slight modification improves" presumption. Mutations simply do not work to "improve" something as though there were a goal.

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Wings appear to have been arms that developed gliding potential, perhaps as a result of the increased aerodynamic capacity conferred by the insulating feathers. Convergent parallel processes can be seen in bats and pterosaurs and in modern animals such as flying squirrels and gliding frogs.

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This is all slight of hand and smoke and mirrors logic. So common in Darwinism. Make up a story as to how this "could have", "may have" happened by chance and take it as the truth.

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Nature is blind. It has no brain, no goals, no purpose. Your underlying assumption is that is does. It is in fact working to build "better" systems.

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Any origin of species theory must take into account the multiple millions of species and the necessary multiple millions of intermediate forms that should have existed.

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DNA requires protein. Protein requires DNA. Can you say chicken or egg? Obviously they both had to exist simultaneously. Darwinism can't explain that either.

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For if it is true, as the Darwinian model of evolution implies, that all the character traits of living things were gained in the first place as a result of a gradual random evolutionary process, then why should they have remained subsequently so fundamentally immune to that same process of change, especially considering that many diagnostic character traits are only of dubious adaptive significance? It was precisely this fundamental constancy of the unique character traits, or homologies, of every defined taxon which led nineteenth century biology to the theory of types!" (Denton M.J., "Evolution: A Theory in Crisis," Burnett Books: London, 1985, pp.134-135)

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Yes indeed, alex123, natural selection, sometimes called micro-evolution, is the explanation for amazing biodiversity after the Flood.

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Never once (feel free to cite evidence to the contrary!) has natural selection been observed by experiment to result in new organisms, novel structures, or even complex tissues or organ systems.

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at the same time new varieties continually arise through the process of mutation. It is the combination of mutation and selection that generates diversity.

This has never been demonstrated.

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In fact the opposite is true, mutations are harmful.

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You assume that complex structures cannot arise by stepwise mutation/selection process because the absence of any one part causes the entire structure to fail and the organism is not viable without that structure?

Yes, I do. This is an engineering truism.

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If the human body were to come about by natural selection, why are their no vestigial parts?

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ORIGINAL: alex123
The only ‘upheaval’ is the synthetic crisis manufactured by creationists.

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"Today, however, the picture is entirely different. More and more workers are showing signs of dissatisfaction with the synthetic theory. Some are attacking its philosophical foundations, arguing that the reason that it has been so amply confirmed is simply that it is unfalsifiable: with a little ingenuity any observation can be made to appear consistent with it. Others have been deliberately setting out to work in just those areas in which neo-Darwinism is least comfortable, like the problem of the gaps in the fossil record or the mechanisms of non-Mendelian inheritance. Still others, notably some systematists, have decided to ignore the theory altogether, and to carry on their research without any a priori assumption about how evolution has occurred. Perhaps most significantly of all, there is now appearing a stream of articles and books defending the synthetic theory. It is not so long ago that hardly anyone thought this was necessary."

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"The 'modern evolutionary synthesis' convinced most biologists that natural selection was the only directive influence on adaptive evolution. Today, however, dissatisfaction with the synthesis is widespread, and creationists and antidarwinians are multiplying. The central problem with the synthesis is its failure to show (or to provide distinct signs) that natural selection of random mutations could account for observed levels of adaptation."

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This is the same argument-from-incredulity as the ‘irreducible complexity’ and ‘half-an-eye’ arguments and fails for the same reasons.

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Firstly it assumes that a fully-functioning structure has to be generated in one go, which is clearly not the case.

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but there are plenty of far simpler eyes that are perfectly function at some level, through lensless eyes and ‘pinholes’ right down to simple eye-spots....

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Really? The medical profession thinks that most diseases are caused by microbial pathogens. Are they wrong?

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Really? I thought that creationists believed in created ‘kinds’ with a limited ability for variation, not descent from common ancestors? Is this some new definition of ‘creationism’?

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I meant the existence of mechanisms or cellular components that demonstrated clear evidence of design.

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unless you make it from a simpler existing struscture with fewer parts (let’s say, a secretory mechanism)

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These are all very interesting questions, but not beyond the realm of naturalistic explanation.

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Most bacteria are immotile anyway, so ‘motionless’ is hardly ‘helpless’ in the bacterial world!

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Not when there is a simpler precursor and a well-documented process of mutation and selection.

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But the evolutionary precursor is not ‘an eye that does not see’, it is an eye that sees nearly as well as the ‘improved’ version. It wil not be removed by NS for as long as it confers advantage.

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When light strikes the retina a photon is absorbed by an organic molecule called 11-cis-retinal, causing it to rearrange within picoseconds to trans-retinal. The change in shape of retinal forces a corresponding change in shape of the protein, rhodopsin, to which it is tightly bound. As a consequence of the protein's metamorphosis, the behavior of the protein changes in a very specific way. The altered protein can now interact with another protein called transducin. Before associating with rhodopsin, transducin is tightly bound to a small organic molecule called GDP, but when it binds to rhodopsin the GDP dissociates itself from transducin and a molecule called GTP, which is closely related to, but critically different from, GDP, binds to transducin.

The exchange of GTP for GDP in the transducinrhodopsin complex alters its behavior. GTP-transducinrhodopsin binds to a protein called phosphodiesterase, located in the inner membrane of the cell. When bound by rhodopsin and its entourage, the phosphodiesterase acquires the ability to chemically cleave a molecule called cGMP. Initially there are a lot of cGMP molecules in the cell, but the action of the phosphodiesterase lowers the concentration of cGMP. Activating the phosphodiesterase can be likened to pulling the plug in a bathtub, lowering the level of water.

A second membrane protein which binds cGMP, called an ion channel, can be thought of as a special gateway regulating the number of sodium ions in the cell. The ion channel normally allows sodium ions to flow into the cell, while a separate protein actively pumps them out again. The dual action of the ion channel and pump proteins keeps the level of sodium ions in the cell within a narrow range. When the concentration of cGMP is reduced from its normal value through cleavage by the phosphodiesterase, many channels close, resulting in a reduced cellular concentration of positively charged sodium ions. This causes an imbalance of charges across the cell membrane which, finally, causes a current to be transmitted down the optic nerve to the brain: the result, when interpreted by the brain, is vision.

If the biochemistry of vision were limited to the reactions listed above, the cell would quickly deplete its supply of 11-cis-retinal and cGMP while also becoming depleted of sodium ions. Thus a system is required to limit the signal that is generated and restore the cell to its original state; there are several mechanisms which do this. Normally, in the dark, the ion channel, in addition to sodium ions, also allows calcium ions to enter the cell; calcium is pumped back out by a different protein in order to maintain a constant intracellular calcium concentration. However, when cGMP levels fall, shutting down the ion channel and decreasing the sodium ion concentration, calcium ion concentration is also decreased. The phosphodiesterase enzyme, which destroys cGMP, is greatly slowed down at lower calcium concentration. Additionally, a protein called guanylate cyclase begins to resynthesize cGMP when calcium levels start to fall. Meanwhile, while all of this is going on, metarhodopsin II is chemically modified by an enzyme called rhodopsin kinase, which places a phosphate group on its substrate. The modified rhodopsin is then bound by a protein dubbed arrestin, which prevents the rhodopsin from further activating transducin. Thus the cell contains mechanisms to limit the amplified signal started by a single photon.

Trans-retinal eventually falls off of the rhodopsin molecule and must be reconverted to 11-cis-retinal and again bound by opsin to regenerate rhodopsin for another visual cycle. To accomplish this trans-retinal is first chemically modified by an enzyme to transretinol, a form containing two more hydrogen atoms. A second enzyme then isomerizes the molecule to 11-cis-retinol. Finally, a third enzyme removes the previouslyadded hydrogen atoms to form 11-cis-retinal, and the cycle is complete.

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...species have greater of lesser degrees of kinship as measured by morphology, homology and genetic analysis. At the same time the fossil record shows similar diversity and clear overall progressions from early simple organisms limited to a narrow range of ecological niches to later more complex organisms ...

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Science does not deal in ‘truth’, it deals in the best answers that fits the facts; ‘could’ and ‘may’ are quite acceptable in that context; in fact they are the only acceptable terms

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– science does not deal in certainties.

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there are hundreds of examples – fish with necks and weight-bearing limbs, birds with teeth, dinosaurs with feathers and so on. Do you want a list?

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‘Darwinism’ (more properly called ‘evolutionary biology’ – the term ‘Darwinism’ implies that it is some kind of doctrine or religion)

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has nothing to say on the matter. Origin of life (abiogenesis) is a different area of study. ‘Darwinism’, as you quaintly put it, is the study of the evolution of the units of replication, not the origins of those replicators.

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This is a daft statement.

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Once a better eye had been evolved, for example, its genetics would be conserved because any mutation that altered the eye for the worse would be filtered out by NS.

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fully-functioning structure has to be generated in one go

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Vestigial, as in ‘organs that have lost their primary function but have been retained in some form because they still perform a secondary function’? Appendix, coccyx, degenerate muscles in the pinna, the ‘goosebump’ reflex… plus numerous ‘broken’ enzyme pathways (e.g. vitamin C synthesis).

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Several years back I thought that the Darwinian theory was probably the best explanation for the emergence of biotic structures. That was before the stunning details of molecular machines were discovered. As the details of these remarkable machines rolled in, I became more and more skeptical that the random step-by-step process of mutations propounded by Darwinian theory could, in fact, account for what we see. It wasn't common descent (which I accept) or the increase of complexity over time that bothered me. It was the idea that the complex machines we see could come about with no planning or some sort of cognitive factor. Having been a machine designer for many years and designed many complex machines and systems, the probability that such remarkable machines could come about unplanned just seemed beyond rationality.

This is not to say that people haven't tried to construct gradualistic scenarios to account for these machines. The problem is that they seem to be totally oblivious to the combinatorial dependencies that are present in any complex machine. One predominant idea in these scenarios is exaptation. This idea suggests that something that offers some function can be utilized with other components to create a new function. So far so good. This happens all the time in design engineering. You take a gear box that is used for rotary motion, add a worm screw at its output and you've got a linear motion. What is ignored in these "just so" scenarios is that you can't just grab any ole gear box and any ole worm screw and get anything that works. The gear box has to be the right size, power factor, rpm, output size, materials, etc. The worm screw also has to have the right coupling design, pitch, power capacity, length, diameter, etc. And that's only one part of the design. The motor has to be the right type, size, torque, power, rpm, etc. Then there is whatever function is at the end of the worm screw. All these components are interdependent. In every complex function there are combinatorial dependencies.

An illustration of one such "just so" scenario can be found here. It's an animation to illustrate Nick Matzke's proposed Darwinian process to create bacterial flagellum. To the uninitiated this all looks pretty reasonable. From a combinatorial-dependency perspective it looks incredibly improbable.

Let's take a look at this in a little detail. First we have a passive pore that starts things off. Since this is the base of the eventual flagellum one has to ask is the pore the right size that the whip of the flagellum can provide the locomotion we see? If it is too small the resulting whip will not be able to handle the stresses from torsion and coupling. If it is too big the whip will be too bulky to be driven in any effective way by the motor. Then we add the secretion system. Is the pore the right size and of the right protein type for the existing secretion system? If not there will be no coupling of the two and no progress.

Ok now we have a selective pore and an secretion system but does it secrete proteins that will be right for the whip? The whip has to have the right protein shape. In engineering the components of a flexible whip have to be designed to mesh correctly such that there is just the right combination of coupling, flexibility, and rigidity. They also have to be the right material. If they are too soft there will be galling. If they are too hard fatigue cracks will set in and destroy the whip. The same goes for clearances between parts. This is a goldie-locks situation. Things have to be just right or it won't work.

Next we have to add the motor. Let's assume we're very lucky that a motor will fit and couple with what we have so far. However, the motor has to have the rpm and torque to drive the whip just right. If it doesn't have enough torque we won't get what we see. If the rpm is too fast the whip will destroy itself because of the hydrodynamic forces applied to it by the fluid. Then it and all the other components have to be sized just right to reverse or the torsional forces on the wip will rip it apart. Remember the diameter, materials, meshing of parts, etc. in this Darwinian scenario have no idea what will be required later.

I could go on and on but I hope you get the idea of combinatorial dependencies. And things are really worse when you consider the problem of "you just can't get there from here". If one component violates the needed dependencies that must be satisfied, you can't just mutate that one component because every component depends on the others. As any design engineer will attest from their mistakes, you just have to start over. In real design a computer program would probably be written to play what-if scenarios to match the torque required, the materials and configuration of whip components, the bearing size and thickness based on cell wall strength, hydrodynamic factors, torsional and coupling stresses, etc and etc. Also this doesn't even take into account the assembly processes that are required. They also have their own dependencies.

The point is that simplistic just-so stories based on random mutations just aren't adequate from an engineering perspective. There's entirely too much luck involved to be taken seriously. Darwinian proponents will have to do much better than this to convince anyone acquainted with real machines.

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These things are getting awfully long

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The only ‘upheaval’ is the synthetic crisis manufactured by creationists.

Well that would explain this remark:
<snip extract>

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And tons of others... sheesh.

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Firstly it assumes that a fully-functioning structure has to be generated in one go, which is clearly not the case.

Wrong again. It rather admits that the probability of a complex functional machine arising by chance and NS is zero. The same as a 17 part meat-grinder has of assembling itself naturally by shaking up the parts in a box for all eternity. Never going to get a meat grinder!

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Really? The medical profession thinks that most diseases are caused by microbial pathogens. Are they wrong?

I suggest you actually go to mutation data base - many available on the web. Check how many are associated with diseases.

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There also should be billions of "missing links" or intermediate forms in the fossil record - there isn't.

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You really ought to research Behe and others response to the secretory sys. rebuttal - it's pure nonsense.

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Also see - http://mbe.oxfordjournals.org/cgi/content/abstract/msn153 - the flagellum preceded the TTSS in nature and thus the TTSS represents a devolution from flagella rather than flagella being evolved from a TTSS.

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And any normal person looking at the e.coli flagellum without the Darwinian fluff and bluff, sees that its a feat mechanical of engineering and not possible through random m. + ns.

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If measuring through morphology, the correspondence with genetics are few and far between and vice-versa. That's why there are currently no viable Darwinian "trees of life". The systematists see it one way the geneticists another and cladists yet another.

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– science does not deal in certainties.

Ya right, science knows nothing then and using math in science is useless - E=MC^2 isn't true and etc...

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Intermediates are assumed in point one of Darwinism, whenever something is found that resembles something between two others it is automatically called "intermediate" without the slightest grain of proof.

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‘Darwinism’ (more properly called ‘evolutionary biology’ – the term ‘Darwinism’ implies that it is some kind of doctrine or religion)

The term Darwinism is amply found in tons of Darwinist literature.

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So where does evolution begin? With the first replicator? So why does any replicator mutate in the first place seeing that 1st living organism was already perfectly fit to survive?

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This is a daft statement

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Suggest you take up Denton on it yourself, see how far you get.

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fully-functioning structure has to be generated in one go

This is actually what NS requires and we are just pointing it out to you.

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Because NS is blind, it dictates that for a change to be persistent to the next generation, an immediate survival value must be present or there is no reason to keep(filter through death) the change or even for a complete about face to occur.

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This is a painfully slow serial processes.

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Irreducible complexity, on the other hand, dictates that all of the parts have to be developed in parallel because parts, in and of themselves, are use less. If they are useless, they never had any survival value. Therefore, natural selection would never have produced them.

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Quite right. Fortunately, no unequivocably IC structures exist.

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Quite right. Fortunately, no unequivocably IC structures exist.

Plenty of them exist - evolutionists prefer to equivocate!