Macroevolution. Fact, or fantasy ?

Macroevolution. Fact, or fantasy? 

https://reasonandscience.catsboard.com/t1390-macroevolution-fact-or-fantasy

https://www.nature.com/scitable/knowledge/library/macroevolution-examples-from-the-primate-world-96679683/

Macro-Evolution is an atheistic, secular-humanistic, philosophical worldview that requires:
(1) massive/infinite amounts of “natural” small changes;
(2) many beneficial/magical, random genetic mutations, producing novel, more complex structures over eons of time, from a “simple” virus or amoeba, to man; and
(3) Natural Selection – the continued survival (of fittest) of these different/new living Species (cf. speciation) & Families.

NEVER, in over 150 years, since Darwin's book " On the origin of species " was published, has even ONE, amongst hundreds or thousands, if not millions of science papers, provided ONE DEMONSTRATION, and empirical verifiable replicable evidence, that any of the evolutionary mechanisms proposed, could produce a primary macroevolutionary transition zone of speciation and population differentiation.

Virtually all other evolutionists of Darwins period were so impressed by the gaps between genera and by the even greater gaps among the higher taxa that they felt they could not do without saltations. T.H. Huxley was characteristic of this thinking. Saltationism became even more popular after the publications of Bateson (1894) and de Vries (1901-1903)
https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1982.tb05483.x

ERNST MAYR SPECIATION AND MACROEVOLUTION March 15, 1982 
Microevolution and Macroevolution The classical view of macroevolution held by Darwin and the majority of paleontologists up to the present day is that species in the course of their gradual evolution in time change to such a degree that they will become different genera or taxa of still higher rank, and acquire in the process all the adaptations and specializations of the world of organic diversity. Viewing evolution strictly in the vertical dimension, as was done by most paleontologists including Simpson, hardly permitted any other interpretation of evolution. When one carefully studies the writings of those geneticists who also gave thought to macroevolution, one finds that they adopted essentially the same view. Yet some of them felt that this left an unexplained area. This led Goldschmidt to his theory of "hopeful monsters"; it led to other saltational theories, and it led to various claims that the rethinking of evolutionary processes in the last 10 or 15 years had made the evolutionary synthesis obsolete. These are inevitable conclusions for those who think in terms of closed gene pools and of exclusively vertical evolution. Indeed, there are no visible connections between the phenomena studied by mathematical population geneticists and those macroevolutionary processes that are studied by paleontologists and comparative anatomists. Such a connection can be established, however, by making use of the findings of population systematics, and of the horizontal approach to evolution, as studied by the new systematics, because they provide a perfect bridge between micro-and macroevolution. 
 In an article entitled 'The return of hopeful monsters' Gould (1977) writes: "I do predict that during the next decade Goldschmidt will be largely vindicated in the world of evolutionary biology...He broke sharply with the synthetic theory, in arguing that new species arise abruptly by discontinuous variation, or macromutation . . . Goldschmidt went on, every once in a while a discontinuous macromutation might, by sheer good fortune, adapt an organism to a new mode of life, a 'hopeful monster' in his terminology. Macroevolution proceeds by the rare success of these hopeful monsters, not by continuous small changes within populations." 2

Microevolution and secondary speciation is a fact. The macro change however from one organism into another in long periods of time, the change of body plans and evolutionary novelties, phenotypic complexity, and phenotypic novelty is not a fact, not even a theory, or even a hypothesis. Its just fantasy without a shred of evidence. It's not possible.  Show me some examples of observed facts;  please provide and give me empirical data of an unorganized undirected unguided Neo-Darwinian accidental random macro-evolutionary event.

What is a macroevolutionary novelty?
The change/transition, where one "kind" can evolve into another beyond the species level (i.e. primary speciation),  like an organism, randomly changing/transition into a whole entire different organism with new fully functioning biological features, the emergence of new complex functions, a new genus or higher rank in taxonomy. The origin of new body plans, forms, and architecture. The origins of novel branches of the tree of life at levels above that of primary speciation.  The origin and diversification of higher taxa. Of new phyla. From the supposed Last Universal Common Ancestor to unicellular eukaryotic cells. From unicellular to multicellular life.  There Are Six Important Patterns of Macroevolution: Mass Extinctions. Adaptive Radiation. Convergent Evolution.

A list of most-often cited examples include photosynthesis (Hecht, 2013), multicellularity and the “Avalon Explosion” (Shen et al., 2008), animal body plans and the “Cambrian Explosion” (Erwin and Valentine, 2013), complex eyes (Paterson et al., 2011), vertebrate jaws and teeth (Fraser et al., 2010), terrestrialization (e.g., in vascular plants, arthropods, and tetrapods) (Bateman et al., 1998), insect metamorphosis (Labandeira, 2011), animal flight and feathers (Wu et al., 2018, Yang et al., 2019), reproductive systems, including angiosperm flowers, amniote eggs, and the mammalian placenta (Chuong, 2013, Doyle, 2012, Roberts et al., 2016, Sauquet, 2017, Specht and Bartlett, 2009), echolocation in whales (Churchill et al., 2016, Park et al., 2016) and bats (Simmons et al., 2008), and even cognitive skills of modern man (Neubauer et al., 2018).
the shell of turtles (Cebra-Thomas et al. 2005), flight (Prum 2005), flowers (Albert, Oppenheimer, and Lindqvist 2002), the ability of great tits to open bottles of milk (Kothbauerhellmann 1990), the transition from the jaw to the ear of some bones during the evolution of mammals from reptiles (Brazeau and Ahlberg 2006), eyes (Fernald 2006), hearts (Olson 2006), bipedalism (Richmond and Strait 2000), and the origin of Hox genes (Wagner, Amemiya, and Ruddle 2003); The evolution of sirenians,   Ernst Mayr, a major figure of the MS, defined novelties as “any newly acquired structure or property that permits the performance of a new function, which, in turn, will open a new adaptive zone” (Mayr 1963, 602). Coevolution. Punctuated Equilibrium. Developmental Gene Changes.

something that we merely don't have to just put blind faith in?

Robert Shapiro: Darwin “ignored the inconvenient fact that human selection for altered traits has never generated a truly new organismal feature (e.g., a limb or an organ) or formed a new species. Selection only modifies existing characters.“

Eugene K Balon: Evolution by epigenesis: farewell to Darwinism, neo- and otherwise May-Aug 2004
In the last 25 years, criticism of most theories advanced by Darwin and the neo-Darwinians has increased considerably, and so did their defense. Darwinism has become an ideology, while the most significant theories of Darwin were proven unsupportable.

Lynn Margulis:  Although random mutations influenced the course of evolution, their influence was mainly by loss, alteration, and refinement... Never, however, did that one mutation make a wing, a fruit, a woody stem, or a claw appear. Mutations, in summary, tend to induce sickness, death, or deficiencies. No evidence in the vast literature of heredity changes shows unambiguous evidence that random mutation itself, even with geographical isolation of populations, leads to speciation.

The accumulation of genetic mutations were touted to be enough to change one species to another….No. It wasn’t dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact.

Natural selection eliminates and maybe maintains, but it doesn't create... Neo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change [which] led to new species. I believed it until I looked for evidence.

New mutations don't create new species; they create offspring that are impaired.

“For all the accomplishments of molecular biology, we still can't tell a live cat from a dead cat.”

biology is opening the black box, and demonstrating how organisms develop. We are slowly getting out of a state of ignorance in regard of what mechanisms determines cell shape, assignment of their planes of division, tendencies to move, directions and rates of movement, modes of differentiation into particular cell types, and cell death (apoptosis).

The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. The discovery and description of the spatial– temporal distribution of the gene expression pattern during morphogenesis, together with its key regulators, is one of the main recent achievements in developmental biology. Nevertheless, gene expression patterns cannot explain the development of the precise geometry of an organism and its parts in space. 1

One mutation confers resistance to malaria but also makes happy blood cells into the deficient oxygen carriers of sickle cell anemics. Another converts a gorgeous newborn into a cystic fibrosis patient or a victim of early onset diabetes. One mutation causes a flighty red-eyed fruit fly to fail to take wing.

Never, however, did that one mutation make a wing, a fruit, a woody stem, or a claw appear.

Mutations, in summary, tend to induce sickness, death, or deficiencies.


A Million Monkeys . . .
http://www.detectingdesign.com/maquiziliducks.html
Some try to explain this problem by saying that, "A million monkeys typing away will eventually create all the works of Shakespeare... if given enough time."  However, some quick calculations will show that forming just a small phrase of Shakespeare such as, "Methinks it is like a weasel.", would take a million monkeys each randomly typing 100 five-letter words a minute, around one trillion trillion trillion years on average.  Clearly then, random chance is powerless to explain the existence of complex language systems or the evolution of one system into another.  There must be something that helps random chance along.  But what is it?

Methinks it is Like a Weasel
Maybe it is not quite fair to compare the English language to the workings of DNA and proteins.  Some evolutionists might balk at this, but many actually do accept the validity of such a correlation.  This acceptance indicates that evolutionists do generally recognize the coded nature of genetic information systems.  In fact, Richard Dawkins, perhaps the most famous living evolutionary biologist, also explains how evolution might work by appealing to examples of English-phrase evolution.  His “Methinks it is like a weasel†phrase evolution is really quite famous.3  It has convinced many very intelligent people that the theory of evolution easily explains the formation of complex biological language systems.  So, let's look a bit into exactly what Dawkins did.
What Dawkins did was to evolve his chosen target phrase with a computer algorithm that began with a random computer-generated series of letters such as “MWR SWTNUZMLDCLEUBXTQHNZVJQF.”  Dawkins begins with a non-functional meaningless phrase and then evolves  â€œMethinks it is like a weasel† in very short order by having the computer select for those copies that are "closest" in sequencing to, "Methinks it is like a weasel."  It seems almost miraculous to watch this evolution happen before one's very eyes on similar algorithms until one realizes that the computer is selecting based on genotypic similarity to an ideal genotypic sequence - - not on phenotypic changes in function.  None of the intermediate steps in this example of sequence evolution have any phenotypic (English language) function whatsoever.  The intermediate phrases are meaningless, much less beneficial.  These intermediate phrases represent links in an evolutionary chain of function and yet none of the links make any sense in the English language.  
Missing links in the fossil record are not the real problem for evolution.  The really significant missing links are found in genetics.  Where are these missing genetic links?  Without them, all we have are huge neutral/non-beneficial gaps.  Really, what real time examples are there to adequately support the theory of common descent via mindless Darwinian evolution beyond very low levels of functional complexity?

Where Do Complex Organisms Come From?
http://reasonandscience.catsboard.com/t2316-where-do-complex-organisms-come-from#4782


EVOLUTIONARY BIOSCIENCE AS REGULATORY SYSTEMS BIOLOGY 1
https://reasonandscience.catsboard.com/t2318-gene-regulatory-networks-controlling-body-plan-development#4804

Never in the modern history of evolutionary bioscience have such essentially different ideas about how to understand evolution of the animal body plan been simultaneously current. The first is the classic neo-Darwinian concept that evolution of animal morphology occurs by means of small continuous changes in primary protein sequence which in general require homozygosity to effect phenotype. The second paradigm holds that evolution at all levels can be illuminated by detailed analysis of cis-regulatory changes in genes that are direct targets of sequence level selection, in that they control variation of immediate adaptive significance. An entirely different way of thinking is that the evolution of animal body plans is a system level property of the developmental gene regulatory networks (dGRNs) which control ontogeny of the body plan.


Molecular pathways regulating mitotic spindle orientation in animal cells
One primary feature of oriented cell division is the proper positioning of the mitotic spindle relative to a defined polarity axis. In principle, spindle orientation is achieved through signaling pathways that provide a molecular link between the cell cortex and spindle microtubules. These pathways are thought to elicit ( provoke ) both static connections and dynamic forces on the spindle to achieve the desired orientation prior to cell division. Although our knowledge of the signaling molecules involved in this process and our understanding of how they each function at the molecular level remain limited, collective efforts over the years have shed light on the importance of spindle orientation to animal development and function. Moreover, emerging evidence shows an association between improper spindle orientation and a number of developmental diseases as well as tumor formation. 
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631962/

and: Electrical gradients and fields are critical in the 3D function and shape of cells and organs.

Morphogenetic fields in embryogenesis, regeneration, and cancer: Non-local control of complex patterning
Electrical signaling is key for cells to properly interpret their environment, and when this process goes awry, the cells default to a cancer program. While ion flows control cell-level behaviors such as migration, differentiation, and proliferation, bioelectric signals also function as master regulators of large-scale shape in many contexts: a simple signal can induce complex, highly orchestrated, self-limiting downstream morphogenetic cascades. For example, an unmodulated flux of protons can cause the formation of a complete tail of the right rise and tissue composition.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631962/

ALL EXPLANATIONS POINT TO INFORMATION. INFORMATION IS THE KEY. CHANGE THE INFORMATIONAL INSTRUCTIONS, AND THE RESULT IS NOT NEW BODY PLANS, BUT DESEASE, CANCER ETC. IN THE END, THE QUESTION IS: WHERE DOES THE INFORMATION COME FROM THAT DIRECTS THE FORMATION OF NEW BODY PLANS ?


The frailty of adaptive hypotheses for the origins of organismal complexity
There is no evidence at any level of biological organization that natural selection is a directional force encouraging complexity. 
http://www.pnas.org/content/104/suppl_1/8597.full

The argument of no observable evidence
1. There is not even one observable evidence that one kind of species changes into another.
2. All different proofs of evolution show only micro-evolution like the Galapagos finches changing the shapes of their beaks, stickleback fishes undergoing genetic change after the ice age.
3. These two species are still finches and fishes that underwent only some adaptation through microevolution or the limited variation that takes place within the species.
4. According to proponents of evolution, billions of microevolution mutations in the genome can create new alleles, and natural selection preserving those changes will result in evolution.
(a) most mutations will be lost due to drift, so a mutation will have to appear many times before it gets fixed in the population;
(b) necessarily, the mutation rate will always be much greater than the fixation rate;
(c1) Kimura is famous for showing that most mutations are nearly-neutral, and therefore are not subject to selection.
(c2) To understand the effect of the near neutral mutation we can give the example of the aging of our bodies. We can repair teeth, do facelifts, even replace hearts. But it is the cumulative aging of the individual cells (principally due to mutations) which places a specific limitation on our lifespan. This is true even though each individual cell is trivial and entirely expendable. Just as the human body rusts out due to countless microscopic mistakes (all of which in themselves are insignificant), the human genome must also be “rusting out” due to near--neutral mutations [that are very subtle]. No selection scheme can stop this process. This is the essence of the near-neutral mutation problem.
5. The explanation of evolution by mutations has a real problem. 
6. Also, experiments on fruit-flies showed that genetic changes are limited and cannot create new species.
6. Macro-evolution or changing of one species into another is not proven. No genetic changes are reported.
7. Evolution is false; creation by an intelligent God is true.
8. God exists.

Stephen C Meyer , Darwin's doubt pg.218:

Contemporary critics of neo-Darwinism acknowledge, of course, that preexisting forms of life can diversify under the twin influences of natural selection and genetic mutation. Known microevolutionary processes can account for small changes in the coloring of peppered moths, the  acquisition of antibiotic resistance in different strains of bacteria, and cyclical variations in the size of Galápagos finch beaks. Nevertheless, many biologists now argue that neo-Darwinian theory does not provide an adequate explanation for the origin of new body plans or events such as the Cambrian explosion. For example, evolutionary biologist Keith Stewart Thomson, formerly of Yale University, has expressed doubt that large-scale morphological changes could accumulate by minor changes at the genetic level. Geneticist George Miklos, of the Australian National University, has argued that neo- Darwinism fails to provide a mechanism that can produce large-scale innovations in form and structure. Biologists Scott Gilbert, John Opitz, and Rudolf Raff have attempted to develop a new theory of evolution to supplement classical neo-Darwinism, which, they argue, cannot adequately explain large-scale macroevolutionary change. As they note:

Starting in the 1970s, many biologists began questioning its neo-Darwinism's adequacy in explaining evolution. Genetics might be adequate for explaining microevolution, but  microevolutionary changes in gene frequency were not seen as able to turn a reptile into a mammal or to convert a fish into an amphibian. Microevolution looks at adaptations that concern the survival of the fittest, not the arrival of the fittest. As Goodwin (1995) points out, "the origin of species—Darwin's problem—remains unsolved."

John Lennox : There is no publication in the scientific literature – in prestigious journals, specialty journals, or books – that describes how molecular evolution of any real, complex, biochemical system either did occur, or even might have occurred. There are assertions that such evolution occurred, but absolutely none is supported by pertinent experiments or calculations… despite comparing sequences and mathematical modelling, molecular evolution has never addressed the question of how complex structures came to be.

James Shapiro, a biochemist at the University of Chicago, also admits that there are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system; only a variety of wishful speculations. Even the highly critical review of Behe by Cavalier-Smith concedes Behe’s point that no detailed biochemical models exist.

http://www.dcclothesline.com/2014/01/09/44-reasons-evolution-just-fairy-tale-adults/

http://creationwiki.org/Mutation

Mutations either beneficial, negative or neutral are rare instances. They happen on average about once in every 10 million duplications of the DNA molecule (10^7, a one followed by 7 zeroes). For evolution to progress, organisms require a series of related mutations to occur. The odds of getting two mutations that are related to one another is the product of their separate probabilities. If every 10^7 duplications of DNA a mutation occurs the equation would start to look like this; 10^7 x 10^7 or 10^14. a one followed by 14 zeroes, a hundred trillion. Mutations which are related or not would barely change finch beak sizes due to drought, or change the shape of a fly wing.
What are the odds of getting three related mutations? That is, again taking into account the mutation rate of duplicated DNA, one in a billion trillion or 10^21. Suddenly the ocean isn't big enough to hold enough bacteria to make that chance very likely. You can quickly tell that at just three related mutations, evolution via related, dependent mutational change through natural selection as its mechanism to produce truly novel information or molecule-to-man change is woefully inadequate.


http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=639

Micro evolution (intrsapecies adaptions- changes/deletions to existing DNA genes) is a fact.

Macro evolution (jumps to new species- via vastly more complex genes added to DNA) is a myth.

Reducibility of "irreducible" systems

https://en.wikipedia.org/wiki/Irreducible_complexity#cite_note-84

Its interesting that Wiki provides as argument for macro change the fact that a research published in the peer-reviewed journal Nature  showed that computer simulations of evolution demonstrated that it is possible for complex features to evolve naturally..This paper describes a computer simulation and thus contains no actual biology. So rather than provide evidence in the natural world, they resort to computer simulations.

following is the paper :

The evolutionary origin of complex features

http://myxo.css.msu.edu/papers/nature2003/Nature03_Complex.pdf

A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms—computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured. However, no particular intermediate stage was essential for evolving complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection.

In the discussion section, we read: "Some readers might suggest that we 'stacked the deck' by studying the evolution of a complex feature that will be built on simpler features that were also useful. However, that is precisely what evolutionary theory requires..."

Well, no. The Lenski simulation requires that complex systems exhibiting complex functions can always be built up from  simpler systems exhibiting simpler function . Macro change needs to explain many de novo features, like the arise of wings, legs, body organs etc, starting from biological systems which did not have such features at all.  

http://www.ideacenter.org/contentmgr/showdetails.php/id/1319#critique

"The simulation by Lenski et al. assumes that all functioning biological systems are evolutionary kludges of subsystems that presently have function or previously had function. But there's no evidence that real-life irreducibly complex biological machines, for instance, can be decomposed in this way. If there were, the Lenski et al. computer simulation would be unnecessary. Without it, their demonstration is an exercise in irrelevance.

Following are the main critique points :

1.Stacking the Deck: It was pre-ordained that the complex function can be created from the less complex functions (they hand-coded a solution before even running the simulation)--but there is no such guarantee in biology that subsystems can be so easily combined to produce anything useful! The complexity gap between the smaller functions (NAND, etc.) and the target functions (EQU) is not very big. In fact, they were able to create EQU using only 5 of the more primitive logic operation subsystems. This means that as far as logic is concerned, only 5 of the basic logic functions used in the programs are needed to evolve EQU. They created a simulation which they knew could evolve the target function through the subsystems. (This is why I have titled this critique "Evolution by Intelligent Design.")

2.Too Much Selective Advantage: Selective advantage was given to literally every single addition of logic functions in the organisms which evolved EQU. Additionally, every mutation which added code, always added functional line(s) of code, while in nature mutations are never guaranteed to have any meaning or functionality in the environment. This makes the evolution of EQU essentially inevitable, and it does not test irreducible complexity. In a true irreducibly complex system, there will be no selective advantage along an evolutionary pathway. In real world, there is no guarantee that the subsystems you need will necessarily give you a selective advantage along your evolutionary pathway.

3.Illustrating that Irreducible Complexity is Unevolvable: When the aforementioned "selective advantage" was taken away, and fitness only increased when the target function EQU appeared, EQU NEVER EVOLVED in their simulations! This is very significant because it shows that they modeled true irreducible complexity, and that when they did, irreducible complexity could not evolve!

Modeling Irreducible Complexity

The paper made one profound finding when it accurately modeled true irreducible complexity (first full paragraph, pg. 143). Michael Behe has defined irreducible complexity as:
"An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway." (A Response to Critics of Darwin’s Black Box, by Michael Behe, PCID, Volume 1.1, January February March, 2002; iscid.org/)

When Lenski et al. created a simulation with high irreducible complexity, i.e. there was no selective advantage until the target function arose, EQU never evolved! Consider this quote from the Lenski paper:

"At the other extreme, 50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection would not preserve the simpler functions that provide foundations to build more complex features. Indeed, none of these populations evolved EQU, a highly significant difference from the fraction that did so in the reward-all environment (P ~= 4.3 x 10-9, Fisher's exact test)."

In other words, when there is no selective advantage until you get the final function, the final function doesn't evolve. In this case, their simulation probably DID model biological reality because irreducible complexity claims that there is no advantage until you get the final function. In fact in such a scenario, it found that the evolution of such a structure was impossible. In other words, they just proved that irreducible complexity is unevolvable.




The Lenski paper can only be seen as a scientific response to the claims of ID proponents, published in a high profile journal such as Nature. Despite the fact that the authors of the Lenski paper would likely deny this fact, there are many clues which show that the article is intended as a rebuttal to the claims of ID proponents. Not only does this validate the work of ID proponents as posing a legitimate challenge to Darwin's theory, but it also indicates that the claims of ID proponents are eminently testable, falsifiable (though as discussed above, not yet falsified), and therefore also scientific in nature.

The article even attempts to address irreducible complexity without using the term. "Thus, although more than two dozen mutations were used to build EQU, undoing any one of them destroyed this function." They are stating that EQU was irreducibly complex, but yet it evolved. Thus, Exhibit C is as follows: the article directly purports to test the evolution of irreducible complexity but yet never uses the phrase. (Note: It is arguable that their stated conclusions about the evolution of irreducible complexity do not match the findings of their simulations. When EQU evolved, the study did not truly model irreducible complexity because it employed a "reward-all" environment where some function could be gained by adding parts which could also contribute to the final function. When the article properly modeled irreducible complexity, where only EQU was rewarded, EQU never evolved!)

While the author Carl Zimmer quotes co-author Christopher Adami to sing an over-inflated victory song, one important point should not be lost: this study implicitly proves that the claims of ID proponents, such the claim that some biological features are irreducible complexity, are eminently testable via the methods of science. Apparently Nature saw the claim of irreducible complexity as such a threat to evolution that it saw fit to publish a study which attempted to model the evolution of irreducible complexity.

http://www.uncommondescent.com/intelligent-design/macroevolution-microevolution-and-chemistry-the-devil-is-in-the-details/

   “A wide spectrum of researchers – ranging from geologists and paleontologists, through ecologists and population geneticists, to embryologists and molecular biologists – gathered at Chicago’s Field Museum of Natural History under the simple conference title: Macroevolution. Their task was to consider the mechanisms that underlie the origin of species and the evolutionary relationship between species… The central question of the Chicago conference was whether the mechanisms underlying microevolution can be extrapolated to explain the phenomena of macroevolution. At the risk of doing violence to the positions of some of the people at the meeting, the answer can be given as a clear, No.”

Macroevolution, in darwinian fashion, is unverifiable. Not a single evidence they can provide to prove the capacity of natural selection acting on random mutation to grow new fully functioning biological features in an organism. The sudden appearance of some 35 new phyla in Cambrian explosion which were without clear morphological ancestors from pre-cambrian period, within a very narrow geologic time span--which is macroevolution at its face--is indicative of the fact that there were other mechanisms responsible for it. Intelligent Design is in itself an evolutionary mechanism.
Lewin, R. 1980 (Nov 21). Science 210:883.

http://creationwiki.org/Evolution_can%27t_be_replicated
How can macro evolution be repeated? It cannot be repeated, i.e., the theory is not replicable. According to evolutionists, the processes are so slow that we cannot observe the major tenets of the theory, i.e. massive genetic and morphological change and increase in genetic information happening today, because they are either so slow (gradualism) or too fast to show up in the fossil record (punctuated equilibrium). Since the major tenets of the hypothesis cannot be observed, they are not scientific. And such a grand theory cannot be replicated, adding veracity to the claim that evolution is primarily unscientific.

We must ask first whether the theory of evolution by natural selection is scientific or pseudoscientific .... Taking the first part of the theory, that evolution has occurred, it says that the history of life is a single process of species-splitting and progression. This process must be unique and unrepeatable, like the history of England. This part of the theory is therefore a historical theory, about unique events, and unique events are, by definition, not part of science, for they are unrepeatable and so not subject to test. ~ Colin Patterson


Matthews, L. Harrison [British biologist and Fellow of the Royal Society], "Introduction", Darwin C.R., "The Origin of Species by Means of Natural Selection," J. M. Dent & Sons: London, 1976, pp.x,xi, in Ankerberg J.* & Weldon J.*, "Rational Inquiry & the Force of Scientific Data: Are New Horizons Emerging?," in Moreland J.P., ed., "The Creation Hypothesis: Scientific Evidence for an Intelligent Designer," InterVarsity Press: Downers Grove IL., 1994, p.275.

"The fact of evolution is the backbone of biology, and biology is thus in the peculiar position of being a science founded on an unproved theory-is it then a science or a faith? Belief in the theory of evolution is thus exactly parallel to belief in special creation-both are concepts which believers know to be true but neither, up to the present, has been capable of proof"

http://www.talkorigins.org/faqs/macroevolution.html
Both macroevolution and microevolution are legitimate scientific terms.

"Given so much time,
the "impossible" becomes possible,
The possible probable,
And the probable virtually certain,
One only has to wait:
Time itself performs the miracles."
(Wald, G., Scientific American, 1954)

http://whoisyourcreator.com/topics/how-does-evolution-supposedly-work/

1. https://arxiv.org/ftp/arxiv/papers/1205/1205.1158.pdf
2. https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1982.tb05483.x
3. https://answersingenesis.org/creation-scientists/edward-a-boudreaux-theoretical-chemistry/

Professor Boudreaux is Professor Emeritus of Chemistry at the University of New Orleans, Louisiana.

there is not one single instance whereby all the tests essential to the establishment of the scientific validity of evolution have been satisfied.

A number of evolutionists openly admit that the coveted fossil record is devastating to the entire scheme of organic evolution, be it neo-Darwinism, punctuated equilibrium or whatever. It has also been clearly demonstrated that observed similarities between organisms, fossil or living, have absolutely nothing to do with proving evolution per se.


Bryan Bissell Darwinism has NO MECHANISM. PERIOD. Creation has a mechanism that is supported by ALL available inferences from observations of complex functioning systems, 100%. In every other field that would by definition be a falsification of Darwinism. The sole and ONLY reason it's not in this case is because of the rebellion of man against following God's rules of ultimate freedom. Tragic. Show me many demonstrations that mutations/natural selection with NO intelligence involved can create massive amounts of NEW genetic information and develop entirely new organs and cause any species to go into a different phyla. Heck, you can use bacteria if you wish.

Until you DEMONSTRATE that or something close to to with EXPERIMENTAL EVIDENCE, which NO ONE has EVER done so far, you have ZERO mechanism. NADA. ZILCH. ZIP.

I'll be waiting for your experimental evidence. And don't claim that mutations, natural selection, genetic drift or any of them help your case at all. They don't. PERIOD. It's precisely because those involve LOSS of genetic information, NOT GAIN, that Behe and many others know that Darwinism is a fraud.

Darwinism is exactly like claiming to have gone from earth to Mars without any available space vehicle. It HAS NO MECHANISM. PERIOD. NONE demonstrated. NONE proven. PERIOD. You have no testable mechanism for Darwinism nor any inferences that can create anything complex or new. Creations testable mechanism is that creative intelligence has designed every single complex thing that we know the origin of. Then it's a simple inference to creation by God who we have VAST evidence for.


In a laboratory it is not difficult to demonstrate changes in large populations of bacteria and insects, changes in certain characteristics that affect their ability to survive in specific situations. But it has not been possible to demonstrate in a laboratory changes in which one species of living creature can produce an offspring which is similar to, and appears to belong to a different species! An analogy is the difference between chemistry and alchemy. It is possible by chemical means to alter chemical compounds, but it is not possible either by chemistry or alchemy to change lead into gold. From a scientific point of view one can relate to the basic Laws of Natural
Selection as to conclusions from controlled experiments. But there is no scientific evidence to support any assumption that these laws can be extrapolated to explain the alleged birth of an offspring whose species is
different from that of its antecedents.

Gene expression and regulation of cell differentiation

http://reasonandscience.heavenforum.org/t1742-gene-expression-and-regulation-of-cell-differentiation

Its said that gene mutations provide macro evolutionary changes. But if a mutation occurs at one place in the genome, all it can do, is to change the development of a particular part. In order to have macro evolutionary changes, the whole body must develop into a specific new direction , and for example to change from scales to feathers, it needs completely new correct genomic information , and feathers that are not fully formed will not provide any survival advantage.  That means, the whole genetic code must differ, and slight changes must occur in the whole body. There would have to be simultaneous genetic mutations, and all provide change of a specific direction.  Each change would have to consist in a gradual change not only of a specific loci and  mutation, but the whole genetic code would have to change as well in order to move on and provide a change of the body as a whole. Why would we have not to expect to see much bigger variation of hybrid transitional forms half chimp, half human, for example ?

http://www.dnalc.org/view/16759-Concept-37-Master-genes-control-basic-body-plans-.html

The development of an organism — from a fertilized egg, through embryonic and juvenile stages, to adulthood — requires the coordinated expression of sets of genes at the proper times and in the proper places. Studies of several bizarre mutations in the fruitfly, Drosophila, provided keys to understanding the molecular basis of large-scale developmental plans. Early embryonic genes express proteins that set up the orientation and define the body segments of the fly embryo. Then "homeotic" genes act on the segments to make the body parts distinct to each segment. Sequence analysis showed that homeotic genes from Drosophila and vertebrate animals share a 180-nucleotide region, called the homeobox. These homeobox proteins have structures highly similar to the regions of regulatory proteins that bind to DNA promoters and enhancers. Thus, a homeotic protein elicits coordinated expression when the protein binds to a specific promoter or enhancer sequence shared by a number of genes involved in the development of body region or segment.



http://truth4longview.com/2013/10/29/natural-selection-to-the-rescue-scientific-evidence-confirms-biblical-creation/#more-835

It is assumed by believers in evolution that some mutations find a useful purpose. It is proposed that even a slight advantage will be passed onto the next generation, which, exceedingly slowly, transforms one type of creature to another. This process is known as natural selection, but how does natural selection hold up under the light of scientific scrutiny as the directing force behind life’s origin and diversity? Dr. John Sanford, retired Cornell University geneticist, inventor of the “gene gun” and 25 other patented discoveries, uses the following illustration to expose the fallacy of this evolutionary belief.1
According to Dr. Sanford,

Dr. J.C. Sanford, Genetic Entropy: The Mystery of the Genome, Ivan Press, 2005

the amount of information required to transform a single-celled organism into a human being would be greater than the information required to transform the manufacturing plant for a Little Red WagonTM into the Star Ship Enterprise — complete with warp drive engines and holodeck! Can natural selection, acting on accidental changes to the assembly directions of the little red wagon, accomplish this transformation?
Natural selection is similar to the quality control department at the wagon assembly plant and our genetic code is similar to a document containing the entire manufacturing process for the red wagon. Everything needed to manufacture the wagon, including the specifications for all of the materials of construction…all of the individual components…the processes needed to manufacture them…all of the metal press specifications…all of the robotics and programming language…the assembly instructions…the paint specifications…the employee benefits manual… EVERYTHING needed for the wagon’s construction needs to be attached as a manual to the bottom of the wagon. The next wagon to be produced must use only the information in the existing wagon to make the next copy. The quality department (natural selection) can only see the finished wagon, not the enormous amount of information in the manufacturing manual (the genetic code of the wagon). The question is: can random changes in the assembly manual (the genetic code) allow the quality control department (natural selection) to transform the little red wagon into a better wagon and ultimately into the USS Enterprise?
The amount of information contained within the simplest single cell organism (similar to the information required to build a wagon assembly plant) would fill a small library. Suppose you started with a perfect set of instructions in this library and randomly changed hundreds of individual letters throughout the instructions. Very few of these changes would be critical for assembly or cause a faulty wagon which the quality control department (natural selection) would reject. It is far more likely that almost all of the random changes (these are called mutations in living organisms) would result in no noticeable change and the wagons would roll off the assembly line with mistakes in their manuals intact — to be used in the creation of the next generation of wagons. This next generation would then have another set of barely noticeable mistakes added, one random letter mistake at a time. Given enough generations of the wagons, and with every increasing letter-by-letter mistake in their assembly manuals; eventually the point would be reached when wagons could no longer be produced from the instructions because there are so many tiny mistakes present. Large mistakes can be eliminated by natural selection, but not the small mistakes because, one wrong “letter” at a time, they are essentially undetectable in the final product. Yet, in the end they will drive the manufacturing process to extinction the same way one rust molecule at a time will destroy a car. This is exactly what is happening to the human genome at an alarming rate. Thousands of tiny mistakes are building up with each generation.
It would seem that neither mutations, nor natural selection, can remotely justify the dogmatic belief in evolution as the explanation for either life’s development or its origin.


In 1996, biologists Scott Gilbert, John Opitz, and Rudolph Raff wrote in the journal- Developmental Biology- " Genetics might be adequate for explaining microevolution, but microevolutionary changes in gene frequency were not seen as able to turn a reptile into a mammal or to convert a fish into an amphibian. Microevolution looks at adaptations that concern the survival of the fittest, not the arrival of the fittest." They concluded: "The origin of species-Darwin's problem remains unsolved."

Scott Gilbert, John Opitz, and Rudolf Raff, "Resynthesizing Evolutionary and Developmental Biology", Developmental Biology, 173, Article no. 0032, 1996, p. 361.

http://english.pravda.ru/science/mysteries/16-04-2010/113050-evolution-1/

There is no evidence that chance mutations can or will provide increasingly more complex genes for natural selection to act upon so that evolution would be possible from simpler species to more complex ones. Even if a good mutation occurred for every good one there would be hundreds, even thousands, of harmful ones so that the net effect over time will be disastrous for the entire species.

"The theory of evolution is believed to be an incontrovertible fact by the general public and most of the scientific community, and is taught as such by most educators. This should not be the case.
The theory of evolution is a valid scientific hypothesis, but the facts are that it has not been proved beyond a shadow of a doubt. To be proven valid, the theory of evolution must undergo the scrutiny (rigours) of the scientific method. This, however, cannot be accomplished because the millions of years required for experimental testing are beyond the reasonable limit of human observation.
The current 'evidence' for the theory of evolution would not stand up in a court of law while undergoing judicial scrutiny. There would be indications that biased interpretation of data had occurred, as alternative theories could be presented to account for observed and tested facts.
The theory of evolution needs its facade of scientific immutability lifted, and exposed for what it really is - an unproven scientific theory."

http://www.creationscience.com/onlinebook/LifeSciences2.html#wp5485965

Organic evolution, as theorized, is a naturally occurring, beneficial change that produces increasing and inheritable complexity. Increased complexity would be shown if the offspring of one form of life had a different and improved set of vital organs. This is sometimes called the molecules-to-man theory—or macroevolution.

Microevolution vs. Macroevolution. Notice that macroevolution would require an upward change in the complexity of certain traits and organs. Microevolution involves only “horizontal” (or even downward) changes—no increasing complexity. Also note that all creationists agree that natural selection occurs. While natural selection does not result in macroevolution, it accounts for many variations within a very narrow range.

Science should always base conclusions on what is seen and reproducible. So what is observed? We see variations in lizards, four of which are shown at the bottom. We also see birds, represented at the top. In-between forms (or intermediates), which should be vast in number if macroevolution occurred, are never seen as fossils or living species. A careful observer can usually see unbelievable discontinuities in these claimed upward changes, as well as in the drawing above.

Ever since Darwin, evolutionists have made excuses for why the world and our fossil museums are not overflowing with intermediates.

http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/

“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.
The gist of the paper is that

so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.

http://www.uncommondescent.com/speciation/new-pnas-paper-large-related-groups-of-animals-diverge-from-each-other-quite-early-in-their-evolution/

Not the long, slow process advocated by Darwin’s followers.* This has long been known, if course, it just gets conveniently buried in the “We’re working on it” pile, lest anyone ask more basic questions. One burial method is obfuscated prose, for which see below.

Clades reach highest morphological disparity early in their evolution

http://www.pnas.org/content/110/34/13875

There are few putative macroevolutionary trends or rules that withstand scrutiny. Here, we test and verify the purported tendency for animal clades to reach their maximum morphological variety relatively early in their evolutionary histories (early high disparity). We present a meta-analysis of 98 metazoan clades radiating throughout the Phanerozoic. The disparity profiles of groups through time are summarized in terms of their center of gravity (CG), with values above and below 0.50 indicating top- and bottom-heaviness, respectively. Clades that terminate at one of the “big five” mass extinction events tend to have truncated trajectories, with a significantly top-heavy CG distribution overall. The remaining 63 clades show the opposite tendency, with a significantly bottom-heavy mean CG (relatively early high disparity). Resampling tests are used to identify groups with a CG significantly above or below 0.50; clades not terminating at a mass extinction are three times more likely to be significantly bottom-heavy than top-heavy. Overall, there is no clear temporal trend in disparity profile shapes from the Cambrian to the Recent, and early high disparity is the predominant pattern throughout the Phanerozoic. Our results do not allow us to distinguish between ecological and developmental explanations for this phenomenon. To the extent that ecology has a role, however, the paucity of bottom-heavy clades radiating in the immediate wake of mass extinctions suggests that early high disparity more probably results from the evolution of key apomorphies at the base of clades rather than from physical drivers or catastrophic ecospace clearing.

http://www.veritas-ucsb.org/library/origins/quotes/macroevolution.html

"Feathers are features unique to birds, and there are no known intermediate structures between reptilian scales and feathers. Notwithstanding speculations on the nature of the elongated scales found on such forms as Longisquama ... as being featherlike structures, there is simply no demonstrable evidence that they in fact are. They are very interesting, highly modified and elongated reptilian scales, and are not incipient feathers."

   Feduccia, Alan (1985)
   "On Why Dinosaurs Lacked Feathers"
   The Beginning of Birds
   Eichstatt, West Germany: Jura Mus



As one Columbia University biologist put it, “ . . . we lack completely fossils of all intermediate stages between reptilian scales and the most primitive feather.”

http://cryptozoologynews.blogspot.com.br/2011/07/bird-fossils-reveal-lifes-colourful.html





"The central question of the Chicago conference was whether the mechanisms underlying microevolution can be extrapolated to explain the phenomena of macroevolution. At the risk of doing violence to the positions of some of the people at the meeting, the answer can be given as a clear, No.

... Evolution, according to the Modern Synthesis, moves at a stately pace, with small changes accumulating over periods of many millions of years yielding a long heritage of steadily advancing lineages as revealed in the fossil record. However, the problem is that according to most paleontologists the principle feature of individual species within the fossil record is stasis, not change...

[b]"The Modern Synthesis is a remarkable achievement. However, starting in the 1970s, many biologists began questioning its adequacy in explaining evolution. Genetics might be adequate for explaining microevolution, but microevolutionary changes in gene frequency were not seen as able to turn a reptile into a mammal or to convert a fish into an amphibian. Microevolution looks at adaptations that concern only the survival of the fittest, not the arrival of the fittest. As Goodwin (1995) points out, "the origin of species -- Darwin's problem -- remains unsolved."

   Scott Gilbert, John Opitz, and Rudolf Raff (1996)
   "Resynthesizing Evolutionary and Developmental Biology,"
   Developmental Biology 173, Article No. 0032, 1996, p. 361

Lynn Margulis says that history will ultimately judge neo-Darwinism as "a minor twentieth-century religious sect within the sprawling religious persuasion of Anglo-Saxon biology."

   Michael Behe
   Darwin's Black Box (1996), page 26
   Reference given is to: Science Vol. 252, 19 April 1991, pp. 379-381
   Which references: American Zoologist, 30:861-875 (1990)

The history of most fossil species includes two features particularly inconsistent with gradualism: 1. Stasis. Most species exhibit no directional change during their tenure on earth. They appear in the fossil record looking much the same as when they disappear; morphological change is usually limited and directionless. 2. Sudden appearance. In any local area, a species does not arise gradually by the steady transformation of its ancestors; it appears all at once and "fully formed."

(Gould, Stephen J., "Evolution's Erratic Pace," Natural History, Vol. 86, No. 5, May 1977, p.14).

http://creation.com/does-homology-provide-evidence-of-evolutionary-naturalism

The recent information explosion in embryology, microbiology, genetics and especially molecular biology has revealed in minute detail how plants and animals are constructed at the molecular level. If the Darwinian interpretation of homology were correct, then we would expect that the same homologies found at the macroscopic level also exist at the microscopic, biochemical and genetic levels. What researchers in each of these fields often find, has greatly undermined the homology concept. So many exceptions now exist that molecular biologist Michael Denton concluded that the homology theory should be rejected. His main argument is that genetic research has not shown that homologous structures are produced by homologous genes and follow homologous patterns of embryological development. Instead, genetics has found that homologous structures are 'often specified by non-homologous genetic systems' and furthermore, the homology 'can seldom be extended back into embryology'.49

Why do most scientists accept macroevolution theory? A major reason is that it is now the accepted world view of scientists—an idea to which they are exposed from the earliest days of training, and by which they are surrounded daily. Most scientists are influenced by social pressure, and many believers fear recriminations from their fellow scientists if they do not conform to what currently is viewed as correct. To prove their orthodoxy, many scientists have become unscientific and have embraced the religion of 20th century-naturalism.50 Belief in evolutionism requires a credulity induced partly by pressure to conform to a world of science that is saturated with naturalism.

http://www.angelfire.com/pro/kairosfocus/resources/Info_design_and_science.htm

Natural selection is the process by which favorable heritable traits become more common in successive generations of a population of reproducing organisms, and unfavorable heritable traits become less common. Natural selection acts on the phenotype, or the observable characteristics of an organism, such that individuals with favorable phenotypes are more likely to survive and reproduce than those with less favorable phenotypes. The phenotype's genetic basis . . . will increase in frequency over the following generations. Over time, this process can result in adaptations that specialize organisms for particular ecological niches and may eventually result in the emergence of new species. In other words, natural selection is the mechanism by which evolution may take place in a population of a specific organism.

From this, we may immediately observe that natural selection is envisioned as a probabilistic culler of competing sub-populations with varying adaptations coming from another source [usually some form of chance-based variation]. That is, it does not cause the actual variation, it is only a term that summarises differences in likelihood of survival and reproduction and possibly resulting cumulative effects on populations across time. So, when innovations in life-forms require the origin of functionally specific, information-rich organised complexity, we are back to some form of chance variation to explain it, and soon run right back into the FSCI-origination barrier.

Moreover, there are linked issues with the related gambler's ruin challenge (as is discussed here).

For, if a given selection advantage is small and the absolute numbers of the sub-population with the innovation are also relatively low, most of the time, such an innovation will simply be lost due to the overwhelming effects of mere chance on odds of survival and reproduction. In other words, one has to have enough population resources to "spend" for long enough to get to the long-run point where modest differential effects will pay off to one's advantage. And, if we take isolation to a niche without competition as a typical example by which such innovations will have a good chance to grow into a viable sub-population that can then migrate back and compete with then dominate over the original population, we still have not accounted for the rise of information-rich organically coherent innovations, especially at that core body-plan level which expresses itself in the vulnerable early phases of the embryological development process.

http://www.discovery.org/a/2450

David Berlinski

Look — The suggestion that Darwin's theory of evolution is like theories in the serious sciences — quantum electrodynamics, say — is grotesque. Quantum electrodynamics is accurate to thirteen unyielding decimal places. Darwin's theory makes no tight quantitative predictions at all.

Look — Field studies attempting to measure natural selection inevitably report weak to non-existent selection effects.

Look — Darwin's theory is open at one end since there are no plausible account for the origins of life.

Look — The astonishing and irreducible complexity of various cellular structures has not yet successfully been described, let alone explained.

Look — A great many species enter the fossil record trailing no obvious ancestors and depart for Valhalla leaving no obvious descendents.

Look — Where attempts to replicate Darwinian evolution on the computer have been successful, they have not used classical Darwinian principles, and where they have used such principles, they have not been successful.

Look — Tens of thousands of fruit flies have come and gone in laboratory experiments, and every last one of them has remained a fruit fly to the end, all efforts to see the miracle of speciation unavailing.

Look — The remarkable similarity in the genome of a great many organisms suggests that there is at bottom only one living system; but how then to account for the astonishing differences between human beings and their near relatives — differences that remain obvious to anyone who has visited a zoo?

But look again — If the differences between organisms are scientifically more interesting than their genomic similarities, of what use is Darwin's theory since its otherwise mysterious operations take place by genetic variations?

These are hardly trivial questions. Each suggests a dozen others. These are hardly circumstances that do much to support the view that there are "no valid criticisms of Darwin's theory," as so many recent editorials have suggested.

Limited Evolutionary Potential

http://www.detectingdesign.com/galactosidaseevolution.html

And yet, despite these many problems, professors Hall and Miller and many other scientists like them would have us believe that the evolution of even more complex functions than single protein enzymes is still a relatively simple or at least a doable process given a few million or even billion years. Such conclusions might be a bit premature to say the least since many of Hall's mutant E. coli seemed to have more than a little difficulty evolving just one relatively simple single-protein enzymatic function. Hall himself described these strains as having "limited evolutionary potential." 3 Hall noted that with both the lacZ and the ebg genes missing, E. coli bacteria cannot evolve lactase ability at all despite his own efforts and those of several others, such as J. H. Campbell, to test for and observe such evolution over the course of many years (since 1973) totaling hundreds of thousands of bacterial generations.6

Hall did seem to realize somewhat of the implications of discovering that only one mutation was needed to "evolve" efficient lactase activity in lacZ negative E. coli strains. In his paper he said, "The realization that a single mutation in ebgA [ebg = evolved b-galactosidase gene] was sufficient to convert ebg0 enzyme into an efficient lactase was therefore disappointing." 3 The problem, as Hall himself pointed out, is that there are mutations that do not yield changes in protein function toward anything useful to the cell. The proteins that result from these mutations might in fact be useful to another organism somewhere in the universe, but for the particular organism that they have evolved in, they are either neutral in function or nonfunctional . . . or, even worse, detrimental in function.

No cell or organism or even an entire gene pool has an infinite vocabulary. All living things have limited individual vocabularies. Out of the huge number of possibilities for different kinds of proteins of a given length, any one individual cell or gene pool of cells "recognizes" or can use only a small fraction of them in a beneficial way (and this fraction gets exponentially smaller as the level of complexity increases). Therefore, some functions are in fact out of statistical reach for that particular cell, or gene pool of cells, as well as their offspring because they do not recognize, as beneficial, any change in the functions of intermediary proteins along the way toward those sequences that would in fact be beneficial. Such neutral evolution looses the guidance of natural selection as a driving force. Hall describes such evolutionarily-challenged bacterial strains as having "limited evolutionary potential." I propose that every living creature has very limited evolutionary potential.

http://www.john-lee-ministries.org/html/11_ways_to_refute_macro_evolut.html

What prevents the transition from micro to macro evolution ?

http://reasonandscience.heavenforum.org/t1390-macroevolution#3280

http://www.angelfire.com/pro/kairosfocus/resources/Info_design_and_science.htm#macvsmic

In order to explain the origin of the Cambrian animals, one must account not only for new proteins and cell types, but also for the origin of new body plans . . . Mutations in genes that are expressed late in the development of an organism will not affect the body plan. Mutations expressed early in development, however, could conceivably produce significant morphological change (Arthur 1997:21) . . . [but] processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream. For this reason, mutations will be much more likely to be deadly if they disrupt a functionally deeply-embedded structure such as a spinal column than if they affect more isolated anatomical features such as fingers (Kauffman 1995:200) . . . McDonald notes that genes that are observed to vary within natural populations do not lead to major adaptive changes, while genes that could cause major changes--the very stuff of macroevolution--apparently do not vary. In other words, mutations of the kind that macroevolution doesn't need (namely, viable genetic mutations in DNA expressed late in development) do occur, but those that it does need (namely, beneficial body plan mutations expressed early in development) apparently don't occur.6 [Emphases added. Cf a more easily readable (and also peer-reviewed) but longer discussion, with illustrations, here.]

Now, this analysis highlights a significant distinction we need to make: micro-evolutionary changes are late-developing, and do not affect the core body plan and its associated functions. Such mutations are indeed possible and are observed. But, when the mutations get to the fundamental level of changing body plans -- i.e. macro-evolution -- they face the implication that we are now disturbing the core of a tightly integrated system, and so the potential for destructive change is much higher. Consequently, the genes that control such core features are stabilised by a highly effective negative feedback effect: random changes strongly tend to eliminate themselves through loss of integrity of vital body functions.

In response, it is often claimed that sufficient microevolution accumulates across time to constitute macroevolution. But, what we "see" in the fossil record of the Cambrian rocks is just that innovation at the core levels coming first, and coming massively -- just the opposite of what the NDT model would lead us to expect. For, as Dan Peterson summarises in his recent article:

To take just one example, a well-known (and unsolved) problem for Darwinism is the Cambrian Explosion. As noted by Stephen Meyer in the book Debating Design, this event might be better called the Cambrian Information Explosion. For the first three billion years of life on Earth, only single-celled organisms such as bacteria and bluegreen algae existed. Then, approximately 570 million years ago, the first multi-cellular organisms, such as sponges, began to appear in the fossil record. About 40 million years later, an astonishing explosion of life took place. Within a narrow window of about 5 million years, "at least nineteen and perhaps as many as 35 phyla (of 40 total phyla) made their first appearance on Earth...." Meyer reminds us that "phyla constitute the highest categories in the animal kingdom, with each phylum exhibiting unique architecture, blueprint, or structural body plan." These high order, basic body plans include "mollusks (squids and shellfish), arthropods (crustaceans, insects, and trilobites), and chordates, the phylum to which all vertebrates belong."

These new, fundamental body plans appeared all at once, and without the expected Darwinian intermediate forms.

In addition, we should observe in passing that there is also an underlying problem with the commonly encountered natural selection model, in which small variations confer significant cumulative advantages in populations,and cumulate to give the large changes that would constitute body-plan level macroevolution. To see this, let us excerpt a typical definition of natural selection:

Natural selection is the process by which favorable heritable traits become more common in successive generations of a population of reproducing organisms, and unfavorable heritable traits become less common. Natural selection acts on the phenotype, or the observable characteristics of an organism, such that individuals with favorable phenotypes are more likely to survive and reproduce than those with less favorable phenotypes. The phenotype's genetic basis . . . will increase in frequency over the following generations. Over time, this process can result in adaptations that specialize organisms for particular ecological niches and may eventually result in the emergence of new species. In other words, natural selection is the mechanism by which evolution may take place in a population of a specific organism. [Emphases added.]

From this, we may immediately observe that natural selection is envisioned as a probabilistic culler of competing sub-populations with varying adaptations coming from another source [usually some form of chance-based variation]. That is, it does not cause the actual variation, it is only a term that summarises differences in likelihood of survival and reproduction and possibly resulting cumulative effects on populations across time. So, when innovations in life-forms require the origin of functionally specific, information-rich organised complexity, we are back to some form of chance variation to explain it, and soon run right back into the FSCI-origination barrier.

The Origin of Body Plans

Starting in the autumn of 1979, at the European Molecular Biology Laboratory in Heidelberg, two venturesome young geneticists, Christiane Nüsslein-Volhard and Eric Wieschaus , generated thousands of mutations to investigate the genomes of tens of thousands of fruit flies (species: Drosophila melanogaster). They hoped to get them to divulge the secrets of embryological development. In technical jargon, Nüsslein-Volhard and Wieschaus performed "saturation mutagenesis" experiments. After feeding male flies the potent mutation-causing chemical (i.e., mutagen) ethyl methane sulphonate (EMS), Nüsslein-Volhard and Wieschaus bred the males with virgin females. They then examined the offspring larvae for visible defects.

Wieschaus responded more soberly, wondering aloud about whether his collection of mutants offered any insights into how the evolutionary process could have constructed novel body plans. "The problem is, we think we've hit all the genes required to specify the body plan of Drosophila," he said, "and yet these results are obviously not promising as raw materials for macroevolution. The next question then, I guess, is what are—or what would be—the right mutations for major evolutionary change? And we don't know the answer to that." Thirty years later, developmental and evolutionary biologists still don't know the answer to that question. At the same time, mutagenesis experiments—on fruit flies as well as on other organisms such as nematodes (roundworms), mice, frogs, and sea urchins—have raised troubling questions about the role of mutations in the origin of animal body plans. If mutating the genes that regulate body- plan construction destroy animal forms as they develop from an embryonic state, then how do
mutations and selection build animal body plans in the first place?

To build a new animal and establish its body plan, proteins need to be organized into higher- level structures. In other words, once new proteins arise, something must arrange them to play their parts in distinctive cell types. These distinctive cell types must, in turn, be organized to form distinctive tissues, organs, and body plans. This process of organization occurs during embryological development. Thus, to explain how animals are actually built from smaller protein components, scientists must understand the process of embryological development

THE ROLE OF GENES AND PROTEINS IN ANIMAL DEVELOPMENT

As much as any other subdiscipline of biology, developmental biology has raised disquieting questions for neo-Darwinism. Developmental biology describes the processes, called ontogeny, by which embryos develop into mature organisms. Within the past three decades the field has dramatically advanced our understanding of how body plans arise during ontogeny. Much of this new knowledge has come from studying so-called model systems—organisms that biologists can easily mutate in the lab, such as the fruit fly Drosophila and the nematode Caenorhabditis elegans. Although the exact details of animal development can vary in bewildering ways depending on the species, all animal development exemplifies a common imperative: start with one cell, end with many different cells. In most animal species, development begins with the fertilized egg. Once the egg divides into its daughter cells, becoming an embryo, the organism begins heading toward a well- defined target, namely, an adult form that can reproduce. Arriving at that distant target requires the embryo to produce many specialized cell types, in the correct positions and at the right time. Cell differentiation involves coordinating the expression of specific genes in space and time, as the number of cells, taking on their different roles, rises from one to two to four to eight, doubling and doubling until it reaches thousands, millions, and even trillions, depending on the species. The number of cell divisions and the total number of cells reflects the number of different cell types the adult needs. This in turn requires producing different proteins for different cell types. For example, the specialized digestive proteins that service the cells lining the adult intestine differ from proteins expressed in a neuron found in the nerve tract of a limb. They must differ because each performs dramatically different functions. So, during development, the appropriate genes must be turned on, or "up-regulated," and turned off, or "down-regulated," to ensure the production of the correct protein products at the right time and in the right cell types.

Specific proteins play active roles in regulating the expression of genes for building other proteins. The protein actors playing these coordinating roles are known as transcriptional regulators (TRs) or transcription factors (TFs). TRs (or TFs) usually bind directly to specific sites in DNA, either preventing (repressing) or enabling (activating) the transcription of specific genes into RNA. TRs or TFs convey instructions about which genes to turn on or turn off. Their three-dimensional geometries exhibit characteristic DNA-binding features, including a specific domain of 61 amino acids that wraps around the DNA double helix. Other transcription factors include the zinc finger and leucine zipper motifs that also bind to DNA. Transcriptional regulators and factors are themselves controlled by complex circuits and signals transmitted by other genes and proteins, the overall complexity and precision of which is breathtaking.

Painstaking genetic research—performed by Nüsslein-Volhard and Wieschaus and many other developmental biologists—has uncovered many of the key embryonic regulatory genes that help switch cells into their differentiated adult types. This research also uncovered a profound difficulty cutting to the very core of the neo-Darwinian view of life.

“There is no theoretical reason that would permit us to expect that evolutionary lines would increase in complexity with time; there is also no empirical evidence that this happens.” (John Maynard Smith, E. Szathmary—quoted from John Lennox’s book, "God’s Undertaker: Has Science Buried God," 107. most of the following quotations are taken from this masterful book!)

“In the whole experimentally accessible domain of microevolution (including research in artificial breeding and in species formation), all variations have certainly remained within the confines of basic types [species, more or less].” (Siegfried Scherer)

Cell biologist E.J. Ambrose of the University of London argued that it is unlikely that fewer than five genes could ever be involved in the formation of even the simplest new structure, previously unknown in the organism. He then points out that only one in 1,000 mutations is non-deleterious, so that the chance of five non-deleterious mutations occurring is 1 in a million billion replications. [This means that every organism will probably die before it adds a new organ!]

If there are limits even to the amount of variation the most skilled breeders can achieve, the clear implication is that natural selection is likely to achieve much less. It is not surprising that he [Grasse] argued that microevolution could not bear the weight that is often put upon it. (Lennox, 108).

“Well, as common sense would suggest, the Darwinian theory is correct in the small, but not in the large. Rabbits come from other slightly different rabbits, not from either [primeval] soup or potatoes.” (Astro-Physicist, Fred Hoyle)

The traditional understanding of DNA has recently been transformed beyond recognition. DNA does not, as we thought, carry a linear, one-dimensional, one-way, sequential code — like the lines of letters and words on this page… DNA information is overlapping – multi-layered and multi-dimensional; it reads both backwards and forwards… No human engineer has ever even imagined, let alone designed an information storage device anything like it. Moreover, the vast majority of its content is metainformation — information about how to use information. Meta-information cannot arise by chance because it only makes sense in context of the information it relates to. (Alex Williams, Astonishing DNA Complexity Demolishes neo-Darwinism, Journal of Creation 21(3) 2007).

Molecular studies (King and Wilson, 1975) were similarly pointing to Homo sapiens. By heterochrony, one could generate de ‘‘evolution at two levels,’’ one molecular, the other morpho logical. Thus, by the early 1980s, numerous paleontologists and evolutionary biologists (Gould, Stanley, Eldredge, Verba, and most critically, Ayala) came to the conclusion that although macroevolutionary phenomena were underlain by microevolutionary phenomena, the two areas were autonomous and that macroevolutionary processes could not be explained solely by microevolutionary events. 1)

http://www.evolbiol.ru/large_files/gilbert.pdf

Darwins doubt (pp. 410-411)

“This book has presented four separate scientific critiques demonstrating the inadequacy of the neo-Darwinian mechanism, the mechanism that Dawkins assumes can produce the appearance of design without intelligent guidance. It has shown that the neo-Darwinian mechanism fails to account for the origin of genetic information because: (1) it has no means of efficiently searching combinatorial sequence space for functional genes and proteins and, consequently, (2) it requires unrealistically long waiting times to generate even a single new gene or protein. It has also shown that the mechanism cannot produce new body plans because: (3) early acting mutations, the only kind capable of generating large-scale changes, are also invariably deleterious, and (4) genetic mutations cannot, in any case, generate the epigenetic information necessary to build a body plan.”

“Careful examination of the evidence for Darwinian theory should be encouraged”? And these “oldest problems in evolutionary biology” lead me and many others to our being “skeptical.” It is not a matter of politics. I simply do not understand, chemically, how macroevolution could have happened. Hence, am I not free to join the ranks of the skeptical and to sign such a statement without reprisals from those that disagree with me? Furthermore, when I, a non-conformist, ask proponents for clarification, they get flustered in public and confessional in private wherein they sheepishly confess that they really don’t understand either. Well, that is all I am saying: I do not understand. But I am saying it publicly as opposed to privately. Does anyone understand the chemical details behind macroevolution? If so, I would like to sit with that person and be taught, so I invite them to meet with me. Lunch will be my treat. Until then, I will maintain that no chemist understands, hence we are collectively bewildered. And I have not even addressed origin of first life issues. For me, that is even more scientifically mysterious than evolution. Darwin never addressed origin of life, and I can see why he did not; he was far too smart for that. Present day scientists that expose their thoughts on this become ever so timid when they talk with me privately. I simply can not understand the source of their confidence when addressing their positions publicly.

Furthermore, most of my scientist colleagues do not discuss macroevolution very often because they are too busy with their own fields of interest to be sidetracked by such tangential matters. Though the acceptance of macroevolution is rather implicit within their core understandings, most science professors are simply too harried to take much notice of the details. Pondering and thoughtfulness has been pounded and distilled out of many of us; there’s another meeting to attend, another proposal to write, another manuscript to proof, yet another lecture to deliver, 100 more emails to answer, and the anxieties about our futures must be allayed. “The peace which passeth all understanding,” is beyond reach, nay beyond understanding.

Likewise, I do not well-understand the stance of many of my creationist friends regarding their scientific evidence for creation or intelligent design, but they seem to be quite comfortable in most respects with the natural and historical suggestions for its claims. I am happy for them, but I hope that their position does not cause them to trump brotherly love or charity in thought or words. When they write on these topics, they are too quick to cite each other or to refer to 40-year-old studies, and slow to consider the newer findings in the mainstream scientific literature. The scientist is not the creationist’s enemy, and most scientists are quite sincere in producing research that is accurate to the best of today’s measurement abilities. For example, the gross dismissing of radiometric dating experiments that use even multiple corroborating nuclei, not by a mere 20% or even 100%, but by 4-5 orders of magnitude, based on antiquated “scientific” arguments, is unscientific and unfair. Moreover, to simply suggest that “God made it look older than it really is” is also unreasonable. With what else is God deceiving us? The virgin birth, the crucifixion or the resurrection, perhaps? Never. God is not in the business of deception, but in causing man to seek so that he could find. And my creationist friends need some thoughtful explanations for their children because, in my experience, young college-aged people seek truth, and if you threaten them, try to brow-beat them, or show them a select set of cloistered “scientific” data, they’ll smell hypocrisy, and sooner or later in life, reject it altogether.

What a comfort it must be to be pleasantly settled in one camp or the other, but I can not be so settled, and hence I have few tent-fellows. Based upon my faith in the Scriptures, I do believe (yes, faith and belief go beyond scientific evidence for this scientist) that God created the heavens and the earth and all that dwell therein, including a man named Adam and a woman named Eve. As for many of the details and the time-spans, I personally become less clear. Some may ask, What’s “less clear” about the text that reads, “For in six days the Lord made the heavens and the earth”? That is a fair question, and I wish I had an answer that would satisfy them. But I do not because I remain less clear.

I hope that’s satisfactory; I mean for me, a scientist and a Christian, to be unsure of a few things in both science and Christianity. The question is not fundamental to my salvation as a Christian which is based upon the finished work of Jesus Christ, my confession in him as Savior and my belief in his resurrection from the dead. And I used to think that my outward confession of skepticism regarding Darwinian Theory was also of little consequence to my career as a scientist. Specifically, in the past, I wrote that my standing as a scientist was “based primarily upon my scholarly peer-reviewed publications.” I no longer believe that, however.

In the last few years I have seen a saddening progression at several institutions. I have witnessed unfair treatment upon scientists that do not accept macroevolutionary arguments and for their having signed the above-referenced statement regarding the examination of Darwinism. (I will comment no further regarding the specifics of the actions taken upon the skeptics; I love and honor my colleagues too much for that.) I never thought that science would have evolved like this. I deeply value the academy; teaching, professing and research in the university are my privileges and joys. Rice University, from the administration, has always been gracious and open. The president of Rice University, David Leebron, has even written to the faculty that a,

“core value of our university is free and open inquiry. We encourage robust debate on the difficult issues of the day, and we welcome people with many points of view to our campus to better understand those issues and the differences that can divide us. That can and does mean that we sometimes provide a forum for opinions that may be controversial — or even on occasion reprehensible — to many or a few. While we cannot and will not censor the expression of divergent opinions, we do expect those opinions be expressed with civility and with respect for other points of view.”

Hence, by my observation, the unfair treatment upon the skeptics of macroevolution has not come from the administration level. But my recent advice to my graduate students has been direct and revealing: If you disagree with Darwinian Theory, keep it to yourselves if you value your careers, unless, of course, you’re one of those champions for proclamation; I know that that fire exists in some, so be ready for lead-ridden limbs. But if the scientific community has taken these shots at senior faculty, it will not be comfortable for the young non-conformist. When the power-holders permit no contrary discussion, can a vibrant academy be maintained? Is there a University (unity in diversity)? For the United States, I pray that the scientific community and the National Academy in particular will investigate the disenfranchisement that is manifest upon some of their own, and thereby address the inequity.

So what should be taught in schools regarding evolution? As I wrote, I am not a proponent of Intelligent Design for the reasons I state above: I can not prove it using my tools of chemistry to which I am bound in the chemistry classroom; the same tools to which I commensurately bind my evolutionist colleagues. But I think that a better approach might include more teaching about evolution, namely coverage of legitimate scientific criticisms of neo-Darwinism and disputes about the origin of the first life. That would be more balanced.

Some have asked me what I think of the movie, “Expelled. No Intelligence Allowed.” I saw a closed viewing of the movie in February 2008, two months before its public showing. It was difficult for me to watch because it struck so close to home, thus I am sure that my feelings were different than the other non-scientists in the theater. As to the veracity of the specific claims by others in the movie, I cannot judge since I was not walking in their shoes. But here is what I fear: the movie might serve to increase the polarization between the scientific and lay communities. That a subset of the scientific establishment is retarding the careers of Darwinian skeptics is true as far as I have witnessed personally. If there are legitimate scientific skepticisms regarding the extrapolation of microevolution to macroevolution, those skeptics are sometimes stifled through unfair treatment regarding their career advancement; that is real although most scientists would say that such attacks on careers are nonexistent. Most would say such a thing because they are not involved in the skirmish and they are not aware that a colleague down the hall is hemorrhaging. Like many, they are absorbed in their own work because science can be all-consuming. I do not fault them for that. Most scientists, as I said, are far too busy with their own careers to be involved with other’s problems of this sort. A small number of scientists would say that the stifled deserve stifling. Therefore, if attention can be brought to the unfortunate state in science through the movie, let it come. I hope all welcome freedom of speech and freedom of inquiry, even if that freedom threatens one’s own preconceived views or areas of research. But I also hope that the reaction will not be too great on the layperson’s side wherein their disgust induces a politician or two to become incensed in the investigation because of the unnecessarily incendiary portrayals to Nazism, Berlin-walling and church-demolishing in the movie; although entertaining from a theatrical perspective, that part of the movie is taken to an unrealistic extrapolation point. But then again, one who is far more qualified than I am, and further seasoned by fire, believed differently. Viktor Frankl (http://en.wikipedia.org/wiki/Viktor_Frankl), a former Auschwitz inmate wrote in The Doctor and the Soul, that the source for much of the 20th Century’s inhumanity has come from the very origins being discussed here.

“If we present a man with a concept of man which is not true, we may well corrupt him. When we present man as an automaton of reflexes, as a mind-machine, as a bundle of instincts, as a pawn of drives and reactions, as a mere product of instinct, heredity and environment, we feed the nihilism to which modern man is, in any case, prone.

“I became acquainted with the last stage of that corruption in my second concentration camp, Auschwitz. The gas chambers of Auschwitz were the ultimate consequence of the theory that man is nothing but the product of heredity and environment; or as the Nazi liked to say, ‘of Blood and Soil.’ I am absolutely convinced that the gas chambers of Auschwitz, Treblinka, and Maidanek were ultimately prepared not in some Ministry or other in Berlin, but rather at the desks and lecture halls of nihilistic scientists and philosophers [emphasis added].”

If Frankl is correct, God help us.”

https://matthew2262.wordpress.com/category/biology-related/

 Macroevolution and the Diversity of Life


Here, we move from the origin of life to its diversity as observed in the current world and as is generally inferred from the fossil record and geological dating schemes. (It is not my purpose here to challenge the generally accepted dating systems and their "standard" chronology. [Cf. ICR's summary remarks here for a start if you are interested in that secondary issue. Also cf. Wiens' remarks here from the Old Earth Creationist view, as well as J P Moreland, here, on the related Bible interpretation issues. The YEC view is summarised here, in a report on a debate: Ross/Lisle.] Nor is it my purpose to attempt to refute that at some significant level macroevolution may have happened across time. Only, let us take time to rethink the credibility of the claims made by the predominant school of thought on the origin of life.)
The underlying issue to be addressed, then, is that there is reason to infer that the observed and inferred diversity cannot credibly be accounted for on the basis of a fundamentally random process of genetic mutation and a selection filter. For, there is a need to generate FUNCTIONAL and highly complex genetic information that works in an integrated organism by chance processes in the context of blind natural forces. The reason for that, is the observation that this requires FSCI, and the claim that such can be generated through essentially random processes, is not credible. So, it is useful to first cite from Lönnig's recent [2004] paper on "Dynamic genomes, morphological stasis, and the origin of irreducible complexity."
Speaking of the horseshoe crab as an organism that seems to have been morphologically static across 250 million years of fossil record and on into the contemporary world, he notes:

examples like the horseshoe crab are by no means rare exceptions from the rule of gradually evolving life forms . . . In fact, we are literally surrounded by 'living fossils' in the present world of organisms when applying the term more inclusively as "an existing species whose similarity to ancient ancestral species indicates that very few morphological changes have occurred over a long period of geological time" [85] . . . . Now, since all these "old features", morphologically as well as molecularly, are still with us, the basic genetical questions should be addressed in the face of all the dynamic features of ever reshuffling and rearranging, shifting genomes, (a) why are these characters stable at all and (b) how is it possible to derive stable features from any given plant or animal species by mutations in their genomes? . . . .
A first hint for answering the questions . . . is perhaps also provided by Charles Darwin himself when he suggested the following sufficiency test for his theory [16]: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." . . . Biochemist Michael J. Behe [5] has refined Darwin's statement by introducing and defining his concept of "irreducibly complex systems", specifying: "By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning" . . . [for example] (1) the cilium, (2) the bacterial flagellum with filament, hook and motor embedded in the membranes and cell wall and (3) the biochemistry of blood clotting in humans . . . . 

One point is clear: granted that there are indeed many systems and/or correlated subsystems in biology, which have to be classified as irreducibly complex and that such systems are essentially involved in the formation of morphological characters of organisms, this would explain both, the regular abrupt appearance of new forms in the fossil record as well as their constancy over enormous periods of time. For, if "several well-matched, interacting parts that contribute to the basic function" are necessary for biochemical and/or anatomical systems to exist as functioning systems at all (because "the removal of any one of the parts causes the system to effectively cease functioning") such systems have to (1) originate in a non-gradual manner and (2) must remain constant as long as they are reproduced and exist. And this could mean no less than the enormous time periods mentioned for all the living fossils hinted at above. Moreover, an additional phenomenon would also be explained: (3) the equally abrupt disappearance of so many life forms in earth history . . . The reason why irreducibly complex systems would also behave in accord with point (3) is also nearly self-evident: if environmental conditions deteriorate so much for certain life forms (defined and specified by systems and/or subsystems of irreducible complexity), so that their very existence be in question, they could only adapt by integrating further correspondingly specified and useful parts into their overall organization, whichprima facie could be an improbable process -- or perish . . . . 

According to Behe and several other authors [5-7, 21-23, 53-60, 68, 86] the only adequate hypothesis so far known for the origin of irreducibly complex systems is intelligent design (ID) . . . in connection with Dembski's criterion of specified complexity . . . . "For something to exhibit specified complexity therefore means that it matches a conditionally independent pattern (i.e., specification) of low specificational complexity, but where the event corresponding to that pattern has a probability less than the universal probability bound and therefore high probabilistic complexity" [23]. For instance, regarding the origin of the bacterial flagellum, Dembski calculated a probability of 10^{^-234}[22].

Now, first, we must observe that Darwin's proposed test, on at least one major interpretation, is less generous than it first appears: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." For, as Shapiro acidly but aptly noted, on the defects in such an appeal to bare possibility in defense of the RNA world hypothesis -- making a remark that, we observe, inadvertently also applies to his preferred metabolism first scenario -- that:
The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck.
In short, there is a distinct difference and resulting massive, probability-based credibility gap between having components of an irreducibly complex,tightly integrated, information-rich functional system with available energy but no intelligence to direct the energy to construct the system, and getting by the happenstance of "lucky noise," to that system. That is, physical and logical possibility are not at all to be equated with probabilistic credibility -- especially when there are competing explanations on offer -- here, intelligent agency -- that routinely generate the sort of phenomenon being observed.
So, having duly noted this caveat, through reasoning within the generally accepted framework of the geological record, and using a classic abductive approach (If X, then otherwise puzzling facts F1, F2, . . . follow at once; so the facts support but do not prove explanation X; this is the core agenda of science, and its core epistemological characteristic) we can see that irreducible complexity and FSCI, working together, can explain major and otherwise unexplained [for 150 - 200 years] features of the fossil record of life. Of course, this sort of claim has not remained unchallenged, and in particular the case of the bacterial flagellum -- a cellular outboard motor that has an ion-driven rotor tied to a hooked filament, that drives the bacterium as it spins at up to upwards of 10,000 rpm -- has been a focus for debate.
On this, we can sum up the current score by again citing Peterson:

Behe's most famous example is the bacterial flagellum described above. If you take away the driveshaft from the flagellar motor, you do not end up with a motor that functions less well. You have a motor that does not function at all. All of the essential parts must be there, all at once, for the motor to perform its function of propelling the bacterium through liquid . . . . that is precisely what Darwinian evolution cannot accomplish. Darwinian evolution is by definition "blind." It cannot plan ahead and create parts that might be useful to assemble a biological machine in the future. For the machine to be assembled, all or nearly all the parts must already be there and be performing a function. Why must they already be performing a function? Because if a part does not confer a real, present advantage for the organism's survival or reproduction, Darwinian natural selection will not preserve the gene responsible for that part. In fact, according to Darwinian theory, that gene will actually be selected against. An organism that expends resources on building a part that is useless handicaps itself compared to other organisms that are not wasting resources, and will tend to get outcompeted . . . .
Behe the biochemist . . . search[ed] the relevant scientific journals, books, and proceedings of meetings to find out what the Darwinists had really proven about the origin of complex biochemical systems . . . . "There has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems" . . . Behe, recalling the "fierce resistance" he encountered after the publication of Darwin's Black Box, remarks that much of it came from "Internet fans of Darwinism who claimed that, why, there were hundreds or thousands of research papers describing Darwinian evolution of irreducibly complex biochemical systems." Except that there aren't.
Well, this sent the Darwinians scrambling. Kenneth Miller, a biologist at Brown University who argues in favor of Darwinian evolution, made a splash when he announced (and he bolded the language in his article) that "the bacterial flagellum is not irreducibly complex." Miller cited a cellular structure known as the type III secretory system (TTSS) that allows certain bacteria to inject toxins through the cell walls of their hosts . . . .
But . . . the bubonic plague bacterium already has the full set of genes necessary to make a flagellum. Rather than making a flagellum, Y. pestis uses only part of the genes that are present to manufacture that . . . injector instead. As pointed out in a recent article by design theorist Stephen Meyer and microbiologist Scott Minnich (an expert on the flagellar system), the gene sequences suggest that "flagellar proteins arose first and those of the pump came later." If evolution was involved, the pump came from the motor, not the motor from the pump. Also, "the other thirty proteins in the flagellar motor (that are not present in the [pump]), are unique to the motor and are not found in any other living system." . . . In short, the proteins in the TTSS do not provide a "gradualist" Darwinian pathway to explain the step-by-step evolution of the irreducibly complex flagellar motor.

Further to this, Meyer's discussion of the Cambrian life revolution (which -- despite much rhetoric to the contrary -- evidently passed proper peer review by renowned scientists) in the same record shows that the underlying pattern of sudden diversification is particularly present and challenging for the Neo-Darwinian Theory [NDT] at the point where the record first shows a dramatic widening of the range of animal life at the highest level, the phylum, with dozens of basic body plans appearing within a fairly narrow temporal window in the record:

The Cambrian explosion represents a remarkable jump in the specified complexity or "complex specified information" (CSI) of the biological world. For over three billions years, the biological realm included little more than bacteria and algae (Brocks et al. 1999). Then, beginning about 570-565 million years ago (mya), the first complex multicellular organisms appeared in the rock strata, including sponges, cnidarians, and the peculiar Ediacaran biota (Grotzinger et al. 1995). Forty million years later, the Cambrian explosion occurred (Bowring et al. 1993) . . . One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the number of new cell types that emerged with them (Valentine 1995:91-93) . . . the more complex animals that appeared in the Cambrian (e.g., arthropods) would have required fifty or more cell types . . . New cell types require many new and specialized proteins. New proteins, in turn, require new genetic information. Thus an increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information. Molecular biologists have recently estimated that a minimally complex single-celled organism would require between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life (Koonin 2000). More complex single cells might require upward of a million base pairs. Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require orders of magnitude more coding instructions. The genome size of a modern arthropod, the fruitfly Drosophila melanogaster, is approximately 180 million base pairs (Gerhart & Kirschner 1997:121, Adams et al. 2000). Transitions from a single cell to colonies of cells to complex animals represent significant (and, in principle, measurable) increases in CSI . . . .
In order to explain the origin of the Cambrian animals, one must account not only for new proteins and cell types, but also for the origin of new body plans . . . Mutations in genes that are expressed late in the development of an organism will not affect the body plan. Mutations expressed early in development, however, could conceivably produce significant morphological change (Arthur 1997:21) . . . [but] processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream. For this reason, mutations will be much more likely to be deadly if they disrupt a functionally deeply-embedded structure such as a spinal column than if they affect more isolated anatomical features such as fingers (Kauffman 1995:200) . . . McDonald notes that genes that are observed to vary within natural populations do not lead to major adaptive changes, while genes that could cause major changes--the very stuff of macroevolution--apparently do not vary. In other words, mutations of the kind that macroevolution doesn't need (namely, viable genetic mutations in DNA expressed late in development) do occur, but those that it does need (namely, beneficial body plan mutations expressed early in development) apparently don't occur.6 [Emphases added. Cf a more easily readable (and also peer-reviewed) but longer discussion, with illustrations, here.]

Now, this analysis highlights a significant distinction we need to make: micro-evolutionary changes are late-developing, and do not affect the core body plan and its associated functions. Such mutations are indeed possible and are observed. But, when the mutations get to the fundamental level of changing body plans -- i.e. macro-evolution -- they face the implication that we are now disturbing the core of a tightly integrated system, and so the potential for destructive change is much higher. Consequently, the genes that control such core features are stabilised by a highly effective negative feedback effect: random changes strongly tend to eliminate themselves through loss of integrity of vital body functions.
In response, it is often claimed that sufficient microevolution accumulates across time to constitute macroevolution. But, what we "see" in the fossil record of the Cambrian rocks is just that innovation at the core levels coming first, and coming massively -- just the opposite of what the NDT model would lead us to expect. For, as Dan Peterson summarises in his recent article:

To take just one example, a well-known (and unsolved) problem for Darwinism is the Cambrian Explosion. As noted by Stephen Meyer in the book Debating Design, this event might be better called the Cambrian Information Explosion. For the first three billion years of life on Earth, only single-celled organisms such as bacteria and bluegreen algae existed. Then, approximately 570 million years ago, the first multi-cellular organisms, such as sponges, began to appear in the fossil record. About 40 million years later, an astonishing explosion of life took place. Within a narrow window of about 5 million years, "at least nineteen and perhaps as many as 35 phyla (of 40 total phyla) made their first appearance on Earth...." Meyer reminds us that "phyla constitute the highest categories in the animal kingdom, with each phylum exhibiting unique architecture, blueprint, or structural body plan." These high order, basic body plans include "mollusks (squids and shellfish), arthropods (crustaceans, insects, and trilobites), and chordates, the phylum to which all vertebrates belong."

These new, fundamental body plans appeared all at once, and without the expected Darwinian intermediate forms.

In addition, we should observe in passing that there is also an underlying problem with the commonly encountered natural selection model, in which small variations confer significant cumulative advantages in populations,and cumulate to give the large changes that would constitute body-plan level macroevolution. To see this, let us excerpt a typical definition of natural selection:


Natural selection is the process by which favorable heritable traits become more common in successive generations of a population of reproducing organisms, and unfavorable heritable traits become less common. Natural selection acts on the phenotype, or the observable characteristics of an organism, such that individuals with favorable phenotypes are more likely to survive and reproduce than those with less favorable phenotypes. The phenotype's genetic basis . . . will increase in frequency over the following generations. Over time, this process can result in adaptations that specialize organisms for particular ecological niches and may eventually result in the emergence of new species. In other words, natural selection is the mechanism by which evolution may take place in a population of a specific organism. [Emphases added.]
From this, we may immediately observe that natural selection is envisioned as a probabilistic culler of competing sub-populations with varying adaptations coming from another source [usually some form of chance-based variation]. That is, it does not cause the actual variation, it is only a term that summarises differences in likelihood of survival and reproduction and possibly resulting cumulative effects on populations across time. So, when innovations in life-forms require the origin of functionally specific, information-rich organised complexity, we are back to some form of chance variation to explain it, and soon run right back into the FSCI-origination barrier.
Moreover, there are linked issues with the related gambler's ruin challenge (as is discussed here). 
For, if a given selection advantage is small and the absolute numbers of the sub-population with the innovation are also relatively low, most of the time, such an innovation will simply be lost due to the overwhelming effects of mere chance on odds of survival and reproduction. In other words, one has to have enough population resources to "spend" for long enough to get to the long-run point where modest differential effects will pay off to one's advantage. And, if we take isolation to a niche without competition as a typical example by which such innovations will have a good chance to grow into a viable sub-population that can then migrate back and compete with then dominate over the original population, we still have not accounted for the rise of information-rich organically coherent innovations, especially at that core body-plan level which expresses itself in the vulnerable early phases of the embryological development process. 
Pulling the strands of analysis together, we may see that, in light of the evident FSCI embedded in life-forms at cellular level, and its implications, the NDT has a major challenge accounting precisely for the macro-evolution that it sets out to explain. But, by sharp contrast, the concepts of irreducible complexity and FSCI/CSI leading to design as a new paradigm are in fact able to relatively easily account for these phenomena, within the generally accepted geochronological and fossil frameworks. 
Thus, it is fair comment to observe that the design inference seems to better explain the generally accepted framework than the dominant paradigm, NDT. 
This is in addition to the basic fact that, strictly, the NDT does not address the origin of life -- a situation where the dominant school in biology (as seen above), after 50 years of various models, still struggles to find a robust, empirically adequate model. So, whatever objections may be made -- and are often made, sadly, to the point of evident workplace harassment in some cases [cf. US Congress Committee staff investigation summary here and main report here with appendix here; also the earlier OSC Letter here as well as the Klinghoffer reports that publicly broke and now follow up the story] -- this basic contrast of explanatory failure/success should be soberly reckoned with.


http://www.angelfire.com/pro/kairosfocus/resources/Info_design_and_science.htm#macvsmic

Micro- and macroevolution1

Microevolution refers to minor genetic variation in a local population, mainly resulting from the reshuffling of characteristics already present in a species’ gene pool and the influence of natural selection. Macroevolution is the emergence of entirely new and more ‘advanced’ features, leading to the emergence of species of a completely different type. Microevolution is a fact. Macroevolution, or large-scale molecules-to-man transformation, is an unproven hypothesis. As palaeontologist Keith Thompson has said:

no one has satisfactorily demonstrated a mechanism at the population genetic level by which innumerable very small phenotypic changes could accumulate rapidly to produce large changes: a process for the origin of the magnificently improbable from the ineffably trivial.¹

Various examples of microevolution have been observed. For instance, the average beak size of finch populations can change over the course of a few years. Many species of moths and butterflies in industrialized regions have shown an increase in the frequency of individuals with dark wings in response to industrial soot blackening trees. More than 200 insect and rodent species have developed resistance to the pesticide DDT in parts of the world where spraying has been intense. Disease-causing bacteria have made a comeback as strains evolved the ability to defend themselves against antibiotics. (As already noted, some of these changes may involve adaptive rather than random mutations.)
Microevolution can bring about the emergence of a new, but similar, species, if we adopt the orthodox definition that different species do not interbreed. For instance, a study of a species of Siberian greenish warblers that nest and breed in forest habitats encircling the Tibetan Plateau found that warblers from neighbouring habitats readily mate, though their characteristics differ slightly, but that two warbler populations living far apart did not mate and differed strikingly in other characteristics – they can therefore be considered two distinct species.*

*Defining a species as an interbreeding community of organisms is only a theoretical definition. In practice, species are almost always defined by their morphology, and sometimes by their behaviour. Some evolutionists argue that when a population varies continuously over a large range, it constitutes a single species, even though the extremes may be incapable of interbreeding. Note that some populations regarded as different species, such as dogs and wolves, do interbreed freely if allowed to.²

The differences between the two species of warblers are however trivial compared with the differences between a mouse and an elephant, or an octopus and a bee. It seems wildly improbable to expect accidental mutations to change one creature into a completely different one – but Darwinists simply respond with the mantra that ‘improbable does not mean impossible’. They have an unshakeable faith in the ability of random chance, with the help of natural selection, to bring about wildly improbable changes (i.e. perform miracles) again and again for millions upon millions of years. If this were true, ‘chance’ would have to change its name. Recognizing this, biologist Lyall Watson asserted that, instead of acting blindly, ‘chance’ seems to have ‘a pattern and a reason of its own’ as if operating according to a ‘set of cosmic rules’.³
Macroevolutionary change requires changes in very early embryogenesis. During embryonic development, the appropriate genes must be turned on or off to ensure the production of the right protein products at the right time and in the right cell types. As already explained, the protein-coding regions of the genome and the non-protein-coding regions that control gene expression together function as circuits, known as developmental gene regulatory networks (dGRNs). The overall precision and complexity of this system are stunning. Not surprisingly, experiments have shown that mutations affecting the dGRNs that regulate body-plan development have catastrophic effects on the organism, leading to abnormalities or death.⁴ Moreover, the genetic and epigenetic information contained in cells does not explain the form of developing organisms. In short, anything Darwinists say about one organism being transformed into a very different organism (e.g. a fish into an amphibian) purely by random genetic mutations or other physical changes should be taken with a large pinch of salt.

1) http://davidpratt.info/evod1.htm

Mutations and macro-evolution

Micro-evolutionary theory cannot explain how brand new structures and body plans can appear. Such major changes are said to occur because of what is termed macro-evolution. If you read a textbook on this subject, then you will find that there is much detail given about the analysis of alleles in micro-evolution but that for macro-evolution there is simply the bland statement that mutation is the driving force for change – with surprisingly little evidence given or explanation of how this can be. Mutations occur when there is a mistake during replication of the DNA molecule and geneticists recognise two main types. In gene mutation an allele of a gene changes, becoming a different allele. Because such a change occurs at one gene, on one point of the chromosome, it is sometimes called a point mutation. In contrast to this there is chromosome mutation, when segments of chromosomes change. When a point mutation occurs there can be three possibilities: There is substitution of a nucleotide base, addition of a nucleotide base or deletion of a nucleotide base. You will remember that there are four DNA nucleotides A, G, C and T. A always pairs with T on the opposite chain and C with G. If a base is added during replication then one will be added on the other chain also (its complement as described above). If one is substituted then likewise there is a substitution on the opposite chain. You will remember that the nucleotide bases code for amino acids in triplets. There are various possibilities, therefore, when a point mutation occurs. There may be a new amino acid coded for and inserted into the protein (for example, when a substitution results in a different triplet). Or the same amino acid may be coded for (because some amino acids are coded for by more than one triplet) and the mutation is therefore silent. Alternatively, if there is a deletion, there may be a completely new amino acid sequence for the protein coded from that point in the DNA – this is because the reading of the base sequence goes out of phase and totally different triplets may be read from it from that point on.

 This is known as a frame shift mutation and it usually results in a non-functioning polypeptide or protein. Sometimes there may be a new, or substituted, amino acid in the protein chain but this has no known effect and so the mutation is neutral. It appears, for example, that the haemoglobin molecule can have a certain amount of variety without losing its overall function – we know this because of studying haemoglobin molecules from different species. Another possibility is that a triplet may be formed which codes for a stop in the reading (known as a stop codon) – from there the amino acid chain construction will also stop, resulting in an incomplete protein. Sometimes larger sequences of the DNA are deleted, changed or duplicated. Large parts of the DNA molecule, up until very recently, have no known function and mutations in these regions have no obvious effect. 

 Chromosomal mutations involve various alterations in structure which cause harm or loss of function. Increased number of chromosomes (polyploidy) occurs fairly often in plants and can result in new varieties – often larger than the parent plants. It must be emphasised, though, that this does not confer any really new information in the DNA and therefore cannot be a mechanism to explain macroevolution. Cells have numerous sophisticated enzymes which repair mutant sites on the DNA and which prevent the vast majority of mutations being expressed. You may remember me mentioning these in the first chapter, where we looked at the constraints on large sections of DNA replicating without such repair mechanisms (as had to be for the first cells in a Darwinian model). There is a host of specific enzymes, some of which prevent damaging compounds getting to the DNA and others that cut and splice the DNA in numerous ways to remove harmful mutations. These mechanisms go to show that mutations are generally harmful and must be prevented for organisms to survive. As a doctor I am very aware of the devastating effect of mutations in human beings. Mutation, to a doctor, signifies damage and often leads to conditions incompatible with life. 

Can we be sure that mutations are the source of the genetic information that leads to useful new processes and structures in organisms?

 This is the key question that needs to be answered by geneticists. Possibly the most detailed and sophisticated textbook on genetics available is An Introduction to Genetic Analysis by Grifiths, et al.2 These are heavyweights in the genetic world. In their textbook there is a large section on the mutation of genes and chromosomes and another on evolution (a surprisingly small section). Much of what I write here is based on this book and here, if anywhere, we should see the evidence for mutations leading to macro-evolution. We find no such thing. The only mutations that are known to be useful are the acquisition of resistance of certain organisms to external agents such as pesticides or antibiotics. There are, in fact, no recorded instances of the type of macro-evolution that I have discussed above. I will quote from the book: ‘Because mutation events introduce random genetic changes, most of the time they result in loss of function. The mutation events are like bullets being fired at a complex machine; most of the time they will inactivate it. However it is conceivable that in rare cases a bullet will strike the machine in such a way that it produces some new function.’3 I do not think that I am the only one who could not imagine any complex machine being improved by firing a bullet at it. In fact the machinery inside a cell is far more complex than any machine ever constructed. There have been endless attempts to observe mutations over the last half-century. Much of the work done is on fruit flies (Drosophila). They are useful because they are easily bred in captivity, there are a multitude of species and they have rapid breeding cycles. Scientists have repeatedly used methods to greatly increase the mutation rate of fruit flies so that vastly more mutations can be observed. This involves subjecting them to various forms of radiation and also using chemicals (mutagens) that increase mutation rates. The result of this is that we ought to see in the laboratory some direct evidence of mutations causing new functions and forms which could conceivably be useful in the wild. No such mutations have ever been seen. The sorts of mutations that we see are usually harmful, such as stunted wings, deterioration in vision and non-functional alteration in limb position. If we are to accept the Darwinian model then we must test its integrity. As mentioned before in discussing the work of Karl Popper, we need to predict from the theory certain expected results which it will fail if the theory is false. Certainly one prediction is that we should see beneficial mutations on the macro level after decades of subjecting billions of fruit flies to mutagens. On this test the theory fails completely. The geneticist Steve Jones has written an updated (I have to say less well written) version of Darwin’s Origin of Species – Almost Like a Whale4. In his first chapter he enjoys a good attack on creationists. (It is interesting that creationists are nearly always lumped together despite having a great diversity of viewpoints.) He points to the one bit of evolution that we have all seen in our lifetime – that of the AIDS virus HIV. He rightly explains how the virus has, through mutation, changed so that there are varieties. This is the only evolution that he can tell us about that has been observed occurring because of mutation. This deserves comment because it actually reflects the very poor evidence for major change being able to occur through mutation. The AIDS virus, firstly, is a virus – an entity which even virologists cannot say for certain is ‘life’. It is not a cell and is basically a package of RNA that gets into human cells, takes over and causes vast numbers of itself to be replicated. The destruction of cells in the immune system leads to AIDS. Any changes that have been observed through mutation are very small – essentially the virus remains HIV. To parade this as evidence for mutation leading from Pikaia (that chordate seen in the Cambrian explosion) to you and me is simply wrong and merely shows up the paucity of evidence that there is for macro-evolution through mutation. We need to realise what happens when a mutation occurs. There may indeed be some new information in the DNA which could mean that a different amino acid, or series of amino acids, was inserted into a protein. In another chapter we will look in more detail at the complexity of some of the intra-cellular machinery but suffice it to say now that the enzyme systems and workings of a cell are the most complex physical structures in the known universe. When a mutation causes a change to such a system then it needs to confer a definite advantage if it is going to survive into future generations. The systems in the cell are so finely tuned that alterations such as those from mutations are either harmful or make very little if any difference. Try to imagine converting a steam-driven car into a modern petrol-driven one. The changes needed are totally radical and cannot be achieved in tiny steps. To become a petrol engine requires many changes all at once. A mutation is equivalent to putting a different fuel (petrol) into an engine designed to run on steam. It will not work. A totally new engine must be designed from scratch. The systems in a cell are far more complex and they govern the whole of the organism. What we see in the fossil record are many sudden changes which are equivalent to the conversion of a steam engine to a petrol one. We have discussed many of these and you will remember the new body plans of the Cambrian period, the appearance of fish, the appearance of tetrapods, feathers, warm blooded mammals, brains. All of these are macro changes which are not explained on mutation theory. Another problem for the Darwinist is that mutation rates in organisms are very very slow. Even the billions of years that have elapsed are simply not adequate to achieve enough progressive genetic change to bring about evolution. Griffiths, et al., in their book, list some typical mutation rates for point mutations in various genes of bacteria, corn and fruit flies. Mutation rates per generation range from from 2 x 10 to the power -8, to 2 x 10 to the power -4. Griffiths, et al., conclude, and I quote: ‘Mutation rates are so low that mutation alone cannot account for the rapid evolution of populations and species.’5 This is a plain admission that we do not have any idea what has caused macro-evolution. Another problem is that most mutations, if passed on to the next generation, are recessive and so the allele will not become frequent in that population. In fact there seems to be no clear way that, even if the allele is dominant, the mutant organisms can so succeed that the allele becomes the norm. The first mutant organism must be still be able to breed with the original stock in order to have

A leaky faucet: Why Darwinian evolution leads to loss of information

http://www.biologicinstitute.org/post/127739428119/a-leaky-faucet-why-darwinian-evolution-leads-to

In 2010 Mike Behe published a paper in the Quarterly Review of Biology in which he concisely stated the first rule of adaptive evolution : “Break or blunt any functional coded element whose loss would yield a net fitness gain.” By this he meant several things. First, there are indeed adaptive mutations, mutations that yield a benefit to the cell under a particular set of circumstances. Second, the primary way such adaptation occurs is by breaking or inactivating some non-essential pre-existing function, in order to make the cell more fit, more competitive than its neighbors.

Behe was talking about microbes –viruses and bacteria–but it also happens at the cellular level in higher organisms. The best example where this rule is played out is in cancer. Cancers develop when one or more normal functions in a cell are disrupted, broken. The ironic thing is that for the cancer cells, this breaking increases their fitness, their rate of growth and cell division, and thus is beneficial—for them. Normal constraints have been removed, allowing uncontrolled growth. For the cancer cell that’s good, but bad for us, of course. So one can say that cancer is a prime example of what adaptive evolution can accomplish on the multicellular level, by breaking or disrupting some normal function.

What does Behe’s first rule of adaptive evolution say about evolution in general? If most “beneficial” mutations are due to the loss of something rather than a gain of something, we are losing information when most adaptations occur, sometimes irreversibly. Let me give an example.

Ralph Seelke and I published a paper in 2010 where we demonstrated that cells always, or nearly always take the easiest road to success. When given a choice between a simple two-step path leading to repair of two genes needed to make tryptophan, versus a one-step path that eliminated expression of the those genes, only one out of a trillion cells went down the path toward making tryptophan, even though that path would ultimately be much more beneficial. Why did this happen? The genes to be repaired were overexpressed—too much of their products were made. Because one of the genes was broken in two places, no tryptophan could be made. Thus both genes were expensive to keep around. It was easier for the cell to break the useless genes than to repair them—one step instead of two—and the cells, having no foresight, took that path. Some of those cells deleted the genes, thus losing the information needed to make tryptophan for good.

Let me explain in every-day terms. A faucet leaking badly but with no way to hook it up to a hose is entirely useless. While it is relatively easy to repair the faucet, requiring only two parts, the owner of the faucet doesn’t know that. Since he can do without the faucet, he is likely to cap the faucet to stop the expense of the wasted water. But he has lost the ability to water his back yard using that faucet.

Like the clueless owner, evolution has no foresight and does not know there is a big pay-off just two mutations away. If the cells can prevent the overexpression of the tryptophan genes or remove them in a single step, that’s what they will do, especially since there are many more ways to inactivate a gene than repair it. Any cell that does this instantly becomes more fit than its neighbors, because it is spending less energy making useless stuff.

In fact, that is what we observed. Nearly all the cells inactivated the genes (only one out of a trillion didn’t). Some of the cells even deleted the genes, thus losing the capacity to make tryptophan for good. Darwinian evolution travels by the shortest road, without regard for where it’s headed. And if the shortest road is to break an existing function–to lose information–that’s the path it chooses.

I’m sure you can think of parallels in the business world, when only the bottom line, corporate fitness, is what matters, and executives have no long-term vision. They don’t see how some things, if adjusted, may yield big pay-offs. As a result, whole technologies can be decimated or lost in a push for efficiency, technologies that if maintained could prove vital in the future. But fortunately, unlike Darwinian evolution, we do have foresight and can plan ahead. We do have the capacity for innovation, and can make wise choices or correct our mistakes.

The process of innovation is the opposite of the first rule of adaptive evolution. In the biological world, the quickest road to adaptation may be to delete or inactivate genes that are not necessary. But you don’t get new features by deleting information. Building something new, which is what is required to explain the diversity around us, requires more than the happenstance and selection of Darwinian evolution. It requires foresight, planning, and a clear picture of the goal. It requires intelligent design.

The real issue

https://creation.com/images/pdfs/tj/j25_2/j25_2_92-98.pdf

The development of new functions is the only thing
important for evolution. We are not talking about small
functional changes, but radical ones. Some organism had to
learn how to convert sugars to energy. Another had to learn
how to take sunlight and turn it into sugars. Another had
to learn how to take light and turn it into an interpretable
image in the brain. These are not simple things, but amazing
processes that involve multiple steps, and functions that
involve circular and/or ultra-complex pathways will be
selected away before they have a chance to develop into
a working system. For example, DNA with no function is
ripe for deletion, and making proteins/enzymes that have no
use until a complete pathway or nano-machine is available
is a waste of precious cellular resources. Chicken-and-egg
problems abound. What came fi rst, the molecular machine
called ATP synthase or the protein and RNA manufacturing
machines that rely on ATP to produce the ATP synthase
machine? The most basic processes upon which all life
depends cannot be co-opted from pre-existing systems. For
evolution to work, they have to come up from scratch, they
have to be carefully balanced and regulated with respect
to other processes, and they have to work before they will
be kept. Saying a gene can be copied and then used to prototype
a new function is not what evolution requires, for this
cannot account for radically new functionality. Thus, gene
duplication cannot answer the most fundamental questions
about evolutionary history. Likewise, none of the common
modes of mutation (random letter changes, inversions,
deletions, etc.) have the ability to do what evolution requires.
Darwin pulled a bait and switch in his On the Origin
of Species. He actually produced two separate theories:
what I call his special and general theories of evolution.
He went on at length to show how species change. This
was the Special Theory of Evolution and he was preceded
by numerous others, including several creationists, with
the same idea. It took him a long time to get to the point,
but he fi nally said,“… I can see no limit to the amount of change
… which may be effected in the long course of time
by nature’s power of selection.”45
This was his General Theory of Evolution, and this
is where he failed, for he provided no real mechanism for the
changes and was ignorant of the underlying mechanisms that
would later be revealed. To use a modern analogy, this would
be akin to saying that small, random changes in a complex
computer program can create radical new software modules,
without crashing the system.46 Thus, the ‘can mutations
create new information’ argument is really about the bridge
between the special and general modes of evolution. Yes,
mutations can occur within living species (kinds), but, no,
those mutations cannot be used to explain how those species
(kinds) came into existence in the fi rst place. We are talking
about two completely separate processes.

Pierre Grasse on evolution

http://ebd10.ebd.csic.es/pdfs/DarwSciOrPhil.pdf

Pierre Grasse was the most distinguished of French
zoologists, the editor of the 28 volumes of Traite de Zoologie, author of numerous original
investigations, and ex-president of the Academie des Sciences. His knowledge of the living
world is encyclopedic.

Grasse  believed in something that he called "evolution." So did Dobzhansky, but when Dobzhansky
used that term he meant neo-Darwinism, evolution propelled by random mutation and guided by
natural selection.

Grasse used the same term to refer to something very different, a poorly
understood process of transformation in which one general category (like reptiles) gave rise to
another (like mammals), guided by mysterious "internal factors" that seemed to compel many
individual lines of descent to converge at a new form of life. Grasse denied emphatically that
mutation and selection have the power to create new complex organs or body plans, explaining
that the intra-species variation that results from DNA copying errors is mere fluctuation, which
never leads to any important innovation.

The genic differences noted between separate populations of the same species that are so often
presented as evidence of ongoing evolution are, above all, a case of the adjustment of a
population to its habitat and of the effects of genetic drift. The fruitfly (drosophila
melanogaster), the favorite pet insect of the geneticists, whose geographical, biotropical, urban,
and rural genotypes are now known inside out, seems not to have changed since the remotest
times

Grasse insisted that the defining quality of life is the intelligence encoded in its biochemical
systems, an intelligence that cannot be understood solely in terms of its material embodiment
The minerals that form a great cathedral do not differ essentially from the same materials in the
rocks and quarries of the world; the difference is human intelligence, which adapted them for a
given purpose. Similarly,

Any living being possesses an enormous amount of "intelligence," very much more than is
necessary to build the most magnificent of cathedrals. Today, this "intelligence" is called
information, but it is still the same thing. It is not programmed as in a computer, but rather it is
condensed on a molecular scale in the chromosomal DNA or in that of every other organelle in
each cell. This "intelligence" is the sine qua non of life. Where does it come from? . . . This is a
problem that concerns both biologists and philosophers, and, at present, science seems incapable
of solving it.... If to determine the origin of information in a computer is not a false problem,
why should the search for the information contained in cellular nuclei be one?

Grasse argued that, due to their uncompromising commitment to materialism, the Darwinists
who dominate evolutionary biology have failed to define properly the problem they were trying
to solve. The real problem of evolution is to account for the origin of new genetic information,
and it is not solved by providing illustrations of the acknowledged capacity of an existing
genotype to vary within limits. Darwinists had imposed upon evolutionary theory the dogmatic
proposition that variation and innovative evolution are the same process, and then had employed
a systematic bias in the interpretation of evidence to support the dogma. Here are some
representative judgments from Grasse's introductory chapter:

Through use and abuse of hidden postulates, of bold, often ill-founded extrapolations, a
pseudoscience has been created.... Biochemists and biologists who adhere blindly to the
Darwinist theory search for results that will be in agreement with their theories.... Assuming that
the Darwinian hypothesis is correct, they interpret fossil data according to it; it is only logical
that [the data] should confirm it; the premises imply the conclusions.... The deceit is sometimes
unconscious, but not always, since some people, owing to their sectarianism, purposely overlook
reality and refuse to acknowledge the inadequacies and the falsity of their beliefs.

Grasse was an evolutionist, but his dissent from Darwinism could hardly have been more radical
if he had been a creationist. It is not merely that he built a detailed empirical case against the
neo-Darwinian picture of evolution. At the philosophical level, he challenged the crucial doctrine
of uniformitarianism which holds that processes detectable by our present-day science were also
responsible for the great transformations that occurred in the remote past. According to Grasse,
evolving species acquire a new store of genetic information through "a phenomenon whose
equivalent cannot be seen in the creatures living at the present time (either because it is not there
or because we are unable to see it)."

Grasse even turned the charges of mysticism against his opponents, commenting sarcastically
that nothing could be more mystical than the Darwinian view that "nature acts blindly,
unintelligently, but by an infinitely benevolent good fortune builds mechanisms so intricate that
we have not even finished with analysis of their structure and have not the slightest insight of the
physical principles and functioning of some of them."

What was different about Grasse
was that he was willing to give unprejudiced consideration to the possibility that science does not
know, and may never know, how new quantities of genetic infommation have come into the
world.

Intelligent Design: Origin of Species ("Macro-Evolution")

Primer: Summary of Problems with Biological and Chemical EvolutionThere is no good explanation for the origin of complex biochemical features. Molecular and anatomical homology fail to provide evidence for common descent. The fossil record does not show transition from one species to another. Developmental biology fails to support common descent. Genetics and chemistry cannot explain the origin of the genetic code. Neo-Darwinism does not explain the geographical distribution of species. 
http://www.ideacenter.org/contentmgr/showdetails.php/id/1510

The Flawed Evidence for Evolution. Genetic analysis falsifies common descent. An evolutionary tree can be made by comparing the same gene in different organisms, but different genes produce widely divergent trees.
http://ncu9nc.blogspot.com/2012/09/the-flawed-evidence-for-evolution.html

The Cambrian Explosion is Best Explained by Intelligent Design Neo-Darwinism cannot explain why during the Cambrian explosion: Many phyla appeared in a brief period of time. The phyla arose without ancestors. There were very few species at that time. No phylum has ever diversified enough to form another phylum. Yet all of these phenomenon are predicted by intelligent design.
http://ncu9nc.blogspot.com/2014/08/the-cambrian-explosion-is-best.html

The Cambrian Explosion: Biology's Big Bang by Stephen C. Meyer, Marcus Ross, Paul Nelson, and Paul Chien
http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=639

Intelligent Design: The Origin of Biological Information and the Higher Taxonomic Categories, By: Stephen C. Meyer, Proceedings of the Biological Society of Washington, August 4, 2004. The Cambrian explosion, where many new animal types appeared suddenly 530 million years ago cannot be explained by natural causes but is best explained by intelligent design, since intelligence is the only known cause that can create information and complex systems.
http://www.discovery.org/a/2177

Survival of the fakest. Many of the examples claimed to prove Darwinism (the Miller-Urey primordial soup experiment, the similarity of early embryos in different species, the evolutionary tree, homology in vertebrate limbs, peppered moths evolving a darker color as air pollution darkened tree trunks, Darwin's finches, evolution from apes to humans) are false or misleading. 
http://www.discovery.org/articleFiles/PDFs/survivalOfTheFakest.pdf

Why Darwinism is False. The fossil record lacks examples of intermediate species; "early development in vertebrate embryos is more consistent with separate origins than with common ancestry; ... non-coding DNA is fully functional, contrary to neo-Darwinian predictions; ... natural selection can accomplish nothing more than artificial selection—which is to say, minor changes within existing species."
http://ncu9nc.blogspot.com/2012/05/why-darwinism-is-false.html

Video: A Critique of Darwinist Icons "Many of the pillars of Darwinian theory are either false or misleading." The evolutionary tree is false. Homology is not proof of common descent. The classic diagrams showing similarities in embryos of different species were faked. Peppered moths supposedly evolved darker colors because tree trunks were darkened by air pollution, but the moths don't rest on tree trunks. Temporary changes in beak morphology of Galapagos finches were due to changes in the frequency of existing genes and do not explain the formation of new genetic information needed to explain macroevolution. 
http://ncu9nc.blogspot.com/2014/09/video-critique-of-darwinist-icons.html

Newly discovered whale fossil, older than its supposed ancestor species, proves Darwinists rely on flawed logic. 
http://ncu9nc.blogspot.com/2014/09/newly-discovered-whale-fossil-older.html

Nature's best evidence for natural selection does not show that natural selection can cause macroevolution. 
http://ncu9nc.blogspot.com/2014/09/natures-best-evidence-for-natural.html

The missing ancestors of the Cambrian explosion would have been found if they existed. 
http://ncu9nc.blogspot.com/2014/09/the-missing-ancestors-of-cambrian.html

Video: Darwinism on Trial with University of California Berkley law professor Phillip E. Johnson 
http://ncu9nc.blogspot.com/2014/09/video-darwinism-on-trial-with.html

Homologous genes that regulate the development of analogous structures are better explained by intelligent design than natural selection. 
http://ncu9nc.blogspot.com/2014/09/homologous-genes-that-regulate.html

Differences in early embryonic development provide evidence that the animal phyla did not share a multicellular common ancestor. 
http://ncu9nc.blogspot.com/2014/09/differences-in-early-embryonic.html

Lee Spetner explains why natural selection can't produce macroevolution. 
http://ncu9nc.blogspot.com/2014/09/lee-spetner-explains-why-natural.html

Macroevolution   v1.1 2006 Laurence A. Moran

http://bioinfo.med.utoronto.ca/Evolution_by_Accident/Macroevolution.html

Embracing Uncertainty in Reconstructing Early Animal Evolution

http://www.cell.com/current-biology/fulltext/S0960-9822(17)31092-8

The origin of animals, one of the major transitions in evolution, remains mysterious.

Reconstruction of ancient evolutionary radiations is devilishly difficult and will likely require broader sampling of sponge and ctenophore genomes, improved analytical strategies and critical analyses of the phylogenetic distribution and molecular mechanisms underlying apparently conserved traits.

our window through time to the Urmetazoan remains obscured by uncertainty regarding whether sponges or ctenophores are the sister lineage to all other animals. While we concur with the sentiment in the opening quote that “we're not afraid to admit what we don't know” and we revel in the insights that are currently possible regarding the dawn of animal life, we eagerly anticipate future breakthroughs that will allow us to move from ignorance to knowledge in our quest to reconstruct the origin of animals.

But hey, maybe mainstream scientists  will wake up one day to the unconvenient truth, that the foundations lied by Hume et al in the 19th century, that design inference should be excluded a priory by scientific investigation, ( specially when it comes to the quest of historical sciences, and origins ) was a huge mistake, and that the hypothesis of a powerful intelligent cause is valid of consideration, and most probably  explains best the origin of animals and biodiversity.

‘‘Science works on the frontier between knowledge and
ignorance. We’re not afraid to admit what we don’t
know. There’s no shame in that. The only shame is to
pretend that we have all the answers.’’
—Neil deGrasse Tyson, Cosmos: A Spacetime Odyssey

But he is afraid to replace the " i don't know" with " most probably,  an intelligent designer "  - go figure, why.

Macroevolution. Fact, or fantasy?
http://reasonandscience.heavenforum.org/t1390-macroevolution#1982

http://www.ncbi.nlm.nih.gov/pubmed/15612191
In the last 25 years, criticism of most theories advanced by Darwin and the neo-Darwinians has increased considerably, and so did their defense. Darwinism has become an ideology, while the most significant theories of Darwin were proven unsupportable.

But up to that breakthrough recognisance, evolution remains an undisputed and unquestioned fact - how fool.

Macroevolution refers to large-scale evolutionary changes that occur over extended time periods, spanning from the level of species and above. These processes involve more significant changes than those seen in microevolution, which pertains to minor variations at the population level. The term itself, "macroevolution," is somewhat debated in scientific circles—not necessarily in its implications or existence but in its distinction from microevolution.

Let's delve deeper:

1. Definition of Macroevolution
Macroevolution describes evolutionary changes and patterns at or above the species level. This includes:

The emergence of new species (speciation).
The extinction of species.
The origin of major innovations and key adaptations.
The adaptive radiation of a single species into several.
The long-term morphological trends within lineages.
The interactions between large groups of organisms.
2. Boundaries Between Microevolution and Macroevolution
Microevolution involves small-scale changes, typically seen in gene frequencies in populations over short periods. It deals with the function and processes of genes, inheritance, and adaptation within populations. On the other hand, macroevolution observes changes over broader scales, either at the species level or higher taxa (e.g., genera, families, orders).

The distinction isn't always clear-cut. While microevolutionary processes undeniably accumulate over time to contribute to macroevolutionary patterns, there are debates about whether the cumulative effects of microevolution alone can explain all observed patterns of macroevolution.

3. Evidence for Macroevolution
While macroevolutionary changes take place over vast time scales and are thus not directly observable, evidence supporting it includes:

Fossil Record: Fossils document the existence of now-extinct species and provide a timeline for the emergence of major groups of organisms. For instance, the transition from fish to tetrapods, or water to land-dwelling animals, is well-documented in fossils.

Comparative Anatomy: Shared structures, even with different functions, point to common ancestry. For instance, the similar bone structures in the limbs of humans, birds, and whales suggest a shared ancestral lineage.

Molecular Evidence: DNA comparisons can showcase the shared ancestry of diverse species. Molecular clocks, based on mutation rates, can also provide estimates for when two species diverged from a common ancestor.

Biogeography: The distribution of species across the planet provides insights into evolutionary history. For instance, islands often have unique species that closely resemble those from the nearest mainland, indicating adaptive radiations after colonization.

Your references also bring up the concept of "hopeful monsters" and saltational changes (i.e., large, sudden genetic changes leading to new species). While traditionally these ideas were more controversial, they've gained some traction, especially when considering punctuated equilibria—a pattern of evolution in which long stable periods are interrupted by brief periods of rapid change.

4. Concerning the Examples You Provided:
Many of the instances you listed (e.g., emergence of flight, eyes, flowers, etc.) have been extensively researched. For example:

Eyes: The evolution of the eye is a classic example. Simple light-sensitive spots can provide an advantage to an organism by allowing it to detect the direction of light (useful for phototactic organisms). Over time, these spots could have deepened into a cup, allowing for more directional sensitivity. Add a lens, and you get improved focusing. This process of gradual refinement is supported by the diversity of eye structures in existing organisms, ranging from simple light-sensitive spots in some flatworms to complex camera eyes in vertebrates and cephalopods.

Flight: The evolution of flight in birds is documented with fossils that show stages of wing development, starting from two-legged dinosaurs like Tyrannosaurus to transitional forms like Archaeopteryx, which had feathers and features of both dinosaurs and birds.

In conclusion, while macroevolution encompasses changes beyond the typical reach of direct observation due to the time scales involved, evidence from multiple disciplines—paleontology, genetics, comparative anatomy, and more—provides a consistent and compelling framework supporting its occurrence.