by Dr. Angus Menuge

Repeatedly, we have seen that even if gene duplication can make all the parts of an irreducible complex system simultaneously available, Darwinism cannot provide credible solutions to the problems of coordinating these parts and ensuring their interface compatibility.
From my perspective as a teacher of computer programming, this limitation of Darwinism as a problem-solving strategy is surprising. First, consider the analogous problem of coordinating a program's instructions. As programs become more complex, it becomes virtually impossible to get them to work if they are written from the bottom-up, one instruction at a time.
 
With so many details, it is highly likely that some critical task is specified incompletely or in the wrong order. To avoid such errors, programmers find it essential to use top-down design. Top-down design is a problem-solving strategy that begins with an abstract specification of the program task and then breaks it down into several main sub-problems, each of which is refined further into its subproblems. This strategy is epitomized by such things as recipes, where the task is broken down into ingredients and utensils (initialization), and the mixing and cooking of the ingredients (processing), and a specification of what to d when te ds is ready (finalization). The same approach is clear in the instructions too build "partially assembled" furniture, such as a bookcase.
 
First, the assembly of the bookcase is reduced to its major tasks, constructing the frame, back, and shelves. Then each of these tasks is specified in detail. At every level, the order of the tasks is important; for example, the back and the shelves cannot be installed until the frame is complete. A quality top-down design is sensitive to the proper placement of tasks, ensuring that given task is not omitted, redundantly repeated, or performed out of sequence. In this way, top-down design facilitates the proper coordination of problem-solving modules.
 
Unfortunately, natural selection cannot implement top-down design. Natural selection is a bottom-up atomistic process. Tasks must be solved gradually, independent from one another. There is no awareness of the future function of the assembled system to coordinate these tasks. If even intelligent agents (experienced programmers) require top-down design to solve complex problems, it is tendentious to suppose that unintelligent selection can solve problems at least as complex without the aid of top-down design.
 
In fact, even with top-down design, programmers find that it is necessary top do two levels of testing to produce a functional program. One level, unit testing, tests the function of a module in isolation from the whole program. The other level, integration testing, ensures that when all the modules are assembled, they interact in such a way as to solve the overall problem .Both kinds of testing are needed: it is a fallacy of composition to argue that since all the part of a system work, the assembled system will also work.
 
Compare the following examples.
 
Each football player is fit; therefore the team will play effectively.
 
Each brick is sound; therefore, the resulting wall will be strong.
 
The conclusions do not follow because it matters how bricks and players are coordinated, and it matters whether they are compatible. Say that each player is fit but that the offense tries to score only when it has lost possession: the team will be hopelessly uncoordinated. And if each player has a different play for the same circumstance, the team will suffer from incompatible elements.
 
Likewise, if bricks are sound but are piled at random or are incompatible in size and shape, it will be impossible to build an effective wall.
 
Unfortunately, Darwinism commits precisely this fallacy of composition in the case of irreducibly complex systems. It has to suppose that the independent unit testing of atomic components (which natural selection provides)is a plausible way of coordinating and attuning those components for their combined role. But it is not. The majority of subsets drawn from the power sets of sound football players and bricks will be completely dysfunctional when combined as teams or walls.
 
Note: From another perspective, Darwinism is also guilty of the reverse fallacy, the fallacy of division. It argues that because a given "irreducibly complex" system has a function, it therefore must be composed of subsystems with the same or a different function. But by itself the flagellum's motor neither supports locomotion or any other function.

Dr. Angus Menuge is a Professor of Philosophy and Computer Science Concordia at the University of Wisconsin, 12800 N. Lake Shore Drive, Mequon, WI  53097, (262) 243-4249, office  LU221 (upper Luther Hall)
 
Up to date discoveries question evolution
 
There is a new online book Darwin’s Predictions by Cornelius G. Hunter. In the introduction of his book he writes:

Many predictions of evolution have been falsified, including foundational expectations. Evolutionists have added explanations to their theory to account for these problematic findings. The drawback is that this greatly complicates the theory. Scientific theories are supposed to be parsimonious, explaining future findings with simple explanations rather than explaining past findings with complicated explanations.

Therefore evolutionists are faced with a accuracy-versus-parsimony tradeoff. The scientific findings make their original theory inaccurate. That is, the theory does not fit the empirical evidence well. The only way to increase the evolution’s accuracy is to complicate the theory tremendously and sacrifice parsimony. Evolutionists have consistently preferred low parsimony over low accuracy, but either way the theory is problematic.

The theory of evolution has consistently failed and as a consequence it has grown far more complex than anything Darwin ever envisioned. Therefore evolution is not a good scientific theory and in this sense it is comparable to geocentrism. Both theories grew ever more complicated in response to the evidences of the natural world, adding epicycle upon epicycle.

In stark contrast to these evidential problems, evolutionists believe that their theory is a fact. Evolution is a fact, they say, just as gravity is fact. This remarkable claim is an indicator that there is more to evolution than merely a scientific theory. In light of the scientific evidence, the claim that evolution is a fact may seem to be absurd. But it is not.

The fact of evolution is a necessary consequence of the metaphysical assumptions evolutionists make. Metaphysical assumptions are assumptions that do not derive from science. They are made independent of science. These metaphysical assumptions that evolutionists make would be difficult to defend as necessarily true outside of evolutionary circles, but within evolution their truth is not controversial. All of this means that the scientific problems with evolution are relegated to questions of how evolution occurred. The science cannot bear on questions of whether or not evolution occurred.

Cornelius G. Hunter is a graduate of the University of Illinois where he earned a Ph.D. in Biophysics and Computational Biology. He is Adjunct Professor at Biola University and author of the award-winning Darwin’s God: Evolution and the Problem of Evil. Hunter’s other books include Darwin’s Proof, and his newest book Science’s Blind Spot (Baker/Brazos Press).

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The rootless evolution tree
 
Charles Darwin believed that phylogeny, the ascent of all species through time, was expressible as a metaphor he termed the Tree of Life. The modern development of this idea is called the Phylogenetic tree. This branching tree, the central concept of evolution theory is described in his book The Origin of Species, where numerous examples of supposed morphological evolution are given, showing how one species evolved into many. From Darwin’s time till now the imaginary evolution tree underwent many changes. Some are depicting it as very bushy and some even as having independent branches and no roots. Let’s consider to what extent the newest discoveries support the existence of a shaky evolution tree.
 
Surprisingly, the journals The Telegraph and New Scientist published an article titled “Why Darwin was wrong about the tree of life”.  A very cutting statement said, “Charles Darwin’s tree of life is ‘wrong and misleading’, claim scientists.” These articles support neither the evolutionary theory, supposedly now being more advanced than at Darwin’s time, nor that it has no weaknesses. As a matter of fact, two years earlier Ford Doolittle and Eric Bapteste already wrote[1]:
 
Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation.  However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic.  The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree.  Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true.  This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation.  Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.
Although Doolittle and Bapteste don’t deny the evolution theory, as becomes obvious from the last sentence, they nevertheless argue that the TOL is unsupportable and a mere human imagination. Here are some more statements not in favour of the TOL.
 
“We will argue that inclusive hierarchical classifications do not emerge naturally and consistently from the relevant prokaryotic data considered in general (in their entirety). Instead, they have been imposed on them by selective analyses that are based on the assumption that a tree must be the real natural pattern, even if only certain of the data can be trusted to reveal it.” 
“Importantly, Darwin did not and could not test the reality of the tree pattern.  Indeed, one is hard pressed to find some theory-free body of evidence that such a single universal pattern relating all life forms exists independently of our habit of thinking that it should.” 
 
According to the authors of some molecular studies, less than 5% of the data agrees with a TOL model, and regarding the “tree of cells,” the phylogenetic signal is just 1%. Although Doolittle claims, “we understand evolution pretty well, it’s just it is more complex than Darwin imagined. The tree isn’t the only pattern,” Michael Rose, an evolutionary biologist at UC Irvine, opines: “The tree of life is being politely buried – we all know that.”[2]  
 
Recently, one of the titles of a heavily pro-Darwinian magazine New Scientist declared, “Darwin Was Wrong: Cutting Down the Tree of Life.”[3] In the editorial to that issue we can read: “It is now accepted that the tree of life is something we impose on nature in an attempt to make the task of understanding it more tractable”.[4] The editor continues with a warning against creationists, “Expect to find excerpts ripped out of context and presented as evidence that biologists are deserting the theory of evolution en masse.” However, despite of this warning, some quotes are too clear and contradictory to the evolution theory to give any strength to his claim of misquoting.
For example, Eric Bapteste says: “Nobody is arguing – yet – that the tree concept has outlived its usefulness in animals and plants.  While vertical descent is no longer the only game in town, it is still the best way of explaining how multicellular organisms are related to one another – a tree of 51 per cent, maybe.  In that respect, Darwin’s vision has triumphed: he knew nothing of micro-organisms and built his theory on the plants and animals he could see around him.
    Even so, it is clear that the Darwinian tree is no longer an adequate description of how evolution in general works.  ‘If you don’t have a tree of life, what does it mean for evolutionary biology?’”[2]
 
Attempting to save the Darwin theory, Doolittle writes: “downgrading the tree of life doesn’t mean that the theory of evolution is wrong – just that evolution is not as tidy as we would like to believe. Some evolutionary relationships are tree-like; many others are not.” However, again, in the same article, the examples of hybridization and “natural chimeras” found in living examples show that genetic information can cross lineages.  This further complicates the attempt to find a common ancestor of all species. Moreover, showing that sea squirts appear to have unrelated branches of ancestral genes, Graham Syvanen declared: “We’ve just annihilated the tree of life…It’s not a tree any more, it’s a different topology entirely.  What would Darwin have made of that?”
 
References:
1.  W. Ford Doolittle and Eric Bapteste, “Inaugural Article: Evolution: Pattern Pluralism and the Tree of Life Hypothesis,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0610699104, published online before print January 29, 2007.
2.  Charles Darwin's tree of life is 'wrong and misleading', claim scientists  
3.  Why Darwin was wrong about the tree of life, New Scientist
4.  Editorial: Uprooting Darwin's tree, New Scientist

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The globins
The very first genes to evolve by gene duplication, according to scientific hypothesis, were the alpha and beta hemoglobin chains, used to carry oxygen in erythrocytes. Myoglobin, which stores oxygen in muscle tissues, developed from tetrameric hemoglobin. Hemoglobin has two compounds, alpha and beta globins. Now, as hypothesized, from alpha globin the gamma, delta and epsilon globin genes developed, and the duplication of alpha globin resulted in the appearance of epsilon and zeta globin genes. The different globin molecules play an important role in the oxygen metabolism during the different stages of embryonic development, each at the right time. The alpha, zeta and epsilon globins are replaced by the gamma chain in the third month, which is replaced by the beta and delta globins at birth. The site of hemoglobin synthesis also changes from yolk sac to liver to bone marrow during development, so differing environments and transport systems are also involved. This complexity reveals a very fine-tuned, precisely regulated system in which everything happens at the right time. Any disruption in the hemoglobin synthesis will result in various diseases. Neo-Darwinian theorists will have a hard time explaining how embryonic development could take place before this complex system was set up.

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Water Activity and the Challenge for Life on Early Mars
Nicholas J. Tosca,¹ Andrew H. Knoll,¹ Scott M. McLennan²

In site and orbital exploration of the Martian surface has shown that acidic, saline liquid water was intermittently available on ancient Mars. The habitability of these waters depends critically on water activity ^αH₂O, a thermodynamic measure of salinity, which, for terrestrial organisms, has sharply defined limits. Using constraints on fluid chemistry and saline mineralogy based on Martian data, we calculated the maximum ^αH₂O for Meridiani Planum and other environments where salts precipitated from Martian brines. Our calculations indicate that the salinity of well-documented surface waters often exceeded levels tolerated by known terrestrial organisms.

Comment: The fact that a high concentration of salt in the environment kills by drawing water out of microbial cells through the process of osmosis is a big problem for one of the existing theories of life’s origin, namely that life had arisen on Mars and had later been transported to earth planet by Martian meteors. The reason for life’s origin on Mars came from the idea that long time ago Mars was a warm planet with a lot of water. However, according to the Harvard University researchers, the salt content of the Martian ocean 4 billion years ago was too high, higher than in the ocean of the earth planet, and so much unfavorable that even salt-loving microbes, the halophiles, would not survive. But most importantly, according to the life-origin-hypothesis, high salt levels block the assembly of RNA molecules on mineral surfaces and hinder the assembly of fatty acids into primitive cell membranes.
References
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The Cyanobacteria

A protein complex found in cyanobacteria regulates metabolic processes, such as nitrogen fixation and photosynthesis. It also influences the general gene expression within the cyanobacterial cell in response to light-dark cycles (day and night). The complexity of cyanobacteria, although higher and more profound, can be still compared to the harmonious complexity of a Swiss watch. With the ever-increasing discoveries of the cell’s harmonious, interdependent complexities, the purposeful design becomes more and more obvious as seen e.g. in the following text.
 
Structural Insights into a Circadian Oscillator
Carl Hirschie Johnson,[1] Martin Egli,[2] Phoebe L. Stewart[3]
An endogenous circadian system in cyanobacteria exerts a pervasive control over cellular processes, including global gene expression. Indeed, the entire chromosome undergoes daily cycles of topological changes and compaction. The biochemical machinery underlying a circadian oscillator can be reconstituted in vitro with just three cyanobacterial proteins, KaiA, KaiB, and KaiC. These proteins interact to promote conformational changes and phosphorylation events that determine the phase of the in vitro oscillation. The high-resolution structures of these proteins suggest a ratcheting mechanism by which the KaiABC oscillator ticks unidirectionally. This posttranslational oscillator may interact with transcriptional and translational feedback loops to generate the emergent circadian behavior in vivo. The conjunction of structural, biophysical, and biochemical approaches to this system reveals molecular mechanisms of biological timekeeping.

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