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Strengths and weaknesses of evolution theory.

Darwin himself devoted three chapters in the Origin of Species to discussing weaknesses in his own theory and conceded that, “A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides.” 
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Michael Cremo’s opinion
The International Society for Krishna Consciousness has recently joined in the fray. “As an organization that represents the Vaishnava tradition – the largest denomination within the Hindu faith – ISKCON reaffirms the reality that the concept of an intelligent designer is not limited to Christians,” the organization said in a statement. “We join other Hindus, Muslims, people of other faiths, and those who profess no particular faith, in calling for a more balanced and objective exploration of the theory of evolution and its alternatives.” “The theory of evolution should continue to be taught, because it is a fact that most scientists today accept evolution,” contends Michael Cremo, an ISKCON member and scholar of Hinduism’s response to evolution. “But it is also a fact that other scientists, admittedly in the minority, accept some version of intelligent design. Educational institutions should reflect this reality, by making room for a neutral presentation of the alternatives to the Darwinian theory. Let people make up their own minds.”
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Molecular motors

Michael Behe and other researchers revealed the great complexity of one living cell, also called a molecular machine. However, a new study examining groups of molecular motors increase the previously known complexity beyond one particular cell. Researchers at the University of Virginia headed by Laib, a second-year student from Lorton, Va. said “[we]found that molecular motors operate in an amazingly coordinated manner when moving an algal cell one way or the other…this provides a new understanding of the ways cells move."[1] “The new U.Va. study provides strong evidence that the motors are indeed working in coordination, all pulling in one direction, as if under command, or in the opposite direction – again, as if under strict instruction.” It seems that the increasing discoveries of the interdependent, specified complexities in molecular motors, all go in the favor of design argument.
 1.  Laib, Marin, Bloodgood and Guilford, “The reciprocal coordination and mechanics of molecular motors in living cells,” Proceedings of the National Academy of Sciences USA, published online February 12, 2009, doi:10.1073/pnas. 0809849106.

News - Leiden University

The Year of Darwin has got off to a bad start in the Netherlands, where a national reorganization of university budgets has led Leiden University to sack its classical  evolutionary -biology staff.

"There will be no one left who can teach natural selection," says population ecologist Jacques van Alphen, one of half a dozen tenured professors who will lose their jobs on 1 March. Some technicians and postdocs will also be fired.[1]
1. Nature, 12 February 2009, “Dutch university slashes evolution staff”, pages 772-3
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"It's a mistake to suppose that there is a sort of road, with life as its destination, along which a chemical mixture is inexorably conveyed by the passage of time. It isn't just a matter of carrying on doing more of the same, with the amino acids obligingly assembling themselves into proteins and the proteins joining up with nucleic acids, and so on, to eventually make a living thing. It isn't a one-way street like that, and the reason is very basic. Making amino acids is what a physicist would call 'thermodynamically downhill', which means it is a natural process that occurs automatically, like crystallisation. But hooking the amino acids together into long chains to make proteins goes the other way. That is an 'uphill'-a statistically more difficult or unlikely-process. Let me give you an analogy. It's a little bit like going for a walk in the countryside, coming across a pile of bricks and assuming that there will be a house around the corner. There is a big difference between a pile of bricks and a house. Now part of the problem here is that attaching the amino acids together to make proteins costs energy. True, there was no lack of energy on the young Earth, but the problem is not energy per se. Rather, it is how this energy organised itself in such a way as to produce this extremely elaborate thing called a protein." (Davies P.C.W. & Adams P., "More Big Questions," ABC Books: Sydney, Australia, 1998, pp.47-48)


"There is one that I like quite a lot, which is a comparison between flying a kite and flying a radio-controlled plane. A kite is literally hardwired to the controller on the ground. By contrast, a radio-controlled plane has an informational channel. How does the plane perform its aerobatics? You push and pull some levers, and these signals are encoded into electromagnetic pulses. That information is then sent up to the plane and decoded. Note that the radio waves themselves don't push and pull the plane around. The signals encoded in the radio waves merely harness other forces and liberate them to do the job. So the radio channel plays the role of an informational channel rather than a physical push-pull link. What has all this to do with life? As we know it, life is based on a kind of deal struck between two very different classes of molecules. One of these are the nucleic acids, which contain the genetic information encoded in the sequence of their atoms. These molecules can't do very much. It is the proteins, the other class of molecules, that are the real workers in biology. But both types of molecules need the other: the nucleic acids on their own are helpless; the proteins on their own are also helpless. ... This is the ultimate chicken-and-egg problem. The great mystery about the origin of life is, which came first: chicken or egg? Was it the nucleic acids or the proteins? That is the traditional biochemical mystery." (Davies P.C.W. & Adams P., "More Big Questions," ABC Books: Sydney, Australia, 1998, pp.55-56)


















Darwin - an objective scientist?                                              News & Views March 2009
            By Ajit Krishna Dasa

Darwin is often portrayed as a sort of textbook example of a perfect scientist who after objectively observing and studying the diversity of life came to conclude that the most logical explanation for this diversity is that life must have evolved over time from a common ancestor through natural selection. A few weeks ago is saw a video where a person defended Charles Darwin and portrayed him as an honest scientist who simply objectively observed the diversity of life, tried to make sense out of what he saw and then came to accept evolution by natural selection as the most plausible and scientific explanation.

How objective was Darwin?

Most people are under the wring impression that Darwin was the father of evolution theory. That's not true. The idea that life arose from matter and evolved from it had been existing for thousands of years. It can be found in the writings of materialist philosophers from in India, Mesopotamia, Sumeria, Egypt and later Greece. Even though these materialist philosophers did not agree on everything we find in their writings ideas of how life arose from matter in water, that humans evolved from fish, that species evolved from one another, that there was a struggle for survival amongst the living being and that there was a hierarchy of of life from the most simple to the most complex. The writings of these philosophers were well known to many western thinkers and scientists like Benoit de Maillet, Pierre de Maupertuis, Comte de Buffon and Jean Baptiste Lamarck and others who all embraced and propagated the idea. Charles Darwin was greatly influenced by these thinkers.

Not only was Darwin influenced by earlier and contemporary thinkers, he was influenced by materialistic ideas from his very childhood. Both his father, Robert Darwin, and grandfather, Erasmus Darwin, were Freethinkers and members of the Mason order. Erasmus Darwin, who was a physicist and one of the highest ranking members of the Masonic organization, was himself influenced by and played an important role in the formation of the evolution theory. In the 1780's and 90's he wrote two books, "Temple of Nature" and "Zoomania", in which he argued that all life came from a common ancestor and developed through the laws of nature alone. Later the founded the "Philosophical Society" to help him spread his ideas. So Darwin wasn't acting alone. There was a whole anti-religious movement centered around so called Enlightenment ideas to help propagate a materialistic world view. Darwin's important contribution in this connection was that he was the first to offer a usable "scientific" justification for the idea.

While the above does not in disprove evolution by natural selection it does show us that Darwin is often misportrayed. The fact is, however, that he did not coin the idea of evolution by natural selection due to his objective observations in nature. He already had the idea in mind from his very childhood and from earlier and contemporary Enlightenment thinkers. He might, therefore, not have been as objective as many would like him to appear.
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The privileged planet

Code to embed            

In this movie not all views are necessarily according to the Hare Krishna standpoints.

Eye evolution - The Pax-6 challenge evolution
 
According to researchers of the Basel University, the Pax-6 gene had a crucial role in eye development of mammals, amphibians, fish and insects. Surprisingly, the new discovery revealed an exact similarity between human and mouse Pax-6 proteins, and their 90% and 94% genetic sequence similarities with the fruit fly genetic sequence. This straightforwardly questions the Darwinistic evolution theory, as Gehring and his colleagues remarked:
 
"This was [an unexpected result] because of the long-standing dogma.. that the insect compound eye was non-homologous to the vertebrate camera eye, and that the two types of eye had evolved independently." [1]
 
Considering the great difference of the vertebrate and insect eyes, as paleontologist Simon Conway Morris remarks, these findings are really puzzling.[2]
 
References:
1. Walter J. Gehring and Kazuho Ikeo (1999), Pax 6: mastering eye morphogenesis and eye evolution, Trends in Genetics, Volume 15 pp.371-377
2. Simon Conway Morris (1998), The Crucible of Creation; The Burgess Shale And the Rise of Animals, 1st Ed, Oxford University Press
   ---------------------------
Punctuated Equilibrium (PE)
 
One of the proofs of the gradualistic evolutionary hypothesis comes from the fossil record, which supposed to display gradual transformations from simple to more complex species. However, even after nearly 40 years of discussions, there is no consensus among paleontologists whether the fossil record shows this gradual change. In the beginning of the 1970s, Stephen Jay Gould and Niles Eldredge came up with the idea of sudden evolutionary changes occurring after long periods of stasis. The name of their new hypothesis became known as punctuated equilibrium.
 
For some biologists, “punctuated equilibrium” is a radical idea. The term was coined in the 1970s to describe an uneven pace of evolution in the fossil record. But because it posits that evolution happens in bursts, punctuated equilibrium goes against the notion that evolution inches forward in tiny steps, guided by natural selection.[1] 
 
The nature of evolutionary changes, recorded by the fossil record, has long been controversial, in particular regarding the relative frequency of gradual change versus stasis within lineages. Over 250 sequences of evolving traits were fit by using a maximum likelihood to three evolutionary models: directional change, random walk, and stasis. Evolution in these traits was rarely directional; in only 5% of the fossil sequences, directional evolution was most strongly supported. The remaining 95% of the sequences were divided nearly equally between random walks and stasis. Variables related to body size were significantly less likely than shape traits to support stasis. The rarity with which directional evolution was observed in this study corroborates a key claim of punctuated equilibria and suggests that true directional evolution is infrequent or, perhaps more importantly, of short enough duration so as to rarely register in paleontological sampling.[2]
 
Before proceeding to PE, let’s briefly look at directional and random walk evolution.
 
Directional evolution
 
Paleontologists rather like to study the fossil lineages that show the hypothetical change than those, which remain static. The above mentioned 5% of directional evolution is made up by comparing morphological similarities of species. However, as the forces causing the genetic and morphological changes are unknown, this puts a great question mark on the “fact” of hypothetical directional evolution.
 
"It is often lamented that studies of present-day populations provide only the briefest snapshot of evolution and tell us little about the evolutionary forces that have shaped a particular trait or organism in the past. Although ancestral phenotypes can be reconstructed with phylogenetic methods or directly determined from fossils, neither approach reveals the evolutionary processes that created these phenotypes.  Even if these historical data could help, there is considerable uncertainty associated with the reconstruction of ancestral character states. A fossil record is missing for most taxa and incomplete for others. As a result, a direct link between the action of micro-evolutionary forces detected in studies of contemporary populations and patterns of speciation and macro-evolution has been difficult to make, yet this is a central problem in evolutionary biology".[3] 
 
Random walk and information theory
 
Considering the above mentioned random walk of evolution, both the Darwinistic theory and the hypothesis of punctuated equilibrium emphasize randomness or a random walk of evolution, because this suites the main tenet of their concept, namely that evolution is undirected. With the rise of modern systems and information theory, however, the strength of the randomness argument is dimming, because information is just the opposite of randomness. For example, how did information collect in the first DNA and from where that information came from? Moreover, from where and how the first biological process that could read DNA information come into being?
 
Briefly, “information theory shows that the laws of nature, as understood by modern science, are insufficient to account for the origin of life. The basic argument [through mathematical models] is the following. The laws of nature and the corresponding mathematical models of physical reality can all be described by a few simple, mathematical expressions. This means that they possess a low information content. In contrast, there is good reason to suppose that the intricate and variegated forms of living organisms possess a high information content. It can be shown that configurations of high information content cannot arise with substantial probabilities in models defined by mathematical expressions of low information content. It follows that life could not arise by the action of natural laws of the kind considered in modern science”.[4]
 
Problems of PE
 
Although PE is an interesting explanation for a sudden appearance of new species, thus giving answer to troubling features of fossil records, a very important question is not yet clarified, namely, does the mechanism of PE actually work? According to researches done in 2001, it seems not.
 
…"metapopulation structure, habitat loss or fragmentation, and environmental stochasticity can be expected to greatly accelerate the accumulation of mildly deleterious mutations, lowering the genetic effective size to such a degree that even large metapopulations may be at risk of extinction"…[4a]
 
Briefly, according to this research the fundamental mechanisms of PE lead to extinction and not to evolution. In other words, the danger for extinction greatly increases when (1) a part of the population of a particular species becomes disconnected, (2) when there is a change of environment, (3) or due to habitat fragmentation (breaking up of the natural environment of plants and animals). All these three factors are central mechanisms of PE.
 
The cause of the greater extinction of the species nowadays is described in the following passage of BBC scientific news.
 
"The point has often been made that temperatures have increased before in the Earth's past; but the rate now is 100 times greater. And whereas in those times there were large areas of natural habitat, now it's much more difficult for animals to change or migrate; plus there's loss of genetic diversity, habitat fragmentation - it's just much more difficult for species than 1,000 years ago."[5]
 
A similar study on habitat fragmentation and extinction of the species was written by Burkey and Reed.
 
“Across the globe, much current research reflects concerns about the effect of habitat fragmentation on the viability of species and populations. This is an immediate and important concern for the Kingdom of Thailand, where decisions about land use are at a critical juncture. Thailand is in danger of losing species that play a special role in Thai culture and history, such as the Asian elephant (Elephas maximus) and the tiger (Panthera tigris). We provide a selective review and synthesis of the effects of habitat fragmentation on extinction risk”.[6]
 
Here is another astonishing example. Studying collared lizards in the Missouri Ozarks, researchers from Washington University in St. Louis showed that habitat fragmentation doesn’t result in speciation but rather extinction.[7]
 
All these discoveries pose serious problems to the concept of evolution as explained by PE because of the lack of its mechanism. Thus the more plausible explanation of the history of the species is the concept of needful design.
 
“The explanatory success of punctuated equilibrium depends upon the existence of a mechanism that can produce rapid macro-evolutionary change. As Foote and Gould note elsewhere, the punctuationalist model of Cambrian evolution requires a mechanism of unusual “flexibility and speed.”[a] As yet, however, neither Foote, Gould nor anyone else has identified such a mechanism with any genetic or developmental plausibility”.[8]
 
Some quotes on Further Difficulties with PE:
 
“The absence of transitional forms also represents a severe (if relatively lesser) difficulty for punctuated equilibrium. Note that both standard neo-Darwinian and more recent punctuationalist versions of evolutionary theory predict (or expect) many more transitional intermediates than the fossil record actually preserves…At present, paleontologists lack clear ancestral precursors for the representatives of, not just one new phyla, but virtually all the phyla represented in Cambrian explosion.”[14]
 
“The Cambrian explosion show a radically different 'top down' pattern. Major differences in form and body plans appear first, with no simpler transitions before them. Later, some minor variations arise within the framework of these separate and disparate body plans. This has completely stumped neo-Darwinists. Others have tried to explain it away by proposing big leaps of evolutionary change-the so-called punctuated equilibrium idea-but even this can't account for the 'top down' phenomenon. In fact, punctuated equilibrium predicts a 'bottom up' pattern; it just asserts that the increments of evolutionary change would be larger. Yet if you postulate intelligent design, the 'top down' pattern makes sense, because it's the same pattern we see in the history of human technological design.”[12]
 
CONCLUSION: Valentine and Erwin concluded that, “neither of the contending theories of evolutionary change at the species level, phyletic gradualism or punctuated equilibrium, seem applicable to the origin of new body plans”[9] and thus, we now require “a [new] theory for the evolution of novelty, not diversity.”[10]
 
“The fossils of the Cambrian Explosion absolutely cannot be explained by Darwinian theory or even by the concept called 'punctuated equilibrium,' which was specifically formulated in an effort to explain away the embarrassing fossil record," and according to the words of Meyer "When you look at the issue from the perspective of biological information, the best explanation is that an intelligence was responsible for this otherwise inexplicable phenomenon.”[13]
 
References:
1. Mark Pagel, Chris Venditti, Andrew Meade, “Large Punctuational Contribution of Speciation to Evolutionary Divergence at the Molecular Level,” Science, 6 October 2006: Vol. 314. no. 5796, pp. 119-121, DOI: 10.1126/science.1129647.
2. The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages, by Gene Hunt Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, MRC 121, P.O. Box 37012, Washington DC 20013-7012
3. Directional selection is the primary cause of phenotypic diversification, Loren H. Rieseberg,* Alex Widmer, A. Michele Arntz, and John M. Burke, Department of Biology, Indiana University, Bloomington, IN 47405-3700, July 29, 2002.
4. Richard Thompson, Mechanistic and Non-mechanistic Science, Information Theory And the Self-organization Of Matter, p 94.
4a. Metapopulation extinction caused by mutation accumulation, Kevin Higgins* and Michael Lync, PNAS February 27, 2001 vol. 98 no. 5 2928-2933
5. Climate response risks to nature, By Richard Black, Environment Correspondent, BBC News
6. Burkey, T.V. and Reed, D.H., The effects of habitat fragmentation on extinction risk: Mechanisms and synthesis, Songklanakarin J. Sci. Technol., 2006, 28(1) : 9-37
7. Disrupting evolutionary processes: The effect of habitat fragmentation on collared lizards in the Missouri Ozarks, Alan R. Templeton*, Robert J. Robertson, Jennifer Brisson, and Jared Strasburg, PNAS May 8, 2001 vol. 98 no. 10 5426-5432
8. Meyer et al, Darwinism, Design and Public Education, p 343.
a. Michael Foote and Stephen J. Gould, “Cambrian and Recent Morphological Disparity,” Science 258, (1992): 1816.
9. J.W. Valentine and D.H. Erwin, “Interpreting Great Developmental Experiments: The Fossil Record,”
pp. 74-77. See diagram on p. 92.
10. Ibid., p. 97.
11. The Case for a Creator, Lee Strobel, 2004, pp. 238-239
12, Ibid pp 242
13. Ibid pp 238
14. The Cambrian Explosion: Biology’s Big Bang, 2001 by Stephen C. Meyer, P. A. Nelson, and Paul Chien, pp 9.

   ---------------------------
The genetic code
 
The genetic code is a set of rules and instructions in a gene telling the cell how to make a specific protein by arranging sequences of 4 types of nucleotides, A – adenine, U – uracil, G – guanine and T – thymine. The genetic code has 64 codons or triplets of nucleotides and it defines the cell's information at its most fundamental level. The combination of many nucleotides (A, U, G, T) or genetic codes, form a gene. A combination of many genes make a chromosome and all the chromosomes together are called the genome, which in humans, for example, equals a sets of 3 billion nucleotides.
 
In the 2002 Nature magazine, Gerald Joyce of the Scripps Institute[5] wrote about his research on the genetic code, the RNA world and the origin of life. His article was quite optimistic, while not avoiding to mention some serious difficulties as well. Here are few points he raised:
 
1. A largely open question concerns the origin of the genetic code. The aminoacylation of RNA initially must have provided some selective advantage unrelated to the eventual development of a translation machinery.
2. The next step towards the origination of the genetic code was the formation of peptide bonds between amino acids that were attached to RNA. The products of this reaction must have conferred some selective advantage, even though the peptides probably would have been too small and too heterogeneous in sequence to function as catalysts. It is not clear, however, how the detailed assignments of the genetic code were made.
 
The origin of the genetic code is still a big puzzle. Both in chemistry and biology, one of the greatest mysteries is to understand which was the first: the genetic code or the protein. In the Feb. 17 (2004) issue of Current Biology, Eörs Szathmáry wrote:
 
“How do you get from the primordial soup to the genetic code?  The snag is that, in contemporary biological systems, there is a division of labour between nucleic acids and proteins: the former store genetic information and the latter exert function. Genetic information is expressed with the help of proteins, which are encoded by nucleic acids. We seemed to be at an impasse: no genes without proteins and no proteins without genes – the classic ‘chicken and egg’ problem”.[1]
 
Of course, immediately after this, Eörs Szathmáry also proposed a speculative solution saying, “it now seems that the primordial soup may not have been that important, and that we may not need a genetic code for early life.” So what is his proposal? He suggests that the RNA performed both the enzymatic functions and the storing of information. However, even if we accept his reasoning for the sake of argument, he fails to explain how the need of the primordial soup and the genetic code is eliminated.
 
DNA, RNA – Genetic code – Protein
 
The process of protein production from the information in the genetic code[7] implies that proteins cannot be made without DNA and RNA and that cells cannot operate without proteins. Even the simplest known cell must pass volumes of coded information from one generation to the next. The only way we know to store and copy that much information is with a genetic molecule, such as DNA or RNA.[8]
 
“Because DNA provides the genetic code for protein synthesis, it is conceivable that DNA may have formed in the primitive earth environment as a consequence of RNA activity. Then DNA activity could have led to protein synthesis (see Chapter 10).”[6] This idea of the “RNA World” hypothesis is very controversial, namely if RNA is synthesized by RNA, where did the first RNA come from?
 
In his article in Scientific American, Horgan mentions another chicken-and-egg problem, namely the interdependence of RNA (and DNA) and phosphorus. He writes: "But as researchers continue to examine the RNA-world concept closely, more problems emerge. How did RNA arise initially? RNA and its components are difficult to synthesize in a laboratory under the best of conditions, much less under plausible prebiotic ones. For example, the process by which one creates the sugar ribose, a key ingredient of RNA, also yields a host of other sugars that would inhibit RNA synthesis. Moreover, no one has yet come up with a satisfactory explanation of how phosphorus, which is a relatively rare substance in nature, became such a crucial ingredient in RNA (and DNA)."[9]
 
Another genetic code – another problem
 
Sequencing and mapping the human genome was the first essential step for scientists to study where genes for diseases such as cancer are located. But in studies to identify the complex factors that make those genes active or inactive, molecular genetic researchers at the University of Virginia have discovered a new area outside the DNA itself that may show existence of another type of genetic code.
 
Professor David Allis from the University of Virginia says: “The cell is somehow making choices about using histone methylation to turn a gene on or off…and we believe that what is telling the cell to make those choices is an overall code that may significantly extend the information potential of the genetic DNA code itself”.[2]
 
This discovery adds a problem to the already great puzzle of evolution, namely it increases the already quite well known complexity of the cell and creates a chicken-or-egg-like enigma, i.e. how and when DNA and protein became interdependent. In other words, if DNA codes for chromatin, how can it be expressed if chromatin wasn’t there from the start to activate the gene?
 
Optimal codons or biochemical synonyms
 
 A codon, as an integral part of genetic code, is a sequence of three base pair nucleotides that codes for either a specific amino acid or the end of a protein. It is also called a ‘biochemical synonym.’ Usually, in any language words can be replaced with appropriate synonyms. The same was thought about codons, until recently, when scientists discovered that the ‘biochemical synonyms’ are not completely interchangeable.[3] In other words, there are particular codons that are optimal for producing functional proteins. These biochemical synonyms are called optimal codons. (D. Allan Drummond et.al.[4])
 
Error-minimization
 
 The primary function of the genetic code embodied in DNA is to determine the presence of particular proteins, mostly enzymes, which in turn control the processes of chemical activity in the cell, and thus ultimately determine the development, maintenance and functioning of organs and of the organism as a whole.[10] It would be enormously harmful to the cell if in this process the genetic code failed to translate the stored information of DNA into the functional information of proteins.
 
 An amazing feature of genetic code is its robustness to resist and minimize harmful mutations that are more numerous than any occasional beneficial mutations. Fine-tuning within the genetic code facilitates a surprising ability of minimizing errors, namely allowing the cell's biochemical information systems to make mistakes and still communicate critical information with minimal distortion.

In conclusion, as we have seen hints of functional fine-tuning and design, we would like to suggest the ID theory as a solution for the above mentioned problems. 
 
References:
1. Eörs Szathmáry, “Magazine: From biological analysis to synthetic biology,” Current Biology, Vol 14, R145-R146, 17 February 2004.
2. http://www.virginia.edu/insideuva/2001/24/code.html C. David Allis, U.Virginia. Byrd Professor of Biochemistry and Molecular Genetics, Aug. 10-23, 2001
3. A "Silent" Polymorphism in the MDR1 Gene Changes Substrate Specificity, Chava Kimchi-Sarfaty,* Jung Mi Oh, In-Wha Kim, Zuben E. Sauna, Anna Maria Calcagno, Suresh V. Ambudkar, Michael M. Gottesman. 26 January 2007:
4. Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution, D. Allan Drummond1,Go To Corresponding Author,andClaus O. Wilke2
5. The antiquity of RNA-based evolution, Gerald F. Joyce, Nature 418, 214-221 (11 July 2002) | doi:10.1038/418214a
6. Alcamo and Schweitzer, CliffsQuickReview Biology , 2001, pages 94-96
7. a. Messenger RNA copies the base sequence of a DNA segment (gene) letter by letter. RNA nucleotides quickly make a copy of the information from only one side of the double helix. A long, single-stranded messenger RNA molecule carries all the information of one gene. The genetic code defines a one-to-one correspondence between three bases and an amino acid.
b. Transfer RNA and ribosomal RNA play a central role in protein synthesis.
c. A transfer RNA molecule is a physical representation of genetic code—at one end you have three bases that are linked to the corresponding amino acid at the other end.
d. A ribosome provides the chemical machinery needed to link amino acids together in the exact order dictated by the messenger RNA. Eventually, a complete protein is assembled.
8. Origins of Life, part 1, Professor Robert M. Hazen, p112.
9. (Horgan, John [Senior Writer, Scientific American], "In The Beginning...," Scientific American, February 1991, p.103. Ellipses in original)
10. The Evolution of Designs: Biological Analogy in Architecture and the Applied Arts by Philip Steadman
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Orphans in the Genes: An Evolutionary Puzzle Is Growing  
 
“The genomes of most newly sequenced organisms contain a significant fraction of ORFs (open reading frames) that match no other sequence in the databases. We refer to these singleton ORFs as sequence ORFans. Because little can be learned about ORFans by homology, the origin and functions of ORFans remain a mystery. However, in this era of full genome sequencing, it seems that ORFans have been underemphasized”.[1]
 
ORFan genes  are sequences of DNA that code for protein. They are defined as ORFs (Open Reading Frames), having no sequence homologs in other genomes.[3] Thus there is no evidence of possible evolution of the ORFan genes. Scientists hoped that genome sequencing would solve the mystery of ORFans, but did that help? It seems not. According to Siew and Fischer from the Ben Gurion University, even after sequencing about 60 microbial genomes, difficulties became even greater than before. In other words, the results of genome sequencing did not reveal intermediate sequences or more matches.
 
If proteins in different organisms have descended from common ancestral proteins by duplication and adaptive variation, why is it that so many today show no similarity to each other? Why is it that today we do not find any of the necessary “intermediate sequences” that must have given rise to these ORFans? Do most ORFans correspond to rapidly diverging proteins? If so, how rapidly do they diverge, and what are the forces involved in their rapid evolution? Is their rate of change constant or did the rapid changes occur only at specific times? Do these rapidly evolving ORFans correspond to nonessential proteins or to species determinants?
 
Thoroughly investigating the microbial genomes, Siew and Fischer found that 20% to 30% of the sequences belong to the ORFan category. As they predicted during the sequencing of the 100th genome, the number of ORFans increased to about 25,000 and this automatically increased the number of whys, namely the problem of the already existing mystery of the origin and function of ORFans.
 
We conclude that the increasing number of ORFans suggests that, as our knowledge of nature’s sequence diversity continues to grow, ORFans may entail an intrinsic phenomenon in evolution, and that a global view of the protein world needs to encompass the ORFan sequence families in addition to the large sequence families containing proteins conserved [i.e., unevolved] in numerous organisms.[1]
 
To prove the evolution theory, evolutionists usually focus on the similarities but often forget to mention the troubling differences without any traceable evolutionary link, like in this case the ORFans.
 
The origin of the ORFans
 
The origin of microbial ORFans, having no detectable homology to other ORFs in the databases, is one of the unexplained puzzles of the post-genomic era. Several hypotheses on the origin of ORFans have been suggested in the last few years, most of which based on selected, relatively small, subsets of ORFans. One of the hypotheses on the origin of ORFans is that they have been acquired through lateral transfer from viruses. Here we carry out a comprehensive, genome-wide study on the origins of ORFans to quantify the strength of current evidence supporting this hypothesis.
 
Results:
“We performed similarity searches by querying all current ORFans against the public virus protein database. Surprisingly, we found that only 2.8% of all microbial ORFans have detectable homologs in viruses, while the percentage of non-ORFans with detectable homologs in viruses is 7.9%, a significantly higher figure”.[2]
 
This means that because there is less homology between ORFans and viruses than non-ORFan genes, there is no evidence that viruses are a significant source of ORFans. Horizontal gene transfer from a virus has not shown to be the source of ORFans in other organisms and thus it can’t be taken for granted that, for example, a novel ORFan gene in a fruit fly came from a virus. It’s more a conjecture.
 
The ORFans of the Flagellum
 
The flagellum of the E-coli bacteria has two ORFan genes whose ancestry is not known even till today. The structure of these ORFan genes, in average about 300 nucleotides and, moreover, their precise function, leads to question both the idea of their gradual evolution and/or the random assemblage of the nucleotides into a fully functional, complex system. Generally, all ORFan genes are specific to one bacterium, like in this case of the flagellum, and thus they deny the concept of common ancestry from Darwin’s theory.
 
Conclusion
 
It is precisely this point — the large number of putative genes with no known function — that has been the biggest surprise in genome sequencing. The genome of the archaeon, Aeropyrum pernix, for example, contains more than 1,500 ORFs — 57% of its total gene content — not recognizable in any other organism by computer searching.[4] And more than 40% of the approximately 4,000 ORFs found in the Mycobacterium tuberculosis, one of the best-studied bacteria of the past century, fall in the same category.[5] In every genome examined so far, at least a quarter of the genes remain 'hypothetical,' in that no function can be ascribed to them. After a long history of biochemical and genetic examination, how could so much remain unknown?
 
The hypothetical ORFs fall into two categories: those that are found in a variety of organisms, and which almost certainly encode functional proteins; and those that are unique to particular lineages. The latter can sometimes be attributed to runaway gene duplication; many of the unidentified genes in the A. pernix are in this category.[4] The extra ORFs in this case are unusually small, thus pushing the ratio of number of genes-to-genome size high above expectation (Fig. 1); not all of them may encode proteins. In contrast, there are large numbers of unidentified genes in a variety of organisms that look conventional in every way. Where these unique sequences come from and what they do remain baffling mysteries.[6]
 
We can conclude that, because of all these problems regarding ORFan genes, the evolution theory is still far from suitable to explain the origin of life.
 
  References
1. Twenty thousand ORFan microbial protein families for the biologist? , N Siew, D Fischer, 2003
2. On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer, Yanbin Yina and Daniel Fischera,b
aComputer Science and Engineering Dept. 201 Bell Hall, University at Buffalo, Buffalo, NY 14260-2000, US
bBioinformatics/Dept. of Computer Science, Ben Gurion University, Beer-Sheva 84015, Israel
3. Fischer D, Eisenberg D: Finding families for genomic ORFans. Bioinformatics 1999, 15(9):759-762
4. Kawarabayashi, Y. et al. DNA Res. 6, 145–152 (1999).
5. Cole, S. T. et al. Nature 393, 537–544 (1998). 
6. Biodiversity: Microbial genomes multiply,  Russell F. Doolittle, Nature 416, 697-700 (18 April 2002) | doi:10.1038/416697a

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Design - an inappropriate concept in evolutionary theory
W. J. Bock
Journal of Zoological Systematics and Evolutionary Research, (February 2009) 47(1), 7-9
 
Abstract: The concept of accident in evolution refers to causes which are stochastic with respect to selective demands arising from the external environment and acting on the organism, while the concept of design refers to causes which meet the requirement of these selective demands. The condition 'with respect to selective demands' is generally forgotten so that evolutionary changes are described as being design modifications. Design is an invalid synonym for adaptation. Furthermore, it implies a designer and has been used by some authors before Darwin to argue that design in organisms demonstrates the existence of a designer and hence a plan. Yet if evolution depends on two simultaneously acting causes, one of which is accidental, then the process of evolution and all attributes of organisms are accidental. The concept of design is inappropriate in biology and should be eliminated from all biological explanations.
 
Comment:
 
In the very beginning of his essay, Professor Walter Bock quotes from the letter of Darwin written to Asa Gray in 1860: "I am conscious that I am in an utterly hopeless muddle. I cannot think that the world, as we see it, is the result of chance; and yet I cannot look at each separate thing as the result of design."
 
Like Darwin, the evolutionary biologist Ernst Mayr has a similar opinion. He wrote: "Given all this, the conclusion is inevitable: we find in all organisms a fitting together of inborn actions or structures so perfect that one can hardly avoid such terms as "design" or "purposefulness"."
 
Bock, like any other evolutionist, very much dislikes the word "design" and tries to go beyond Darwin and Mayr proposing to the scientific community to give up it's usage and find another technical word. The reason is that "the term design carries with it too many undesirable connotations, such as the existence of a creator, and therefore it should not be used in evolutionary theory. Design could be replaced with non-accidental or non-stochastic, but these substitute terms are awkward and not really informative. Darwin developed his theory of organic evolution in part as an explanation of the appearance and perfection of adaptations to counter the idea of design as advocated by Paley and accepted then by almost everyone in the western world, including biologists."
 
The alternative words Bock proposes to be used by biologists are "paradaptation and adaptation" for, as he writes, "they do not carry any baggage in the form of unwanted connotations, such as a designer or an adapter."
 
Although seemingly a good proposal, still not everyone is of the same opinion, like Paul Nelson who says: 'He [Bock] claims that his terminology does not "carry any baggage in the form of unwanted connotations", but they do!' 
 
According to Bock ( 1967:67), “Those aspects of a feature that are dependent upon, resulting from, or under the control of chance-based evolutionary mechanisms may be termed paradaptive (from ‘para’ and ‘adaptive’), meaning ‘besides adaptive’ in the sense that these aspects are not dependent upon selection and hence cannot be judged in the range of adaptive to nonadaptive. Paradaptive aspects of a feature only depend upon the accidental evolutionary mechanisms and hence may be either adaptive or nonadaptive according to whether they are accepted or rejected by selection.”
 
In the rest of this essay we will briefly mention natural selection because in other places there is more elaboration. After discussing “accident” in evolution we will consider whether Bock’s rejection of the word design from the scientific language is proper or not.
 
Although according to some critics Bock (1969a:441) only seemingly contradicts himself, saying that adaptive or nonadaptive differences within paradaptive aspects are determined “according to whether they are selected or rejected by selection,” taking the importance of natural selection from the viewpoint of Kauffman creates great difficulty.
 
"FOR as long as he can remember Stuart Kauffman [Kauffman, Stuart A. [Theoretical biologist, Santa Fe Institute, New Mexico, USA] has held a deep conviction about nature: that natural selection cannot be the sole or even the most important source of order in the biological world. Almost three decades ago, Kauffman, then a young medical student at the University of California, San Francisco, set out to prove he was right and that the rest of the biological community was wrong. `What I found was profound,' says Kauffman. `I knew that then and I'm still convinced of it.' ... `The results were so powerful, and seemed to confirm what I felt instinctively must be true, that I dismissed natural selection as being totally unimportant,' says Kauffman." (Lewin, Roger [biochemist, former editor of New Scientist and science writer], "Order For Free," New Scientist, 13 February 1993, Supplement, pp.10,11)
 
In similar manner Carl Sagan in 1992 wrote: “Some of the underlying emotional reasons for rejecting natural selection were later vividly expressed by the playwright George Bernard Shaw: `[T]he Darwinian process may be described as a chapter of accidents. As such, it seems simple, because you do not at first realize all that it involves. ... if this sort of selection could turn an antelope into a giraffe, it could conceivably turn a pond full of amoebas into the French academy.' ... George Bernard Shaw, Back to Methusaleh: A Metabiological Pentateuch (New York: Brentano's, 1929), p. xlvi. The last sentence is in fact the modern evolutionary point of view." (Sagan C. & Druyan A., "Shadows of Forgotten Ancestors: A Search for Who We Are," [1992] Arrow: London, 1993, reprint, pp.63-64, 428n.)
 
Bock’s other weak point is the concept of accident. Here are two examples, food for thought that can give insight whether accident can result in anything useful.
 
1. Three teams of researchers from Boston College, the University of Groningen, Netherlands, and Tohuku University, Japan, have independently designed and synthesized a single-molecule rotary motors, capable of spinning in a single direction. Molecular motors are protein/enzyme complexes that generate movement in the cell. [1],[2] The motors can be driven by UV radiation and heat or chemical energy.
 
The whole structure of molecular motors were carefully designed and synthesized. The light-and-heat-driven motor depends on the "unique combination of axial chirality and the two chiral centers" in the molecule positioned "just right" in three-dimensional space.[3] The chemically-driven motor is dependent upon chirality as well as the fine-tuning of multiple molecular substituents.[4]
 
Obviously, the motors were a product of neither an accident nor the mere workings of natural laws of chemistry and physics. In fact, the chemically-driven motor, comprised of only 78 atoms, took Boston College's brilliant team more than four years to build.[5] If it takes researchers four years to construct a molecular motor, how likely is it that molecular motors that occurs in nature is the result of accidents?
 
2. Having random letters fall into place to make a single meaningful sentence, by accident, is numerically not feasible. The same is true for any functional strings of nucleotides. If there are more than several dozen nucleotides in a functional sequence, we know that realistically they will never just “fall into place”. This has been mathematically demonstrated repeatedly.[6] Thus, strings of nucleotides cannot arise randomly but rather a pre-existing “concept” is required as a framework upon which a sentence or a functional sequence must be built.
 
All in all, intelligent design is a must and accident is excluded. For the sake of argument, if we could just calculate all the required accidents of the history for hypothetical evolution of species, the number would surpass zillions and zillions. There is no reason to believe why even one accident should have been able to give a correct, fine tuned account of all the other accidents. “If the world's finest minds can unravel only with difficulty the deeper workings of nature, how could it be supposed that those workings are merely a mindless accident, a product of blind chance?”[8] Ultimately, using the phrase “by accident”, only indicates ignorance of cause and design.
 
Thus, as these few evidences show, it is appropriate to use the word “design” in scientific explanations, not only because of both practical and philosophical reasons but even realistically and linguistically “what justification is there for a word which is simply the opposite of some other words? A word contains its opposite in itself.”[7].
 
"Given all this, the conclusion is inevitable: we find in all organisms a fitting together of inborn actions or structures so perfect that one can hardly avoid such terms as "design" or "purposefulness"." And actually, we cannot.
 
References:
1. T. Ross Kelly, Harshani De Silva, and Richard A. Silva, "Unidirectional Rotary Motion in a Molecular System," Nature 401 (1999): 150-52
2. Nagatoshi Koumura et al., "Light-Driven Monodirectional Molecular Rotor," Nature 401 (1999): 152-55.
3. Koumura et al., 154.
4. Kelly et al., 150-152.
5. Anthony P. Davis "Synthetic Molecular Motors," Nature 401 (1999): 120-21
6. Sanford, Mystery of genome p124
7. Syme, the Newspeak editor, in George Orwell’s, 1984
8. Davies, Superforce p235-36