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Various evidences for design

Irreducible complexity.

According to the definition of Michael Behe the irreducible complex
system is "a single system composed of several well-matched
interacting parts that contribute to basic function, wherein removal
of any one of the parts causes the system to effectively cease
functioning." In other words, when in a particular biochemical system
all the parts are interdependent, namely no one of the parts can
function separately they are said to be a functional, irreducible
complex system. According to Dembski, irreducible complexity is a type
of specified complexity. The specified pattern is thesimultaneous co-
occurrence of components required for the system to have minimal
function.Conclusively, irreducible complexity indirectly points to
intelligent designer because a specified complexity can be a result
only of premeditation and planning.

The example of irreducibly complex systems are the biochemical systems
composed of many components. If any part would be missing the
biochemical systems would not function at all. It is like a human body
unable to function without brain, heart, lungs or bones. Many man-made
systems show similar irreducible complexity and so what to say about
biochemical systems?

Chicken-and-egg systems.

The first and biggest chicken-and-egg puzzle is what was first, the
DNA or a protein because both had equal importance for life’s
appearance. In general, the interdependence of many or at least two
components within any biochemical system give rise to the chicken and
egg problem, namely which component came the first and how it could
exist and start to function at all without other component(s). One
another compelling example for this chicken-and-egg problem is the
interdependence of ribosome and a protein. In other words, proteins
can't be made without ribosomes, and ribosomes can't be made without
proteins. Thus, the interdependence of biochemical components within
biochemical systems points to intelligent design.

Fine-tuning.

Just as most of the man-made systems require a high-degree of
precision to function properly, similarly in many biochemical systems
there is a very high level of precise fine tuning. For example, the
enzyme active sites are exquisitely fine-tuned molecular systems.
Sometimes slight repositioning of active site chemical groups in space
readily compromises the functional efficiency of enzyme-mediated
catalysis. Another, recent discovery is that protein binding depends
on the exact placement of only a few amino acids located on the three-
dimensional surface of the folded protein. As each month there are
more and more reports of biochemists about the biochemical fine-
tuning[1], it becomes more and more obvious that biochemical
structures and activities depend on the precise location and
orientation of atoms in three-dimensional space. Thus biochemical fine-
tuning points to the fact of intelligent design.

Optimization.

Many biochemical systems are optimized according to a purpose and
their optimality like a high performance are far better than of the
systems made by great human engineers and designers. For example,
scientists have found that certain components of ribosomal RNA are
chemically modified by the cell’s machinery to structurally fine-tune
one region of the ribosome (called the A-site). This region actively
participates in protein synthesis. Such structural fine-tuning
optimizes the ribosome to balance the accuracy and speed
of protein production. Optimization is associated with intelligent
design and such optimization within biochemical systems is highly
necessary for the survival of the biochemical system.

Biochemical information systems

“The cell's biochemical machinery is an information-based system.
Moreover, the chemical information inside the cell exists as encoded
information and the genetic code (the rules used to encode the cell's
information) defines the cell's biochemical information system.

By itself, the cell's encoded information offers powerful evidence for
an Intelligent Designer.[since there is] a type of fine-tuning in the
rules that form the genetic code. For example, these rules impart to
the genetic code the surprising capacity to minimize errors.

Error-minimization properties in the genetic code allow the cell's
biochemical information systems to make mistakes and still communicate
critical information with high fidelity. (Rana Fazale, FYI: I.D. IN
DNA – Deciphering Design in the Genetic Code) In terms of
functionality and performance, biochemical information systems are
much more complicated systems than anything ever made by human beings.
For example, all biological information systems have "molecular
interpretation machines" for the purpose of interpreting genetic
code. Without these ‘interpreters’ the genetic information could not
be expressed, or "implemented" by the cells.
The question that also arise here is: because they are interdependent,
what was the first, the molecular interpretation machine or the
designer of the message (sender) in biological information systems.
Thus this is another chicken-and-egg problem as well.

Structure of biochemical information.

More than only the information-based biochemical systems are their
structural features, such as language structure, the organization and
regulation of genes.[In the biochemical systems], there are hints of a
language structure, akin to that seen with ordinary languages, in the
lengths of non-protein coding DNA. [2]

Just as human information is structured according to syntactics,
semantics, and pragmatics the same properties also apply to
biochemical information. Syntactics in human information refers to the
ordering of symbols or letters and in biochemical information it
refers to ordering the sequence of nucleotides and amino acids. Here
the ordering has nothing to do with whether the arrangement has
meaning. Semantics refers to the meaning or the interpretation of a
word, sentence, or other language and as it always happens some
sequences will have meaning (red) and others not (sjw). Pragmatics
means the acceptance of particular meaning of some sequence as agreed
upon between two parties – the sender and the recipient. Only after
receiving a meaningful information the recipient can take action. As
Bernd-Olaf Küppers explains: “The identification of a character as a
"symbol" presupposes certain prior knowledge . . . in the form of an
agreement between sender and recipient. Moreover, semantic
information is unthinkable without pragmatic information, because the
recognition of semantics as semantics must cause some kind of reaction
from the recipient”. [3]

So, just as human beings use language for communication, the RNA, DNA,
polypeptides etc. also have their particular language. As Bernd-Olaf
Küppers explains: "The analogy between human language and the
molecular-genetic language is quite strict.... Thus, central problems
of the origin of biological information can adequately be illustrated
by examples from human language without the sacrifice of exactitude.”
During this last decade, microbiologist and biochemists discovered
that many organisms within their skin, saliva and sweat have small
peptides that have antimicrobial activity, and so, an importance for
the immune system.

[4]
Examination of antimicrobial peptides detected in them combinations of
sequences similar to phrases used in language and just as any language
has its grammatical rules how the sentences are constructed, 684 rules
of biochemical grammar were discovered. Using these parameters, the
scientists produced 42 new antimicrobial peptides that displayed
antimicrobial activity analogous to the peptides found in nature.
Comparing these artificial, newly made peptides with similar peptides
composed from a same type of amino acids but having random sequences,
the random peptides lacked activity, just like an unorganized usage of
words to construct a sentence gives no any meaning. As scientists get
more knowledge about the chemical composition of the cell's
structures and contents, they starting to get deeper understanding of
the relationship between the structure of biomolecules, their function
and how the cell stores and manages the information necessary to carry
out life's activities. Finally, the existence of fine tuned structures
like the biochemical language, which bears a strong similarity to
human languages, organized into meaningful information; and a strict
molecular grammar are all
indications for an Intelligent Design.

Biochemical codes.

Within the cell there is a highly complex symbolism in the form of
biochemical codes. More precisely, the biochemical code in DNA or RNA,
made up of a long chain or sequence of nucleotides, codons, and genes,
determine the characteristics of an organism. Thus, the biochemical
code is the heart of the cell’s information system. The encoded
information of all the three types of biochemical codes: the genetic
code, the histone code and the parity code of DNA needs an intelligent
designer to generate them.

Genetic code fine-tuning.

The rules comprising the genetic code that are better designed than
any conceivable alternative have a surprisingly great capacity to
minimize errors and fine tune as the genetic code translates stored
information into functional information. Due to its essential function
of error minimization, fine tuning and complexity, the random
appearance of the genetic code, is very questionable. ‘The genetic
code is not a `frozen accident'’.[5] And moreover, the possibility to
evolve a genetic code, as functional as one found in nature is 1 in
106. Thus, studying the genetic code's origin the molecular biologists
have discovered a fundamental evidence for Intelligent Design—a type
of
fine-tuning in the rules that form the genetic code.

Quality control.

All the cells have a very important and sophisticated quality control
systems by which bad, damaged, useless or improperly produced proteins
are destroyed. They reside within the informational structure of DNA
in the form of a parity code. The destruction processes or quality
control procedures are critical for the cell if it is to maintain
proper biochemical operations.[6] For example, occasionally a mistake
can occur in pairing of A-adenine to T-thymine and G-guanine to C-
cytosine, i.e. a wrong information is transmitted. Quality
control systems in the cell check and correct these errors that might
occur during DNA replication and transcription or remove protein waste
which could otherwise cause neurodegenerative disorders, like for
example the Huntington’s Disease. Thus, the life-important quality
control systems, without which there would be a great degree of
genetic degeneration and quick extinction of the species, are another
proof for intelligent design.

Molecular convergence.

Nowadays molecular biologists describe five different types of
molecular convergence.
1. Functional convergence describes the independent origin of
biochemical functionality on more than one occasion.
2. Mechanistic convergence refers to the multiple independent
emergences of biochemical processes that use the same chemical
mechanisms.
3. Structural convergence results when two or more biomolecules
independently adopt the same three-dimensional structure.
4. Sequence convergence occurs when either proteins or regions of DNA
arise separately but have identical amino acid or nucleotide
sequences, respectively.
5. Systemic convergence is the most remarkable of all. This type of
molecular convergence describes the independent emergence of identical
biochemical systems.

For example, examining the amino acid sequences of over six hundred
peptidase enzymes[7] the scientists from the Cambridge University (UK)
discovered that, from an evolutionary viewpoint, the peptidases had
over sixty separate origin events.

A similar discovery was made by the scientists of the National
Institutes of Health. Scrutinizingly observing the protein sequences
from 1,709 EC (enzyme commission) classes, they found that although
105 of them had proteins that catalyzed the same reaction, still they
must have had separate evolutionary origins.[8]

These and many other examples show highly specified complexity, which
could certainly not be produced independently from one another, by
blind, thoughtless, random natural process. Rather molecular
convergence indicates a common blueprint for all these systems, which
further indicates a must of intelligent design. Thus whenever
different non-related, complex biochemical systems and/or
biomolecules with independent origins are structurally, functionally,
and mechanistically identical, that certainly indicates a common
blueprint, a molecular convergence that reflects intelligent design,
rather than random natural process of creation.

Strategic redundancy.

The genetic code determines how a protein is to be constructed by
using four chemical nucleotides A-adenine, T-thymine, G-guanine, and C-
cytosine. The repetition of messages in the genetic code are to reduce
the probability of errors, namely they are like responsive backup
circuits. According to Run Kafir et all. (2006), genetic redundancy
makes genomes robust to the harmful effects of mutations, namely that
there is always a functional copy of a particular gene available. It
was also shown that these duplicated genes that serve as a backup, are
normally inactive but become active when the duplicated genes become
damaged. About how elegantly this system is designed, the researches
said: "We suggest that compensation for gene loss is merely a side
effect of sophisticated design principles using functional
redundancy."[9] We agree in toto, all this reveals a very careful
design.

Trade-offs and intentional suboptimization. Biochemistry is recently
discovering trade-offs and suboptimization in many biochemical
systems, by which their overall optimal performance is achieved. How
suboptimization balances trade-offs is seen in the examples like
protein synthesis, the carbon fixation reaction of photosynthesis etc.
The example of the rubisco – Rubisco or the “ribulose-1,5-biphosphate
carboxylase/oxygenase” is the most important enzyme in the process of
photosynthesis that catalyzes the first major step of carbon fixation
in the creation of sucrose and similar molecules. Because it is very
slow compared to other enzymes; it can fix only a few carbon dioxide
molecules per second, genetic engineers were trying to optimize this
enzyme for higher carbon dioxide removal. However, it was discovered
that rubiscos in a low carbon dioxide-to-oxygen environment convert
carbon dioxide and ribulose 1,5-bisphosphate into a six-carbon
compound at a relatively slow rate, and rubiscos in relatively high
carbon dioxide-to-oxygen environments complete the carbon fixation
reaction more rapidly. Thus the researchers from the National Academy
of Sciences concluded that "despite appearing sluggish and confused,
most rubiscos may be near-optimally adapted to their different gaseous
and thermal environments..[10] In Other words, rubiscos found
throughout nature are perfectly optimized for their environments and
the slow carbon fixation reaction is a necessary trade-off for this
enzyme to make the difficult discrimination between carbon dioxide and
molecular oxygen. Conclusively, just as optimization is a distinctive
characteristic of the well-designed device by an engineer, similarly
optimization and fine-tuning within the biochemical systems indicates
the work of an intelligent design.
..

NOTES:
1. Some papers that give examples for biochemical fine-tuning are:
Won-Ho Cho
et al., "CDC7 Kinase Phosphorylates Serine Residues Adjacent to Acidic
Amino
Acids in Minichromosome Maintenance 2 Protein," Proceedings of the
National
Academy of Sciences, USA 103 (August 1, 2006): 11521-26; Daniel F.
Jarosz et
al., "A Single Amino Acid Governs Enhanced Activity of DinB DNA
Polymerases on
Damaged Templates," Science 439 (January 12, 2006): 225-28; William H.
McClain,
"Surprising Contribution to Aminoacylation and Translation of Non-
Watson-Crick
Pairs in tRNA," Proceedings of the National Academy of Sciences, USA
103 (March
21, 2006): 4570-75;
2. [S. Aw, CEN Tech. J., Vol. 10, No. 3, p:308 1996, (see Physical
Review
Letters, Vol. 73, p:3169-3172)]
3. Küppers, Information and the Origin of Life, 32-33
4. 12. Michael ZaslofF, "Antimicrobial Peptides of Multicellular
Organisms,"
Nature 415 (January 24, 2002): 389-95.
5. Has Natural Selection Shaped The Genetic Code? S. J. Freeland et
al.
Princeton University, March 11, 1999
6. Additional reading: Shu-ichi Matsuzawa et al., "Method for
Targeting Protein
Destruction by Using a Ubiquitin-Independent, Proteasome-Mediated
Degradation
Pathway," Proceedings of the National Academy of Sciences, USA 102
(2005):
14982-87.
7. Peptidases are proteins that break down other proteins by cleaving
bonds
between amino acids.
8. Galperin, Walker, and Koonin, "Analogous Enzymes," 779-90.
9. Ran Kafri et al., "The Regulatory Utilization of Genetic Redundancy
through
Responsive Backup Circuits," Proceedings of the National Academy of
Sciences,
USA 103 (2006): 11653-58.
10. Guillaume G. B. Tcherkez, Graham D. Farquhar, and T. John Andrews,
"Despite
Slow Catalysis and Confused Substrate Specificity, All Ribulose
Bisphosphate
Carboxylases May Be Nearly Perfectly Optimized," Proceedings of the
National
Academy of Sciences, USA 103 (May 9, 2006): 7246-51.