Various evidences for design 

Irreducible Complexity 
According to the definition of Michael Behe, an 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 none 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 the simultaneous co-occurrence of components required for the system to have minimal function. Conclusively, irreducible complexity indirectly points to an intelligent design because a specified complexity can be a result only of premeditation and planning. 
Examples of irreducibly complex systems are 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, 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 ribosomes and proteins. 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 there are more and more reports by biochemists about biochemical fine-tuning [1] each month, 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. Their optimality, like a high performance, is far better than of 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 Design 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 a 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 arises here is: because they are interdependent, what was 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 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. 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 a sequence as agreed upon between two parties – the sender and the recipient. Only after receiving 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, microbiologists and biochemists discovered that many organisms within their skin, saliva and sweat have small peptides that have antimicrobial activity and are therefore important for the immune system.[4] Examination of antimicrobial peptides detected in the combinations of sequences lead to the discovery of 684 rules of biochemical grammar, similar to grammatical rules for sentence structure in language. 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 the 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 has no meaning. As scientists get more knowledge about the chemical composition of the cell's structures and contents, they are starting to get a deeper understanding of the relationship between the structure of biomolecules, their function, and the way the cell stores and manages the information necessary to carry out life's activities. Finally, the existence of fine tuned structures organized into meaningful information, like biochemical language which bears a strong similarity to human language, and a strict molecular grammar are indications for 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 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 three types of biochemical codes, the genetic code, the histone code, and the parity code of DNA, require intelligent designer to generate them.  
 
Genetic Code Fine-tuning 
The rules comprising genetic code, which 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. Because of its essential function of error minimization, fine-tuning and complexity, random appearance of the genetic code is very questionable. “The genetic code is not a ‘frozen accident’.”[5] 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, molecular biologists have discovered fundamental evidence for Intelligent Design—a type of fine-tuning of the rules that form the genetic code.  
 
Quality Control 
All cells have a very important and sophisticated quality control system 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 its proper biochemical operation. [6] For example, occasionally a mistake can occur in the pairing of A-adenine to T-thymine and G-guanine to C-citozine, i.e. 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 the Huntington's disease. Thus, the vital quality control systems, without which there would be a great degree of genetic degeneration and quick extinction of the species, are another proof of 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 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] 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, 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 for intelligent design. 
Thus, whenever different, non-related, complex biochemical systems and/or biomolecules with independent origins are structurally, functionally, and mechanistically identical, there is certainly an indication of a common blueprint, a molecular convergence that reflects intelligent design, rather than random natural process of creation.   
 
Strategic Redundancy 
Genetic code determines how a protein is to be constructed from 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 there is always a functional copy of a particular gene available. It was also shown that these duplicated genes that serve as a backup and are normally inactive, become active when the duplicated genes become damaged. About how elegantly this system is designed, the researchers 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 careful design. 
 
Trade-offs and Intentional Sub-optimization 
Biochemists have recently discovered trade-offs and sub-optimization in many biochemical systems, by which their overall optimal performance is achieved. How sub-optimization balances trade-offs is seen in examples like protein synthesis, 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 a well-designed device, similarly, optimization and fine-tuning within biochemical systems indicates the work of intelligent design. 
 

NOTES: 

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.