Defending the Christian Worlview, Creationism, and Intelligent Design
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Defending the Christian Worlview, Creationism, and Intelligent Design

This is my personal virtual library, where i collect information, which leads in my view to the Christian faith, creationism, and Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity


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Defending the Christian Worlview, Creationism, and Intelligent Design » Intelligent Design » Information Theory, Coded Information in the cell » How does programming in biology point to God?

How does programming in biology point to God?

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Otangelo


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How does programming in biology point to God?

https://reasonandscience.catsboard.com/t3083-how-does-programming-in-biology-point-to-god

Maybe you are a layperson, and are curious to understand a bit better what the "Central Dogma of molecular biology" is -  but have a difficult grasp to understand what it is all about. I like to use analogies from real life to make things more clear.

Let's suppose you invent a recipe to make a Gourmet Hamburger and write the recipe on a Word document, and save it on the hard disc of your computer.  You have a Japanese friend and only communicate with him using the Google translation program. (He only speaks Japanese). Now he wants to try out your Gourmet Hamburger  and asks you to send him the recipe a copy per email. So you write an email, annex the Word document, and send it to him. When he receives it, he will use Google Translate and get the recipe in Japanese, written in kanji, in logographic Japanese characters which he understands. With the information at hand, he can make the Gourmet Hamburger exactly as described in the recipe. In order for that communication to happen, you use at your end 26 letters from the alphabet, syntax,  semantics, and pragmatics, to write the receipt, and your friend has 2,136 kanji characters that permit him to understand the receipt in Japanese. Google Translate does the translation work.  
Now he can make the Gourmet Hamburger at his end.

To perform the job it is rather effortless, when we have the ability to cook, invent a fine recipe, and have a basic grasp to use a computer. Now lets think a bit more about the complexity to have this job done. What has to be invented from scratch for your Japanese friend to be able to make the Gourmet Hamburger ?

1. A language (English) and an alphabet, using syntax, grammar, and semantics
2. A second language (Japanese), and Kanji 
3. Computer with a hard disc.
4. The recipe to make Gourmet Hamburger and store the Word document with the recipe on the hard disc of the PC.
5. Another computer as backup system (otherwise the PC can break, and the information is lost)
6. An e-mail service and using it to create an e-mail, and annex a copy of the Word document with the recipe
7. Sending the Word document with the recipe to your friend
8. Inventing the Google Translate software program, and program it to translate from English to Japanese
9. Using the computer at the receivers end to get the email with the Word document
10. Using Google Translate to generate the translation
11. Taking the recipe in Japanese and make the Gourmet Hamburger

Now think about the complexity to have this job done. Inventing languages, algorithms, and programs, a recipe, store, send, translate and receive information, are all actions performed by intelligence.  Nobody in its sane mind would ascribe all these things to the action of random chance, right? So any logical person would agree with me, that all these tasks are ALWAYS performed by intelligence, right? I mean, just think about how long humanity took to invent computers, the internet, Google Translate, and implement it....

Okay, now lets see how that works in the cell. 
In the cell, it is essential to make proteins, which are molecular machines, veritable working horses. The recipe to make them (equivalent to the recipe of the Gourmet Hamburger) is written and stored in genes through DNA, which are extremely long chains of molecules that contain all the information necessary for the life functions of a cell. The individual molecules that make up DNA are called nucleotides. In order to get proteins, a similar process has to occur inside the cell, as with the recipe for your Japanese friend to be able to make the Gourmet Hamburger. While the recipe is written on a Word document saved on your computer, in the cell, the recipe (instructions or master plan) for the construction of proteins, is stored in the genome. It has to be sent to the Ribosome, the factory that makes proteins, which does the translation (remember your friend, using Google Translate at his end). While your Japanese friend, once he receives the message in Japanese, in Kanji, still has work to do, namely to follow the instructions to make the Gourmet Hamburger, the Ribosome does both jobs, translation of the information AND making proteins, the final product, all in one step. Smart, that!! The very translation also will produce the desired end product.

While you use the 26 letters of the alphabet to write your recipe, the Cell uses DNA, 4 nucleotide "letters". They are four different organic bases, which are adenine (A), guanine (G), cytosine (C) and thymine (T), 
and while your Japanese friend uses kanji at his end, the cell uses the amino acid alphabet, consisting of 20 amino acids to get the message in translated form. 

The way by which DNA stores the genetic information consists of triplet codons equivalent to words, consisting of a sequence of three DNA nucleotides. These triplets form "words". While you used words to write sentences to write the Gourmet Hamburger recipe, the cell uses codon "words" to write sentences which are called genes. With four possible nucleobase "letters", A,G,C,T,  the triple-nucleotide "words" can give 4^3  (4x4x4=64 possible words which can be made up from these 4 letters) = 64 different possible "words" (tri-nucleotide sequences). That's the entire genetic language, consisting in 64 words.  In the standard genetic code, three of these 64 codons (UAA, UAG, and UGA) are stop codons. That is like punctuation marks in the alphabet. It instructs when a sentence ends.

There has to be a mechanism to extract the information in the genome, and send it to the ribosome, which is at another place in the cell, often free-floating in the cytoplasm. The message contained in the genome is transcribed by a very complex molecular machine, called RNA polymerase. (That's like making a copy of the recipe and annex it in the email) It makes a transcript, a copy of the message in the genome, and that transcript is sent to the Ribosome. (The email with the recipe arrives at your Japanese friend's end) That transcript is called messenger RNA or typically mRNA. Once the messenger RNA arrives at the Ribosome, translation can begin (the Ribosome does what Google Translate does)

In communications and information processing, code is a system of rules to convert information—such as assigning the meaning of a letter, word, into another form, (as another word, letter, etc.) In translation, 64 genetic codons or "words" are assigned to 20 amino acids. (equivalent to the kanji characters)  It refers to the assignment of the codons to the amino acids, thus being the cornerstone template underling the translation process. Assignment means designating, ascribing, corresponding, correlating.

The Ribosome does basically what Google Translate does. But while Google Translate just gives the recipe in another language, and your Japanese friend still has to make the Gourmet Hamburger,  the Ribosome actually makes in one step the end product, which are proteins. That translation process is staggeringly complex.

Now lets list the components required that have to exist in order for the cell to be able to make proteins, starting from the recipe stored in the genome:

1. An alphabet, letters, (A), guanine (G), cytosine (C) and thymine (T), and 64 codon "words", a language, syntax, grammar, and semantics
2. The second language  (setting up the amino acid alphabet consisting of 20 amino acids)
3. The medium to store the message (DNA, polymer strands, genes, the genome)
4. The recipe (instructional complex prescribed  information to make proteins) stored it in DNA.
5. The machinery to duplicate the information to have life going and multiplying (DNA replication, we know only of that mechanism generating heredity)
6. The machine to extract and transcribe  the message (RNA polymerase)
7. The medium to send the message (transcribed messenger RNA)
8. The translation code/cipher (genetic code) from mRNA to amino acids
9. The machine/factory that performs the translation (the ribosome)
10. Programming of the machine to know both languages, to make the translation (making the adapter molecules, tRNA, and aminoacyl tRNA synthetases which recognize which amino acid to charge and add to the nascent polypeptide chain)
11. Now the translation can be performed (which produces the proteins)

1. D
2. D → A & B & C
3. A & B & C → requires Intelligence
4. Therefore Intelligence

A: Information, Biosemiotics (instructional complex mRNA codon sequences transcribed from DNA)
B: Translation mechanism (adapter, key, or process of some kind to exist prior to translation = ribosome)
C: Genetic Code
D: Functional proteins

1. Life depends on proteins (molecular machines) (D). Their function depends on the correct arrangement of a specified complex sequence of amino acids.
2. That depends on the translation of genetic information (A) through the ribosome (B) and the genetic code (C), which assigns 61 codons and 3 stop codons to 20 amino acids
3. Instructional complex Information (Biosemiotics: Semantics, Syntax, and pragmatics (A)) is only generated by intelligent beings with foresight. Only intelligence with foresight can conceptualize and instantiate complex machines with specific purposes, like translation using adapter keys (ribosome, tRNA, aminoacyl tRNA synthetases (B)) All codes require arbitrary values being assigned and determined by agency to represent something else (genetic code (C)). 
4. Therefore, Proteins being the product of semiotics/algorithmic information including translation through the genetic code, and the manufacturing system (information directing manufacturing) are most probably the product of a divine intelligent designer.

The problem of translation through the Ribosome is threefold:

1. The origin of Information stored in the genome.
1. Semiotic functional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process.
2. This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic code is like suggesting that a rainbow can write poetry... it is never going to happen!  Physics and chemistry alone do not possess the tools to create a concept. The only cause capable of creating conceptual semiotic information is a conscious intelligent mind.
3. Since life depends on vast quantity of semiotic information, life is no accident, and provides powerful positive evidence that we have been designed. A scientist working at the cutting edge of our understanding of the programming information in biology, he described what he saw as an “alien technology written by an engineer a million times smarter than us”

2. The origin of the adapter, key, or process of some kind to exist prior to translation = ribosome
1. Ribosomes have the purpose to translate genetic information into proteins. According to Craig Venter, the ribosome is “an incredibly beautiful complex entity” which requires a minimum of 53 proteins. It is nothing if not an editorial perfectionist…the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products…  They are molecular factories with complex machine-like operations. They carefully sense, transfer, and process, continually exchange and integrate information during the various steps of translation, within itself at a molecular scale, and amazingly, even make decisions. They communicate in a coordinated manner, and information is integrated and processed to enable an optimized ribosome activity. Strikingly, many of the ribosome functional properties go far beyond the skills of a simple mechanical machine. They can halt the translation process on the fly, and coordinate extremely complex movements. The whole system incorporates 11 ingenious error check and repair mechanisms, to guarantee faithful and accurate translation, which is life-essential.
2. For the assembly of this protein making factory, consisting of multiple parts, the following is required: genetic information to produce the ribosome assembly proteins, chaperones, all ribosome subunits and assembly cofactors. a full set of tRNA's, a full set of aminoacyl tRNA synthetases, the signal recognition particle, elongation factors, mRNA, etc. The individual parts must be available,  precisely fit together, and assembly must be coordinated. A ribosome cannot perform its function unless all subparts are fully set up and interlocked.
3. The making of a translation machine makes only sense if there is a source code, and information to be translated. Eugene Koonin: Breaking the evolution of the translation system into incremental steps, each associated with a biologically plausible selective advantage is extremely difficult even within a speculative scheme let alone experimentally. Speaking of ribosomes, they are so well-structured that when broken down into their component parts by chemical catalysts (into long molecular fragments and more than fifty different proteins) they reform into a functioning ribosome as soon as the divisive chemical forces have been removed, independent of any enzymes or assembly machinery – and carry on working.  Design some machinery which behaves like this and I personally will build a temple to your name! Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. The origin of the ribosome is better explained through a brilliant intelligent and powerful designer, rather than mindless natural processes by chance, or/and evolution since we observe all the time minds capabilities producing machines and factories.

3. The origin of the genetic code
1. A code is a system of rules where a symbol, letters, words, etc. are assigned to something else. Transmitting information, for example, can be done through the translation of the symbols of the alphabetic letters, to symbols of kanji, logographic characters used in Japan.  In cells,  the genetic code is the assignment ( a cipher) of 64 triplet codons to 20 amino acids.
2. Assigning meaning of characters through a code system, where symbols of one language are assigned to symbols of another language that mean the same, requires a common agreement of meaning. The assignment of triplet codons (triplet nucleotides) to amino acids must be pre-established by a mind.
3. Therefore, the origin of the genetic code is best explained by an intelligent designer.

How does programming in biology point to God?  Inform11

https://reasonandscience.catsboard.com

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