The central dogma of intelligent design

The central dogma of intelligent design

https://reasonandscience.catsboard.com/t2714-the-central-dogma-of-intelligent-design

The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It is often stated as "DNA makes RNA and RNA make protein.


See how following six biological production workflows which are called the central dogma, are analogous to man-made manufacturing processes, outlined afterwards:

1. applies to the genetic code, which equals a computer code
2. applies to DNA which is an information storage system
3. applies to the gene regulatory network, which activates and selects the information in the DNA library at the right location, at the right time, to be expressed
4. applies to the information stored in DNA and epigenetic codes to make Cells, which are factories, that make as products, copies of themselves in small variations. 
5. applies to transcription, where DNA is transcribed by RNA polymerase enzyme complexes into messenger RNA, and then transmitted to the Ribosome to be translated.
6. applies to ribosomes which translate the digital information stored in DNA, and transmitted by messenger RNA, into proteins, which are the analogue tridimensional form of proteins


Let us suppose that the headquarters of a company is located in the u.s., where products are invented by a team of engineers, projected and developed to their maturity. A prototype is made, tested to its satisfaction, and ready for serial production.  The companies industrial manufacturing park constituted of various interconnected factories, full of machines, and production lines will be raised and build in China. Before the products can be manufactured, the factory has to be built at the right, strategic location, with ease to get the materials delivered, easy to find employees, and ease to export the products to its final destinations. So the engineers of various faculties need to know how to establish the following production flow which is essential in order to make everything work:
  

1. The establishment of a language based on codes and signs, and a common agreement of meaning,  but also a common agreement of signs for designing the engineering plans and drawings. The information of the blueprints and instruction manuals is codified, complex, and instructional.

2. Further, a storage medium of the information to make the factory and its products is needed. Traditionally, it was paper and pen. Today, computers and software programs like Autocad, and a hardrive to store the information.

3. The information specialists ( computer programmers etc. ) will need to develop a library and storage system, and tag each blueprint, so they know where to find it when needed. The engineers will send during the time period along the factory building the needed blueprints in a sequential manner. They know how to find the right plans in the library, select them, and send them to Chinese colleagues.

4. The engineers will have to decide and come to an agreement what they want to make, and how ( cars, machines, toys etc. ), the products precise size, parts, materials, and how the final product has to work and function. And use the language, to draw the blueprints and produce the descriptive information, designs with memorial etc. 

The production facility must be conceptualized to produce the intended product. A factory that makes toys cannot be employed to make cars. The product must be described in all details, and how to be assembled, once the subparts have been made. The materials of the products employed must be described and informed:  how and where to find the right ones, how to import them into the factory, how to reject materials that are inappropriate to be imported, how to transform them into useful form, ( material purity, density, colors, size, form etc. ) and, once the product has been processed and made, it is ready, pack and tag it, to be shipped to its final destination.
 
They need also to establish and instruct how to construct the factory facility, its buildings -where to find the right materials of the factory building, how to bring them to the construction site, process them ( bricks need to be made in its right shape, and the right materials ) and build the factory, establish the factory  size, wall size, height, dimensions, compartments, localization, etc. The same applies to all the machines, their energy supply - they need to inform how to produce the energy , store, retrieve, to fuel the machines and fuel all the processes of the factory, where  first to get the materials that will be used as fuel, where to dispose the waste material, and recycle facilities; production rate and quality control, etc. Manuals to fix the machines if something drives havoc, and skilled people that can perform the repairs when needed.  Inform where to get the raw materials to make the  machines for production, how to transport them and where to place them, and correctly interconnect them, retrieval facility of the stored raw materials when required in its right quantity, where to conduct them to be processed, and once the factory machine is ready, and construct everything in order for the facilities to be ready to start production. Many factories also produce machines that are delivered to the assembly factories, where they are united and interconnected into assembly lines. All this must be informed in detailed manner and requires huge quantities of specified complex information. 

5. A mechanism of transmission of the information from the u.s. to China is required. Traditionally the plans drawings and instruction manuals were sent by post, FedEx and so on, but today, we have modern communication channels, like the world wide web. That is, extracting the blueprints, drawings and plans, from the HD, annex it to an email, send it, and the receiver will be able to save the received information from the email on his computer hard drive, use translation programs which translate the message into Chinese, and he eventually prints the blueprint out, and hands it over to the employees. First to those, which are trained to make and build the factories etc. and afterwards, to the workers in the factories, that will actually manufacture the products.

6. Since the drawings, blueprints and designs are made in English, and the workers are Chinese, that construct the factory, and the products, afterwards, a translation program has to be made which translates the plans from english to Chinese so they can understand the instructions. The rules of any communication system are always defined in advance by a process of deliberate choices without physical constraints. There must be prearranged agreement between sender and receiver, otherwise, communication is impossible. By definition, a communication system cannot evolve from something simpler because evolution itself requires communication to exist first.
 
In both cases, all depends essentially on foresight and intelligence and establishing teleological goals. For this reason, I call above analogy the central dogma of intelligent design.

1. High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design.
2. Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.
4. Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems.

The interdependent and irreducible structures required to make proteins
https://reasonandscience.catsboard.com/t2039-the-interdependent-and-irreducible-structures-required-to-make-proteins4.

To make proteins, and direct and insert them to the right place where they are needed, at least 25 unimaginably complex biosyntheses and production-line like manufacturing steps are required. Each step requires extremely complex molecular machines composed of numerous subunits and co-factors, which require the very own processing procedure described below, which makes its origin an irreducible  catch22 problem.

Wanna Build a Cell? A DVD Player Might Be Easier
https://reasonandscience.catsboard.com/t2404-wanna-build-a-cell-a-dvd-player-might-be-easier

Wanna Build a Cell? A DVD Player Might Be Easier Imagine that you’re building the world’s first DVD player. What must you have before you can turn it on and watch a movie for the first time?

A DVD. How do you get a DVD? You need a DVD recorder first. How do you make a DVD recorder? First, you have to define the language. When Russell Kirsch (who we met in chapter Cool created the world’s first digital image, he had to define a language for images first. Likewise, you have to define the language that gets written on the DVD, then build hardware that speaks that language. Language must be defined first. Our DVD recorder/player problem is an encoding-decoding problem, just like the information in DNA. You’ll recall that communication, by definition, requires four things to exist:

1. A code
2. An encoder that obeys the rules of a code
3. A message that obeys the rules of the code
4. A decoder that obeys the rules of the code

These four things—language, the transmitter of language, message, and receiver of language—all have to be precisely defined in advance before any form of communication can be possible at all.

The central dogma of intelligent design

The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It is often stated as "DNA makes RNA and RNA makes protein.

See how following six biological production workflows which are called the central dogma, are analogous to manmade manufacturing processes, outlined afterwards:

1. applies to the genetic code, which equals to a computer code
2. applies to dna which is a information storage system
3. applies to the gene regulatory network, which activates and selects the information in the DNA library at the right location, at the right time, to be expressed
4. applies to the information stored in DNA and epigenetic codes to make Cells, which are factories, that make as products, copies of themselves in small variations.
5. applies to transcription, where DNA is transcribed by RNA polymerase enzyme complexes into messenger RNA, and then transmitted to the Ribosome to be translated.
6. applies to ribosomes which translate the digital information stored in DNA, and transmitted by messenger RNA, into proteins, which are the analog tridimentional form of proteins


Let us suppose that the headquarters of a company is located in the u.s., where products are invented by a team of engineers, projected and developed to their maturity. A prototype is made, tested to its satisfaction, and ready for serial production.  The companies industrial manufacturing park, constituted of various interconnected factories, full of machines, and production lines, will be raised and build in China. Before the products can be manufactured, the factory has to be built at the right, strategic location, with ease to get the materials delivered,easy to find employees, and ease to export the products to its final destinations. So the engineers of various faculties need to know how to establish following production flow which is essential in order to make everything work:
 

1. The establishment of a language based on codes and signs, and a common agreement of meaning,  but also a common agreement of signs for designing the engineering plans and drawings. The information of the blueprints and instruction manuals is codified, complex, and instructional.

2. Further, a storage medium of the information to make the factory and its products is needed. Traditionally, it was paper and pen. Today,  a computer hardrive to store the information.

3. The information specialists ( computer programmers etc. ) will need to develop a library and storage system, and tag each blueprint, so they know where to find it, when needed. The engineers will send during the time period along the factory building or product manufacturing  the needed blueprints in a sequential manner. They know how to find the right plans in the library, select them, and send them to the Chinese colleagues.

4. The engineers will have to decide and come to an agreement what they want to make, and how ( cars, machines, toys etc. ), the products precise size, parts, materials, and how the final product has to work and function. And use the language, to draw the blueprints and produce the descriptive information, designs with memorial etc.

The production facility must be conceptualized to produce the intended product. A factory that makes toys cannot be employed to make cars. The product must be described in all details, and how to be assembled, once the subparts have been made. The materials of the products employed must be described and informed:  how and where to find the right ones, how to import them into the factory, how to reject materials that are inappropriate to be imported, how to transform them into useful form, ( material purity, density, colors, size, form etc. ) and, once the product has been processed and made, it is ready, pack and tag it, to be shipped to its final destination.

They need also to establish and instruct how to construct the factory facility, its buildings -where to find the right materials of the factory building, how to bring them to the construction site, process them ( bricks need to be made in its right shape, and the right materials ) and build the factory, establish the factory  size, wall size, height, dimensions, compartments, localization, etc. The same applies to all the machines, their energy supply - they need to inform how to produce the energy , store, retrieve, to fuel the machines and fuel all the processes of the factory, where  first to get the materials that will be used as fuel, where to dispose the waste material, and recycle facilities; production rate and quality control, etc. Manuals to fix the machines if something drives havoc, and skilled people that can perform the repairs when needed.  Inform where to get the raw materials to make the  machines for production, how to transport them and where to place them, and correctly interconnect them, retrieval facility of the stored raw materials when required in its right quantity, where to conduct them to be processed, and once the factory machine is ready, and construct everything in order for the facilities to be ready to start production. Many factories also produce the machines that are delivered to the assembly factories, where they are united and interconnected into assembly lines. All this must be informed in detailled manner and requires huge quantities of specified complex information.

5. A mechanism of transmission of the information from the u.s. to china is required. Traditionally the plans drawings and instruction manuals were sent by post, fedex and so on, but today, we have modern communication channels, like the world wide web. That is, extracting the blueprints , drawings and plans, from the HD, annex it to an email, send it, and the receiver will be able to save the received information from the email on his computer hard drive, use translation programs which translate the message into chinese, and he eventually prints the blueprint out, and hands it over to the employees. First to those, which are trained to make and build the factories etc. and afterwards, to the workers in the factories, that will actually manufacture the products.

6. Since the drawings, blueprints and designs are made in english, and the workers are chinese, that construct the factory, and the products, afterwards, a translation program has to be made which translates the plans from english to chinese so they can understand the instructions. The rules of any communication system are always defined in advance by a process of deliberate choices without physical constraints. There must be prearranged agreement between sender and receiver, otherwise communication is impossible. By definition, a communication system cannot evolve from something simpler because evolution itself requires communication to exist first.

In both cases, all depends essentially on forsight and intelligence, and establishing teleological goals. For this reason, i call above analogy the central dogma of intelligent design. To make proteins, and direct and insert them to the right place where they are needed, at least 25 unimaginably complex biosyntheses and production-line like manufacturing steps are required. Each step requires extremely complex molecular machines composed of numerous subunits and co-factors. DNA and RNA is required to make proteins. But proteins are required to make DNA and RNA, which makes its origin an irreducible catch22 problem.

1. High information content (or specified - instructional complexity) and irreducible complexity and systems interdependence constitute strong indicators or hallmarks of (past) intelligent design.
2. Biological systems have a high information content (or specified - instructional complexity) and utilize subsystems that manifest irreducible complexity.
3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.
4. Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems.

Although it is obvious that different species will have different ways of doing things, there are complex functions that are shared. These provide the foundation for most biological systems; e.g. the flow of information from DNA to RNA to protein is the paradigm utilized in virtually all species. From an engineering perspective, there are a number of complex functions of cellular machines (e.g. DNA replication, mRNA translation into protein) that are essentially the same throughout the biological kingdom. These complex functions often depend upon mechanisms that are observed across species, even though some of the protein components involved in these mechanisms might be different.

Mitch Leslie Origin and Evolution of the Ribosome 2010 Sep;
The modern ribosome was largely formed at the time of the last common ancestor, LUCA. Hence its earliest origins likely lie in the RNA world. The PTC peptide transferase center and tRNAs clearly existed before LUCA.

Introduction: What Is DNA?
What however is ignored or rarely considered is the fact that the first self-replicating cell already required to have a minimal amount of information stored in a minimal set of genes to make a minimal set of proteins. In fact, no life form without DNA is known

The ribosome is a basic machine that has been optimized in bacteria to function under a wide variety of conditions. Humans and other mammals have similar ribosomes, but some components are adapted to a mammalian environment and respond to different control mechanisms. However, improvements to the basic machine of the ribosome can potentially be transferred to human ribosomes, such as heat tolerance. This is again analogous to the car industry. Different manufacturers have produced cars with different designs, but the basic mechanisms that allow cars to accelerate, brake, and turn are essentially the same, albeit with different parts. 

As functions or mechanisms are shared, we can look at the steps involved in a given function in a single cell type to understand how molecular components would interact to produce similar quantifiable functions in other cells. These shared functions are described, in this text, as “functional modules” which we define as a minimal set of molecular components working together to yield a measurable activity or a function. 

Many complex functions are the result of multiple tasks that need to be completed in sequence or in neighboring regions of a cell. These functions culminate in emergent properties, i.e. when multiple functional modules are coordinated to perform a multistep task. Without the proper coordination of the functional modules, the complex function cannot be completed.

An emergent property is the outcome of many steps and many modules in a complex function. Cells are highly engineered robust machines.




https://www.nature.com/scitable/topicpage/introduction-what-is-dna-6579978/#:~:text=Deoxyribonucleic%20acid%2C%20more%20commonly%20known,have%20DNA%20within%20their%20cells.&text=In%20other%20words%2C%20whenever%20organisms,passed%20along%20to%20their%20offspring.