Wanna Build a Cell? A DVD Player Might Be Easier

Wanna Build a Cell? A DVD Player Might Be Easier 1

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, 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.

A camera sends a signal to a DVD recorder, which records a DVD. The DVD player reads the DVD and converts it to a TV signal. This is conceptually identical to DNA translation. The only difference is that we don’t know how the original signal—the pattern in the first DNA strand—was encoded. The first DNA strand had to contain a plan to build something, and that plan had to get there somehow. An original encoder that translates the idea of an organism into instructions to build the organism (analogous to the camera) is directly implied.

The rules of any communication system are always defined in advance by a process of deliberate choices. 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. You can’t make copies of a message without the message, and you can’t create a message without first having a language. And before that, you need intent. A code is an abstract, immaterial, nonphysical set of rules. There is no physical law that says ink on a piece of paper formed in the shape T-R-E-E should correspond to that large leafy organism in your front yard. You cannot derive the local rules of a code from the laws of physics, because hard physical laws necessarily exclude choice. On the other hand, the coder decides whether “1” means “on” or “off.” She decides whether “0” means “off” or “on.” Codes, by definition, are freely chosen. The rules of the code come before all else. These rules of any language are chosen with a goal in mind: communication, which is always driven by intent. That being said, conscious beings can evolve a simple code into a more complex code—if they can communicate in the first place. But even simple grunts and hand motions between two humans who share no language still require communication to occur. Pointing to a table and making a sound that means “table” still requires someone to recognize what your pointing finger means.

A number of special natural laws can be derived from general natural law NLI-4: 2
- NLI-4a: Every code is based on a mutual agreement between sender and receiver.
- NLI-4b: There can be no new information without an intelligent sender.
- NLI-4c: Every information transmission chain can be traced back to an intelligent sender.
- NLI-4d: The assignment of meaning to a set of symbols is a mental process requiring intelligence.

According to NLI-4, there is an intelligent originator at the beginning of every information transmission chain. If this principle is applied consistently to biological information, an intelligent originator is necessary here as well.


DNA Is a Structure That Encodes Biological Information
What do a human, a rose, and a bacterium have in common? Each of these things — along with every other organism on Earth — contains the molecular instructions for life, called deoxyribonucleic acid or DNA. Encoded within this DNA are the directions for traits as diverse as the color of a person's eyes, the scent of a rose, and the way in which bacteria infect a lung cell.
http://www.nature.com/scitable/topicpage/dna-is-a-structure-that-encodes-biological-6493050

Transmission of intra-cellular genetic information: A system proposal
The model of a transmission system of genetic information is concerned with the identification, reproduction and mathematical classification of the nucleotide sequence of single stranded DNA by the genetic encoder. Hence, a genetic encoder is devised where labelings and cyclic codes are established. The establishment of the algebraic structure of the corresponding codes alphabets, mappings, labelings, primitive polynomials (p(x)) and code generator polynomials (g(x  )) are quite important in characterizing error-correcting codes subclasses of G-linear codes.
http://www.sciencedirect.com/science/article/pii/S0022519314003233

The Information in DNA Is Decoded by Transcription
DNA is essentially a storage molecule. It contains all of the instructions a cell needs to sustain itself. These instructions are found within genes, which are sections of DNA made up of specific sequences of nucleotides. In order to be implemented, the instructions contained within genes must be expressed, or copied into a form that can be used by cells to produce the proteins needed to support life.

The instructions stored within DNA are read and processed by a cell in two steps: transcription and translation. Each of these steps is a separate biochemical process involving multiple molecules. During transcription, a portion of the cell's DNA serves as a template for creation of an RNA molecule. (RNA, or ribonucleic acid, is chemically similar to DNA, except for three main differences described later on in this concept page.) In some cases, the newly created RNA molecule is itself a finished product, and it serves an important function within the cell. In other cases, the RNA molecule carries messages from the DNA to other parts of the cell for processing. Most often, this information is used to manufacture proteins. The specific type of RNA that carries the information stored in DNA to other areas of the cell is called messenger RNA, or mRNA.
http://www.nature.com/scitable/topicpage/the-information-in-dna-is-decoded-by-6524808









1. Perry Marshall, Evolution 2.0, page 153
2. http://www.0095.info/en/

More information : The genetic code, insurmountable problem for non-intelligent origin
http://reasonandscience.heavenforum.org/t2363-the-genetic-code-unsurmountable-problem-for-non-intelligent-origin

The Touchstone of Life Molecular Information, Cell Communication, and the Foundations of Life, Werner R. Loewenstein,  page 176


To start, we will try to define the basic elements in this intercellular network in terms of information theory. That theory, specifically its branch, communication theory, specifies five stages for any communication system, regardless of its form: an information source, an encoder, a communication channel, a decoder (or receiver), and a user. The information source generates the information to be transmitted; the encoder transforms the information into a suitable message form for transmission over the communication channel; and the decoder performs the inverse operation of the encoder, or approximately so, for the user at the other end of the channel.

This elementary series may be expanded by any number of substages, depending on the complexity of the network involved. For our purposes it will be useful to add a substage after the encoder, a transmitter, for we find such a go-between in all communications beamed out of the DNA. This stage—in effect, a second encoder—converts the information in the message into yet another form and, more often than not, there are more than one transmitter reissuing information down the line. Let's call the output of such transmitters signals, for short. Given the above definitions, the equivalent stages in intercellular communication may be readily identified, though now and then we get into a jam because the biological vocabulary was largely coined before the informational logic of the communicating molecular chains was understood. However, there is no problem of terminology that a lexicon won't fix. Try this word list, for instance, for the channels of communication entailing hormones of the lipid (steroid) variety:

DNA = information source
transcription machinery = encoder
messenger RNA = message
translation machinery/ hormone synthesis/release apparatus    = transmitter
hormone = signal
DNA-headgate multiplex = decoder or receiver
DNA polymerase = user

Things get more tricky with communications entailing hormones of the protein sort. Then, there may be transmitters both in the membrane and in the cytoplasm of the target cell—a long series of retransmissions—and even more than one user, when the communication lines fork. In biology those retransmitters are collectively called receptors, though occasionally I will fall back on the communication-theory term, to remind us that they are not end stages. Communication channels with multiple transmitters are not so easily tracked down in cells. The seasoned sleuth here looks first for the user of the message—if he finds a user, he knows he has come to the end of a line. He then backtracks along the signal chain and, though he may not always strike a rich vein, at least he can hope to come up with the basic elements of the channel. Many an intercellular communication channel was bagged precisely that way.

It ensured that the cellular communication channels are normally rather free of interference from extraneous signals and electromagnetic fields. No human manufacturer of communication equipment offers such a warranty—just try out your car radio under an electric power line!

Only at much shorter wavelengths do the signal molecules become appreciably disturbed and, as we get to wavelengths of one-tenth of a micrometer or smaller, the signal molecules begin to dance on the razor's edge. However, there is only one type of particle with a wavelength of that sort to pose real danger: the photons in the ultraviolet. And these get largely filtered out by the ozone and water in the atmosphere The information transmitted through these channels is largely free of external interferences. It is as solidly bottled up as the message sent by our stranded mariner across the sea.

In plain language the second of Shannons  theorem says roughly this: if one cannot eliminate noise, a message can be transmitted without significant error and without loss of transmission rate if the message has been properly encoded at the source. This came as a surprise to everyone when the notion made its debut fifty years ago. Just think what the theorem promised: an error-free transmission in a noisy channel, without lowering the transmission rate, and all you have to do is come up with precisely the right code! It's a good thing that one cannot argue with a theorem, or else there would be quite a few skeptics. Well, the promise has since been fulfilled by scores of applications in communication engineering, and the theorem sits high in science's pantheon. As for biological communication, this theorem holds the key to the question of how the messages get through those noisy molecular channels, as will become clear in the following pages. It turns out that Lady Evolution ( really ????!! since when has evolution forsight and knowledge ?  )  knew the theorem all along, and our knowledge of it will help us unweave a little her multi-cellular organismic fabric and afford us a rare glimpse into her master strategy.

The Virtues of Redundant Small Talk
First off, let us consider the basic strategy Evolution (sic) uses to solve the noise question. ( amazing. Evolution has problem solving capacities ) The problem is how to get, by thermal teeter-totter, a molecular signal through a communication channel—how to beat the statistical odds. To do so, the cells make signal molecules in multiple copies and send one copy after another through their channels. This, as we said, is the poor man's method, a straightforward tack: where one molecule singly must surely fail, one molecule in a hundred thousand or a hundred million has a sporting chance. We see intuitively that the dispatching of more and more copies of a signal will eventually beat the odds. One actually can calculate those odds with the aid of probability theory. Although this theory had a somewhat frivolous beginning— it originally was started to get an advantage at the gambling table — it eventually acquired solid-rock foundations thanks to a set of axioms by the mathematician Kolmogoroff. This is the same set that the whole edifice of statistical mechanics in physical chemistry rests on. 

Thus, by bringing to bear probability theory on the movement of the signal molecules, we can find out whether an intercellular channel is up to snuff. All we need to know is the channel space (the signal dilution volume) and the average net velocity of the signal molecules (which, over the short range, is given by the molecules' diffusion rates in the lipid bilayer or in the cytoplasm and, over the long range, by their convection rates in the blood and other body liquids). Indeed, the answer turns out to be positive in all cases tested so far; the number of molecular copies is enough to virtually ensure a signal throughput. A rather modest number of signal copies goes a long way because the probability of a throughput failure decreases exponentially with the number of copies. Here is how this works: assume that the individual signal molecule in a channel has the chance of one in a thousand to get through; then, the chance that a thousand copies would be lost altogether is 1/e, about 0.37; with ten thousand copies that chance falls to about 5 x 10"5 and with one hundred thousand copies it dwindles to 4 x 10"44.

There is no simpler formula for defeating communication noise than that copy method; the recurrency of the same information, the redundancy, decreases the probability of transmission error. It is the same formula we use when we try to communicate with someone across a noisy street or send an SOS from the middle of the ocean. But why did cells turn to such an artless method? There is nothing sophisticated about redundancy, for sure. The answer can be given in four words: beggars can't be choosers. It was all that cells could afford at the start of their information endeavor. Later on when they began to cooperate, it is true, they had amassed considerable information capital and had mastered the art of extracting signals out of extrinsic signal noise. But their original (internal) communication scheme goes back to the dawn of the Cell Age when the luxury of processing out random noise was unaffordable. So, throughout the ages they stuck to their basic guns—they modified and recombined old information and produced signals in large editions. To copy or change information costs a lot less than to create new information, and copying one's own is no crime in Evolution's bailiwick. However, there is a penance for being so uninventive: delay—it takes then a good while to get a message across. Although the tautology decreases the transmission errors in a channel, the transmission rate decreases too. Thus, the messages have to be kept short if one wants to say something in a reasonable time. Redundancy obviously is not practical for long speeches, but it is OK for short utterances. And this is precisely what cells go in for. They keep the communiques between them to the bare bones and save their long speeches, the transmission of the lengthy strings of DNA and RNA information, for their internal business transactions. Indeed, compared to the large hunks of information we have seen circulating inside the cells, the information flowing between them isn't much— intercellular communication is small talk, we might say.

Accurate Information Transmission Through Dynamic Biochemical Signaling Networks 1

How signaling networks perform their core functions in the presence of noise is a fundamental question.

Signaling Networks: The Origins of Cellular Multitasking 2

One characteristic common to all organisms is the dynamic ability to coordinate constantly one's activities with environmental changes. The function of communicating with the environment is achieved through a number of pathways that receive and process signals, not only from the external environment but also from different regions within the cell. Individual pathways transmit signals along linear tracts resulting in regulation of discrete cell functions. This type of information transfer is an important part of the cellular repertoire of regulatory mechanisms. However, as increasingly larger numbers of cell signaling components and pathways are being identified and studied, it has become apparent that these linear pathways are not free-standing entities but parts of larger networks. Several articles in this review series describe in exquisite detail how individual classes of signaling pathways are organized and function. As we understand the details of such functional organization and move to the next level of analyzing integrated cellular functions, it will become increasingly important to identify and study the properties and capabilities of signaling networks as a whole.

One of the more surprising revelations that is coming from the initial studies of networks and component interactions in different cell types is that there may be a general signaling network that receives signals from cell type–specific inputs (i.e., receptors) and engage cell type–specific machinery. The molecular identity of the signaling components and their interacting partners may be cell type–specific, but the overall function of these components and the logic of the circuitry is preserved from cell type to cell type. We will compare two cell types, T cells (Dustin and Chan, 2000 [this issue of Cell]) and the postsynaptic region of glutamatergic synapses, to develop this argument. Signaling networks are likely to have a variety of emergent properties and capabilities. We will describe some of our current insights into how signaling networks are organized and how this dynamic spatial organization can lead to higher order cellular capabilities. As an example of such capabilities, we further develop the concept that the ability of a cell to regulate spatially resolved multiple functions in a coordinated manner arises from the organization of signaling pathways into networks.



1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813785/
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619409/

All cellular functions are irreducibly complex

http://reasonandscience.heavenforum.org/t2179-the-cell-is-a-interdependent-irreducible-complex-system

The problem of information

It has to be explained:

- The origin of the complex, codified, specified, instructional information stored in the genome and epigenetic codes to make the first living organism
- The origin of the genetic Code
- How it got nearly optimal for allowing additional information within protein-coding sequences
- How it got more robust than 1 million alternative possible codes
- The origin of the over a dozen epigenetic codes
- The origin of the information transmission system, that is the origin of the genetic code itself, encoding, transmission, decoding and translation
- The origin of the genetic cipher/translation, from digital ( DNA / mRNA ) to analog ( Protein )
- The origin of the hardware, that is DNA, RNA, amino acids, and carbohydrates for fuel generation
- The origin of the replication/duplication of the DNA
- The origin of the signal recognition particle
- The origin of the tubulin Code for correct direction to the final destination of proteins

none of the above items can be explained by evolution since evolution depends on all this.