Machines that make machines?

[Techne]

An interesting article authored by Antoine Danchin from the Pasteur Institut was recently published and is sure to bring forth much discussion.

Bacteria as computers making computers
The abstract:

Various efforts to integrate biological knowledge into networks of interactions have produced a lively microbial systems biology. Putting molecular biology and computer sciences in perspective, we review another trend in systems biology, in which recursivity and information replace the usual concepts of differential equations, feedback and feedforward loops and the like. Noting that the processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers. However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge. Microbial genomes are organized into a paleome (the name emphasizes the role of the corresponding functions from the time of the origin of life), comprising a constructor and a replicator, and a cenome (emphasizing community-relevant genes), made up of genes that permit life in a particular context. The cell duplication process supposes rejuvenation of the machine and replication of the program. The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments.

The quantum teleportation experiments have demonstrated that information can be viewed as a fundamental irreducible property of physics (informationalism). Information in the sense that energy supervenes on information. Energy is understood to be the ultimate foundation of all matter in this universe. From Einstein's equation, E=mc^2, all matter was ultimately created out of energy, and is theoretically reducible to energy. From there it can also be derived that time comes to complete stop at the speed of light. In addition, the first law of thermodynamics states that energy cannot be created or destroyed. The quantum teleportation experiments showed the entire information content (properties) of one photon can be teleported instantaneously onto another photon whereby the second photon assumes the complete identity of the first photon, while the first photon loses its complete identity. So from there, energy can be viewed to supervene on information, and information can be viewed as a fundamental category of Nature.

Systems biology is moving in that same direction, as viewing cells as computers with machinery and software makes it possible to view information as a fundamental category of nature and all future developments of systems biology can include this concept when looking at cells.

There are many interesting passages in this article. A few of these are going to be highlighted for discussion.
From the article:

Historically, systems biology follows on from molecular biology, a science based on many concepts more closely linked to arithmetic and computation than to classical physics or chemistry. Molecular biology relies heavily on concepts such as ‘control’, ‘coding’ or ‘information’, which are at the heart of arithmetic and computation. To accept the cell as a computer conjecture first requires an exploration of the concept of information, in relation to the concept of genetic program.

Cellular processes are exquisitely controlled and carried out by remarkable biomolecular machines. The software needed to coordinate these processes is located in a fairly optimal genetic code that is optimized for evolution and maintains its own functional integrity.

From the article:

The Austrian mathematician Kurt Godel showed that arithmetic (the science of whole numbers) can make statements about itself. To substantiate this remarkable claim, which implies that just manipulating whole numbers with the rules of arithmetic can generate novel information, G¨odel used a simple trick. He coded the words used in Number Theory as integers (e.g. four, which is quatre in French, vier in German and tessera in Greek, can be coded by 4) and used the corresponding code to translate propositions of arithmetic. This generated a large whole number, which could be manipulated by the rules of arithmetic, and after a sequence of operations, this manipulation generated another whole number. The latter could be decoded using the initial code. Godel’s trick was to drive the sequence of operations modifying the initial statement, to lead to a very particular conclusion. When decoded, the manipulated sequence translated into a particular proposition, which, briefly, stated: ‘I am impossible to prove’. In other words, arithmetic is incomplete, i.e. some propositions of arithmetic can be understood as valid; yet they cannot be proven within the frame of arithmetic. But this ‘incompleteness’ can also be seen as a positive feature; it is what allows the creation of new information – in Godel’s case, the statement of a fact of which the world was previously unaware. In his book, Hofstadter showed that the genetic code, which enables the world of nucleic acids to be translated into the world of proteins, which in turn manipulate nucleic acids, behaves exactly as Godel’s code does. This implies that manipulating strings of symbols, via a process that uses a code, can generate novel information. Of course, in the case of nucleic acids and proteins, there is no Godel to drive the process, and no need for one: while Godel knew what he was aiming at, living systems will accumulate information through recursivity, without any design being required. We only perceive a design because the end result is familiar to us, and thus seems more ‘right’ than any other possible result. But what we commonly term the ‘genetic program’ because it unfolds through time in a consistent manner is not a programme with an aim – it is merely there, and functions because it cannot do otherwise.

Why can't the function of the program be to actively manipulate information as a means to an end… self-replication and preservation. Later in the article something similar to this is actually suggested:

From the article:

The reluctance of investigators to regard information as an authentic category of Nature suggests that, at this point in the present review of the literature, it may still be difficult for the reader to accept that a cell could behave as a computer. Indeed, what would the role of computation be in the process of evolution? We have already provided some elements of the answer to the question: Turing showed that the consequence of the process of computation along the lines he outlined is that his machine would be able to perform any conceivable operation of logic or computation by reading and writing on a data/program tape. Stated otherwise, and in a way that is easier to relate to biology, the machine manipulates information and, because arithmetic is incomplete [as illustrated in the introduction above (Hofstadter, 1979)], it is able to create information. The machine is therefore in essence unpredictable (Turing, 1936–1937), but not in a random way – quite the contrary, in a very interesting way, as lack of prediction is not due to lack of determinism, but due to a creative action that results in novel information. If the image is correct, then it shows that living organisms are those material systems that are able to manipulate information so as to produce unexpected solutions that enable them to survive in an unpredictable future (Danchin, 2003, 2008a).

There we go, organisms can be viewed as entities that are able to manipulate information as a means to an end. Why would it be difficult to accept that cells to behave like computers? Yet, cells are capable of more than computers, e.g. self-replication and autonomous manipulation of information.

The article continues to discuss at length the parallels between our own created information processing systems (computers) and molecular processes fundamental to life. With more and more information being gathered on cellular mechanisms, cells can be seen as computers (machines expressing various programs), that are not only able to govern cellular processes needed to sustain the software, but also contains the necessary software and machinery to reproduce the computing machine while replicating its program.

 

[Techne]

In order to demonstrate the validity of viewing cells as computers that are able to manipulate information, consider the following finding.

The Ribosome: Perfectionist Protein-maker Trashes Errors

ScienceDaily (Jan. 9, 2009) — The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist.

It turns out, the Johns Hopkins researchers say, that the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products which, as workhorses of the cell, carry out the very business of life.

"What we now know is that in the event of miscoding, the ribosome cuts the bond and aborts the protein-in-progress, end of story," says Rachel Green, a Howard Hughes Medical Institute investigator and professor of molecular biology and genetics in the Johns Hopkins University School of Medicine. "There's no second chance." Previously, Green says, molecular biologists thought the ribosome tightly managed its actions only prior to the actual incorporation of the next building block by being super-selective about which chemical ingredients it allows to enter the process.

Because a protein's chemical "shape" dictates its function, mistakes in translating assembly codes can be toxic to cells, resulting in the misfolding of proteins often associated with neurodegenerative conditions. Working with bacterial ribosomes, Green and her team watched them react to lab-induced chemical errors and were surprised to see that the protein-manufacturing process didn't proceed as usual, getting past the error and continuing its "walk" along the DNA's protein-encoding genetic messages.

"We thought that once the mistake was made, it would have just gone on to make the next bond and the next," Green says. "But instead, we noticed that one mistake on the ribosomal assembly line begets another, and it's this compounding of errors that leads to the partially finished protein being tossed into the cellular trash," she adds.

So what is being monitored by the ribosome? Information. Material representations (amino acid sequence vs DNA sequence) of information. But, it does not only monitor it, it manipulates it as a means to an end... fidelity.

To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis.

"These are not subtle numbers," she says, noting that there's a clear biological cost for this ribosomal editing and jettisoning of errors, but a necessary expense.

"The cell is a wasteful system in that it makes something and then says, forget it, throw it out," Green concedes. "But it's evidently worth the waste to increase fidelity. There are places in life where fidelity matters."

The ribosome is optimized to manipulate information for fidelity.

 

[Bishadi]

what a great thread!

on observation;

perhaps the differences to observe between a quantum frame and 'computer' or electrical model is the capacity of variable

the current binary, analog (on and off) model of chemical reductions, offers little method of defining the state of interacting operators of the various wavelengths of potential upon the variety of interrelating structures.

such as when one catalyst creates a change, that energy released can become the catalyst of the next, then to change the temperature (ambiant wavelength across the field) then complete systems can change within the very same cast of variables (for example; having a fevor to create antibodies)


just writing my thoughts

 

[Techne]

Information (not the material) can be seen as the basis of reality .
Cell manipulating information as a means to an end... homeostasis.

Consider yet another fascinating finding.
Molecular Machine Turns Packaged Messenger RNA Into A Linear Transcript

ScienceDaily (Feb. 13, 2009) — For RNA, the gateway to a productive life outside the nucleus is the nuclear pore complex, an amalgamation of 30 kinds of proteins that regulates all traffic passing through the nuclear membrane. New research from Rockefeller University shows that one of these proteins magnetically couples with a special molecule — a helicase — to form a machine that unpacks balled-up messenger RNA particles so that they can be translated.

Cells at the core are information processing systems. Parallels between our own designed information processing systems (computers) cellular systems are there and are very useful in guiding research. However, it must be kept in mind that comparing our own measly designed models (like computers) to cellular mechanics and machinery could hamper discovering ever more intricate systems and codes in cells (e.g. epigenetic code).
Taking cues from designs in nature, it would be a prudent exercize in humilty to not overstretch our analogous designs to the designs in nature when we can learn so much more about these designs. E.g. Biomimicry.


The article continues:

The work illuminates a previously unknown stage in the process by which genetic information is read and converted to proteins. In humans and other higher organisms, the genetic information that is encoded in the DNA is stored inside the nucleus, while the factories that convert DNA instructions into proteins are located in the surrounding cytoplasm. As those instructions — messenger RNA particles — pass through the nuclear membrane, numerous proteins that cover and protect the delicate messenger RNA molecules must be stripped off.

Several RNA processing mechanisms exist to prepare the RNA molecule for future translation. A few include polyadenylation, 5'-capping, splicing etc. Every step of the process has a quality control systems with checks and balances in order to make sure good quality proteins are formed.

André Hoelz, a research associate in John D. Rockefeller Jr. Professor Günter Blobel’s Laboratory of Cell Biology, and his colleagues solved the crystal structure of a complex located on the cytoplasmic side of the nuclear pore — nucleoportin Nup214 coupled with helicase Ddx19. They then performed a series of biochemical experiments to further parse the interactions between these two molecules and to elucidate their mechanism of action.

“We found that the messenger RNA protein package and Nup214 competitively bind to the helicase, one after the other,” Hoelz notes. Each time the helicase binds the ball of messenger RNA and protein, it strips one protein molecule off. “The process is akin to a ratchet mechanism for messenger RNA export.” The result, Hoelz speculates, is a linear messenger RNA transcript that travels on to the ribosome, where it delivers instructions for building proteins.

The work may also clarify a cause underlying acute myeloid leukemia, which is associated with mutations to Nup214. “Patients with mutations in Nup214 that remove the docking site for the helicase are likely to have a messenger RNA export defect,” Hoelz says.

Fascinating work that further demonstrates the validity of viewing cells as computers that are able to manipulate information as a means to an end.

 

[Walter L. Wagner]

Isn't it nice to know that our cells function properly without any conscious input from ourselves. Very nice computer programs evolved over eons of time to which we our indebted not only to our immediate ancestors [parents, grandparents, mitochondrial-Eve, et al.], but to all the eons of evolutionary time.

Sure would be a shame to see us accidentally destroy that by some ignorant machine-makers who only have a modicum of understanding of the intricacies of nature.

 

[Slacker47]

Very interesting. What would the cells need to continuously function, in terms of food? I am sure that electrical currents would still be the method of computation, but how would one "feed" thier computer? This topic has been around for a couple of years, and I still cant see how to apply the idea. However, I am all for it in order to reduce the huge amount of toxic chemicals associated with computers. Good luck!

 

[Enmos]

Computer programs ?? :bugeye: