The Ribosome: Perfectionist Protein-Maker Trashes Errorhttp://reasonandscience.heavenforum.org/t1661-ribosomes-amazing-nano-machines
One machine common to all life on Earth is the ribosome. Its strongly conserved nature, and the common sense observation that it makes everything else, indicates its central position in evolution. The ribosome is not a single tool but a workshop split into two major parts, all created (using E. coli as an example) from around 7,400 amino acids, and around 250,000 atoms, all primed to use the strongest possible codon-amino acid mapping out of a practically endless range of possibilities.
Ribosomes can be so numerous as to make up 25% of the cell mass of E. coli. A striking feature of the ribosome is that, even given the large assorted collection of subunits, it self-assembles in vitro!
The core of the ribosome is RNA, supporting the idea that early forms of life relied on RNA rather than DNA. But if such a workshop is necessary to create proteins, whether from templates of RNA or DNA – from where could the ribosome come from? More vexing still for Darwinism is how editorial precision could arise in a system in which errors themselves were the key to prolific reproductive success at the start. Why change a winning hand?
New discoveries are being made about the ribosome all the time. Relevant to Darwinism, in 2009 Nature published some new discoveries by Johns Hopkins researchers concerning the remarkable actions of the ribosome’s ruthless quality control editor; if you think I tend to anthropomorphise molecules, note how the researchers detail -
..a new “proofreading step” during which the suite of translational tools called the ribosome recognizes errors, just after making them, and definitively responds by hitting its version of a “delete” button.
It turns out.. ..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.”
“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.”
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 Green says is “shocking” and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis.
The translation process in the ribosome to occur, the ribosome must be able to proceed and go through the full translation sequence, it must be fully functional, no intermediate evolutionary stage will do it : beside this, it consists of two main subunits, ( beside a significant number of co-factors , which help in the build up process of the ribosome ) which makes it a irreducible complex system.
Replication most probably would not occur at pre-stage of a common ancestor, so evolution cannot be proposed as a driving factor at this stage.
RNA replication in the lab makes use of extensive investigator interference. Chemicals like amino acids, aldehydes, and sugars (other than ribose) are arbitrarily excluded. Very specific activation agents are used to encourage replication (ImpA for adenine, ImpG for guanine, ImpC for cytosine, and ImpU for uracil). The concentration of the chemicals (especially cytosine and ribose) is billions and billions of orders of magnitude higher than what one would expect under plausible prebiotic conditions.
Shajani Z :
Ribosome assembly needs the contributions of several assembly cofactors , including Era, RbfA, RimJ, RimM, RimP, and RsgA, which associate with the 30S subunit, and CsdA, DbpA, Der, and SrmB, which associate with the 50S subunit. These subunits would have no function of their own, why then would random processes produce them without a final goal and no forsight of function ?
Five following conditions would all have to be met in the biosynthesis process of the Ribosome:
C1: Availability. Among the parts available for recruitment to form a biological system consisting of multiple parts, there would need to be ones capable of performing the highly specialized tasks of the specific system, even though all of the items serve some other function or no function in another system where they were recruited from.
C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.
C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.
C4: Coordination.The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if the subunits are put together in the right order, they also need to interface correctly.
The parts must be coordinated in just the right way: even if all of the parts of a ribosome are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.
C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if the subunits are put together in the right order, they also need to interface correctly.
Resumed : For the assembly of a biological system of multiple parts, following steps must be explained : the origin of the genome information to produce all subunits and assembly cofactors. Parts availability, synchronization, manufacturing and assembly coordination through genetic information, and interface compatibility. The individual parts must precisely fit together. All these steps are better explained through a super 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, producing machines and end products.
The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist
Johns Hopkins researchers, reporting in the journal Nature January 7, have discovered a new "proofreading step" during which the suite of translational tools called the ribosome recognizes errors, just after making them, and definitively responds by hitting its version of a "delete" button.
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.
and it's this compounding of errors that leads to the partially finished protein being tossed into the cellular trash," she adds.
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. "The cell is a wasteful system in that it makes something and then says, forget it, throw it out,"
That looks all ingeniously designed.......
http://www.nytimes.com/2009/10/08/science/08nobel.html?_r=0Besides the implications for biomedical research, another consequence of the ribosome work was to resolve an old “classic chicken and egg problem” , Dr. Berg of the National Institute of General Medical Sciences explained. If ribosomes are needed to make proteins but they are also made of proteins, which came first?
J.Sarfati : the DNA information requires a complex decoding machine, the ribosome, but the instructions to build ribosomes are on the DNA. And decoding requires energy from ATP, built by ATP-synthase motors, built from instructions in the DNA decoded by ribosomes … “vicious circles” for any materialistic origin theory, as leading philosopher of science Karl Popper put it .
http://newswire.rockefeller.edu/2013/08/14/structural-biologist-interested-in-ribosome-assembly-to-join-rockefeller-faculty/What’s more, it’s something of a chicken-and-egg problem. “You need the machinery to be in place in order to manufacture proteins, but the machinery itself is made of proteins that must be manufactured,” Klinge says.
well, as far as i know without ribosomes there is no protein synthesis, without protein synthesis there is no life, without life there is no evolution so ribosomes cant come to existence via evolution so how did the form?
Facing these facts, i believe theists are justified to hold the position, that design explains best the origin of Ribosomes, and the origin of life.