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Ribosome a diligent proofreader

As you’re reading this keep in mind it’s all due to a random dance of atoms. No design here. Matter, chance, and POOF it’s alive. Yeah right.

From Science Daily

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.

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.

“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.

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 research was funded by the National Institutes of Health with support from the Howard Hughes Medical Institute.

In addition to Rachel Green, Hani S. Zaher, also of Johns Hopkins, was author of the paper.

Adapted from materials provided by Johns Hopkins Medical Institutions.

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34 Responses to Ribosome a diligent proofreader

  1. (sarcasm alert)

    Do we SEE the designer doing the editing? No.

    Therefor how can you say the ribosome was designed?

    You people and your metaphysics…

    But anyway it will be very interesting to investigate thjis- as in how does the ribosome “recognize”, ie how does it “know” what it is supposed to be producing?

    This whole process must have been something of a shock to the investigators. And I would say another nail in the coffin of Darwinism.

  2. Joseph,

    You just don’t understand the process. At some time in the past this version of the ribosome was selected for. Cells that contained this version were more likely to survive and thus we have a version that is better at proof reading.

    Here it is in Dr. Green’s own words.

    ” ‘I’m happy to be pulled back from trying to recapitulate the RNA World,’ Green notes. ‘But understanding that world is part of what pulls me to the ribosome. When you open it up, its core being is a nest of RNA. I’m happy to be studying the thing that won out in evolution.’ ”

    In other words it was selected. What a wonderful concept selection is. It is better than scaffolding or co-option but not quite as powerful as emergent. With magic tools like these how could you doubt the Darwinian theory of evolution.

  3. 3

    “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.”

    Exactly what one would predict would be programed into a nanobot. A designer can select among slightly-less-than-perfect alternatives for one that is “good enough.” But a nanobot has no ability to choose along a continuum. So the designer designed it to select for “perfect or nothing.”

  4. Error-control systems in a system allegedly created by errors in copying genetic code. Will wonders never cease.

  5. The ribosome- a genetic compiler!

    Think about it-

    What happens to a newly written or modified computer code that has an error?

    I bet if we were to watch we would see the compiler doing its thing right up to the point the error occurs and then spits it out much faster than if the code was OK, ie error free.

    Now I am not saying that I have years of experience with coding errors, but if I did then the correlation would be obvious. ;)

  6. Error-control systems in a system allegedly created by errors in copying genetic code. Will wonders never cease.
    ——————–

    Brilliant! Evolution did it by natural selection…or not. It doesn’t matter. Evolution does whatever it wants, whenever it wants, by any means it wants and they all work to bring us these amazing non-designed machines.

    Also, it’s about time you get it through you heads that materialism isn’t a religion. It’s science. That’s why it’s ok to teach materialism in the science classroom. There are no religious implications in materialism.

    Chance explains everything! Once, in my alphabet soup, I saw the word cow. Cow! Right there in my bowl. What are the chances? It can’t be much harder to make a real cow if you have 400 billion years and a few spare electrons.

    While I’m at it….aliens may have invented the ribosome. I don’t know. It’s an amazing thing so I bet they might could have but if they did then I still don’t know where their ribosomethingies came from.

    Ah….the life of an intellectually fulfilled atheist is so nice.

  7. The enzyme machine that translates a cell’s DNA code into the proteins of life is nothing if not an editorial perfectionist.

    A compiler of a computer code is nothing if not an editorial perfectionist.

    The source code has to be “perfect” in order to get the object code.

    Again not that I would have experience with such a thing.

    Biologists need to be introduced to and experience computer science.

    Then this sort of discovery wouldn’t be so “shocking”.

  8. 8

    Joseph said,

    I bet if we were to watch we would see the compiler doing its thing right up to the point the error occurs and then spits it out much faster than if the code was OK, ie error free.

    What if the error were one of logic and not say, syntax? Do you know of a compiler that can weed out all errors?

  9. Sort of a funny spin from Green. She calls the process “wasteful” when the system identifies and throws out a toxic component inserted by a troll trying to hack the system. I’d be thrilled if the human-engineered systems that I work with every day had anything that even approached this kind of error-handling capability. Fantastic might be a better word.

  10. What if the error were one of logic and not say, syntax?

    The output would reflect such an error.

    If not was it really an “error”?

    Do you know of a compiler that can weed out all errors?

    I don’t know of a singular compiler that can do such a thing, but that doesn’t mean one doesn’t exist or couldn’t exist.

    Today’s computer programming has at least two stages of error checking-

    1- the compiler
    2- the output, as in is it what was wanted/ intended?

    But you are right. I should have been more specific about the errors compilers can assess.

    Point taken.

    My point is we already knew the ribosomes helped in the translation- mRNA to polypeptide and a compiler’s job is also to translate.

    Now this error stopping feature is further evidence, not for analogy, but for the reality that the ribosome is a compiler.

    And it also tells us why that Craig Venter can synthesize a ribosome but cannot get it to synthesize proteins- no software to run it- See “Life: What a Concept!” page 51

  11. 11

    Dave, thanks for the best posts on UD.

  12. A long time ago some one made a statement about gravity,what goes up must come down.Once an object goes up beyond down gravity,where does it go? Should that page be changed?Apparently NASA has figured out that equation. Are they sharing it?

  13. Thanks DaveScot,

    Equally amazing as the process of alternative RNA splicing.

  14. Got a question I would like to ask Einstein if he were still alive.In written words how would you write$999,999,999.99+$.01=`s answer first in North AMerican currency then in Euopean currency and then do the math to show the difference and then write that answer in words.A reason to know why economics is in such a mess.YES? going for walk

  15. geoffrobinson,

    Nice observation. Thanks.

    Plus, error-driven error-correction would have had to have “emerged” very early in the process.

    Your comment also illustrates a special product of the random-error model, i.e., locktite logic.

  16. What is the naturalistic mechanism posited by Darwinian theorists that explains why random mutation over long time periods moves in a direction to assemble rather than destroy or to improve or advance a certain thing rather than a regress?

  17. jerry:

    Here it is in Dr. Green’s own words.

    ” ‘I’m happy to be pulled back from trying to recapitulate the RNA World,’ Green notes. ‘But understanding that world is part of what pulls me to the ribosome. When you open it up, its core being is a nest of RNA. I’m happy to be studying the thing that won out in evolution.’ ”

    Yeah, and the funny thing is that the ribosome is mainly RNA, possibly selected in the RNA world with the remarkable purpose to translate mRNA derived form DNA to generate proteins in the future protein world… What is that, Natural Selection or Natural Prophecy?

    SteveB, why should we be surprised of a “wasteful” process, when it seems that the human genome is 98.5% junk DNA? Obviously, evolution treasures wastefulness…

    And Joseph, obviously a compiler, however good, cannot recognize all errors. After all, it is only, like the ribosome, a very well designed machine. For really smart errors, the designer himself has to work at debugging (and, as we know, success is not always ensured).

  18. After reading something like this I always wonder if people like Green wonder if maybe there might be some problems with the Darwinian explanation for such wonders. Do they wonder, but wonder about the ramifications of expressing their wonderment?

  19. And Joseph, obviously a compiler, however good, cannot recognize all errors.

    I would never categorically deny the possibility.

    After all, it is only, like the ribosome, a very well designed machine.

    I take that to mean it matters who designed it and for what purpose.

    For really smart errors, the designer himself has to work at debugging (and, as we know, success is not always ensured).

    Perhaps we could write a program that would help him/ her.

    Sometimes the programmer is just to close to their program, meaning they are “boxed” in. And that means looking outside of the box. Sometimes another programmer is OK, but I would think that a program could do it much faster and maybe even more efficiently.

  20. Dave !!!!

    This is crazy! We all know that mutational “errors” are actually the GOOD fuel for evolution! So, this ribosome article must be a mistake..and the author of it must be a fanatical creationist!

    Stop the propaganda!

    :P

  21. Barry Arrington: 3

    “Exactly what one would predict would be programed into a nanobot. ”

    Totally wrong, I work with robotic systems and they can be easily programmed to make selections based on how closely they match a target, you can even get them to alter their selection criteria based on feedback.

  22. J Guy: 20

    These are errors in protein synthesis, not in DNA replication. Errors in DNA replication are the ones that get inherited.

    I knew a guy once that was using genetic algorithms to design logic circuits with in built error checking systems. The traditional (intelligently designed) systems used two sets of logic, one to perform the function and another to check the first circuit for errors. Obviously if there was an error in the second circuit it couldn’t detect errors. The evolved version was a single circuit (i.e no separate error checking sub-unit) where any fault (usually in the form of a faulty gate) would generate a fault signal – it had evolved a self checking error checker. Neat stuff but I know that examples and analogies from computer science aren’t always good illustrations of evolution.

    “Biologists need to be introduced to and experience computer science.”

    BTW, this guy worked in a research group full of biologists.

  23. Laminar

    I’ve been working with computer automated equipment all my life. What Barry was trying to say is that nanobots can only respond as they’re instructed. If the programmer doesn’t anticipate any specific contingency the robot won’t be able to invent an appropriate response to it. If we look at “evolution” as the programmer of these nanobots, and we take into account that evolution is reactive, not proactive, it can’t program reactions into the bots for future contingencies, anticipating different possible future situations is proactive and being proactive is something that only intelligent agents do. So Barry rightfully says the nanobot does the only thing it can do which is pass a perfect copy or destroy an imperfect copy. It can’t make any independent decisions.

  24. These are errors in protein synthesis, not in DNA replication.

    The errors were BEFORE protein synthesis.

    Errors in DNA replication are the ones that get inherited.

    Only the errors which do not get corrected and do not disable the organism from reproducing.

    “Biologists need to be introduced to and experience computer science.”

    BTW, this guy worked in a research group full of biologists.

    What is the relevance? Did the biologists learn anything from him?

  25. DaveScot:

    I don’t see that interpretation at all. Barry says that a designer can look at imperfect options and select ones that are good enough but that a small robot cannot select for anything except ‘perfect or nothing’. To me this translates as ‘Machines are incapable of selecting or rejecting things based on how closely they match a pattern, they can only select for exact matches’. This seems to fly in the face of a lot of pattern matching algorithms I’ve come across, for example handwriting recognition.

    We are basically talking about a cellular mechanism that has a high quality filter for selecting or rejecting its products. You seem the be saying that evolution can only produce high quality filters, not low quality ones as that would require foresight.

    “Evolution … can’t program reactions into the bots for future contingencies … so … the nanobot does the only thing it can do which is pass a perfect copy or destroy an imperfect copy.”

    You appear to be arguing that this is exactly what you would expect evolution to produce – a non-foresighted mechanism?

  26. Joseph:

    A lot of biologists I know work closely with computer scientists, some biologists also have degrees in computer science (And I know some computer scientists with degrees in biology).

  27. GAs are really cool tools, and if properly guided can help optimize antennas, circuits, and a variety of practical applications. The interesting thing about computer scientists who are also Darwinists is that they know from experience the limitations of GAs as a tool yet at the same time they believe the biological system is somehow able to overcome said limitations without any intelligent input at all. I say “somehow” because every time I’ve seen people acknowledge the limitations they cannot at the same time define exactly how undirected processes can do it.

  28. DaveScot: … anticipating different possible future situations is proactive and being proactive is something that only intelligent agents do.

    Is Gil’s checkers app an intelligent agent? If not, I’m curious how it plays so well without anticipating possible future situations.

  29. A lot of biologists I know work closely with computer scientists, some biologists also have degrees in computer science (And I know some computer scientists with degrees in biology).

    How many is “a lot”?

    And how many of these scientists with degrees in computer science and computer scientists with degrees in biology think that life owes its existence and subsequent diversity to blind, undirected processes?

  30. Is Gil’s checkers app an intelligent agent?

    Gil is. And as Dr Meyer has pointed out all CSI in an application can be traced back to an intelligent agency.

  31. Joseph – Are you asking for a statistical breakdown of all the people I know and what their various degrees are in or are you just implying that I am a liar?

    Given the wide use of computers across all sciences for everything from data visualisation to modelling it shouldn’t be at all surprising that computer scientists work closely with, and sometimes also are, biologists.

    I’m pretty certain that they ALL accept MET as the only credible scientific theory that explains the diversity of life today. I’m not sure what they think about the origin of life and I know some of them are religious.

    “And as Dr Meyer has pointed out all CSI in an application can be traced back to an intelligent agency.”

    Do you have a source for this claim so I can take a look myself?

  32. Do you have a source for this claim so I can take a look myself?

    please see minute 5:30 of this video for the direct Meyer Quote:

    Intelligent Design vs. Evolution – Dr. Meyer

    http://www.godtube.com/view_vi.....1b53f962a8

  33. Given the wide use of computers across all sciences for everything from data visualisation to modelling it shouldn’t be at all surprising that computer scientists work closely with, and sometimes also are, biologists.

    I agree. Why hire a programmer when you can do it yourself? Never mind, a non-biologist might make a mistake in modeling a subject he or she does not fully comprehend due to an error in communication. I know for certain I would not attempt such a project without a biologist close at hand. Then again, a Darwinist biologist would probably insert unverified assumptions into models…but there’s going to be a level of bias and some assumptions no matter who you are.

    I’m pretty certain that they ALL accept MET as the only credible scientific theory that explains the diversity of life today.

    A generalized belief based largely upon social pressure is very different from knowing enough about the topic in order to explain why its credible. I know engineers who maintain a belief in Darwinism but they cannot explain the foundation for this belief, other than that they were taught to believe it.

    I used to be the same way, btw. After all, why would my instructors mislead me? But it was not a closely cherished belief and I felt no need to defend it when it became obvious it could not be substantiated.

    I’m not sure what they think about the origin of life and I know some of them are religious.

    Religious? As if the worldview and beliefs of agnosticism and atheism are not a factor… I’m not sure if you knew this but out of the people I know the vast majority of religious people who are also now ID proponents used to be Darwinists.

  34. Is Gil’s checkers app an intelligent agent?

    Gil is. And as Dr Meyer has pointed out all CSI in an application can be traced back to an intelligent agency.

    I was hoping that someone could actually answer the question. If his app is not an intelligent agent, then which premise in the following argument is wrong?

    P1. Only intelligent agents anticipate different possible future situations.

    P2. Gil’s app anticipates different possible future situations.

    C. Therefore, Gil’s app is an intelligent agent.

    And yes, I know that Gil’s app was designed to anticipate future possibilities, but that doesn’t address the above argument. (And if we too were designed to anticipate future possibilities, does the fact that we were designed negate our intelligent agency?)

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