Wednesday, October 2, 2013

Rare Codons Near the Beginning of a Gene Control Protein Expression Level

More Fine-Tuning

Various studies have shown that in order to produce a protein evolution would need roughly 10^70 attempts to get close enough for natural selection to take over. That is a 1 with 70 zeros after it. The number of attempts possible, on the other hand, is far less. One study concluded that 10^43 attempts may be possible. It is important to understand how tiny 10^43 is compared to 10^70. 10^43 is not about half of 10^70. It is not even close to half. In fact 10^43 is an astronomically tiny sliver of 10^70. Furthermore that study concluded that 10^43 attempts may be possible assumed, as a starting point, the existence of bacteria. In fact it assumed the Earth is covered with them. And bacteria, as every freshman knows, contain proteins. So in order to evolve a protein, evolutionists assume the prior existence of proteins, and still fail to resolve the problem. But we really haven’t even begun to address the problem.

Genes that code for proteins do not merely code for a string of amino acids that happens to perform some simple function. For beyond this, a gene codes for an incredible level of complexity. It has been discovered, for instance, that gene sequences are cleverly arranged to complement the cell’s error correction mechanisms and so minimize copying errors. On top of that information, the gene also contains signals that help to control the speed at which the new protein is synthesized. These signals have been found to be quite sophisticated.

Protein coding genes also influence how the protein synthesis process should work. Specifically, in addition to specifying the amino acids to be used in making the new protein, genes also include signals for which particular amino acid-bearing machine (the tRNA) should be used.

And once the new protein is synthesized, it must avoid the propensity of proteins to stick to each other and form fibrils in what is known as an amyloid. As one researcher explained, “The amyloid state is more like the default state of a protein, and in the absence of specific protective mechanisms, many of our proteins could fall into it.”

The problem is that short protein segments of say half a dozen amino acids can be self-complementary and sticky. If these sticky patches are on the exterior of a protein, then multiple copies of the protein can attach and form a growing and dangerous amyloid fibril.

Not surprisingly the cell has several mechanisms to protect against protein fibrillation. And beyond these protective mechanisms, the gene sequence itself arranges the protein’s amino acid sequence such that sticky patches are safely hidden away in the protein interior. This is a major threat to proteins and one evolutionist hypothesized, “Most proteins have evolved to fold in a way that effectively conceals their amyloid-prone segments.”

And there is yet more information the gene must carry. Not only must the protein not aggregate, but it may require transportation instructions that help it to be shuttled to the right place in the cell.

Also, some genes are overlapping with other genes. In other words, the stretch of DNA where a gene resides may be shared with another gene entirely. So the genetic information is now doubled. And even if this is not the case, researchers are increasingly finding that genes perform multiple tasks. In what is known as gene sharing, the protein product of a gene may carry out several separate and distinct functions. As one researcher concluded, “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms.”

Consider the p53 protein for example. It is a tumor suppressor, a gene regulator, and it plays a role in cell growth, death and DNA repair. In another example, a protein was discovered to undergo a dramatic structural and functional change. When a phosphate group is attached to the right place the protein switches from (i) helping to translate the RNA copy of a gene into a new protein to (ii) working on making the RNA copy of the gene.

So you can see that the job of evolving a protein consists of far more than merely finding a simple function, which itself is far beyond evolution’s capabilities, even according to the evolutionist’s own numbers.

Now new research reveals yet more information in the gene. It has been known for years that it is crucial that the mRNA copy of the gene is not too stable. Otherwise it cannot be used to synthesize the protein. So the gene, when transcribed by RNA polymerase, must not produce an mRNA transcript that folds up too tightly.

The new research shows that rare codons that appear early in a gene sequence influence the mRNA stability, and in so doing strongly influence that protein expression level. In other words, built into a gene sequence are instructions that can control how much of the corresponding protein to make.

One wonders how many more signals are buried in genetic sequences.

46 comments:

  1. "Various studies" - citation needed.

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    Replies
    1. And if they are legitimate, peer reviewed, studies, will it make a difference to you?

      Delete
    2. They might make a difference for you. What was expected of you back when back when were doing accademic work?

      Delete
    3. "And if they are legitimate, peer reviewed, studies, will it make a difference to you?"

      No. At that point the pseudo-skeptics will cry foul, stating that "the researchers of the paper believe in evolution", so that any inference to the contrary found within their data must be irrelevant.

      Delete
    4. It's this paper, the same one he's quote-mined and misrepresented several times before on this blog.

      Experimental Rugged Fitness Landscape in Protein Sequence Space

      Here's the paragraph he quote-mined.

      "The question remains regarding how large a population is required to reach the fitness of the wild-type phage. The relative fitness of the wild-type phage, or rather the native D2 domain, is almost equivalent to the global peak of the fitness landscape. By extrapolation, we estimated that adaptive walking requires a library size of 10^70 with 35 substitutions to reach comparable fitness. Such a huge search is impractical and implies that evolution of the wild-type phage must have involved not only random substitutions but also other mechanisms, such as homologous recombination. Recombination among neutral or surviving entities may suppress negative mutations and thus escape from mutation-selection-drift balance. "

      Man, it's a good thing lying for Jesus doesn't count on your heavenly "personal record". Not sure about lying for the DI's paycheck though.

      Delete
    5. Rich: "Various studies" - citation needed.

      CH: And if they are legitimate, peer reviewed, studies, will it make a difference to you?

      Rich: They might make a difference for you.


      In other words, "no".

      Delete
    6. lifepsy"

      No. At that point the pseudo-skeptics will cry foul, stating that "the researchers of the paper believe in evolution", so that any inference to the contrary found within their data must be irrelevant.

      That is precisely that argument that is used. And if you respond by explaining that you also have studies from those who don't believe in spontaneous origins, then they dismiss those papers as well because, after all, those papers come from people who don't believe, so they are biased. This is a gold mine of fallacies. If one ever needed proof of what evolution is all about, just look to the evolutionists.

      Delete
    7. Such a huge search is impractical and implies that evolution of the wild-type phage must have involved not only random substitutions but also other mechanisms, such as homologous recombination. Recombination among neutral or surviving entities may suppress negative mutations and thus escape from mutation-selection-drift balance.

      Such a huge search space is not just "impractical" (an incredulous evolutionist? What a rare specimen.), its probability is exactly zero. Why? It's because any complex or even simple combination of genetic sequences is guaranteed to be quickly destroyed by subsequent deleterious random mutations long before the gene can be viable enough to replicate. The whole natural origin of life thing is too silly to even contemplate. I'm sure it causes some kind of brain damage. Thorton here is a case in point.

      Delete
    8. Thorton here is a case in point.

      Thorton is what is known as a troll. His goal is simply to disrupt. He hasn't a clue about the science, makes a fool of himself, and just pops right back up come the next post.

      Delete
    9. LOL! Looks like I hit a nerve.

      Speaking of making a fool of oneself, let's not forget this gem by you.

      Cornelius Hunter September 21, 2013 at 2:41 PM

      oleg: Propose a testable alternative, Cornelius, and Penny and coworkers will test it against the evolutionary model. Until then, your protestations ring hollow.

      1. I've already done that. I tested creation and it came out unquestionably true.


      Maybe someday you'll post those results where you tested Creation and it came out unquestionably true. I'll be the first in line to congratulate you on your Nobel Prize. :D

      Delete
    10. LOL! Looks like I hit a nerve.

      The usual “LOL”? Check.
      Accusation of lying? Check
      Lying about paychecks? Check.

      Yes, that was quite a nerve. Really surprised us with those brand new accusations. This is a troll in action.


      Maybe someday you'll post those results where you tested Creation

      Like I said, hasn't got a clue. But do you have to prove my point so fast?

      Delete
    11. Cornelius Hunter

      Like I said, hasn't got a clue.


      LOL! But I'm not the one who got caught in an amazingly dumb lie, claiming to have "tested creation and it came out unquestionably true."

      Too late to erase that embarrassment now CH, it's already been archived for posterity. Just part of your growing legend.

      Delete
    12. LOL!

      Oh, there you again. Quote mining also, but that's standard.

      Nothing like a troll who thinks he's onto something, but has no clue about the science. I guess you couldn't understand the paper even if you did read it.

      Delete
    13. So tell me Trollton, what probability did I come up with?

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    14. Cornelius Hunter

      I guess you couldn't understand the paper even if you did read it.


      We'll never know since you don't have such a paper.

      Why don't you link to it for the lurkers for them to read? Show them that you're not just a paid political shill for a right-wing religious organization who pissed away his chances at a real science career?

      Show us that creation science CH.

      Delete
    15. Let's try that again just in case you missed it Trollton. What exactly was that probability and my explanation to oleg that you quote mined out? As usual, we won't hold our breath.

      Delete
    16. You forgot to link to your supposed paper where you "tested creation and found it unquestionably true."

      What are the lurkers to think?

      Delete
    17. That's what we expected. Once a quote miner, always a quote miner. But when evolutionists make fools of themselves, they never actually realize it.

      Delete
    18. What are the lurkers to think?

      Um, probably that all of your many, many accusations of lying and quote mining are, in fact, coming from within.

      Delete
    19. Darn CH, I was really hoping you'd link to that paper you claimed to have written which you "tested creation and it came out unquestionably true." I was all ready to put it right next to your famous talk on thylacines and wolves in the Creationist Hall of Fame.

      But sadly your bluff was called and you folded like wet tissue. There is no such paper.

      What a bitter disappointment it must be for your fanboys, knowing now that you were just making it up again.

      Delete
    20. Amazing, the quote mining continues. To which we can now add denial. It is like that Monte Python skit where you pay for an argument.

      Delete
    21. (takes a quick peek in)

      Dozens of blustering posts by CH but still no paper.

      What a surprise.

      Delete
    22. Thorton:

      Dozens of blustering posts by CH but still no paper.

      Sorry but you don't get off that easy. No slinking away this time. You get one more chance: What exactly was that probability and my explanation to oleg that you quote mined out, and please explain this "paper" you have contrived.

      Delete
    23. The probability of you blustering and not producing the paper you claimed where you ""tested creation and it came out unquestionably true" is 1.0.

      That would be the paper which when I asked you to produce it before you replied "I guess you couldn't understand the paper even if you did read it.".

      I'm sure it's embarrassing for you to get caught in such an egregious lie. But maybe you should have thought of that before you told it.

      "

      Delete
    24. Thorton:

      CH: Sorry but you don't get off that easy. No slinking away this time. You get one more chance: What exactly was that probability and my explanation to oleg that you quote mined out, and please explain this "paper" you have contrived.

      Thorton: The probability of you blustering and not producing the paper you claimed where you "tested creation and it came out unquestionably true" is 1.0. That would be the paper which when I asked you to produce it before you replied "I guess you couldn't understand the paper even if you did read it.".


      I gave you three chances to undo your quote mine and you just couldn’t bring yourself to do it. That would undermine this latest false accusation.


      I'm sure it's embarrassing for you to get caught in such an egregious lie. But maybe you should have thought of that before you told it.

      And yet another false accusation. You have quote mined, erected strawmen, and made false attacks here literally for years. You fire for effect, ignore corrections, and just keep spewing your lies in all directions. Darwin’s God definitely gets a P for patience on this one. The times that I have corrected your false accusations not only go unacknowledged, you just come right back the next time with the same lie. Personal conduct matters my friend, it really does. Just because you’re hidden behind a computer screen somewhere doesn’t mean it doesn’t. I wish you well friend.

      Delete
    25. CH -

      I'm confused. You seem to be rattled, but you really DID claim you had tested Creationism. Here are you words:

      OLEG: "Propose a testable alternative, Cornelius, and Penny and coworkers will test it against the evolutionary model. Until then, your protestations ring hollow."

      CORNELIUS: "1. I've already done that. I tested creation and it came out unquestionably true."

      Now why are you getting annoyed with Thorton for pressing you on this? He isn't quote-mining you - you said it there in black and white. Did you mis-speak? Did you mean something completely different by those words? If so, I really don't see how that is Thorton's error.

      Delete
    26. Ritchie:

      Null hypothesis testing is notoriously slippery. Go here for a funny introduction:

      http://www.null-hypothesis.co.uk/science//item/what_is_a_null_hypothesis

      The Penny paper is the height of junk science which I was commenting on. A creationist could achieve the same level of certainty as Penny did (and get the exact same probability). I'm not saying the creationist would be any more correct than the Penny paper, just that the method proves essentially nothing. It is a joke. You need to understand this In order to understand the exchange between oleg and me, not to mention not quote mining it.

      Delete
  2. I'd like to see a source for the "various studies" as well. It's not that i doubt you, and I am a proponent of ID (one might even call me a creationist!). I'd just like to have a source if I throw that number out there at someone.

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    Replies
    1. Here is a starting point:

      http://darwins-god.blogspot.com/2012/03/these-new-protein-findings-are-problem.html

      Delete
    2. It's always good practice when trying to prop up your lies to link to other places where you made the same lies as a reference. Really convincing.

      Delete
    3. What lies? I don't see any liar here besides you, Thorton.

      Delete
  3. Okay:

    Rich: "Various studies" - citation needed.

    CH: And if they are legitimate, peer reviewed, studies, will it make a difference to you?

    Rich: They might make a difference for you.

    In other words, "no".

    1. Is it wrong for me to ask for citations?
    2. Should you have provided them?
    3. Is a critical assessment of primary materials good practice?
    4. Have you attributed to me a position I didn't advance?
    5. Is that an honest thing to do?
    6. What are Jesus' views on that?

    Thanks in advance.

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    1. You're an effing moron, Hughes. Jesus would bury his foot up your asteroid orifice. Is that Christian enough for you? LOL.

      Delete
    2. That's a very interesting interpretation of scripture, Louis. Which verses in particular led you that that conclusion?

      Delete
    3. Rich:

      1. Is it wrong for me to ask for citations?

      Not if your request is genuine. Citations, and science in general, make no difference to evolutionists.


      2. Should you have provided them?

      No. not if they don't make any difference to you. With evolutionists its about moving goal posts, not the evidence or the science. Sorry, I'm not going to fetch the evidence for you so you can then decide that peer review no longer matters.

      3. Is a critical assessment of primary materials good practice?

      It is ironic that evolutionists, who believe in spontaneous origins, ask questions like this, as though they have some sort of empirical higher ground.


      4. Have you attributed to me a position I didn't advance?

      I asked you a simple question, with a very simple answer. Would legitimate, peer-reviewed papers actually make any difference to you? A simple "Yes" would have been just fine. But you diverted instead. The simple fact is that peer reviewed papers really don't make any difference to evolutionists. Otherwise we wouldn't even be debating any of this.

      Delete
    4. Watching CH flounder and flop to avoid providing his sources is a scream! Almost as funny as listening to him bellyache about Judge Jones and Inherit The Wind

      Better than any comedy show on TV!

      Delete
  4. I'd like to look at the primary materials and the arguments they advance before forming an opinion. I see nothing wrong with this. You appear to be bellyaching about "I asked you a simple question, with a very simple answer." and yet do precisely that 4 times (not answering the other 2 questions).

    You're also having a bit of trouble with cause and effect. Generally the cause comes before the effect you have to do stuff to see the outcome. I hope this helps.

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    1. Rich:

      I'd like to look at the primary materials and the arguments they advance before forming an opinion. I see nothing wrong with this.

      Terrific, you can see my response to SonuvaDawg.

      Delete
  5. Hughes:

    That's a very interesting interpretation of scripture, Louis. Which verses in particular led you that that conclusion?

    I was being gentle. Choose one:

    1. Get a foot buried up your asteroid orifice.
    2. Get barbecued to a crisp by fire from heaven.

    Which would you rather have? LOL.

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  6. CH: "It is important to understand how tiny 10^43 is compared to 10^70. 10^43 is not about half of 10^70. It is not even close to half. In fact 10^43 is an astronomically tiny sliver of 10^70."

    It's like Hunter has never heard that information is the logarithm of the number of states. (He has of course, he merely pretends to.)

    Let me make it simple. If a password contains 70 bits, that would be 2^70 combinations. If you have found the first 43 bits, you only need to get 27 more. Which means that you are more than half way towards figuring out the password.

    2^43 is a tiny sliver of 2^70, but that is irrelevant. 43 bits is more than half the information in 70 bits.

    ReplyDelete
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    1. Which means that you are more than half way towards figuring out the password.

      Two problems. First, "half way" doesn't help. This isn't "half way" on the first try. Or the millionth try. These are extremely conservative estimates of the best you can do. 10^43 is orders of magnitude way too high, and 10^70 conservatively low for most real proteins.

      Second problem, we're not dealing with information here. We're dealing with required evolutionary experiments. Logarithms don't help.

      What is needed is some remarkable way to construct and/or follow extremely narrow pathways in the hyper dimensional search space, to arrive at real proteins. Until then we have the curse of dimensionality. Even by the evolutionist’s own ridiculously optimistic numbers the probability of a single, rather simple, protein evolving is 1 in 10^27. That’s with a time window that is way too long, number of attempts that is way too high, protein that is incredibly simple and, oh by the way, the preexistence of proteins! So the real probability is far worse than 1 in 10^27. But even that number, by any scientific standard, is impossible. The science is telling us that evolution is false. And, oh by the way, that’s just one protein.

      Perhaps that will change and some clever way to find proteins may well be possible. It just isn't what science is telling us right now. Furthermore, if it was found to be possible, then it certainly seems that it would be an astonishing property of matter and natural law that truly would require a multiverse to explain.

      So at this point it is what it is. We know what science is telling us. We need to honestly acknowledge the science. Future findings may always reveal something different, but that may or may not happen. You can either acknowledge the facts of science, or live in denial.

      Delete
    2. oleg, I appricate the example but I think it is extremely poor at making your point.

      This is because by it's very nature a password it useless without the whole thing. If I had a password (that was hashed as ALL passwords should be, and that is crucial) even if you had guess all but 1 character you would be no closer to finding it.

      This is because you would have no way of knowing you had got that close.

      Like a gene for a protein, even one 90% similar may be of no use at all. So to make out like getting 50% of it is any use at all is bonkers.

      Making it worse, in the case of mutation driven changes, is the fact that you have no mechanism for stopping changes to your exising "bits" so even if you got to 50% of the bits required there is no guarantee at all the subsequent changes won't ruin your progress.

      If you think about it, it will almost cirtainly guarntee that you never EVER make the goal.. the closer you get the more that can go wrong.

      Delete
  7. Excellent post Dr. Hunter.! Thanks for your hard work. Just to let you know that some of your readers do genuinely appreciate your efforts.

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  8. Not sure what the big song and dance is about.

    On the point about amlyoid-prone segments, more insight can be found here:
    http://www.nature.com/news/2010/100407/full/464828a.html

    A few "quote mines" for the more lazy among us:

    "It seems that most proteins have evolved to fold in a way that effectively conceals their amyloid-prone segments" ..because..
    From over 12,000 proteins (with known 3d structures) examined, they found that 95% of the predicted amyloid-prone segments within them are buried within the structures of their host proteins, and that those that are exposed are too twisted and inflexible to zip up with partner segments.

    It's almost like DNA knows something.

    "If you had a machine that could generate protein sequences randomly, you would only rarely get one that can remain stable in the globular, soluble state,"

    Rarely indeed, but life is full of suprises!

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  9. For the umpteenth time, probability isn't valid in determining if a theory is true or probability true. This is because you would need to know all of the possible outcomes

    For example..

    CH: What is needed is some remarkable way to construct and/or follow extremely narrow pathways in the hyper dimensional search space, to arrive at real proteins.

    Exactly, how do you know that "real" proteins (that currently exist) were intentional outcomes, and therefore the only possible outcomes? Please be specific.

    IOW, probability is only valid for making decisions *inside* an existing theory, which is exactly the context of the paper you keep referencing.

    Specifically, the paper doesn't suggest that the kind of life we observe today was specifically chosen and therefore the only possible outcomes. Some other kind of carbon based life could have evolved with different proteins, etc.

    At which point your objections based on probability is simply more hand waving.

    ReplyDelete