1. Evolution or Design? Duons

Have you ever tried writing palindromes? How about writing phrases that can be read the same way in either direction? Here are some examples:
A man, a plan, a canal: Panama
Live not on evil
Was it a car or a cat I saw
These sentences were no doubt designed…
Can you imagine writing a book that can be read forwards and backwards containing 2 different stories that made sense? Not an easy task…

Watch the video and pay special attention to the following examples:

  1. Alternative splicing of RNA that produces multiple proteins from one gene
  2. Duons – Overlapping sequences that code for both protein expression and transcription factor binding sites simultaneously
  3. Dual coding genes in which one sequence is read in multiple frames to produce completely different protein

The magnitude of the dual coding problem in DNA would be the equivalent of writing a novel that could be read in either forward over reverse directions making two different stories both of which made sense…

And don’t forget that according to Darwinists the dual coding in DNA simply evolved, right?

403 Replies to “1. Evolution or Design? Duons”

  1. DNA_Jock
    Ignored
    says:

    colewd: Do you consider binding ATP to be a protein function in itself?

    Yes, I do. Keefe et al. selected for binding, rather than catalysis, for a rather boring and irrelevant technical reason. If not for the technical hurdle, they could have achieved similar results selecting for specific catalysis. BTW, do you consider binding to biotin to be a protein function in itself?

    colewd: This is based on the faulty assumption that binding to substrate A has anything to do with binding to substrate B. When mutating to substrate B the sequence is still facing the large void of non functional space.

    This is wrong. Proteins that fold are adjacent to other proteins that fold in the “vast” sequence space.

    Were not binding to small molecules were binding to large proteins. P53 has to evolve surfaces that bind to all 10 in order for apoptosis to work. Each protein is much larger then ATP. P53 has been around along time as a molecule that performs apoptosis.

    And it turns out that binding to large proteins is easier than binding to small molecules.

    Granting their pre existence for the sake of argument, p53 had to evolve a sequence that would fold into a protein structure that would bind to all 10 proteins in order to gain the advantage of cell death. In itself this is a miraculous event without guidance.

    You might want to consider the possibility that the other ten proteins were also evolving in their ability to interact with p53 (whether directly or indirectly), or you could stick with your argument from personal incredulity. Your choice.
    Fun fact: if, in the sequence space of 20^80, ATP-binding proteins arise at 1 in 10^11, that means that there are 10^93 different ways of binding ATP. That’s a helluva lot of needles in the haystack.

  2. Corneel Corneel
    Ignored
    says:

    DNA_Jock: You might want to consider the possibility that the other ten proteins were also evolving in their ability to interact with p53 (whether directly or indirectly), or you could stick with your argument from personal incredulity.

    I was wondering about that. Binding 10 proteins sounds very impressive, but how many functional domains are actually involved? I would hazard a guess that in some of these interactions p53 is the substrate, as a consequence of the need to tightly regulate its activity (phosphorylation and such) and of course several different proteins may simply bind the same domain.

    Oncology is not my area of expertise, but I do recognise juggling with numbers.

  3. Entropy Entropy
    Ignored
    says:

    colewd:
    This is based on the faulty assumption that binding to substrate A has anything to do with binding to substrate B. When mutating to substrate B the sequence is still facing the large void of non functional space.

    Why would that be a faulty assumption? The faulty assumption is to imagine that every molecule ever bound by a protein is completely different from every molecule ever bound before.

    Also, did you not understand that there’s plenty of successful proteins to evolve from? There’s, again, plenty of proteins, all with different affinities to many small and large molecules. Not only that, there’s lots of domains, with all kinds of activities, that can be exchanged between proteins. You’re just assuming that all of those proteins did not exist. That P53 had to do all of that from scratch in one go.

    colewd:
    Were not binding to small molecules were binding to large proteins.P53 has to evolve surfaces that bind to all 10 in order for apoptosis to work. Each protein is much larger then ATP. P53 has been around along time as a molecule that performs apoptosis.

    You’re the one who mentioned small molecules in the first place. Either way, you continue making mistakes I already explained to you before. Binding to other proteins in not a big deal, There’s plenty of potential surfaces for interactions, and plenty of proteins already interacting, plenty of domains that already tend to interact with each other. You’re assuming, again, that there’s only one way of evolving things, and that such way is always from scratch.

    colewd:
    Granting their pre existence for the sake of argument, p53 had to evolve a sequence that would fold into a protein structure that would bind to all 10 proteins in order to gain the advantage of cell death. In itself this is a miraculous event without guidance.

    There’s plenty of proteins that already fold. Putting together a few domains, each one that folds in itself, each one with different activities, each one with different binding partners, is no big deal. Remember: P53 did not have to evolve all of those interactions in one go from scratch!

    The “guidance” is provided by the evolutionary processes. By the different needs fulfilled by the ancestral proteins to P53. We’re talking about evolution Bill. This is a process going on for billions of years. You underestimate the role of the history of these molecules and imagine that every feature in a human protein evolved in humans. Well, no. They evolved across lots of organisms other than humans. The P53 family has been around for quite a while.

    colewd:
    Random change from a functional sequence. The odds are large that it walks toward non function.

    Nah. You’re forgetting that there’s such a thing as purifying selection, and that there’s tons of copies of each gene available for variation to occur.

    I think I’ve produced some beautiful and clear explanations. Somehow I suspect that you haven’t read them all too carefully.

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