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Micro RNAs and Design inference.

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http://www.nature.com/nrm/journal/v9/n9/pdf/nrm2472.pdf

“MicroRNAs (miRNAs) are known to regulate gene expression at the level of translation, but how does this affect what proteins are produced? Two recent papers have shown that individual miRNAs can affect the expression of hundreds of proteins.

One known as miR-223 seems to function as a rheostat to finely adjust protein output.

Another miRNA let-7b is can fine-tune protein production from thousands of genes.

Individual miRNAs can have an effect on global protein expression, and protein repression is likely to be mediated by a specific complementary sequence target region in the corresponding messenger RNA. The emerging picture is that miRNAs do not have just a small number of mRNA targets — they function at the transcriptional and translational level to subtly modulate what specific proteins are produced.”

Do the exact complimentary target sequences for these miRNAs being present on many mRNAs coding for different proteins, mean that all these sequences and proteins have a common ancestor, or were the target sequences derived independently?

The study of miRNAs and their target mRNAs and proteins may be good ID research, as I suspect that many unrelated proteins are controlled by the same miRNA. Because the target sequence is the same, that seems to imply strongly that design, rather than descent with modification, was involved.

http://www.nature.com/nrm/journal/v9/n9/pdf/nrm2472.pdf

Comments
Because there are 4 Cs 3 Ts and a G in the sequence. That is 8!/(4!*3!) = 280 ways to arrange those bases. The other issue is that this sequence only has to be in the 3' UTR acoring to the article. That means that it just has to appear anywhere within 5 thousand basepairs, or so, of the gene. So, you just have to get 6-8 basepairs to lineup out of 5000. get the idea?10_3_3
August 28, 2008
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My trusty windows calculator in scientific mode says that 4 x^y 8 equals 65536. I'd guess your Excel is still working.DaveScot
August 28, 2008
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Well, I have not followed all the discussion, but obviously there is no doubt that the possible combinations of an 8 nucleotide sequence are exactly 4^8, that is 65536 (if my Excel is still working).gpuccio
August 28, 2008
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10_3_3 I wonder at your math. Taking the example of base 10, there are 10^1 different ways of putting a one place number together. There are 10^2 different ways of putting a two place number together. There are 10^3 different ways of putting a three place number together. There are 10^4 different ways of putting a four place number together. The genetic code uses a base 4 number system. How do you figure that an 8 figure base four number only has 280 possibilities?idnet.com.au
August 28, 2008
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idnet, The last part of my post above is wrong (don't know what I was thinking when I posted...). I shouldn't post when I'm tired. any way, what I should have said (and what I was thinking to begin with) was that given the sequence of DNA in the binding site there are only 8!/(4!*3!) = 280 ways of arranging the bases. anyway...10_3_3
August 27, 2008
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re: nuclear transfer citation This the one ? http://www.bioone.org/perlserv/?request=get-abstract&doi=10.1095%2Fbiolreprod.104.031302&ct=1steveO
August 27, 2008
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Dave, Thanks for the response. While I do agree that both RNA plays a large role in development and that maternal effect plays a large role in early development, I don't think that it maternal RNA plays that large of an overall role in the complete development of the adult organism. The problem that I see with this, is that while DNA is quite stable, RNA is fairly unstable and degrades quickly in the cytoplasm. I can not find where I had read this, but I seem to remember reading that maternal RNAs are nearly exhausted early in the blastocyst stage. I know that maternal RNA does affect some phenotypes that persist into adult organism though (snail shell coil direction is a text book example), so maybe... Also, thanks for checking on the citation for me. I'm not the most organized person, so I understand loosing citations.10_3_3
August 27, 2008
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10_3_3 RNA is a good candidate for epigenetic storage of high level architecture. Think of DNA as a dictionary and the RNA content of the cytoplasm as a novel. That seems the easiest way to address your point about RNA molecules in the cytoplasm having a template sequence in nuclear DNA. re; nuclear transfer citation I was reviewing Dembski/Wells "The Design of Life" before it was published and when I read evo-devo subsection 2.7, page 50, 2nd paragraph on nuclear transfers:
For example, when an egg's genes are removed and replaced with the genes from another type of animal, development follows the pattern of the original egg until the embryo dies from lack of the right proteins. (The rare exceptions to this rule involve animals that could normally mate to produce hybrids.)
I was skeptical and asked them for a citation. Jonathan sent me the citations in an email. I read them online to confirm the text in the book then eventually deleted the email. I checked the CD just now and the citation isn't there but Jonathan does have more notes on developmental program storage citing microtubule arrays which are built by inherited centrosomes and also membranes whose structure is also inherited rather than specified in nuclear DNA. DaveScot
August 27, 2008
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idnet, I do understand what you're saying but there are a couple of things that I think you're missing. First, it is often the case that RNAi binding sites can be degenerate. So, lets say that 7 out of the 8 base pairs need to match, then we're down to ~1/16000 or if we let 2 bases be mismatched then it drops down to ~1/4000. Now then, both your calculation and mine above assume that these binding sites are arising de novo. This is clearly the wrong probability to calculate. As there are only 4 bases in DNA and the exact location of the binding site is not that critical, the chance of 6 of the 8 base pairs arising by chance, I don't think is that unreasonable. Also, remember that these binding sites are *very* GC rich and are in genic regions. There are only so many combinations of 8 bases in a row when most are Gs and Cs that you can have. In fact if we let all bases be equal there are 4 choose 8 = 70 possible combinations. So, really I think the bigger problem is keeping these binding sites from showing up where they're not wanted.10_3_3
August 26, 2008
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10_3_3 You are not impressed by repeated sequences of 8 base pairs. Each specific base pair sequence of length n, has a probability of 1/n^4. An 8 pair sequence has a pobability of 1/4^8 or ~ 1/64000. To have two that match I think we need to multiply the probabilities of each. Get the drift? After seeing the same target sequence not a couple but hundreds of times, and in the protein target groups that give the right combinations for function, doesn't design spring to your mind?idnet.com.au
August 26, 2008
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Dave, Any guesses as to the cytoplasmic component is responsible? I am guessing that you don't think it's RNAi as you state that "there doesn’t seem like enough data storage space in a few billion base pairs of nuclear DNA to specify all the detail in a mammal" and RNAi is encoded in the nuclear DNA. Do you happen to have the citation for the nuclear transfer experiment? sounds like an interesting read.10_3_3
August 25, 2008
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Hi, Im new. I was wondering if someone could point me towards some good information on the dynamics of interactions between cell machinery. Also am interested in information on how localized and isolated environments with generally consistent weather patterns and external stresses could be responsible for the vast diversity of the life forms within them. Thanks!joshuarolandblume
August 25, 2008
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10_3_3 I'm talking about far more than the maternal effect. I was being literal about the cytoplasm determining whether a cell is destined to become a fly or a horse (fly/horse taken from title of geneticist Sermonti's book "Why a Fly is not a Horse"). In it he writes the only thing we know for certain about why a horse is a horse and not a fly is because its mother was a horse. In Dembski's latest book are references to nuclear transfer experiments showing that when an enucleated egg of one species receives a nucleus from a different species development (until it spontaneously aborts - none live to adulthood in interspecies nuclear transfer) proceeds along the path of the species of the egg, not the nucleus. So by what we know right now what makes a horse a horse instead of something else resides outside the nucleus. This makes sense because from an engineering point of view there doesn't seem like enough data storage space in a few billion base pairs of nuclear DNA to specify all the detail in a mammal or similarly complex animal. It's enough room to store a component library of the nuts and bolts required to build individual cells of different types but not the whole animal. There is a vast amount of potential storage space outside the nucleus. DaveScot
August 25, 2008
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the tip of the iceberg in where heritable information that determines whether a cell is destined to become a horse or a fly is actually stored.
I guess it doesn't make the difference between a horse and a fly but in Chrysomya rufifacies it at least makes the difference between males and females.sparc
August 25, 2008
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idnet, I am a little confused here. Are you saying that you don't think that this target sequence could have arisen independently across the genome? I don't think it's that unthinkable. The targets are only 7-8 base pairs long. They are often degenerate (meaning they don't have to be the exact sequence) and these are highly GC rich. this last point is critical because genic regions are often also GC rich, so the probability of these targets arising near genes is higher than if they arise in a region of the genome with a uniform distribution of base pair composition. Dave, I think what you're talking about is a well known phenomenon called "maternal effect".10_3_3
August 25, 2008
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Off topic: Anyone noticed this on global warming?Borne
August 25, 2008
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As I've written several times before in several places I think we're seeing the tip of the iceberg in where heritable information that determines whether a cell is destined to become a horse or a fly is actually stored. It's in the cytoplasm not the nucleus. The mechanism for inheritance in this case isn't duplication but rather more direct - a portion of the mother cell's cytoplasm is sectioned off and given to the daughter cell in the process of making the new cell. DaveScot
August 25, 2008
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OFF TOPIC (Sorry): I couldn't find a way of bringing this to the attention of UD, so apologies for the threadjack: http://www.boingboing.net/2008/08/25/mickey-mouse-bridges.html I think this is right up UD's street. Jtenstrings
August 25, 2008
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idnet.com.au So you think we may be seeing "evolutionary convergence" at the microscopic level, right?Granville Sewell
August 25, 2008
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