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DNA has a molecular ambulance

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From BioTechniques:

A molecular motor that transports damaged DNA is also necessary for its repair.

Double-strand breaks in DNA are a source of stress and sometimes death for cells. But the breaks can be fixed if they find their way to repair sites within the cell. In yeast, one of the main repair sites resides on the nuclear envelope where a set of proteins, including nuclear pore subcomplex Nup84, serves as a molecular hospital of sorts. The kinesin-14 motor protein complex, a “DNA ambulance,” moves the breaks to repair sites, according to a new study in Nature Communications (1).

“To think of motor proteins moving DNA inside cells-it was very surprising,” said corresponding author Karim Mekhail at the University of Toronto. “In the beginning, we thought that there must be some other way to explain these findings. But the more we tested, the more we realized that kinesin-14 must be mediating the movement of damaged DNA.” More.

Just a random event, for sure. Like that plague of Boltzmann brains floating over your desks… Oh wait, you better not think this one out too clearly.

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Comments
Mung, I'll get to your crazy test another time. :)Upright BiPed
September 4, 2015
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REC, are you actually asking if we change the codon to a different codon, will we get a different amino acid presented for binding? Really? You present it as if it’s some deep challenge that your ID opponents should be wary of – like it demonstrates something of significance about how and why codon/amino acid relationships are established in the cell. I’m sitting here reading these questions from you: “Lets re-arrange a Trp codon. Does the amino acid incorporated change?” -and- “ If I rearrange the nucleotide bases ‘AUG’ that code for methionine, does the amino acid incorporated change? Yes or no.” ... and I’ll be darned if I can make anything out of it other than you are actually asking if we change the codon, does the effect change. Good grief. Rec, having a certain amino acid presented for binding at a certain point in time is a translated effect. Keep that in mind – a temporal effect brought into being under the control of a translated representational medium. It requires one arrangement of matter to evoke the effect, and another arrangement of matter to physically establish what the effect will be. There are very specific physical reasons for this to be the case – not the least of which is the presence of inexorable law. And like every other translated effect ever known to exist, it’s a relational architecture that must preserve the discontinuity between the arrangement of the medium and its effect within its system. It’s not sort-of like it, it’s not kinda like it; from a strict physics perspective, it’s exactly like every other translated effect ever observed. These are demonstrable facts that stem from observation, theory, and experimental confirmation by some of the brightest minds of the past 100 years – and these facts are not going away just because of someone’s ideological preference to imagine the system as a local entity that’s reducible to its physical properties. It isn’t. Get over it. Translation stems from contingent organization, not dynamics. And frankly, this is only the tip of the observations that clarify the genetic translation system. There’s plenty more. Perhaps instead of wasting your own time by regurgitating toothless counter-observations (like “it’s just chemistry folks”) maybe you should wonder why you were taught the genetic translation apparatus without being given a core understanding of what translation is to begin with. Of course, we all know the deal here – the zero tolerance policy regarding ID. Do what you gotta do. As for myself, I am off to spend a long weekend with my toes in the surf, sipping a Tecate with my wife, listening to some Ska. cheersUpright BiPed
September 4, 2015
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"Aminoacyl-tRNA synthetases control the process of adding the AA to its specific tRNA. The materialistic explanation is the enzymes recognize the shape and/ or chemical signal of the tRNA as they diffuse through the system." Specifically, they bond with the anticodon. This is quantifiable, and can be performed with purified and synthetic material. Physical perturbation of the system changes the outcome. What is your (non-materialist?) explanation?REC
September 4, 2015
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UB @55-not quite how the conversation went. At least you credit me for proposing a test based on empirical data. I guess you preferred to bail then offer a response. Anyone else want to take a stab? If I rearrange the nucleotide bases 'AUG' that code for methionine, does the amino acid incorporated change? Yes or no. For those interested, this experiment can be performed with purified components. No external source of information. Physical changes to key players-ribosomes, aatRNA synthetases, etc will change the outcome. There is a physical relationship from codon to amino acid that runs through the tRNA adapter.REC
September 4, 2015
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EugeneS:
Nothing in biology makes sense except in the light of design.
Alicia Cartelli:
Yeah keep telling yourself that, Eugene.
Yeah, and you keep telling yourself the opposite. We're now even. I would go much further than EugeneS: Absolutely nothing in the universe makes sense except in the light of design.Mapou
September 4, 2015
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You failed to answer the question: “I propose a test. Lets re-arrange a Trp codon. Does the amino acid incorporated change?” I too have a test for Upright BiPed. If we take a codon that codes for an amino acid and change it so it still codes for the same amino acid, when does it code for a different amino acid? Extra credit question: Isn't this irrefutable proof that there is no genetic "code"?Mung
September 4, 2015
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UB: bye Don't go! We'll miss you!Mung
September 4, 2015
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PPolish @73, In principle, I agree, but, formally speaking, naturalistic causation is probably enough in physics and chemistry (leaving aside the very important question of how physics and chemistry came to be, of course). I think that science is actually impotent as far as the beginning is concerned. Nature cannot explain itself. How can you 'explain' without first defining what explanation is or should be? Any explanation has to start somewhere necessarily. So is there a naturalistic explanation of how nature itself came to be?! This does not make sense to me.EugeneS
September 4, 2015
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Dionsio- If the DNA has the codons then the mRNA would have the anti-codons and the tRNA would have the original codons, in RNA format. If you say the mRNA has the codons then the tRNA would have the anti-codons. The AA connects to the CCA tail. Aminoacyl-tRNA synthetases control the process of adding the AA to its specific tRNA. The materialistic explanation is the enzymes recognize the shape and/ or chemical signal of the tRNA as they diffuse through the system.Virgil Cain
September 4, 2015
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ppolish @73
“Nothing in biology makes sense except in the light of design.”
Actually,...
“Nothing makes sense except in the Light.”
:)Dionisio
September 4, 2015
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#72 error correction The mRNA contains the complementary triplets of the template strand of DNA, hence the mRNA codons match the coding DNA strand triplets. Therefore the tRNA contains the anticodons. Did I get this right now? Thanks.Dionisio
September 4, 2015
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"Nothing in biology makes sense except in the light of design." Same goes for Chemistry. Ditto Physics.ppolish
September 4, 2015
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Upright BiPed & Virgil Cain Please, help me with these questions: Do the codons in the mRNA relate to AAs indirectly, through the mediation of tRNA anticodons associated to the corresponding mRNA codons? Are the mRNA codons kind of anticodons to the original DNA codons? Where is the direct chemical bond between the AAs and the actual codons? I'm missing that. You may correct any conceptual error in the formulation of my questions too. Thanks. -clueless student PS. Anyone else reading this is welcome to help me too.Dionisio
September 4, 2015
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Yeah keep telling yourself that, Eugene.Alicia Cartelli
September 4, 2015
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Nothing in biology makes sense except in the light of design.EugeneS
September 4, 2015
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Alicia:
Nature is the ultimate trial-and-error experiment, it hasn’t needed foresight to produce the diversity of species and underlying chemistry we see today.
It didn't produce the diversity of species nor the underlying chemistry.Virgil Cain
September 4, 2015
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Eugene, you are confusing the function of a molecule and the evolution of a molecule. When I use the word function, I am simply referring to what the molecule does, due to its chemistry; no evolutionary perspective or “implementation logic” involved. The original conversation was about “foresight” and whether it was necessary. Molecules do not have foresight, as has been said, and their evolution does not involve foresight either. Nature is the ultimate trial-and-error experiment, it hasn’t needed foresight to produce the diversity of species and underlying chemistry we see today.Alicia Cartelli
September 4, 2015
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Dionisio, I share your feelings of awe at the profound design of biological systems.EugeneS
September 4, 2015
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"I enjoy teaching about biology." Poor students.EugeneS
September 4, 2015
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ppolish @51
Interesting how design works on so many levels. It’s fascinating really.
Agree, although "fascinating" seems like an understatement in this case. To those who have worked for a quarter century on engineering design software development projects, just looking at the elaborate cellular and molecular choreographies orchestrated within the biological systems could be extremely humbling. The first time I briefly looked inside a medical school textbook on human development, I lost my concentration at work, to the embarrassing point of being at a technical meeting and not listening to what my supervisor and my colleagues were saying, because I could not stop imagining what I had read in that textbook. What started as simple curiosity later turned into an obsession that ultimately became an irresistible attraction. On another 'embarrassing' occasion, I went out to lunch with a biology professor that was leading a research group working on protein folding mechanisms. That was the first time I heard about such a thing. After a while, the professor noticed I wasn't eating. He asked me if I didn't like the food and suggested that we could order something else for me. I told him the food was delicious, but confessed that I got so hypnotized by his description of the problems they were investigating, that I had forgotten about the food on the table. Declaring that all those marvelous systems are the result of unguided processes could be simply unacceptable to someone who has worked on engineering design software development projects.Dionisio
September 4, 2015
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Alicia, Are you a graduate or a postdoc? "Molecules do not have foresight." This is exactly what all of us here are trying to communicate to you. And yet, functions realize that foresight. Functions achieve a goal, for which they exist. It means that functions are not just molecules. Functions are logic implemented using molecules. Just like human made processors on crystals utilizing the motion of particles of matter in order to produce utility. Your level of understanding is way lower than I expected of a person who claimed to be actively involved in research in biology. How people manage to spend years doing biology without actually understanding what is going on, I don't really know. Carpathian, I totally agree with VC. The level of knowledge you have demonstrated here does not allow you to really make a judgement. REC, Carpathian and Alicia could not tell whether television was television and not just an electric current in the wire if they'd seen it for the first time without being told what it was... A profound level of understanding indeed: - human speech is just sound waves; - circuit boards are just electricity; - biology is just chemistry. Face palm.EugeneS
September 4, 2015
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Yes, Alicia, I know about tRNA and that bond. That is NOT what we are talking about. Obviously you love to equivocate a spew nonsense. Also the tail of tRNAs are all the same- where that bond is. AGAIN- There isn't any bond between the mRNA codons and the amino acids they represent. Stop being such an arse.
I shouldn’t be responding to you Virg, but what can I say, I enjoy teaching about biology.
You need to learn about it BEFORE teaching it. :razz:Virgil Cain
September 4, 2015
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I shouldn't be responding to you Virg, but what can I say, I enjoy teaching about biology. There is a covalent bond formed between the tRNA and its corresponding amino acid in the observed translational system. This is basic stuff, but not really important to the conversation with upright. I think the conversation is a little above your paygrade though. Have a nice day.Alicia Cartelli
September 4, 2015
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Carpathian- Her posts are evidence and substance-free. You wouldn't know so that is OK. But nice to see your cheerleading is still going strongVirgil Cain
September 4, 2015
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Virgil Cain:
Carpathian, Your opinion means nothing. Alicia is full of bluff and bluster.
I see that her comments have much more content pertaining to biology while yours are primarily opinion.Carpathian
September 4, 2015
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Alicia:
I repeat, there is a direct chemical relationship between nucleotide and amino acid.
You mean there can be a direct chemical bond. There isn't any chemical bonds between nucleotides and amino acids in the observed translation systems.Virgil Cain
September 4, 2015
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REC:
A codon doesn’t “represent” anything, except in human made protein translation tables or programs.
So all biology textbooks are WRONG? Is that your "argument"- really?
It physically codes(hence the name) for an amino acid, as translated by the adapter molecule tRNA through hydrogen bonds and physical fit.
LoL! A code means one thing represents another. Codons represent amino acids. They do not become them. That means there isn't any physio-chemical relationship between them.
“I propose a test. Lets re-arrange a Trp codon. Does the amino acid incorporated change?”
It could. It all depends.Virgil Cain
September 4, 2015
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"...the biological ID movement isn’t ready to provide any answers about biology." It's about asking the right questions. Won't find meaningful answers without the right questions. EvoBio Dogma is almost dead. Dead end.ppolish
September 4, 2015
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Upright, recent research has shown that the 2nd nucleotide position of every codon correlates with certain amino acids. I repeat, there is a direct chemical relationship between nucleotide and amino acid. Certain bases correspond with certain amino acids based on their chemical properties. I don't know all the details, but I'm picturing this 2nd nucleotide position/amino acid correlation as a chemical leftover of the early evolution of the system. A system where maybe a single nucleotide was used to code for a certain amino acid or a subset of amino acids with similar properties; the end result being the polymerization of an amino acid chain by the early ribozyme with a reproducible sequence.Alicia Cartelli
September 4, 2015
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REC: ribonucleotide base pairing is responsible for the relationship between a codon and the specific amino UB: no its not REC: I propose a test of right I am UB: Is anyone else surprised by this? REC: I’m wrong, but you people are losers UB: byeUpright BiPed
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