Cell biology Genetics News

DNA has a molecular ambulance

Spread the love

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.

Follow UD News at Twitter!

114 Replies to “DNA has a molecular ambulance

  1. 1
    Andre says:

    ID guy: Wow a molecular ambulance! How did this happen?

    Materialist guy: Evolution is amazing!

    ID guy: The question still, how?

    Materialist guy: It emerged!

    ID guy: How?

    Materialist guy: Are you saying my moral code is inferior to yours?

  2. 2
    Alicia Cartelli says:

    “To think of motor proteins moving DNA inside cells-it was very surprising,”
    What the heck is this guy talking about? It is well known that the motor proteins Kinesin 4, 10 and 7 all move DNA.

    No one said it was a “random event,” come back to planet Earth.

  3. 3
    ppolish says:

    “motor proteins moving DNA inside cells-it was very surprising,”

    Why “surprising” and not “fascinating”. Because of design denial that’s why. Blindwatchmaker mentality.

  4. 4
    EugeneS says:

    Guys, you don’t understand it. Of course, it is not a random event because junk DNA did it!

  5. 5
    bornagain77 says:

    DNA repair mechanisms are found to be very sophisticated. The overlapping repair mechanisms for DNA include, (but are not limited to), the following:

    A proofreading system that catches almost all errors
    A mismatch repair system to back up the proofreading system
    Photoreactivation (light repair)
    Removal of methyl or ethyl groups by O6 – methylguanine methyltransferase
    Base excision repair
    Nucleotide excision repair
    Double-strand DNA break repair
    Recombination repair
    Error-prone bypass
    http://www.newgeology.us/presentation32.html

    Scientists Decipher Missing Piece Of First-responder DNA Repair Machine – Oct. 2009
    Excerpt: The first-responder machine, a protein complex called Mre11-Rad50-Nbs1 (or MRN for short), homes in on the gravest kind of breaks in which both strands of a DNA double helix are cut. It then stops the cell from dividing and launches an error-free DNA repair process called homologous recombination, which replaces defective genes.
    http://www.sciencedaily.com/re.....164106.htm

    A Look at the Quality Control System in the Protein Factory – JonathanM – March 2012
    Excerpt: The DNA damage response (DDR) system is like a cellular special ops force. The moment such damage is detected, an intricate network of communication and recruitment launches into action. If the cellular process for making proteins were a factory, this would be the most advanced quality-control system ever designed.
    http://www.evolutionnews.org/2.....57791.html

    Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010
    Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot.
    http://www.sciencedaily.com/re.....123522.htm

    Electric DNA
    Excerpt: unbroken DNA conducts electricity, while an error blocks the current. Now Dr Barton has found that some repair enzymes exploit this. One pair of enzymes lock onto different parts of a DNA strand. One of them sends an electron down the strand. If the DNA is unbroken, the electron reaches the other enzyme, and causes it to detach. I.e. this process scans the region of DNA between them, and if it’s clean, there is no need for repairs.
    http://creation.com/electric-dna#endRef5

    Researchers discover how key enzyme repairs sun-damaged DNA – July 2010
    Excerpt: Ohio State University physicist and chemist Dongping Zhong and his colleagues describe how they were able to observe the enzyme, called photolyase, inject a single electron and proton into an injured strand of DNA. The two subatomic particles healed the damage in a few billionths of a second. “It sounds simple, but those two atomic particles actually initiated a very complex series of chemical reactions,” said Zhong,,, “It all happened very fast, and the timing had to be just right.”
    http://www.physorg.com/news199111045.html

    Elaborate overlapping DNA repair mechanisms are incompatible with neo-Darwinism in principle:

    The Darwinism contradiction of repair systems
    Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma.
    http://www.uncommondescent.com.....r-systems/

    Contradiction in evolutionary theory – video – (The contradiction between extensive DNA repair mechanisms and the necessity of ‘random mutations/errors’ for Darwinian evolution)
    http://www.youtube.com/watch?v=dzh6Ct5cg1o

    The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective – February 2011
    Excerpt: “Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation.”
    http://www.benthamscience.com/.....OEVOLJ.pdf

  6. 6
    Dionisio says:

    ppolish @3

    Why “surprising” and not “fascinating”.

    Perhaps because their discoveries contradict their reductionist expectations?

    BTW, the new discoveries are rendering the observed complexity more complex than expected, thus making more difficult for the established “just-so” stories to explain many things.

    There are gazillion examples out there:

    http://www.uncommondescent.com.....ent-578360

  7. 7
    ppolish says:

    I agree Dionisio, many discoveries contradict the dogma.

    But if you are going to publish these contradictions, it is politically necessary to act “surprised” or “shocked to learn”.

    Will we get to a point where the design evidence leads authors to be “dismayed” or “saddened to learn”:) Or will that study just not be published:(

  8. 8
    Alicia Cartelli says:

    Boy, you guys are a special brand of stupid.
    Quibbling over researchers using the word “surprising” vs. “fascinating?” Get real. And you guys really love to do it. I’ve seen it a number of times on here.
    They’re just playing the PR game and talking up their research. You guys are completely clueless and out of touch with the real world.

  9. 9
    ppolish says:

    “special brand of stupid” 🙂

  10. 10
    Dionisio says:

    Alicia Cartelli
    Glad to find someone smart like you, who is not a special brand of stupid.

    Can you briefly tell us how exactly are the morphogen gradients formed and how exactly are they interpreted during developmental organogenesis?
    Can you describe for us the exact mechanisms underlying the cell fate specification and determination, intrinsic asymmetric meiotic/mitotic segregation of cell fate determinants?
    Also tell us how those mechanisms came to be.
    You may provide graphical illustrations to support your presentations.
    Please, explain it all in easy to understand terms.
    Remember that you’re addressing a special brand of stupid people.
    Thanks.
    🙂

  11. 11

    Alicia Cartelli @8: I will not respond in kind with name calling. On the contrary, the fact you are here at this site indicates you have an interest (perhaps a passionate interest) in the topic, and thus smart. However, you operate under the handicap of indoctrination – the indoctrination imposed on many of us by the academic elites of this world, in particular those evolutionary biology professors in the ivory towers.

    Stick with me on this if you will:
    1) Read the article once more, and then carefully read BA77’s remarks @5 – in particular the following list:
    A proofreading system that catches almost all errors
    A mismatch repair system to back up the proofreading system
    Photoreactivation (light repair)
    Removal of methyl or ethyl groups by O6 – methylguanine methyltransferase
    Base excision repair
    Nucleotide excision repair
    Double-strand DNA break repair
    Recombination repair
    Error-prone bypass

    This clearly indicates an extremely sophisticated design, but to see this you must get past your indoctroation.

    Now look at the following article “Growing a Bone Requires Foresight” at:
    http://www.evolutionnews.org/2.....98911.html

    Notice carefully that the title of this article is “Growing a Bone Requires Foresight”, emphasis on the word Foresight.
    This directly contradicts a key tenant of Evolution whish says “Evolution is not teleological or goal directed.” The entire article is from http://philosophy.wisc.edu/for.....tes_4.html, an American University in Wisconsin.

    What I hope you catch in this exercise is that virtually all elements of life – from cells to organs to limbs, to bones – all of them – do show very specific “‘goal direction.”

    Do you find it strange that a process (evolution) that is claimed to be “… not teleological or goal directed”, actually produces – across the board – goal oriented and specifically functional end products? Products for example that can execute a beautiful and exacting double play in baseball.

  12. 12
    Virgil Cain says:

    Alicia:

    No one said it was a “random event,”

    Random, as in not planned, happenstance- that is what evolutionism claims produced the diversity of life-> contingent serendipity.

  13. 13
    ppolish says:

    Virgil, it is only an appearance of random.

    Design gives the appearance of random sometimes. Design is awesome. No surprise.

  14. 14
    Dionisio says:

    ayearningforpublius @11 & Virgil Cain @12

    Please, do not distract the attention of Alicia Cartelli.
    Leave her alone.
    She needs time to focus in on the homework @10.
    It’s probably easy task for her, but still it demands some time and concentration.
    The questions @10 can’t be answered by chance.
    🙂

  15. 15
    Virgil Cain says:

    ppolish- I was just explaining to Alicia that evolutionism says the event was random. I don’t think it appears random but evolutionism has to explain its existence by unplanned and happenstance occurrences.

  16. 16
    Alicia Cartelli says:

    Dio, I would never try to explain those things to anyone as special as you guys. Definitely not to someone who asks for a “brief” explanation of “exactly” how something works in biology. If you knew anything about biology, you would know that isn’t possible.
    Read some books, education ain’t free.

    Yearning, a passionate interest in something doesn’t indicate intelligence. Let’s take Dio here, he’s been posting abstracts to the same webpage on UD for who knows how long, and yet he still knows next to nothing about biology.
    Anyways, I did not need to be “indoctrinated” by evolutionary professors. I have had many professors and all they do is present the facts and expect us to learn them. It is up to the student to draw their own conclusions about their validity. Having studied biology for many years, I have formed my own opinions and drawn my own conclusions. The “professors in their ivory towers” that you are probably referring to are simply trying to present the basics of this material to the masses; the people who aren’t highly educated in biology. Unfortunately nutjobs, like the ones here at UD, love to prey on the masses and their lack of knowledge, doing their best to confuse and undermine. Let’s take bornagain and his post for example, he throws a bunch of big, scientific words around (most of which he knows nothing about) in an attempt to blind the reader with science. Basically, he’s saying “look how complex this sounds, it must have been designed by an intelligent being.” Next, he sends us to “evolutionnewsandviews” which has put a spin on a scientific article, making sure to word things in a way that supports their position. You keyed in on the word “foresight,” but the word never actually appears in the actual primary article. Weird, huh?
    All elements of life do not demonstrate “goal direction,” they have a function(s) and they carry out these function(s). End of story. You guys can switch the words out all you want to try to support your side, but the only people you will fool are the fools, and trust me, they will have no effect on where the science is headed.
    And where is the science headed?
    Well, let’s just say it doesn’t look good for you guys.

  17. 17
    Dionisio says:

    Alicia Cartelli @16
    Gotcha! The word “brief” was intentionally part of the test, as a hint, but you misinterpreted it.
    Sorry, but you failed to answer the easy questions @10.
    The correct answer is indeed very brief:
    No one knows all those exact mechanisms yet.
    That’s all. Let’s repeat it, in case you missed it: NOBODY.
    However, as more discoveries are made, and more light is shed on the elaborate cellular and molecular choreographies orchestrated within the biological systems, the old theories are less adequate to explain the observed complexity. That’s why we should look forward, with much anticipation, to reading the newest research papers in the days ahead.
    Got it now?
    Alright, you may go and tell the bad news to your comrades.
    And try to read the latest research papers, lest you fail to pass such an easy test again.
    Remember, some of the stuff you learned is obsolete now.
    🙂

  18. 18
    Alicia Cartelli says:

    Dio, we know a pretty good amount about how these processes work, look up the 1995 nobel prize in physiology.
    It depends just how much detail you want in the explanation.
    No bad news, for me at least.

  19. 19
    Virgil Cain says:

    Alicia- There is a huge difference between knowing how the processes work and knowing how they arose. You cannot model a physio-chemical process producing living organisms and their systems.

    BTW evolutionism relies on the ignorance of the masses. Unfortunately its “experts” don’t know any more than the masses.

  20. 20
    scottH says:

    Alicia
    Serious question, if everyone is a fool here and no one understands evolution, biology, anything, then why are you on this site?

  21. 21
    ppolish says:

    I bet Alicia visits this site because she thinks it is possible that she may be mistaken. A bowel thing I think?

  22. 22
    Alicia Cartelli says:

    Good question. I guess I just love to talk about biology.
    And laugh at you guys of course.
    =)

  23. 23
    Upright BiPed says:

    Alicia,

    Since I’m one of the stupid people here you refer to, perhaps you would be kind enough to enlighten me how you envision a representational organization rising from dynamic properties and chaotic initial conditions. Perhaps you could start off by giving an inventory of the material conditions required by such a system, then providing a scenario by which those material conditions are satisfied.

  24. 24
    ppolish says:

    “And laugh at you guys of course. =)”

    Laughter is the best medicine. How does Nature do that? DNA ambulances are cool sure. Just at a different level. Guided, purposeful. Timing is important too. Both for jokes & ambulances. Nature is awesome, Nature is special. Freaking Special.

  25. 25
    scottH says:

    Alicia
    Thanks, that tells me all I needed to know about you.

  26. 26
    Upright BiPed says:

    Oh well.

    Maybe some other time then.

  27. 27
    Alicia Cartelli says:

    Keep your shirt on upright, I don’t have the time to be constantly checking UD for your oh-so insightful posts.
    Anyways, I’ve seen your “translational system” schtick on here often as well so I’ll keep it short. I’m envisioning some kind of ribozyme that is capable of polymerizing amino acids specifically based on both the chemical properties of the nucleotides within the ribozyme as well as the chemical properties of the amino acids themselves. I’m not saying the system is as complex as what we see in living organisms today, but it is “representational organization.”

    Ppolish, are you high?
    Next time you see someone with cancer, or some congenital defect, pick any disease really; make sure to let them know that “laughter is the best medicine.” I’m sure they’ll really appreciate it.

  28. 28
    ppolish says:

    Alicia, google “smiling cancer kids” and check out the “images”. Say a prayer for them – it can’t hurt can it? It can’t.

  29. 29
    Dionisio says:

    ayearningforpublius @11

    Very insightful commentary. Thank you.

  30. 30
    Dionisio says:

    Alicia Cartelli @16

    Let’s take Dio here, he’s been posting abstracts to the same webpage on UD for who knows how long, and yet he still knows next to nothing about biology.

    Thank you for giving me undeserved credits, but let me correct something you wrote about me:

    next to nothing

    should read more accurately:

    next to nothing

    I’m morally and intellectually destitute.

    But I don’t want any exaltation or credits from this dying world.

    My identity is in Christ, Who made you and me.
    His grace is sufficient.
    Don’t need anything else.
    I’ll pray for you.

  31. 31
    EugeneS says:

    “All elements of life do not demonstrate “goal direction,” they have a function(s) and they carry out these function(s). End of story.”

    Function is by definition teleologic. Function is something useful, and has by its own nature, a purpose. Function is about “in order to”. And “in order to” is a synonym of foresight. End of story.

    Comments 5 and 11 are nice.

  32. 32

    Dionisio @29: Thanks … I’ve polished it up a bit at
    ayearningforpublius.wordpress.com/2015/09/03/either-modern-evolutionary-biology-is-goal-directed-or-it-is-false

  33. 33
    Upright BiPed says:

    Oh I see

    So, your thinking of a ribozyme. And it’s gonna have some nucleotides. And some amino acids.

    powerful.

  34. 34
    Dionisio says:

    Upright BiPed @33

    Since you seem to understand what she wrote, can you explain it to me? Thanks.
    I definitely didn’t get it. But again I belong in the special kind of stupid group.
    🙂

  35. 35
    Dionisio says:

    ayearningforpublius @32

    Thanks.

  36. 36
    EugeneS says:

    UB,

    You have mail. 🙂

  37. 37
    Virgil Cain says:

    Alicia seems to be nothing more than a bloviating arse. She doesn’t have any answers and her attempt at ridicule proves she is a bully-wannabe. How typical and still pathetic.

  38. 38
    EugeneS says:

    Alicia,

    I am sure you know that every function in biology has a key word that describes it. I am sure you know that this word is ‘recognize’.

  39. 39
    Alicia Cartelli says:

    PPolish, I’d rather spend time researching and finding better cures for cancer.

    Always a good chat with you, Upright.

    Eugene, that was an awesome game of telephone you played with yourself there.
    “Foresight” is knowing what will be needed in the future. Molecules do not have foresight. They are present in the cell or they’re not, and they carry out a specific function when the necessary pieces are in place. Also, the term “recognize” in biology doesn’t mean what most people think when they hear the word. When a molecule “recognizes” another, it simply means it happened to crash into it when floating around the cell and the binding sites met in the correct orientation.

    Sorry, but you guy really have no idea what you are talking about. Thanks for the laughs though.

  40. 40
    Virgil Cain says:

    It’s obvious that Alicia has no idea what she is talking about- all bluff and bluster. People like Alicia give science a bad name.

  41. 41
    Upright BiPed says:

    Always a good chat with you, Upright.

    I didn’t think anything else needed to be said. It’s obvious from your response that you not only have no coherent answers, but you don’t even comprehend the question – otherwise you wouldn’t imagine a system that accomplishes its task any differently that the actual system in place.

  42. 42
    Alicia Cartelli says:

    My system carries out the same representational function as the actual system in living organisms today. It just does so in a simpler manner. Certain nucleotides favoring the binding of certain amino acids within the polymerizing ribozyme is the driving force behind the evolution of the system I proposed, to the system we see today. I am assuming the necessary amino acids and nucleotides are already present, but they do not necessarily need to be the same amino acids and nucleotides in use today.

  43. 43
    Upright BiPed says:

    Nucleotides don’t determine relationships within extant cells. That’s not how translation works in the real world.

  44. 44
    REC says:

    @43: “Nucleotides don’t determine relationships within extant cells.”

    “Determine relationships” is, perhaps to you, a more interesting phrase than to me, but don’t we all agree ribonucleotide base pairing (hydrogen bonds and size) is responsible for the relationship between a nucleic acids codon and the specific amino acid to be incorporated into protein?

  45. 45
    Virgil Cain says:

    Alicia:

    My system carries out the same representational function as the actual system in living organisms today.

    The rate that amino acids are bonded influences the final form. Also you have to account for your system.

  46. 46
    Virgil Cain says:

    REC:

    “Determine relationships” is, perhaps to you, a more interesting phrase than to me, but don’t we all agree ribonucleotide base pairing (hydrogen bonds and size) is responsible for the relationship between a nucleic acids codon and the specific amino acid to be incorporated into protein?

    There isn’t any physio-chemical relationship between a codon and the amino acid it represents. The relationship is arbitrary and because of that it is evidence for coding agent.

  47. 47
    Virgil Cain says:

    Alicia, Intelligent Design would include cells having foresight and the ability to move molecules around as it seems fit to do.

  48. 48
    Upright BiPed says:

    #44

    No, we don’t agree. The arrangment of a codon does not establish the relationship between a codon and an amino acid. That’s not how translation works in the real world.

  49. 49
    REC says:

    “a codon and the amino acid it represents”

    A codon doesn’t “represent” anything, except in human made protein translation tables or programs. It physically codes(hence the name) for an amino acid, as translated by the adapter molecule tRNA through hydrogen bonds and physical fit.

    “arrangment of a codon does not establish the relationship between a codon and an amino acid. ”

    I propose a test. Lets re-arrange the codon. Does the amino acid incorporated change?

    I’m not going to launch into a language critique here, but it is interesting when a well defined physical process gets murkier by the use of “relationship” and “representation”

  50. 50
    Upright BiPed says:

    Is anyone else (genuinely) surprised the REC doesn’t know how the relationships between codons and amino acids are established in the extant translation system?

  51. 51
    ppolish says:

    I’m not surprised. Interesting how design works on so many levels. It’s fascinating really.

  52. 52
    REC says:

    @50-

    “Is anyone else (genuinely) surprised the REC doesn’t know how the relationships between codons and amino acids are established in the extant translation system?”

    I’m (genuinely) surprised at the crap tone ID supporters take. With the death of ID, I guess this is the inevitable shift from denial to anger. Next comes bargaining.

    But what is wrong with the statement: a codon “physically codes(hence the name) for an amino acid, as translated by the adapter molecule tRNA through hydrogen bonds and physical fit?”

    I could go into detail about aaRS, but again, we’re talking about biochemical forces connecting the codon to the amino acid.

    Cue “direct” “representation” “arbitrary” etc., and so on. None of this makes you of Joe right when you say that there is no physical relationship.

    You failed to answer the question: “I propose a test. Lets re-arrange a Trp codon. Does the amino acid incorporated change?”

  53. 53
    Carpathian says:

    Virgil Cain:

    Alicia seems to be nothing more than a bloviating arse. She doesn’t have any answers and her attempt at ridicule proves she is a bully-wannabe. How typical and still pathetic.

    She obviously knows more about biology than you or most IDists do.

    The fact that you cannot see this is evidence that the biological ID movement isn’t ready to provide any answers about biology.

  54. 54
    Virgil Cain says:

    Carpathian, Your opinion means nothing. Alicia is full of bluff and bluster.

  55. 55
    Upright BiPed says:

    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: bye

  56. 56
    Alicia Cartelli says:

    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.

  57. 57
    ppolish says:

    “…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.

  58. 58
    Virgil Cain says:

    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.

  59. 59
    Virgil Cain says:

    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.

  60. 60
    Carpathian says:

    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.

  61. 61
    Virgil Cain says:

    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 strong

  62. 62
    Alicia Cartelli says:

    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.

  63. 63
    Virgil Cain says:

    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. 😛

  64. 64
    EugeneS says:

    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.

  65. 65
    Dionisio says:

    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.

  66. 66
    EugeneS says:

    “I enjoy teaching about biology.”

    Poor students.

  67. 67
    EugeneS says:

    Dionisio,

    I share your feelings of awe at the profound design of biological systems.

  68. 68
    Alicia Cartelli says:

    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.

  69. 69
    Virgil Cain says:

    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.

  70. 70
    EugeneS says:

    Nothing in biology makes sense except in the light of design.

  71. 71
    Alicia Cartelli says:

    Yeah keep telling yourself that, Eugene.

  72. 72
    Dionisio says:

    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.

  73. 73
    ppolish says:

    “Nothing in biology makes sense except in the light of design.”

    Same goes for Chemistry. Ditto Physics.

  74. 74
    Dionisio says:

    #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.

  75. 75
    Dionisio says:

    ppolish @73

    “Nothing in biology makes sense except in the light of design.”

    Actually,…

    “Nothing makes sense except in the Light.”

    🙂

  76. 76
    Virgil Cain says:

    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.

  77. 77
    EugeneS says:

    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.

  78. 78
    Mung says:

    UB: bye

    Don’t go! We’ll miss you!

  79. 79
    Mung says:

    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”?

  80. 80
    Mapou says:

    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.

  81. 81
    REC says:

    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.

  82. 82
    REC says:

    “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?

  83. 83
    Upright BiPed says:

    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.

    cheers

  84. 84
    Upright BiPed says:

    Mung, I’ll get to your crazy test another time.

    🙂

  85. 85
    Upright BiPed says:

    Dio,

    Send me an email to contact (-at-) complexitycafe (-dot-) com and I’ll answer your question directly.

    You’ll have to figure out a way to convince me that you are you.

    🙂

  86. 86
    Mung says:

    You’ll have to figure out a way to convince me that you are you.

    Even better, convince him that you are not someone else.

    That’s what I did.

    Hint: He accepts DNA samples.

  87. 87
    Dionisio says:

    UB and Virgil Cain

    This mRNA translation discussion seems a little off topic for this thread, but that’s fine with me.

    Since the transcription and translation mechanisms seem consistent through most cell types, I did not study them until this discussion now.

    I’ve ben more interested in the processes that cause the cellular diversity and their spatiotemporal distributions into interwoven tissues and organs within the biological systems. There’s where design really shines.

    But now that I finally looked into this fundamental genetic mechanism I think I understood your point about the physical discontinuity of the mechanistic components of the protein synthesis process.

    Perhaps the below text made me understand your point:

    The amino acid loaded onto the tRNA by aminoacyl tRNA synthetases, to form aminoacyl-tRNA, is covalently bonded to the 3′-hydroxyl group on the CCA tail. (Wikipedia)

    Apparently the enzyme does the association between the tRNA anticodon and the corresponding AA.

    Hence, the AAs don’t seem to have direct physical association to the anticodons. The association seems to be mediated by the given enzyme.
    Apparently the AAs get consistently attached to the CCA tails of corresponding tRNA molecules. The anticodon domains of the tRNA are the physical connection to the corresponding mRNA codons.

    The mentioned enzyme is the heroe that realizes the association between the anticodon domains of the tRNA and the AAs.

    Hence, in no moment the AAs appear directly bound to the codons or anticodons.

    Did I get this right now?

    Thanks.

  88. 88
    Dionisio says:

    UB, Virgil Cain

    Apparently this is the closest the AAs physically get to the mRNA codons:

    (mRNA codons) – (tRNA anticodon + tRNA CCA tail) – AA

    My question is: how do the aminoacyl tRNA synthetase enzymes associate the tRNA anticodons with the corresponding AAs?

    Where is that correspondence established?

    When?

    I’ll try to look for that info, but if someone else can post it here, I will appreciate it.

    Thanks.

    – clueless student

  89. 89
    Box says:

    Alicia Cartelli: 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.

    It is utterly nonsensical to look at a molecule in isolation and term its involvement in chemical reactions “function”. It doesn’t make sense, because one cannot speak coherently about “function” without the context of a larger system. “Function” is teleological and always implies a hierarchical relationship.

  90. 90
    Box says:

    Alicia Cartelli: Nature is the ultimate trial-and-error experiment, it hasn’t needed foresight to produce the diversity of species (…) we see today.

    Natural selection can only operate on viable organisms. IOW the production of viable organisms is entirely up to chance — trial-and-error. It’s relevant to quote Dawkins here:

    But, however many ways there may be of being alive, it is certain that there are vastly more ways of dead, or rather not alive. You may throw cells together at random, over and over again for a billion years, and not once will you get a conglomeration that flies or swims or burrows or runs, or does anything, even badly, that could remotely be construed as working to keep itself alive.
    [Dawkins]

    Natural selection has zero creativity; all it does is eliminate viable organisms — which isn’t helpful.
    So, how did humans come into existence?
    Evolutionist: “By chance alone, despite natural selection.”

  91. 91
    EugeneS says:

    I agree with those who say everything is designed. Of course, everything is designed except God, the Designer. But that is a matter of faith. Our conversation was much narrower as it was about biology. And I paraphrased the well known quote. The only difference between biology and everything else is perhaps that in biology design is scientifically recognizable (and yet that the designer is God, is remarkably still a matter of faith). So the primacy of faith is not compromised.

    I do not agree with the position that religious faith in Creator has scientific evidence in the strict sense of this word. It has pointers to it, for want of a better word, not scientific evidence. Otherwise, it is not faith anymore but a ‘proved theorem’.

    However, design is a different matter, strictly speaking. Design is only compatible with religious faith in the Creator of everything and the Giver of moral law, but strictly speaking does not entail it.

  92. 92
    Virgil Cain says:

    REC:

    What is your (non-materialist?) explanation?

    Programming- specifically the enzymes are programmed to recognize their specific tRNAs.

  93. 93
    Dionisio says:

    UB, Virgil Cain

    Here’s some additional information to answer my own questions posted @88:

    The attachment of amino acids to the 3?-end of tRNAs is catalyzed by the aminoacyl-tRNA synthetase (aaRS) family of proteins.

    aaRSs are ubiquitous and essential but only eukaryotes and a handful of bacteria have the full set of 20 enzymes, one for each canonical amino acid in the genetic code.

    tRNAs: Cellular barcodes for amino acids

    Edited by Manuel Santos

    Rajat Banerjee, Shawn Chen, Kiley Dare, Marla Gilreath, Mette Praetorius-Ibba, Medha Raina, Noah M. Reynolds, Theresa Rogers, Hervé Roy, Srujana S. Yadavalli, Michael Ibba

    DOI: http://dx.doi.org/10.1016/j.febslet.2009.11.013

    http://www.febsletters.org/art.....5/abstract

    It seems like the association between the anticodons and the AAs is facilitated by the existence of a specific enzyme from the aaRS family for each canonical AA in the genetic code, although apparently there are some variations of that ‘script’ as explained in the above referenced paper.

    Apparently every tRNA anticodon can be associated with the catalytic effect of a corresponding aaRS enzyme in order to attach the corresponding AA to the CCA tail of the given tRNA molecule.

    The aaRS enzymes seem to recognize both the anticodon domain and the CCA tail of the tRNA molecules, hence they can mediate the association between each mRNA codon and the corresponding canonical AA in the genetic code.

    Did I get this right this time?

    Again, I had not studied the transcription/translation mechanisms, but I’m glad I looked into this now, so I could understand what y’all were discussing about.

    The transcription/translation mechanisms, along with their corresponding post-transcriptional and post-translational mechanisms, undoubtedly very interesting, seem like basic regulatory (common) “tools” compared to higher level mechanisms underlying morphogenesis (morphogen gradient formation and interpretation) and cell fate specification/determination (intrinsic asymmetric division).

  94. 94
    Virgil Cain says:

    Dionisio- You are doing great. There isn’t much more to it- for example getting the right tRNA to the ribosome at the right time.

  95. 95
    bornagain77 says:

    as to:

    Alicia Cartelli: Nature is the ultimate trial-and-error experiment, it hasn’t needed foresight to produce the diversity of species (…) we see today.

    Aside from the fact that atheists live in outright denial of the design and purpose, (i.e. foresight), they see in nature and in life:

    “Yet the living results of natural selection overwhelmingly impress us with the appearance of design as if by a master watchmaker, impress us with the illusion of design and planning.”
    Richard Dawkins – “The Blind Watchmaker” – 1986 – page 21

    Michael Behe – Life Reeks Of Design – 2010 – video
    https://www.youtube.com/watch?v=Hdh-YcNYThY

    living organisms “appear to have been carefully and artfully designed”
    Lewontin

    “The appearance of purposefulness is pervasive in nature.”
    George Gaylord Simpson

    Francis Crick, co-discoverer of DNA, seems to have been particularly haunted by this illusion of seeing design everywhere he looked in molecular biology:

    “Biologists must constantly keep in mind that what they see was not designed, but rather evolved.”
    Francis Crick – What Mad Pursuit

    “Organisms appear as if they had been designed to perform in an astonishingly efficient way, and the human mind therefore finds it hard to accept that there need be no Designer to achieve this”
    Francis Crick – What Mad Pursuit – p. 30

    And aside from the fact that it is impossible for atheists to put their money where their mouth is and to live their lives as if there truly were no purpose for their life:

    The Heretic – Who is Thomas Nagel and why are so many of his fellow academics condemning him? – March 25, 2013
    Excerpt:,,,Fortunately, materialism is never translated into life as it’s lived. As colleagues and friends, husbands and mothers, wives and fathers, sons and daughters, materialists never put their money where their mouth is. Nobody thinks his daughter is just molecules in motion and nothing but; nobody thinks the Holocaust was evil, but only in a relative, provisional sense. A materialist who lived his life according to his professed convictions—understanding himself to have no moral agency at all, seeing his friends and enemies and family as genetically determined robots—wouldn’t just be a materialist: He’d be a psychopath.
    http://www.weeklystandard.com/.....tml?page=3

    Darwin’s Robots: When Evolutionary Materialists Admit that Their Own Worldview Fails – Nancy Pearcey – April 23, 2015
    Excerpt: Even materialists often admit that, in practice, it is impossible for humans to live any other way. One philosopher jokes that if people deny free will, then when ordering at a restaurant they should say, “Just bring me whatever the laws of nature have determined I will get.”,,,
    When I teach these concepts in the classroom, an example my students find especially poignant is Flesh and Machines by Rodney Brooks, professor emeritus at MIT. Brooks writes that a human being is nothing but a machine — a “big bag of skin full of biomolecules” interacting by the laws of physics and chemistry. In ordinary life, of course, it is difficult to actually see people that way. But, he says, “When I look at my children, I can, when I force myself, … see that they are machines.”
    Is that how he treats them, though? Of course not: “That is not how I treat them…. I interact with them on an entirely different level. They have my unconditional love, the furthest one might be able to get from rational analysis.” Certainly if what counts as “rational” is a materialist worldview in which humans are machines, then loving your children is irrational. It has no basis
    within Brooks’s worldview. It sticks out of his box.
    How does he reconcile such a heart-wrenching cognitive dissonance? He doesn’t. Brooks ends by saying, “I maintain two sets of inconsistent beliefs.” He has given up on any attempt to reconcile his theory with his experience. He has abandoned all hope for a unified, logically consistent worldview.
    http://www.evolutionnews.org/2.....95451.html

    Existential Argument against Atheism – November 1, 2013 by Jason Petersen
    1. If a worldview is true then you should be able to live consistently with that worldview.
    2. Atheists are unable to live consistently with their worldview.
    3. If you can’t live consistently with an atheist worldview then the worldview does not reflect reality.
    4. If a worldview does not reflect reality then that worldview is a delusion.
    5. If atheism is a delusion then atheism cannot be true.
    Conclusion: Atheism is false.
    http://answersforhope.com/exis.....t-atheism/

    And aside from the fact that it is impossible for atheists to even do science in the first place without presupposing teleology on some level:

    tel·e·ol·o·gy
    Philosophy
    the explanation of phenomena by the purpose they serve rather than by postulated causes.
    Theology
    the doctrine of design and purpose in the material world.

    Design Thinking Is Hardwired in the Human Brain. How Come? – October 17, 2012
    Excerpt: “Even Professional Scientists Are Compelled to See Purpose in Nature, Psychologists Find.” The article describes a test by Boston University’s psychology department, in which researchers found that “despite years of scientific training, even professional chemists, geologists, and physicists from major universities such as Harvard, MIT, and Yale cannot escape a deep-seated belief that natural phenomena exist for a purpose” ,,,
    Most interesting, though, are the questions begged by this research. One is whether it is even possible to purge teleology from explanation.
    http://www.evolutionnews.org/2.....65381.html

    “virtually all of science proceeds as if ID is true – it seeks elegant and efficient models; it reverse engineers biological systems; it describes evolution in teleological terms; it refers to natural forces and laws as if there is some kind of prescriptive agency guiding matter and energy; it assumes that the nature of the universe and human comprehensive capacity have some sort of truthful, factual correspondence.”
    William J Murray

    “to say that a stone falls to earth because it’s obeying a law, makes it a man and even a citizen”
    – CS Lewis

    And aside from the fact that it is impossible for atheists, or anybody else for that matter, to describe molecular biology without abundant reference to words that imply agency, purpose, and design, (i.e. foresight):

    The ‘Mental Cell’: Let’s Loosen Up Biological Thinking! – Stephen L. Talbott – September 9, 2014
    Excerpt: Many biologists are content to dismiss the problem with hand-waving: “When we wield the language of agency, we are speaking metaphorically, and we could just as well, if less conveniently, abandon the metaphors”.
    Yet no scientist or philosopher has shown how this shift of language could be effected. And the fact of the matter is just obvious: the biologist who is not investigating how the organism achieves something in a well-directed way is not yet doing biology, as opposed to physics or chemistry. Is this in turn just hand-waving? Let the reader inclined to think so take up a challenge: pose a single topic for biological research, doing so in language that avoids all implication of agency, cognition, and purposiveness1.
    One reason this cannot be done is clear enough: molecular biology — the discipline that was finally going to reduce life unreservedly to mindless mechanism — is now posing its own severe challenges. In this era of Big Data, the message from every side concerns previously unimagined complexity, incessant cross-talk and intertwining pathways, wildly unexpected genomic performances, dynamic conformational changes involving proteins and their cooperative or antagonistic binding partners, pervasive multifunctionality, intricately directed behavior somehow arising from the interaction of countless players in interpenetrating networks, and opposite effects by the same molecules in slightly different contexts. The picture at the molecular level begins to look as lively and organic — and thoughtful — as life itself.
    http://natureinstitute.org/txt.....ell_23.htm

    Life, Purpose, Mind: Where the Machine Metaphor Fails – Ann Gauger – June 2011
    Excerpt: I’m a working biologist, on bacterial regulation (transcription and translation and protein stability) through signalling molecules, ,,, I can confirm the following points as realities: we lack adequate conceptual categories for what we are seeing in the biological world; with many additional genomes sequenced annually, we have much more data than we know what to do with (and making sense of it has become the current challenge); cells are staggeringly chock full of sophisticated technologies, which are exquisitely integrated; life is not dominated by a single technology, but rather a composite of many; and yet life is more than the sum of its parts; in our work, we biologists use words that imply intentionality, functionality, strategy, and design in biology–we simply cannot avoid them.
    Furthermore, I suggest that to maintain that all of biology is solely a product of selection and genetic decay and time requires a metaphysical conviction that isn’t troubled by the evidence. Alternatively, it could be the view of someone who is unfamiliar with the evidence, for one reason or another. But for those who will consider the evidence that is so obvious throughout biology, I suggest it’s high time we moved on. – Matthew
    http://www.evolutionnews.org/2.....nt-8858161

    The formal Darwinism project – June 2015
    Excerpt: Today, as molecular biologists choose to call some of their discoveries ‘mechanisms’, and ascribe ‘functions’ to enzymes, they use purposive language and so they also adopt the design approach. It is arguably impossible to undertake work in many areas of biology without doing so: purpose in explanations has great power, and attempts to do without it in ethology,,, have long ago been abandoned as unworkable.
    of note: *Ethology is the scientific and objective study of animal behaviour
    https://scientiasalon.wordpress.com/2015/06/15/the-formal-darwinism-project/

    Aside from all that hidden teleology that is in the atheists worldview, in regards to goal directed processes, (i.e. teleology), atheist have another huge elephant in the living room that they live in denial of.

    Specifically, embryological development, where one cell turns into the final ‘reproducing adult product’ of trillions of cells, is clearly a massively goal directed process.

    The Deeper Issues of the Worm Video Debate: P.Z. Myers’s Misdirection – Paul Nelson – May 7, 2015 (with C. elegans video link)
    Excerpt: ,,,while Myers agrees that evolution possesses no foresight, he overlooks the key logical point that natural selection operates only downstream of successful (i.e., functional) novel variations.,,,
    Given that reproduction is a necessary condition of natural selection, however, selection is powerless to act until reproductive capability comes online. Randomly arising mutations must therefore construct novel developmental pathways “on their own” — with crash-and-burn of the whole system as the most likely result.,,
    http://www.evolutionnews.org/2.....95891.html

  96. 96
    bornagain77 says:

    FLIGHT: The Genius of Birds – Embryonic development – video
    http://www.youtube.com/watch?v=-Ah-gT0hTto

    Moreover, in humans themselves, as all teenagers are well aware, reproductive capability does not ‘come online’ until practically all of the goal directed process of development has already occurred.
    To say that Darwinists lack a coherent explanation as to how these amazing, massively, goal directed processes of development can possibly occur, with reproductive capability being so far downstream in the process, is a gross understatement.

    When one considers the sheer magnitude of the developmental process involved in creating a human out of a billion-trillion protein molecules, “without foresight” is certainly not the term that comes to one’s mind,

    Alexander Tsiaras: Conception to birth — visualized
    http://www.youtube.com/watch?v=fKyljukBE70

    Mathematician Alexander Tsiaras on Human Development: “It’s a Mystery, It’s Magic, It’s Divinity” – March 2012
    Excerpt: ‘The magic of the mechanisms inside each genetic structure saying exactly where that nerve cell should go, the complexity of these, the mathematical models on how these things are indeed done, are beyond human comprehension. Even though I am a mathematician, I look at this with the marvel of how do these instruction sets not make these mistakes as they build what is us. It’s a mystery, it’s magic, it’s divinity.’
    http://www.evolutionnews.org/2.....57741.html

    Frank Turek Christ Community Church (April 2015) – video – (goal directed embryogenesis 27:10 minute mark)
    https://youtu.be/iKFfq-IwcrM?t=1629

    HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE – Stephen L. Talbott – May 2012
    Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,,
    Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling… and so on without end. Yet the coherence of the whole is maintained.
    The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?”
    The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary.
    Two systems biologists, one from the Max Delbrück Center for Molecular Medicine in Germany and one from Harvard Medical School, frame one part of the problem this way:
    “The human body is formed by trillions of individual cells. These cells work together with remarkable precision, first forming an adult organism out of a single fertilized egg, and then keeping the organism alive and functional for decades. To achieve this precision, one would assume that each individual cell reacts in a reliable, reproducible way to a given input, faithfully executing the required task. However, a growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type. (Loewer and Lahav 2011)”,,,
    And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.,,,
    http://www.netfuture.org/2012/May1012_184.html#2

    Moreover as if all that was not completely devastating to the proposed unguided material processes of neo-Darwinian evolution, in metamorphic creatures, such as in butterflies, the miracle of development happens twice before reproductive capability comes online.
    Dr. Paul Nelson, at the 12:21 minute mark of the following video, comments that metamorphosis is, by all rights, a miracle with no possible naturalistic explanation as to how it came about:

    The Miracle of Development Part 1 – Origins with Dr. Paul A. Nelson – video – April 2013
    http://www.youtube.com/watch?v.....age#t=736s

    Moreover this miracle of metamorphosis is widespread:

    From Discovering Intelligent Design: My How You’ve Changed – May 26, 2013
    Excerpt: Holometabolism (complete metamorphosis) is the most common and complicated form of insect maturation. The diverse group that undergoes this type of process includes butterflies, moths, beetles, fleas, bees, ants, and many kinds of flies.,,,
    It is exceedingly difficult to understand the origin of holometabolism in Darwinian evolutionary terms. Neither the larval nor the pupal stage is capable of reproduction — only the adult is. In particular, the pupal stage is an all-or nothing proposition. It must complete the process and become an adult, or it will die without ever reproducing.
    The liquefied organism must be completely rebuilt. For this to occur, large amounts of information — encoding the larval body plan, the mechanisms of transformation during metamorphosis, and the adult body plan — must exist before the larva enters this stage. An organism could not survive complete metamorphosis unless the entire process was fully programmed from the beginning. Such a large jump in complexity requires forethought and planning — things that don’t exist in Darwinian evolution. As one evolutionary entomologist acknowledges:
    “… the biggest head-scratcher in evolutionary biology would have to be the origin of the holometabolous insect larva.”
    http://www.evolutionnews.org/2.....72521.html

    Moreover, besides butterflies, and other insects, it turns out that some, (perhaps many?), of the Cambrian creatures also harbored this amazing ‘2 for 1’ metamorphic capability that butterflies and other insects possess:

    The Enigma of Metamorphosis Is Hardly Limited to Butterflies – October 2011
    Excerpt: Even more mysteriously, it appears that the most ancient phyla were metamorphic from the beginning, based on the few larval forms that have been preserved. This suggests that these Cambrian animals had not one but two or more developmental stages at the outset,,,,
    http://www.evolutionnews.org/2.....51541.html

    Metamorphosis Is Widespread – Ann Gauger – video
    http://www.youtube.com/watch?v=GkD-jd1imaI

  97. 97
    Dionisio says:

    Virgil Cain @92

    Programming- specifically the enzymes are programmed to recognize their specific tRNAs.

    Yes, the fact that a precise spatiotemporal regulatory system guarantees the presence of tRNA carriers and specific aaRS enzymatic proteins for catalyzing the association of the translated mRNA codons with their corresponding AAs, in order to synthesize other proteins, is indeed amazing.

    Complex complexity. 🙂

  98. 98
    Dionisio says:

    UB

    Thanks for the email answer.

    Have a good weekend.

  99. 99
    Virgil Cain says:

    Perry Marshall has a challenge for evos on the origin of information:

    The Origin of Information: How to Solve It

    Here is the setup: The Atheist’s Riddle: Skeptics Attempt To Solve It

  100. 100
    Alicia Cartelli says:

    No, mapou, we’re not even close to even. You guys are lightyears behind and not going anywhere fast.

    Like I said, Upright, always a good chat with you.

  101. 101
    Virgil Cain says:

    Alicia Cartelli- Please go soak your head as you are lightyears behind and you don’t have a clue.

    You are always good for a laugh, though. Come back when your position has an explanation for what we observe happening inside a cell.

  102. 102
    Alicia Cartelli says:

    Virg, buddy, remember when you tried to tell me there were no covalent bonds between RNA and amino acids in the translational system and I had to correct you?

    The first half of your comment 76 also makes no sense. The codon is always on the mRNA and anticodon always on the tRNA. End of story. Dio actually sounds like he knows what he’s talking about more than you do. (That’s not good for you).

    I really need you to stop trying to talk about biology, I might die from laughter.

  103. 103
    Virgil Cain says:

    Alicia- You screwed up because you don’t know anything. There aren’t any bonds between the mRNA codon and the amino acid they represent. I told you that and you still choose willful ignorance.

    Biologists also say the codon is on the DNA- sense/ anti-sense. So stuff it.

    You are obviously just an ignorant arse.

    My comment in 76 could be understood by a middle school biology student. It’s very telling that it went over your pointed head.

  104. 104
    Alicia Cartelli says:

    Virg, your statement was:
    “There isn’t any chemical bonds between nucleotides and amino acids in the observed translation systems.”
    And it is completely and utterly incorrect.

    And no, codons cannot be on both the sense/antisense strands of DNA, you would get two different predicted protein sequences from them.

    Wrong again Virg, thanks for playing. Goodbye!

  105. 105
    Virgil Cain says:

    Alicia- CONTEXT- we were talking about the mRNA codons- so grow up.

    And no, codons cannot be on both the sense/antisense strands of DNA, you would get two different predicted protein sequences from them.

    Codons can be on both, Alicia. Both sides can be transcribed. That means it all depends on which is the codon. But tat wasn’t even the point you moron.

    Your ignorance, while amusing, means nothing.

  106. 106
    Dionisio says:

    Virgil Cain @103

    There aren’t any bonds between the mRNA codon and the amino acid they represent.

    That seems correct. Apparently, for every canonical AA associated with the genomic code there’s a specific aaRS enzyme that recognizes the tRNA anticodon domain and attaches the corresponding AA to the tRNA CCA tail.

    I don’t recall seeing anywhere in the available literature that I reviewed any reference to direct bonds between the codons and the AAs. However, I know nothing about biology, hence it’s possible that your interlocutor has access to paywalled academic papers that contain the latest research information unavailable to you and me.

    BTW, you may talk all you want to about biology or anything else you want to. Don’t let the voices of this dying world tell you what to do. They have no clue whatsoever, but sadly they are not aware of the miserable condition they’re in.

    I was in that same condition for a long time, but God graciously pulled me out of that path that leads to eternal separation from His glory. Hallelujah!

    I pray for our interlocutors. They don’t know that God loves them too. We are not better than them. Perhaps some of them will be graciously rescued from their hopeless situation before it’s too late.

  107. 107
    Mung says:

    Virgil Cain:

    If you say the mRNA has the codons then the tRNA would have the anti-codons.

    I just don’t see what Alicia finds so hilariously funny about this.

  108. 108
    Virgil Cain says:

    It’s the following she finds funny:

    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.

    She doesn’t realize that is all perspective. That is why I included the “If” at the front of both sentences. Meaning Alicia is also ignorant of English

  109. 109
    Axel says:

    I love these invective ‘rumbles’! Two cage-fighters I think Alicia is winning as she manages to send Virg into transports of fury. But that may be because she’s doing the atheists’ thang of talking genuine twaddle and putting her ‘case’ across with a certain feline hauteur, that’s getting under Virg’s skin. Even her name is kinda feline, isn’t it? Alicia. Slides rather than rolls off the tongue.

    But I hope she’s not like the French general, Giraud, who was described by a fellow-officer as having ‘the uncomprehending eyes of a porcelain cat – so stately.. and stupid.’

    I dinnae ken though. So, I may be reviled by both, though I think they have enough scientific ‘stuff’ to keep them occupied.

  110. 110
    Virgil Cain says:

    Dionisio:

    I don’t recall seeing anywhere in the available literature that I reviewed any reference to direct bonds between the codons and the AAs. However, I know nothing about biology, hence it’s possible that your interlocutor has access to paywalled academic papers that contain the latest research information unavailable to you and me.

    That would be big news and trumpeted by evos everywhere. No trumpets means no big news. 😎

  111. 111
    Virgil Cain says:

    LoL! @ Axel- Alicia is winning by misrepresentation and equivocation. Oh wait, that’s not winning at all…

  112. 112
    Axel says:

    From a cage-fighting perspective it looks that way, though, Virg. It may be precise, but I think ‘twaddle’ is a passable precis of ‘misrepresentation and equivocation’.

    But ‘you moron’ is not very gallant, said to a lady, Virg, however loudly it made me explode with laughter!

    ‘Toodaloo’ was good, Alicia!

  113. 113
    Virgil Cain says:

    From a cage-fighting perspective Alicia has been body slammed and knocked out. “Toodaloo” was all she had- and she ran away after another huge misrepresentation. “you moron” was very accurate and I doubt Alicia Cartelli is a lady, Axel.

  114. 114
    Axel says:

    Heck, I shoulda thought of that. The multiverse starts here!

Leave a Reply