Monday, October 5, 2009

Replicating Damaged DNA

You probably remember that before a cell can divide into two daughter cells its DNA must be replicated into two duplicate copies. But what you didn't learn in high school biology class is what happens when the DNA is damaged. First let's review normal DNA replication.

Normal DNA Replication

DNA consists of pairs of long molecular strands, and a small army of proteins performs a series of fascinating and complex tasks to make a copy of these paired strands. At designated starting points the strands are separated and each strand then serves as a template upon which a new copy of the other, complementary strand is synthesized.

In the end, the result is two pairs of strands where originally there was just one pair. One intriguing aspect of this operation is that the synthesis is performed in opposite directions on each strand. That is, as the strands are unzipped a "Y" is formed. On one of the single strands, the proteins synthesize a new strand continuously as the original DNA strands are unzipped. This way, as more strand becomes exposed it quickly is covered with a newly synthesized strand.

On the other single strand, however, the proteins synthesize the new strand in the opposite direction, away from the unzipping action. This makes sense because paired DNA strands are chemically anti-parallel. But this makes for a complex process.

As the strand is exposed due to unzipping, the proteins start close to the intersection of the "Y" at the location that has most recently been exposed. The proteins then move away from the intersection as they synthesize the new strand.

At some point the proteins halt, move back toward the intersection of the "Y", and begin the process again on the newly exposed section of strand. Hence on one of the strands replication is continuous (the "leading" strand), and on the other strand replication is discontinuous (the "lagging" strand).

Did it Evolve?

Can you see why evolution is not a very good scientific theory? Evolutionists want us to believe that, in addition to the DNA molecule and its information, this incredible DNA replication process just arose all on its own. And of course this is only the beginning (the DNA has to be used somehow, for instance).

How do evolutionists respond to such criticism? They say that with evolution we are not allowed to be incredulous. Why? Because such disbelief is not scientific.

This means that with evolution one need not search for likely explanations. It is the perfect venue for speculation. Of course anything can happen, but the evolution narrative makes fairy tales appear likely by comparison. How many miracles are we supposed to swallow? Well here is one more.

The normal DNA replication process won't work very well when DNA is damaged, by radiation for example. When such damage is detected the normal copying machines are paused and a special "sloppier copier" is ushered in to do the job. This backup copying machine is able to replicate a damaged section of DNA by not reading it so precisely. This means that there are more copying errors, but a copy with more errors is better than no copy at all.

So now we are to believe that in addition to the normal DNA copying machines, this "sloppier copier" also just happened to evolve along with helper machines that tell it when and where to go to work.

It is remarkable that the theory of evolution is taken seriously. What is utterly astonishing, though, is that evolutionists insist that, every bit as much as gravity, it is a fact.


  1. This shows how crazy complex DNA repair is:

    How could this be the result of a random process?

  2. this shows how crazy the process of ketchup becoming thinner when you whack the bottle is:

    how could this be the result of a random process?

  3. "this shows how crazy the process of ketchup becoming thinner when you whack the bottle is:

    how could this be the result of a random process?"


  4. I don't see the connection between ketchup and an example of complex machinery with lots if interdependant parts.

    And the post is about how cells cope wioth damaged DNA. I just posted an example.

  5. just showing that even the seemingly simplest things are incredibly complex. does this mean that the shear-thinning process was designed? this is esp. true since we still don't totally understand how this process occurs, despite decades of research. furthermore, ketchup is a non-Newtonian fluid and thus represents a glaring example of failed Newtonian theory. yet Newtonianists still insist their theory is as much a fact as the theory of gravity. unbelievable.

  6. Khan: Your analogy with ketchup is completely inadequate. We're not talking about fluid dynamics or mere physical laws, we're talking about a process that does specific and organized work.
    Comparing DNA rep. to flowing ketchup is like comparing the photocopy process to mere flowing ink.

  7. The complexity of flowing ketchup is probably contained in the laws that govern fluids. But the complexity of a cell does not follow from the laws of physics and chemistry.

    And why is ketchup non-Newtonian?

  8. Hitch, but if ink didn't flow then the photocopier wouldn't work, would it? and a very complex, specific set of molecular interactions (which are still not well understood) involving numerous interdependent parts have to happen to make it flow correctly. so are fluids designed as well?

  9. "The complexity of flowing ketchup is probably contained in the laws that govern fluids." if you know how, NASA and the entire physics community would like a word with you.

    ketchup is non-Newtonian because it doesn't conform to the assumption of constant viscosisty in Newton's formulations. just another example of a failed Newtonian assumption.

    "But the complexity of a cell does not follow from the laws of physics and chemistry. "
    are you saying that cells break laws of chemistry and physics? again, the entire scientific community would like to know how


  11. Thwe orgin of cells cannot be explained by the laws of physics, just like the origin of watches can't.

    And where does Newton talk about viscosity?

    I imagine that ketchup is like the three body problem. Complex calculations are beyond humans ability to predict, but nothing happens that violates the laws of physics.

  12. so, in your opinion, are both the origin of cells and the flow of ketchup "beyond humans ability to predict"? if so, why do you claim one requires design and the other doesn't? they are both mysteries, but neither one violates any fundamental laws of physics or chemistry.

  13. Hey Moiz Khan, Its very obvious that you spend a LOT of time trying to justify your atheist evolutionary stance. Why do you think this is? Ok, I'll tell you! You were born with a moral code that KNOWS there is a God.

  14. thanks for the bogey moment

  15. By the way Moiz Khan, your website seems to be a self-glorification cry for help.

  16. whatever. are you going to answer my questions or not?

  17. Again the reasoning presented is ... poorly thought-out. The strategy: list a complex system carrying out a precise function. List all its parts. Then imply that it came about "all by itself" (as opposed to through a process of inheritance, mutation, and selection over a very long period of time) without precursors which acted a bit differently or with (gasp!) different machinery.

    The response to my claim will surely be an attempt to put the onus on me to prove to your satisfaction that exactly what I said happened: that there were precursors, I know what they are, and I can demonstrate them thusly. But that would miss the point and the entire context here: Cornelius is saying that it's unreasonable to think these systems could have evolved. With a tiny bit of biological knowledge, I can think up all kinds of reasonable pathways he has not excluded. Furthermore, inheritance and selection are well-demonstrated in biology, as opposed to a successful and predictive design inference. There's a nice saying by Orgel that applies (almost always, here): evolution is cleverer than you are.

    It's pretty funny that he set up a tiny martyr complex, too... oh no, he's "not allowed" to be incredulous of evolution, it isn't scientific! It would be just terrible if some poorly-reasoned denialism earned disrepect!

  18. The origin of cells does violate second thermodynamics. Ketchup flow is merely hard to predict. And I'm not sure that hard to predict equals complexity.

  19. To the best of my knowledge a the evolution of a complete knew protein pathway or structure has not actually been observed. Correct me if I'm mistaken.

  20. "THe origin of cells does violate second thermodynamics"

    really? in what way?

  21. Because complex things can't put themselves together.
    All that entropy. And adding enrgy to the system would tend to break it apart, not put it together. Unless it is added in very controlled way. This is what machines do. They control the enrgy flow through a system. Buit machines were created by clever people.

  22. Or if the energy is absorbed in a semi-controlled fashion...

    Let's start with some basics. If cells violate any of the laws of thermodynamics, state how and why. I expect actual calculations.

    If 'complex things' can't put themselves together, you need a coherent and reliable definition of what constitutes a 'complex thing'. Otherwise, who would know when what you're claiming applies and who would know whether it can even be said to be accurate? Is the solar system complex enough for you? It sure doesn't seem to need a designer, I'm sure you're quite comfortable with the physics explaining the formation of such ordered systems.

    If you throw some amphiphilic compounds into water (polar), they will group with the polar ends to the water and lipophilic ends on the 'inside' of something which is or resembles a micelle. Is that complex enough? Who could say, but it sure is a property emerging straight from the chemistry (literally adding the compound and observing).

    Add such compounds and sonicate and you can get liposomes. Again, not terribly specific reagents or methods and you get a membrane.

  23. Things that have interconnecting parts that fit and act together would be a good definition of complexity. And the function of cells does not violate second thermodynamics, but the origin of cells does spntaniously from small molecules does.

  24. And the cell membrane is extemely complex. It has kinds of receptors and gates and such.
    And the complxity is critical to the function of the cell. Nothing like a bubble membrane.

  25. Adn what your describing is a process done ina lab by intelligent scientists. All that sonicating, and adding of reagents. We already konw that scientists can make complex things. The trick is finding out how to do it ina purely natural environment.

  26. How does the origin of cells violate the second law of thermodynamics? Again, I asked for your math, as would be required. You might find the problem in your statement when attempting to do so.

    Cell membranes are chock full of proteins. It doesn't make a liposome any less of a membrane, even made of the same 'base' stuff as our own membranes!

    If adding reagents = intelligent design, Anonymous, then all of the discoveries in chemistry require a designer. So would the laws of physics by extension: not the written laws or written chemistry, but the actual things going on. In other words, you're trying to tell me that if we add sulfuric acid to benzene and NO2, a resulting aromatic compounding is too tinged with design to happen 'naturally', that merely being in the same *area* is too much design. How have you determined this? Furthermore, if you're asking for operational science but won't accept situations where scientists add reagents and observe, you're asking for the impossible, by definition.

    The facts remain the same: single or double-layered membranes emerge from pretty simple actions, the properties of amphiphilic compounds in a polar environment (you can also get similar, but reversed, situations in apolar environments). I don't doubt that were this not demonstrated, you'd find the very emergence of membranes far too complex to happen 'by themselves'.

  27. A liposome would not work for a cell. Cells need the complex membranes. So saying that liposomes can form membranes doesn't help explain how life formed.

    And the rules are that the onjly explanations naturalistic ones. That means that you have to explain how cell membranes formed under naturalistic conditions without intellignet intervention. I'm not talking about discovering things. I'm talking about making things. You can't say that the fact that something was made in a lab by humans means that it can be made in nature without intervention. Inventions, not discoveries require intervention.

  28. I'd be happy with a situation that can be found in nature. If sulfuric acid, benzene and NO2 can be found toghetrh in nature, then that wouldn't need intervention.

  29. A plasticv bag is a membrane, but it won't work for a cell.

  30. According to this article, evolution can be thought of as an increase in entropy in the environment.

    But that only works if you've already got the mechanisms in place. I'm asking about the origin of the cell, and those mechanisms.

    Entropy can be descibed as the natural log of the number of states a system can be in times Boltzman's constant. Now, since the number of states small molecules can be in is much greater if they do not join to form a cell, then the joining of small molecules to form a cell results in a loss of entropy. I hope I got the math right.

  31. Anonymous said, "A liposome would not work for a cell. Cells need the complex membranes. So saying that liposomes can form membranes doesn't help explain how life formed."

    It does, as it shows that the phosopholipid component is something which forms spontaneously fairly mundanely. And that wasn't even my point, the point was in demonstrating that your lack of imagination is not equivalent to reasonable doubt or refutation. If it weren't so easy for liposomes or micelles to come about, I don't doubt you'd be telling me how terribly complex they are and difficult for them to come about it is. You might even try to sell me some nonsense about how it violates the second law of thermodynamics because the molecules are 'coming together'. Sound familiar?

    "And the rules are that the onjly explanations naturalistic ones."

    OK? What's the context of this comment? I'm guessing you're responding to my point about the impossibility of your apparent request, which is for operational science which doesn't have people manipulating the scenario? You haven't been terribly specific about what's so bad and designerish about adding amphiphilic compounds to water, so I came up with a very reasonable explanation.

    "That means that you have to explain how cell membranes formed under naturalistic conditions without intellignet intervention."

    That doesn't follow. Naturalistic is not equivalent to, 'you can't design and manipulate experiments', I have no idea why you'd even think that unless it's a response to having bad ID arguments pointed out. Do you honestly think that every experiment in operational science isn't scientific? Even if that 'rule' existed (it doesn't), it doesn't follow that I need to provide any explanation to you at all. Designer-by-default is theistic presupposition.

    Plastic bags aren't single or double-layered amphiphilic membranes... why not stop trying to come up with gotcha responses (which don't work) and read up on science instead? I'm going to get tired of correcting you soon, as you don't actually admit to learning or correcting yourself when wrong.

    "I'd be happy with a situation that can be found in nature. If sulfuric acid, benzene and NO2 can be found toghetrh in nature, then that wouldn't need intervention."

    They can be, easily. However, I'm pretty sure you missed my point with respect to membranes. It's about using pure doubt (not skepticism) and the limits of your imagination as guides to whether or not biology works a particular way or came about in a certain way.

    I answered your use of the PhysOrg article in another thread... I don't think you understand what they were saying, as it works against your general ideas.

    You didn't use any math, Anonymous, you listed a concept in physical chemistry which is extremely useful in considering entropy and then misused it. First, the applicability of the model works only if you are considering a closed system. You will find that it fails in open systems because disequilibrium is a fact of the universe. If you have determined that cells as well as their precursors are closed systems, go ahead and demonstrate it. It's in conflict with our current understanding.