Wednesday, July 25, 2012

Bacterial Protein Acetylation: The Dawning of a New Age

Molecular biology is not only a story of complex molecules, machines and processes but also of massive information flow via a variety of molecular messages. And while information flow is often associated with the DNA macromolecule, there are less celebrated but ubiquitous armies of molecular machines that are busy attaching, modifying and removing small chemical tags to and from both DNA and proteins. It is a massive information network and these chemical tags—such as methyl, hydroxyl and phosphate groups—act as a sort of molecular modifier or barcode regulating a diverse array of cellular functions. Another molecular barcode is the acetyl group, long thought to be mainly at work in eukaryotes, has now found to be important in bacteria as well. It is, as one evolutionist put it, the “dawning of a new age.” (click above)

According to evolutionists, life began simple and gradually increased in complexity. Therefore early life should be simpler life. And so evolutionists have continually been surprised to find high complexity throughout the living world. As the research paper concluded:

Bacteria have long been considered simple relatives of eukaryotes. Obviously, this misperception must be modified. From the presence of a cytoskeleton to the packaging of DNA to the existence of multiple post-translational modifications, bacteria clearly implement highly sophisticated mechanisms to regulate diverse cellular processes precisely.

With evolution we now must believe that even protein acetylation miraculously appeared very early in the history of life. This would require (i) the enzymes to attach and remove the acetyl groups, (ii) the capability to attach those groups at the right place and under the right conditions, and (iii) of course right influence such that the presence of the acetyl groups produced the needed functional modification.

And all of this must have occurred spontaneously. As per evolutionary theory, the changes must have occurred at random. In other words, the need at hand could not have influenced the changes. Those astronomically unlikely, incredibly complex, changes must have arisen to create the phenomenal protein acetylation functionality, so that it then could be selected for. There is no scientific evidence for a long, gradual series of designs leading to this capability. Even for a single protein this evidence is lacking.  It is yet another example of dashed expectations even in this New Age.

49 comments:

  1. ,,,It is interesting to point out that even the protein machinery that replicates DNA is found to be vastly different:

    Did DNA replication evolve twice independently? - Koonin
    Excerpt: However, several core components of the bacterial (DNA) replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic (DNA) replication apparatus.
    http://nar.oxfordjournals.org/cgi/content/full/27/17/3389

    There simply is no smooth 'gradual transition' to be found:

    Was our oldest ancestor a proton-powered rock?
    Excerpt: In particular, the detailed mechanics of DNA replication would have been quite different. It looks as if DNA replication evolved independently in bacteria and archaea,... Even more baffling, says Martin, neither the cell membranes nor the cell walls have any details in common.
    http://www.newscientist.com/article/mg20427306.200-was-our-oldest-ancestor-a-protonpowered-rock.html?page=1

    Problems of the RNA World - Did DNA Evolve Twice? - Dr. Fazale Rana - video
    http://www.metacafe.com/watch/4564682

    An enormous gap exists between prokaryote cells and eukaryote type of cells. A crucial difference between prokaryotes and eukaryotes is the means they use to produce ATP (energy).
    http://www.trueorigin.org/atp.asp

    Mitochondria - Molecular Machine - Powerhouse Of The Cell - video
    http://www.metacafe.com/watch/5510941/

    On The Non-Evidence For The Endosymbiotic Origin Of The Mitochondria - March 2011
    http://www.uncommondescent.com/intelligent-design/on-the-non-evidence-for-the-endosymbiotic-origin-of-the-mitochondria/

    On the Origin of Mitochondria: Reasons for Skepticism on the Endosymbiotic Story -
    Jonathan M. - January 10, 2012
    Excerpt: While we find examples of similarity between eukaryotic mitochondria and bacterial cells, other cases also reveal stark differences. In addition, the sheer lack of a mechanistic basis for mitochondrial endosymbiotic assimilation ought to -- at the very least -- give us reason for caution and the expectation of some fairly spectacular evidence for the claim being made. At present, however, such evidence does not exist -- and justifiably gives one cause for skepticism.
    http://www.evolutionnews.org/2012/01/on_the_origin_o054891.html

    Further note:

    Bacteria Too Complex To Be Primitive Eukaryote Ancestors - July 2010
    Excerpt: “Bacteria have long been considered simple relatives of eukaryotes,” wrote Alan Wolfe for his colleagues at Loyola. “Obviously, this misperception must be modified.... There is a whole process going on that we have been blind to.”,,, For one thing, Forterre and Gribaldo revealed serious shortcomings with the popular “endosymbiosis” model – the idea that a prokaryote engulfed an archaea and gave rise to a symbiotic relationship that produced a eukaryote.
    http://www.creationsafaris.com/crev201007.htm#20100712b

    Even more problematic for evolutionists than the unexplained gap between prokaryote and eukaryote is that even within the 'bacterial world' there are enormous unexplained gaps of completely unique genes within each different type of bacteria:

    ORFan Genes Challenge Common Descent – Paul Nelson – video with references in description
    http://www.vimeo.com/17135166

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  2. Once again, the evidence is not on the side of evolutionists. How many more outs does their "theory" get?

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  3. And all of this must have occurred spontaneously.

    With spontaneously you mean without Jesus, right? Jesus woke up one day and decided to add some acetylation capabilities to his little creatures the bacteria. That's your theory?

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    Replies
    1. So you're not interested in offering some kind of critique, just insults?

      Just curious, what makes you think Jesus sleeps?

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    2. Jason Kay

      So you're not interested in offering some kind of critique, just insults?


      What exactly do you think need critiquing? It's the same standard boilerplate personal incredulity that's been offered here for years, i.e.

      "ZOMG look how complex this is, it's really really really complex, therefore JEEBUS!"

      The OP wasn't exactly a scientific assessment of the data, ya know?

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    3. Personal incredulity, my foot. The complexity argument against evolution and the spontaneous arrival of life is an extremely powerful argument. Most critics like to point out that the odds are astronomical. I think they are missing the target. There is absolutely zero probability that complex life could have arisen on its own, let alone evolve into complex species. The reason is that the forces that are trying to destroy life are orders of magnitude more plentiful than the constructive forces.

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    4. This is your theory. And the scientists should search for evidences against it.
      But, if these evidences will be found, the theory can be moddified or the data should be on suspect, and you can say that the gaps will be filled anytime.
      The theory of evolution should be replaced for the good health of science. But, in the case of the present state of science can not provide an alternative, the conclusion is: "the science does not have a good explanation".

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    5. Exactly- we do not need a replacement before canning a failed "theory".

      Delete
    6. If a replacement is not necessary, then how do you get around the problem of extrapolating data without an explanatory theory?

      To use an example, why didn't observations of neutrinos traveling from the LHC to OPRA immediately falsify Einstein's theory that nothing can travel faster than the speed of light? Because they had yet to develop an alternative theory to explain those same observations.

      In other words, observations are meaningless in the sense you're referring to without an alternative explanation to interpret them.

      And when we finally did come up with an explanation for the observations it ended up being an error in how the experiment was performed.

      So, observations tell us nothing either way without an explanatory framework to extrapolate them.

      Of course, if you'd like to enlighten us with a way to extrapolate observations without first putting them into an explanatory framework that actually works, in practice, I'm all ears.

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    7. Scott:
      If a replacement is not necessary, then how do you get around the problem of extrapolating data without an explanatory theory?

      Why do we need a theory before we can extrapolate data?

      Even without Einstein the observation of faster than light neutrinos would be fascinating and something to study.

      If we observed anti-biotic resistence we wouldn't need any theory of evolution to observe it and then attempt to explain it.

      Observations tell us quite a bit- they are the stuff of science and give us something to figure out.

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    8. Joe G: If we observed anti-biotic resistence we wouldn't need any theory of evolution to observe it and then attempt to explain it.

      We start with a single bacterium, and allow it to reproduce. After we have a large number, we expose them to antibiotics. Most of them die, but a few survive. These survivors are allowed to reproduce, and we see that their offspring are also able to survive exposure to antibiotics. We notice differences between the genomes of the resistant survivors and the parent. One of these differences is consistent across many such experiments.

      Let's call this "evolution".

      Now, we're curious as to whether this change in the genome was in response to the exposure to antibiotics. Can you suggest how we might test this?

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    9. Zacho-

      That has nothing to do with what I said. Also both ID and YEC are OK with bacteria gaining resistance to anti-biotics, ie evolution.

      So please go bother someone else with your equivocating nonsense.

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    10. Joe G: If we observed anti-biotic resistence we wouldn't need any theory of evolution to observe it and then attempt to explain it.

      Joe G: That has nothing to do with what I said.

      YOU brought up observations of antibiotic resistance. YOU claimed we wouldn't need any theory of evolution to explain those observations.

      In fact, we can directly observe evolution. Then we asked you how we might determine whether the evolved trait was in response to the exposure to antibiotics. For some reason, you didn't answer.

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    11. Zacho- the "theory" of evolution is total nonsense as it is too vague to be of any use.

      Also your continued equivocation just proves how dishonest you are.

      I have nothing else to say to you but I will keep exposing your dishonesty

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    12. We do NOT need a theory of evolution to OBSERVE bacterial resistance to anti-biotics. We can produce one by figuring out the how/ why some bacteria are resistant and some are not.

      IOW Zacho you are still ignorant of how science operates.

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    13. Joe G: We do NOT need a theory of evolution to OBSERVE bacterial resistance to anti-biotics.

      No, we don't, but we do need one to explain how bacterial populations change over time. In particular, we asked you how we might determine whether the evolved trait was in response to the exposure to antibiotics. This has implications for medicine.

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    14. Zacho- we have been over and over this and you refuse to understand what I have said.

      So go pound sand.

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    15. YOU brought up observations of antibiotic resistance in bacteria. We pointed to direct observations of evolution of that resistance, and an important question concerning that evolutionary process.

      You can't or won't answer.

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    17. Joe G: We can then figure out why some are resistant and some are not and then propose one.

      The observation of interest is that clonal bacteria have different responses to antibiotics, and that resistance appears to be a heritable trait. What do you call this process of change in a population?

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    18. Well you can call it whatever you want. The observation fits in well with baraminology, so you could call it variation within a Kind.

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  4. Nice post. A couple of questions for the evolutionists: How did the ability to survive evolve? Did it evolve before the ability to duplicate? If so, how did it evolve without duplication?

    Inquiring minds and all that.

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  5. Louis Savain

    How did the ability to survive evolve?


    What do you mean by "the ability to survive"?

    Everything has the ability to survive Louis, it's an inherent property of matter. There are rocks in the Canadian shield that have survived over 4 billion years. The only real question is for how long can something last. The usual way to survive is to avoid being destroyed by external forces, either through happenstance or by deliberate action.

    Did it evolve before the ability to duplicate? If so, how did it evolve without duplication?

    It didn't. Evolution only happens when you have imperfect replication, inheritance, and a competition for resources.

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    1. But your position can't even explain replication. And evolution can happen without any competetion.

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    2. Go have another donut Chubs.

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    3. Thorn:

      Everything has the ability to survive Louis, it's an inherent property of matter.

      Wow. Arguing with evolutionists is like pulling teeth. Why would I be talking about inanimate matter? Isn't evolution concerned with living organisms? Let me rephrase my questions in a simpler way that you may be able to parse.

      A living organism has a lifespan. During that life, it uses various mechanisms to stay alive, right? How did this ability (the mechanisms of life) evolve (it evolved, right?) without the ability to replicate? And I dare say that the ability to replicate depends on the ability to stay alive long enough to do so.

      The circular basis of the theory of evolution is so blatant and in your face, so injurious to logic, that one is forced to conclude that Paul Feyerabend was right when he wrote in Against Method, "the most stupid procedures and the most laughable result in their domain are surrounded with an aura of excellence. It is time to cut them down to size and to give them a lower position in society."

      Feyerabend was speaking of scientists in general but he might as well have been talking about evolutionists in particular. It would be funny if it weren't so pathological. ;-(

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    4. Louis Savain

      A living organism has a lifespan.


      Define what you mean by a "living" organism. The first pre-biotic self replicators are generally not considered to be living.

      As I've pointed out many times, the boundary between "non-life" and "life" is extremely blurred and hard to define. It usually comes down to a matter of definition.

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    5. _"As I've pointed out many times, the boundary between "non-life" and "life" is extremely blurred and hard to define. It usually comes down to a matter of definition"

      A matter of definition? you are living in a fantasy world.
      There are "physical" realities about physical structures, even what human mentality conceptualizes as "life".
      You are so inept in your position that you "argue" for. that you expose your ultra simplicity regarding these matters. You and Liddle and the others, are simpletons that have no excuse for your meaningless banterings, especially in light of the current evidences that come forth on a regular basis that totally defy your explanitory philosophy. Your ingorance is no longer an excuse. And your personal preferential treatment of "scientific" data has long since been discarded as "force fitting the evidence to bolster the preferred explanation" Get out of here and let REAL science proceed. You vandals.

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    6. bpragmatic

      A matter of definition? you are living in a fantasy world.
      There are "physical" realities about physical structures, even what human mentality conceptualizes as "life".


      Alright then, let's hear your definition of life, and your objective test to determine if an object qualifies as alive.

      Are viruses alive? How about HeLa cells?

      Please support your answers with evidence.

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    7. life = info processing resulting in function.

      You should write a letter to Origin of "life" researchers.

      Delete
    8. First of all, why is it the responsibility of the critics of evolution to provide a definition for life? One would think that, since evolutionists claim to know how life evolved, that it would be incumbent upon them to define it and explain how its evolution began.

      Second, why is life so hard to define? I suspect that this is yet another dirty deception coming from the evolutionist camp. To define life, it suffices to identify the processes that are required for it. Off the top of my head, I would include some sort of metabolic system: the ability to intake the right nutrients and use them for both cell construction, maintenance, repair and protection, and the energy needed to accomplish all these things. I could probably think of more things to add but it's past my bedtime.

      PS. My questions remain: How this all the life mechanisms evolve without the ability to replicate? And how did the ability to replicate evolve without the ability to live? No BS, please.

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    9. At the 37 min. 15 sec. mark of this following video,

      Evidence for an Engineered Universe
      http://www.youtube.com/watch?v=nLd_cPfysrE

      Dr. Walter Bradley talks a little bit about the OOL problem and states:

      What Distinguishes living systems from non-living systems?

      All living systems

      Process energy

      Store information

      Replicate

      He comments further: Now that's not all they do, but they (living systems) all do that:

      Of course this bare minimum definition of a living system misses the most important question of 'what is life', i.e. it misses thinking, sentience, consciousness, it misses the most important definition that we use to judge whether a human is actually alive. This 'minor detail' of consciousness, as to exactly when it "emerged" is of no small importance as to properly defining 'life' as even this atheist author admits:

      Mind and Cosmos - Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False - Thomas Nagel - November 2012 (projected publication date)
      Excerpt: If materialism cannot accommodate consciousness and other mind-related aspects of reality, then we must abandon a purely materialist understanding of nature in general, extending to biology, evolutionary theory, and cosmology. Since minds are features of biological systems that have developed through evolution, the standard materialist version of evolutionary biology is fundamentally incomplete. And the cosmological history that led to the origin of life and the coming into existence of the conditions for evolution cannot be a merely materialist history.
      http://ukcatalogue.oup.com/product/9780199919758.do

      Further notes:

      God Versus Science: A Futile Struggle By J Roy Singham - May 2012
      Excerpt: Materialists believe that matter is unconscious, a tenable opinion. But they also believe that consciousness is an illusion. That belief is absurd, almost madness.
      http://ezinearticles.com/?God-Versus-Science:-A-Futile-Struggle&id=6940055

      "As a man who has devoted his whole life to the most clear headed science, to the study of matter, I can tell you as a result of my research about atoms this much: There is no matter as such. All matter originates and exists only by virtue of a force which brings the particle of an atom to vibration and holds this most minute solar system of the atom together. We must assume behind this force the existence of a conscious and intelligent mind. This mind is the matrix of all matter."
      Max Planck - The Father Of Quantum Mechanics - Das Wesen der Materie [The Nature of Matter], speech at Florence, Italy (1944)(Of Note: Max Planck Planck was a devoted Christian from early life to death, was a churchwarden from 1920 until his death, and believed in an almighty, all-knowing, beneficent God.

      This following video is very good for highlighting the very different perspectives that Theism and Materialism have on classifying exactly what 'life' is:

      The Mystery Of Life - God's Creation & Providence - video
      http://www.metacafe.com/watch/4193364

      Of course, besides consciousness, I think any basic definition of the basis of life that does not include at least some reference to the one who defeated death on the cross is woefully incomplete!

      John 11:25
      Jesus said to her, “I am the resurrection and the life. Whoever believes in me, though he die, yet shall he live,

      Natalie Grant - Alive (Resurrection music video)
      http://www.godtube.com/watch/?v=KPYWPGNX

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    10. computerist29

      life = info processing resulting in function.


      You've just introduced three more vague undefined terms - information, processing, and function.

      I could argue that by your definition, a star is alive because its fusion processes the information in hydrogen and results in a light / heat output function.

      Told you the divide between "life" and "non-life" is not easy to define.

      Delete
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    12. Perhaps someone should buy thorton a dictionary as all three words "information, processing, and function" are defined

      Delete
    13. Chubby G

      For an ignoramus like you the divide between "life" and "non-life" is not easy to define


      I notice you can't define the boundary or given any objective way to test for it Chubs.

      Perhaps someone should buy thorton a dictionary as all three words "information, processing, and function" are defined

      Then why don't you define them Chubs as they apply to the pre-biotic processes being discussed.

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    16. As expected, Chubby Joe can't provide his definitions. Oh well Chubs, go ahead and put your head back in that feed trough. Stop when you hit the metal bottom though.

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    17. As expected thoorton the liar cannot read- geez puppet it's the last comment in this thread- the one that contains the definition of life.

      But thanks for continuing to prove that you are a human reject.

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    18. Wipe your chins Chubs. You're drooling again.

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  6. OT: Science & Human Origins: Interview With Dr. Douglas Axe - podcast - July 25, 2012
    http://intelligentdesign.podomatic.com/entry/2012-07-24T21_33_53-07_00

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  7. puppet liar:
    The first pre-biotic self replicators are generally not considered to be living.

    Please reference the evidence for these non-existent pre-biotic self replicators.

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    Replies
    1. Go have another burrito Chubs. Extra cheese.

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  8. puppet loser:
    Alright then, let's hear your definition of life, and your objective test to determine if an object qualifies as alive.

    1- Must contain a genome (Yockey)

    2- Must be able to or have come from reproduction

    3- Response to stimuli (yes plants respond to stimuli)

    4- metabolism

    5- Growth

    6- composed of one or more cells

    7- adaptation

    8- homeostasis

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  9. When dealing with liberals, I've found that after you've countered their facts, and their arguments, they begin by asking for definitions of things. It's their way of running away and hiding.

    As Jack Nicholson said: "[They] can't handle the truth!"

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    1. The sad part is it is as if they think biologists don't know what it is they are supposed to be studying. No diff between geology and biology.

      Is it a rock or just a survivor in stasis?

      With that mindset it is easy to get life from non-life.

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