Friday, April 2, 2010

DNA Methylation in Bacteria

How do bacteria respond to environmental challenges and signals so quickly and effectively? In addition to genetic modifications there are a series of non genetic, or epigenetic, modifications. Genetic modifications change the sequence of nucleotides that, for instance, comprise a protein-coding gene. In that case the resulting protein is modified to better handle the environmental challenge. Epigenetics, on the other hand, involves various other types of modifications. For instance, the three-dimensional structures of proteins may be dramatically altered, or tiny chemical signals—methyl groups—may be added to certain proteins or DNA sequences. As with genetic modifications, many of the epigenetic modifications are heritable, so the adjustments are passed on to later generations.

Consider the methylation of DNA. This occurs at certain target sites along the DNA sequence where specific short DNA sequences appear. These sequences are found by special proteins as they move along the DNA. The special proteins search for these sequences and add a methyl group to the adenine base that appears within the sequence. The protein binds to the DNA, twists the helix so the adenine base rotates into a precisely shaped pocket in the protein, and the protein then facilitates the transfer of the methyl group from a short donor molecule to the adenine.

The short donor molecule does more, however, than just supply a methyl group. It also actually helps to control the special protein. How does this work? Of course the short donor molecule binds to the pocket of the special protein so the methyl group is ready for transfer. But the donor molecule also binds to another site on the protein. This binding serves to alter the structure of the protein, enhancing its function. So the special protein is designed to do its job when it is charged with a donor molecule.

But not all of the DNA target sequences are methylated. This complex DNA methylation function doesn’t occur if the target sequence is protected by another protein that binds to the sequence. This protein binds to some of these DNA target sequences but not all. The result is a particular DNA methylation pattern which influences which genes are expressed, and therefore how the bacteria interacts with the environment.

This DNA methylation pattern is propagated to the daughter cells when the bacteria divides. When such division occurs the DNA must, of course, be replicated. The double helix is separated and new complementary strands are synthesized on each strand. At the DNA target sequences there is an adenine on both strands. If both adenines are methylated, then after replication the two newly formed DNA helices will each contain only a single methylated adenine—the original adenines are methylated but the new adenines that were added are not.

These hemimethylated sequences are rectified by other proteins, which methylate the lone, unmethylated, adenines. The result is that after cell division, the two new bacteria cells have inherited the full DNA methylation pattern established in the original cell. You can read more about this and other bacterial epigenetic mechanisms in this review paper.

This is one small chapter of the epigenetics story that helps to explain the incredible adaptation capabilities we observe in both single and multiple cell organisms. The idea that such capabilities evolved is, of course, not motivated by science. Evolutionists once claimed that adaptation was obvious proof of evolution, but in fact biological adapation is yet another massive problem for evolution.

14 comments:

  1. Is there scientific doubt as to whether species go extinct? Is there scientific doubt that the rabbit-population of Australia has exploded over the past 100 years?
    Evolution isn't natural selection. Evolution is 'the process of development' (evolution, part 'III', Oxford English Dictionary online edition). Natural selection is one account, among others, of how stability can be achieved in an evolving state of affairs, or put in biological terms: the change of organic structures over time.

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  2. Cornelius Hunter: The idea that such capabilities evolved is, of course, not motivated by science.

    There's a pattern emerging.

    CH: This biological process is very complex.
    CH: Therefore, it's a massive problem for evolution.
    CH: Therefore, religion drives science.

    That means arguing the particulars of your post don't seem particularly relevant. We know that evolutionary processes can generate complexity, so your argument is unfounded—whether or not the modern Theory of Evolution is on solid ground.

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  3. Here is the referenced paper...
    http://www2.hawaii.edu/~scallaha/SMCsite/MIcro671Links/25-Epigenetics/CasadesusRev.pdf

    Zachriel, while I agree the Dr. Hunter's innuendo that such capabilities didn't evolve "...is, of course, not motivated by science", the articles are still interesting.

    I look at it with a bias towards orchestrated quantum effects. Sometimes the evidence is supportive, other times it neither supports nor contradicts. I will look at this in detail on this basis.

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  4. Per:


    "Is there scientific doubt as to whether species go extinct?"

    No

    "Is there scientific doubt that the rabbit-population of Australia has exploded over the past 100 years?"

    No.

    "Evolution isn't natural selection."

    Agreed.

    "Evolution is 'the process of development' (evolution, part 'III', Oxford English Dictionary online edition)."

    False. Evolution is the theory that the species arose strictly via natural laws and processes.


    "... or put in biological terms: the change of organic structures over time."

    False. On that definition even divine creation falls under evolution.

    The problem here is that evolutionists equivocate on their own idea. This is typical. The genre consistently, for centuries, mandates strict naturalism, and then when questioned about their absurdities, evolutionists pose the proverbial "who me?", back pedaling and saying all they ever claimed is that there has been change over time.

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  5. Per: ... or put in biological terms: the change of organic structures over time.

    Cornelius Hunter: False. On that definition even divine creation falls under evolution.

    Genesis 2:22
    And the rib, which the LORD God had taken from man, made he a woman, and brought her unto the man.

    That's hardly what any fair reading of Per's statement would entail. Biological evolution refers to descent with modification, that is, change in the heritable traits of populations over time. The Theory of Evolution includes many related claims and observations, including descent with modification, natural variation, natural selection and Common Descent.

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  6. Zach:

    =====
    That's hardly what any fair reading of Per's statement would entail. Biological evolution refers to descent with modification, that is, change in the heritable traits of populations over time. The Theory of Evolution includes many related claims and observations, including descent with modification, natural variation, natural selection and Common Descent.
    =====

    I know this is probably hard to believe, but evolutionists commonly do, in fact, use the very argument, quite literally, that Per is using. Perhaps in this case Per actually was using shorthand, and meant what you are saying, but that is not typical.

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  7. Zachriel:
    We know that evolutionary processes can generate complexity...

    How, exactly, do scientists know that?

    I don't think there would be all these blogs debating the theory of evolution if that were true.

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  8. I just posted this on After the Bar Closes. It has been suggested they are better at determining CSI than ID Proponents. I have also posted this on Telic Thoughts.

    Here are two number sequences one contains "Complex Specified Information" the other was generated from random.org. I even used random.org to choose the order of presentation. I tried not to bias this with any CSI detection I knew about, either for or against. However, it could be argued I purposely avoided biasing the use of Benford's Law (i.e. Lewis). There is an implied "0" at the start of both sequences.

    Sequence A:
    65640787712341033747653810908791305757774532

    Sequence B:
    67958708262272571011298115782181530329759049

    Tomorrow Morning I will give a clue by separating groups of numbers. Tomorrow evening I will give the answer.

    If you want to keep score, 2 points for guessing right this evening. 1 point for guessing right after the clue. Those that are bold enough can get 3 points. It is permissable to guess one way first and a different way second. Therefore, there is no reason not to guess early.

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  9. Unfortunately, I have to make a correction. I worked the problem out as if I didn't know the answer, and I found an oops. My mistake will provide a hint. I need to update 14 digits. I am updating both. I used Random.org to update the random sequence.

    New Sequence A:
    65640389793390444627653810908791305757774532

    New Sequence B:
    67958532340412126851298115782181530329759049

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  10. Zachriel: We know that evolutionary processes can generate complexity...

    Doublee: How, exactly, do scientists know that?

    Because evolutionary processes are a mathematical class that can be studied. They are quite capable of exploring environments and problem-spaces that exhibit the kinds of order we see in nature. We can also directly observe adaptive evolution in nature.

    Doublee: I don't think there would be all these blogs debating the theory of evolution if that were true.

    The argument regarding design is not constrained by evidence. ID is a social and political movement, not a scientific program.

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  11. Zachriel:

    There's a pattern emerging.

    CH: This biological process is very complex.
    CH: Therefore, it's a massive problem for evolution.
    CH: Therefore, religion drives science.


    This is so true and concisely stated. Dr Hunter, you are not making much impression with this fallacious non-sequitur, nor does it improve with repetition.

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  12. As promised, here is another hint with leading zero and spaces added.

    New Sequence A:
    06564038979339044462 76538109087913057577 74532

    New Sequence B:
    06795853234041212685 12981157821815303297 59049

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  13. More information

    Sequence A Decimal:
    06564038979339044462 76538109087913057577 74532

    Sequence A Binary:
    000000101101100011000001001101010110010000111010100100100011001101110
    001000010011000101101111111001011001011111101001001111001110100101001
    010010001100100100

    Sequence A Octal:
    00554301152620724443156 10230557713137511716451 221444

    Sequence A Hexadecimal:
    05B1826AC8752466E 4262DFCB2FD279D29 12324


    Sequence B Decimal:
    06795853234041212685 12981157821815303297 59049

    Sequence B Binary:
    0101111001001111101110001000001010101000101101110100111100001101
    1011010000100110010101100100001100000110100101011010110010000001
    1110011010101001

    Sequence B Octal:
    0571175610125055647415 1320462544140645326201 163251

    Sequence B Hexadecimal:
    5E4FB882A8B74F0D B42656430695AC81 E6A9

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  14. Evolution isn't a theory. There might be theories of evolution, but they are certainly not what evolution is.

    Evolution is not a uni-linear account, or any account for that matter, of species history. Evolution is something that occur to some thing(s) over time, namely development. Natural selection is one way of accounting for why that change happens, there has been other accounts before and after Charles Darwin.

    Maybe the reason to why 'evolutionists' have put forth similar claims about evolution, is that they study evolution, and know that it isn't an idea any more than fire is an idea. There surely is ideas and theories about fire, and how to make one, but it certainly IS none of those.

    Why would it be absurd for some people to take an interest in patterns that to them seem apparent, being it religion or otherwise?

    // Best wishes.

    Per Guterstam Christoffersson

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