Biological Strength of Spirit?

I read today that what can only be described as a group of geniuses in Illinois has been quietly making amazing discoveries about the molecular processes involved in DNA, including the fascinating field of epigenetics.

The DNA contains four different nucleic acid bases, called Adenosine, Cytosine, Guanine and Thymine, or ACG and T.  C and G bond together, as do A and T, making the rungs of a long and beautifully coiled ladder of data.

This vast two-dimensional storage system only a few atoms wide (if an atom were a grain of sand, the smallest visible object would need to be at least 4 metres wide) is twisted, coiled and supercoiled repeatedly to such an extent that the collections it forms, the chromosones, become visible through a microscope.

Cytosine

The field of epigenetics deals with a newly discovered layer of meaning superimposed on the DNA itself.  Epigenetic processes seem to be influenced by the experiences and lifestyle of an individual, and leave markers which can survive for many generations – the effects are so long lasting in successive generations of laboratory animals that some researchers believe the markers laid down can’t be turned off.

Methylated cytosine

These processes don’t change the arrangement of the letters, but instead, they can change one of the base molecules – usually cytosine, sometimes adenosine – by swapping one of its hydrogen ions to a more complex methyl group.  It’s as if they swap a capital letter instead of the same letter in lower case.  The 4-character information remains the same, but the changed letter is read differently by the other equipment in the cell.  Therefore while the DNA remains intact, the proteins which it is supposed to make can be switched on or off.  Up until recently, it was thought that this was the main extent of changes caused by “methylation”.

DNA in the grip of methyltransferase (DNMT1)

Above you can see the little molecular machine grabbing the DNA, finding the right sequence and adding a methyl group to the cytosine.   Now, you may well ask, from where do those little machines come from, that is, where are their designs stored and how are they assembled?  How should I know?  I’m only a programmer!

This process is almost always carried out to cytosine bases lying in the sequence:

CG
GC

So as both DNA strands have a cytosine, both strands will be converted with a methyl group. When the DNA is replicated, each of the new DNA double helices will have one old strand, complete with methyl groups, and one new strand, which is not methylated.  But all the machinery has to do is find such a group, and apply the modification to the cystine on the other strand.  Impressive though, for a machine which can’t see and doesn’t seem to have any kind of a memory in which to store its instructions.  What makes it act the way it does?

How to measure the forces need to break apart strands of DNA (http://www.ks.uiuc.edu)

Well, who knows – or to be more precise: it’s a hotly debated topic at present.  But now to the real story: the catchily-named Theoretical and Computational Biophysics Group did a rather clever thing.   By trying to break apart strands of DNA before and after methylation, they proved:

..a role of methylated DNA physical properties needs to be reconsidered as a direct epigenetic control factor. We found through novel and extremely extensive force measurements comparing non-methylated and various methylated DNAs that methylation affects the propensity for mechanical DNA strand separation to a significant degree.

This means that methylation doesn’t just accent the language of DNA, it makes the DNA itself stronger – tougher to break apart – which is important because your DNA, much like your wealth or your beautiful girlfriend, is subject to constant break-ins or attempts to rip it off altogether.

Yes, even on the molecular level there are crooks and predators on the make.  What a neighborhood!  Some attacking machinery from bacteria tries to splice in their own, alien, DNA into ours to mess up the activity of our cells.  So any process which makes the DNA stronger is a boost to our immune systems.

It took some pretty strong DNA to turn this Carrera marble into Moses. I think the horns were a misinterpretation of the Aramaic or Hebrew. But nobody wanted to tell Michelangelo that

It may well be that the resistance some people have to disease is a direct result of epigenetics.  Perhaps the susceptibility to addictions in materialist societies is a result from weakened genetics.  It is striking that in the last days of the Raj, virtually all the male children became alcoholics, something hardly seen before.

Perhaps the races which have had to cope with slavery and oppression by raising their spiritual values in non-violent protests have also increased the resilience of their DNA.  It is true that African Americans led the way in practically all sports, once freed from the chains of slavery.  Perhaps the well researched but otherwise inexplicable tendency of families with strong moral backgrounds to produce men of genius is because of beneficial changes to the DNA by virtue of, well, of virtues – if so, perhaps virtues and vices, far from being arbitrary and meaningless concepts, have biological reflections of their own.

Of course, making statues to preserve myths doesn't suit our advanced civilisation today. Cardiff, the capital of Wales is well known across the UK for its vibrant nightlife

Anyway, it is already known that positive attitudes can defeat the onset of infections or improve the recovery time from illnesses.  From this, and in the light of The TCBG’s work, it’s not much of a leap to suppose the epigenetic system to be closely tied to our emotional state, and an important part of the biology reflecting our strength of spirit.  And to all, a good night.

…………………………………………………………………………………………………………………………

Next week!  How to make this amazing bit of machinery for uncoiling knots:

DNA Gyrase from E.Coli is an enzyme which helps untangle, un-knot and relax supercoils in its DNA. It does so by binding to a strand of DNA, cutting both strands and then, while keeping hold of both cut ends, passing another piece of double stranded DNA through the gap. It then reseals the double stranded break.

Essentially it allows portions of the large circular bacterial genome to pass through itself, to prevent knotting and entanglement. A number of antibiotics (e.g. Simocyclinone D8) target this enzyme, since it is essential to the organism’s survival. Humans also have a form of this enzyme but its construction is different and we are thus not affected by the antibiotics.

(http://beautifulproteins.blogspot.com/)

About iain carstairs

I have a great interest in both scientific advances and the beauty of religion, and created www.scienceandreligion.com about 15 years ago with the aim of finding common ground between the scientist and the believer, and to encourage debate between the two sides.
This entry was posted in Biology, Cytosine, Designs in nature, DNA Methylation, Epigenetics, Genetic damage, Human genome, Materialism, Nanotechnology, Natural Intelligence, Proteins and tagged , , . Bookmark the permalink.

7 Responses to Biological Strength of Spirit?

  1. Lori says:

    Another wonderful entry and work Iain! Thank you.

  2. That’s an awesome explanation of the atomic mechanics of epigenetics. I was just reading about epigenetics in the lastest National Geographic. Their article on twins suggests the differences between twins are epigenetic. But they didn’t get into the mechanics of it. It was a high-level overview of gene expression, and not a single hydrogen ion was mentioned.

    You get the why and how of that figured out, you’ll probably end up reinventing both science and religion! I suspect you’d also make serious inroads on updating evolution theory to go beyond randomness into something more meaningful.

    • I’m glad you enjoyed it! Hopefully that sentiment strengthened your methylating processes and triggered an oxytocin rush, heping evolution in every way. In other words, Happy New year.

      Actually I did get that NG issue on your recommendation, but didn’t include anything from it, as it seemed more visual and I think I rely on images too much sometimes. Good article, though, very striking. It occurs to me that twins even disprove random mutations, since if a human has say 100 trillion cells (some say 400 trillion, but I don’t know either way) then a case of twins developing to virtually indistinguishable results means the significant error is negligible. It’s like a handy random mutation test system right in front of us – 100,000,000,000,000 practically perfect copies made in two separate experiments.

      The idea of chromosones changing their number by accident (eg two chromosones fusing to produce our chromosone 2) in order to prevent interbreeding seems especially weird, since errors would have to occur in all the duplication and error checking equipment at the same time, and in one generation, so any member of any species would be liable to the same disruption. In a world with 7,000,000,000 people, each of whom show 100,000,000,000,000 cell duplications, that’s a total of 700,000,000,000,000,000,000,000 experiments. You would expect random mutations to be causing absolute chaos on a daily basis.

      Instead.. hmm, nothing!

      Science estimates that 70% of mutations will be harmful, with 30% conferring a slight benefit. A benefit so slight that it isn’t detectable (in twins) could never translate into “more children” in a species producing only one or two, or at most, a handful of children per family, compared to the vastly greater number being produced by the standard models all around. Such a tiny difference would be over-ruled by a hundred other factors, like, the weather, or who is nearest to mate with. Even a vastly superior individual could still only manage a handful of children in its brief period of family life, and in any case its superiority would have to be compromised by reliance on a standard-issue mate.

      And how could a small advantage (say 3 extra hairs on its chin per generation) translate into greater survival, when all are facing a savage wind of -50 degrees celsius, or a drought? Take a more dramatic change: ten extra hairs on its knee, or toenails that grow 2cm per month instead of 1.8cm (yes, all this is random). What good is any of that when facing a need to feed ten children and two grumpy wives?

      If random lucky-fluke evolution were true, then in a species with millions of progeny, like ants, you would expect a vastly greater rate of mutation. Instead, there doesn’t seem to be any, even over 500 million years.

      Speaking of which! –I know you’re interested in ants: you might like this film if you haven’t already seen it:

      http://www.dailymail.co.uk/sciencetech/article-2095335/Underground-ant-city-Brazil-rivals-Great-Wall-China-labyrinth-highways.html

      This stand-alone experiment was a great opportunity to use wits to interpret new findings. But no, no, no. Instead the scientist over-rules what his brain is shouting at him, for the sake of temple dogma:

      “Everything looks like it has been designed by an archiect. A single mind.” [pause – we completely see his point] “..but of course, that isn’t true..” [D’oh!]

      Of course, it IS!

      • #1, I definitely got into the wrong line of work. Excavating an ant megalopolis is where it’s at.

        #2, I hope if someone ever pumped ten tons of concrete into my house, they would first check all the rooms to remove the guitars and comic books.

  3. That is exactly right – they simply must check for partially completed paintings. And the black felt tip pen I have with a certificate proving it came from Jack Kirby’s desk.

    Very few scientists today are willing to take these precautions simply because they are so excited to be pouring tons of cement. At best it’s not the worst but still not good – and at worst it’s not even the least best.

    Yep, you is preachin’ to the choir!

  4. Pingback: The Story So Far | ScienceAndReligion.com

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