## Thursday, March 24, 2005 ... //

### DNA backup: inheriting from grandparents

Many of us - and our computer managers - often back up their data. Something may go wrong in which case there is still a chance to avoid the worst. They just return to the previous version.

The DNA code is a natural example of a large data file. Mutations and natural selection keep on editing this file - many files, in fact. Usually it was assumed that we inherit the file from our parents only (plus some mutations). If a piece of the DNA code of both parents is damaged, then the son or daughter has bad luck. There's no way to fix it.

Or is there?

David Goss has pointed out a new fascinating discovery in genetics described in the New York Times:

The biologists at Purdue University have found that 10 percent of off-spring of a plant are able to repair a genetic problem of both parents. The only acceptable explanation that the biologists have been able to propose is the following:

• The organisms carry not only the parents' code, but also a cryptic backup of the code from the grandparents (and maybe beyond). This code is sometimes used if something goes wrong with the parents' code.

Let me philosophize a bit. If you remember your biology classes, you know that there are dominant and recessive genes. Recessive genes are those that are inconsequential in a heterozygous genotype (i.e. in which there are two copies of an allele that differ). My countrymate Gregor Mendel, the father of genetics, has described many examples of recessive genes of a plant. But I guess that he would have assumed that if both parents have an important segment of the DNA damaged, it can't get fixed. But it can.

I feel that it is morally right to say that the backup of the critical DNA code is analogous, if not an example, of a recessive gene. More philosophically: if Nature can do something that we can, be sure that it's possible that it has been able to develop this technology after those billions years of attempts - and only an experiment can show whether it has actually developed it. Nature is wicked smart, and DNA code backup may be another example.

The stored data do not seem to be in the form of DNA - a copy of the same sequence does not seem to appear in the DNA strand. The second most likely explanation is then RNA - it's less stable than DNA and it was assumed that it can never be used as a primary source of the genetic information. Well, maybe it can, at least in the extreme cases.

It is not know whether the same phenomenon may be observed for other types of organisms. If it is so, a popular theory designed to explain the existence of sexes - namely as a tool to avoid excess mutation - could be in trouble because the DNA backup could be far more efficient in doing the same job.

#### snail feedback (8) :

Lots of questions one can ask:

e.g.,

1. How does the mechanism work whether to revert to the grandparents' gene or not? i.e., how do you know when to restore from backup?

2. Does the mechanism work both ways? Specifically, will a plant with a normal HOTHEAD gene (say by reversion) that has an abnormal grandparent, sometimes produce offspring that revert to the abnormal gene? i.e., how do you know which version is correct, the primary or the backup?

I am wondering of the perspective views of those who engage in string theory, would have a bend towards questions like this, as you present the article?:)

Sean speaks about how once you learn the ideas of GR and QM, one may sense the momentum of things as a interesting feature embedded in ones thinking?

In the case of genetic predisposition, how could something go back and change itself?

Are we not breaking laws here? Okay, we have the article,yes.

If such things are possibe at that level what is to say,that the cyclical naure of the universe could not go through and re-express itself? That this feature in genetical expression.....that we could not understand this context about going back and speaking to the grandfather?

You see where this is leading to I am sure.:)

I am a bit skeptical about the conclusion without seeing the detail of the research. If only 10% of plants are able to "recover" then a more natural explanation is natural selection.

In billions of years of evolution, DNAs are evolved by natural selection which results in:

1.The chemical form of the specific DNA is more stable than a random combination of a random DNA, so that it is less likely to be altered by natural forces like ultraviolet, vibration or heat.

2.The DNA is more surviveable, both in the natural environment of Darwinism, and amoung all the cells within the same physical body.

So I would speculate that the artificially altered (just altered a little bit) DNA is unstable in the specific segment that's altered, and is not good in surviveability compare with the original.

So it either mutate back to the original form by random process, hence get a better chance of surviving, or it die out by natural selection, during the long process of growing from a single cell to a whole plant.

That is quite possible. An astronomical number of split and mutations happen during the process of growing from one single cell to a baby. Countless "bad" cells are eliminated during the process, so that at the end it is much more likely than not that a heathy baby is born.

Lubos do you know a perfectly healthy human body would contain a couple hundred different cancer cells at any given time? During normal situations those natural cells have no changce of survival in the body and so it would grow into cancer. But if chance gives one of the cancer cell looks more stable and more surviveable, it takes over and you get cancer.

Quantoken

Quanto,

There is a deeper question here about what momentum might have impart such designs in nature?

It looks like a marvelous discovery," said Dr. Elliott Meyerowitz, a plant geneticist at the California Institute of Technology. Dr. David Haig, an evolutionary biologist at Harvard, described the finding as "a really strange and unexpected result," which would be important if the observation holds up and applies widely in nature.

Years ago in private research, such seedling and field generation was looked at.

Under controls( others who were engaged with university), this did not produce any significant effects under the controls of producing superior seedlings. But the very idea, presented other questions about the plan, and as it would unfold.

Such questions about emergenece forces one to wonder about the design of the universe?

Electrostatic fields applied on eggs at early stages of morphogenesis are claimed to have strange effects on the morphogonesis of several organims. More ancient forms of organism grow from treated eggs. Also plants develop series of leaves representing various stages in evolution.

This allows to play with the idea that the intronic "junk" portion (95 per cent for humans) could contain among other things genetic archive realizing ontogeny recapitulates phylogeny principle at the genetic level.

One can of course wonder whether the archive contains also part representing genes which are not yet realized since the harsh environment does not yet allow this (saints cannot live in market economy).

Ciba Geigy effect was discovered by Ebbner and Schuerch. See http://www.pukshofer.com/Privat_Home/Projekte/Ciba_Geigy/Ciba_Geigy.htm and http://www.s-line.de/homepages/keppler/elektrofeld.htm .

Matti Pitkanen

A warning to Arun about point #2.

It could be sloppy thinking that made you write "abnormal".
Don't forget that that grandparents
are (by definition) successful geno/phenotypes. ;-)

It is possible that, if the future environment rather suddenly changes to some very stressful extent, a previously 'recessive gene' type of 'backup resource' could be unmasked to allow a lineage to relatively readily re-adapt (using a previously relict piece of code) to this new but in the phylogeny of the lineage not unprecedented environmental challenge.

To Lubos:
May be if you stop partying (as much as you do;) you can get enough time to nicely finish off the fundamental physics fase of your career and instead put you formidable analytical abilities into

Comment apropos Quantokens call about cancers:

Many (or most) kinds of primary malignant tumours are obviously co-caused by some chronic (frequent or longterm) exposure to a chemical, kinetic or radiant irritant (with or without apparant symptoms of inflamation) - e.g. by smoking or snuffing tobacco, by having breathed-in shafing asbestos fibres (in lungs), by some adverse dietary ingredient or habit that has overworked an organ (such as the liver (possibly undiagnosed cirrhosis), alimentary canal (possibly undiagnosed polyps, ulcers), bile duct (possibly undiagnosed gall stones) or kidneys (possibly undiagnosed kidney stones), by sun-bathing (in the case of fair skinned people), etcetera.

The adaptive-phylogenetic origin of "cancerous behaviour" of single cells in multicellular animals 'suggests itself' if one imagines what survival promoting options were available to the individuals of the amoebic era in the phylogeny of fauna.

Picture an prototypic "irritating cloud type situation" in the primordial sea (most typically produced by a volcano) wherein single-/soft-celled creaure were often trapped and repeatedly having
its withdrawal reflex induced (by irritating cloud particles).

There could have been only two adaptive responses to being in such a situation and not seriously depleted of vital energy and thereby either dead and/or reproductively disadvantaged:

1.
- "Hibernation" (a self-inhibition that outpaces and preempts the maladaptive exhaustion caused by the withdrawal reflex that the irritant would otherwise be free automatically to induce)

2.
- As if a last ditch gamble on
self-replication to produce a by
mutation rendered immune or even 'irritant-eating' offspring - before the for reproduction required vital resources have become too depleted.

[In my view, the last option, of these two and only options, says something fundamental (if ever so simply so) and fairly instructive and not only as far as cancers are concerned. %}]

P

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