Plants Can Fix Bad Genes (from parents -so inheritance concept revision)

[papau]

http://www.latimes.com/news/science/la-na-genetics23mar23,1,6674474.story?coll=la-news-science&ctrack=2&cset=true

THE NATION
Plants Can Fix Bad Genes, Study Shows
By Karen Kaplan
Times Staff Writer

March 23, 2005

Upending prevailing genetic theory, a team of scientists at Purdue University has discovered a mechanism in plants that allows them to correct defective genes from their parents by tapping into an ancestral data bank of healthy genetic material.

In essence, the plants back up the evolutionary path and use past genes to restore traits that would otherwise be lost, according to a study published Tuesday in the online version of the journal Nature.

The finding proposes "an extraordinary view of inheritance," the scientists said in their paper.

The mechanism appears to be a way for self-fertilizing plants, which are more likely to suffer from the negative consequences of inbreeding, to maintain a healthy level of genetic diversity and increase their chances of survival.

It could also be a way for plants to adapt to changing environmental conditions by having a store of diverse traits at their disposal, the scientists said.

The proposal offers a radical addition to the widely embraced laws of Mendelian genetics, which date back to the mid-1800s. They hold that plants and animals inherit only two copies of a gene — one from each parent. If both copies were defective, a plant would have no ability to correct the error.<snip>

[papau]

1. So will human RNA fix defective Human DNA? - future research will answer

The plants "can recover DNA variants that have come from one of their great-grandparents, even if their immediate parent did not contain the variant," wrote molecular biologists Detlef Weigel and Gerd Jurgens in an accompanying article.

The researchers said the plants must contain a normal version of the hothead gene, although they searched the plants' genomes and were unable to find it.

That has led them to believe that the genetic information could be contained in the plant's RNA, a close cousin to DNA that is thought to be a less reliable vessel of genetic information.

Each of the steps necessary for RNA to modify the genes in DNA has already been demonstrated in other research, the scientists said.

[Celebration]

3. junk dna?

I would bet on "junk dna" instead of RNA. Just a hunch however.

http://www.sciencentral.com/articles/view.php3?type=article&article_id=218392305

[fasttense]

2. Wow, the wonders of this world continually amaze me. n/t

[bemildred]

4. Forms of error correction and redundancy are to be expected.

It's fairly interesting that this manifests in self-fertilizing
plants, where it would be most needed. In general, it is easy to
predict that the mechanisms of genetics are much more complicted than
we presently understand, and hard to say exactly how.

[YankeyMCC]

5. wow

I mean...well wow.

[hunter]

6. I wrote about this when I saw it in LBN...

...and of course, being LBN, it sank like a stone. I was going to get around to posting it here but I'm happy to see you beat me to it, papau!

The common comparisons of genes to computer programs and blueprints can be quite deceptive.

It's becoming very clear that life on earth has evolved various means of evolving -- that there are mechanisms in life's toolkit that make the process of evolution more effective.

Populations of organisms that can evolve quickly when they are faced with some sort of environmental stress are more likely to survive than populations that cannot.

At first we thought of evolution as a process where essentially random mutations were simply selected for or against -- a process of "natural selection" that was easily explained using our genes-as-blueprints analogies. Mutant genes that are not benificial are weeded out of a population, and mutant genes that are benificial are reproduced and amplified within a population.

The next step in our understanding of the process was to model genes as chunks of code that could be duplicated and shuffled around into new, more competitive configurations. This model has led to a much more sophisticated understanding of natural selection. These so-called "genetic algorithms" are the subject of cutting-edge research in genetics, computing, and evolutionary biology. For examples my quick "I'm feeling lucky" google search took me here:

http://www.aic.nrl.navy.mil/galist

But such "genetic algorithm" models do not explain everything.

It seems this duplication and shuffling of genes, along with the sorting and collection of "random" mutations, is somehow a contolled process. Duplications, shufflings, and mutations of genes that are unlikely to be useful to an organism's descendents are somehow suppressed through a variety of unknown mechanisms, one of which may have been described above.

(Before anyone jumps in at this point claiming to see some "Invisible Hand of God" here, that's not at all what I'm talking about. The mechanism for these processes are unkown, but not supernatural.)

As always, we discover life's toolkit to be much more sophisticated than we thought it was...

I don't agree with the author that this is a "radical addition to the widely embraced laws of Mendelian genetics," perhaps because I've been very keen on these sorts of research for the past twenty-five years. It's been clear for many years now that genes are not the static entities Mendel described.

The "radical" aspect of this -- which is not so radical when you actually think about it -- is that the capacity of a population to evolve or not to evolve is, in itself, an evolved trait.

[bemildred]

7. Nice. Everything has layers.

The genetic system is self-referential.

[bemildred]

8. FWIW, self referential computing programs can get pretty strange too.

It's called self-modifying code. It's pretty much anathema in
software engineering circles, but not because it's not interesting.

[phantom power]

11. yeah, and for exactly this sort of reason

Let self-modifying software go to town, and it quickly becomes impossible to understand :-)

Biology, on the other hand, is under no obligation whatsoever to be easy for us to understand.

I read somewhere that they've discovered that the gene->protein transcription sequence is often not the full story. A gene gets decoded into a protein, but then that protein is further modified by *other* proteins, until it reaches it's final form.

Yeah. We've got along way to go...

[bemildred]

12. That is what led me to think of it.

Write only code; I used to be handed some of that to decipher
once in a while. This has the same sense of ad hoc-ery and
changing the rules underneath you to it. But when you allow
self-modifying code, yikes!

[phantom power]

13. What I find strange is...

that many people cite this kind of over-complexity as some kind of evidence for "intelligent design", when in fact that's completely backwards. No intelligent designer would employ the astonishing rube-goldberg hacking that's being applied to biological genomes, or the gene-->protein decodings.

Reminds me of my neighbor, who likes to use the example of retinal cells. He says there are something like 30 chemical steps that are involved in translating an incoming photon into a neural signal out the back of the retina. He sees this as some kind of disproof of evolution. I see it as completely irrefutable *proof* of evolution. No decent engineer would create such an over-engineered solution, never mind supposedly all-knowing, all-powerful engineer!

My explaination of this, which involved genetic-programming examples, didn't make much of an impression. Oh, well.

[bemildred]

16. A good point, it is a sign of something that grew somehow,

not of something that was put together. But I find the whole
idea that something cannot exist without something else to
"create" it just a grammatical bungle. One is then left with the
question of what "created" the creator, and so on, an infinite
regression. And when you find yourself trailing along in such
an infinite progression, you may be sure you made a logical
mistake in the beginning. The fact is that things just are,
coming into being of themselves, and one may easily observe it
all around one, there is no little animacule inside the machine
running it.

[hunter]

14. My favorite computer ever was the Atari 800.

I did a lot of experiments with "self modifying" code on that machine, often in various attempts to fit complex graphics programs into the very limited memory space. I eventually upgraded two Atari 800XL machines to 256K using a common Atari hobbyist "bank switching" technique, which made my self-modifying codes even more reckless and exciting!

You are correct, the gene-to-protein transcription sequence is not the entire story. If you want to use a movie industry analogy, there is a lot of "post production" going on. The mRNA transcribed from the "genetic" DNA is edited, and then the proteins made from those edited mRNA strands are themselves edited.

It doesn't take any great leap of faith to think that genes themselves can be edited in similar ways.

I think we still suffer under the notion that genes are some sort of fixed plan, when in fact they are as fluid as anything else in life. We are still limited by some theory of "Creation." Even the most ardent atheist can look at Darwin's theories of natural selection as some variation of a "creation science."

If you start from the premise that "In the beginning there was The Genetic Code" then you will find yourself getting into just as much trouble as if you said "In the beginning there was The Word."

Therefore, when I examine any scientific theory I usually start with the premise that the Universe doesn't give a damn what I think, doesn't give a damn what any human being thinks. The Universe is very big, and humanity is very, very small.

Accepting this premise keeps me out of a lot of trouble. I assume the words of humans are nothing more than a small bit of noise in the background of the Great Cosmic Symphony. (And any expalnations of how I reconcile this attitude with my religious beliefs as a Social Justice Catholic are an entirely different essay...)

[bemildred]

15. An excellent premise.

We are here to enjoy the show, as much as we may, not to run things.

[Celebration]

10. Good source--edited to include link

Haha. We use Rense in the 9/11 forum. Why not here?

http://www.rense.com/general62/expl.htm

"To this end they compared the rules of syntax (the way in which words are put together to form phrases and sentences), semantics (the study of meaning in language forms) and the basic rules of grammar. They found that the alkalines of our DNA follow a regular grammar and do have set rules just like our languages. Therefore, human languages did not appear coincidentally but are a reflection of our inherent DNA.

The Russian biophysicist and molecular biologist Pjotr Garjajev and his colleagues also explored the vibrational behavior of DNA. In brief the bottom line was: "Living chromosomes function just like a holographic computer using endogenous DNA laser radiation." This means that they managed, for example, to modulate certain frequency patterns (sound) onto a laser-like ray which influenced DNA frequency and thus the genetic information itself.............

snip

They even captured information patterns of a particular DNA and transmitted it onto another, thus reprogramming cells to another genome. So they successfully transformed, for example, frog embryos to salamander embryos simply by transmitting the DNA information patterns! This way the entire information was transmitted without any of the side effects or disharmonies encountered when cutting out and re-introducing single genes from the DNA.

This represents an unbelievable, world-transforming revolution and sensation: by simply applying vibration (sound frequencies) and language instead of the archaic cutting-out procedure."

[hunter]

9. Here's the Nature News link:

http://www.nature.com/news/2005/050321/full/050321-8.html