Mutation and Human Evolution

Electropollution and chemical contaminations have altered the structure and composition of the organic molecules that circulate in this planet's ecosphere. Much research describes these altered molecules' impact on non-living systems like the earth's carbon, nitrogen and hydrogen cycles - but the science is being buried by the "global warming debate." Similarly, the research investigating the effects of altered organic molecules on living cells and organisms is overshadowed and obscured by the so-called evolution/intelligent design "debates" that pit science against religion - another obviously orchestrated polarization designed to camouflage a real crisis.

This thread is not a forum for debate on whether or not humans mutate and evolve - the premise is that a) humans do mutate and evolve, and b) the mutation/evolutionary process is escalating. The goal is to explain exactly and simply how our electrobiochemically altered world is triggering mutation, and causing an evolutionary crisis.


Premises

1. Altered organic molecules circulating in the ecosphere cause mutations in living organisms;

2. The numbers of altered organic molecules present in the ecosphere have grown exponentially, reached the point of self-organizing criticality and besides affecting the functioning of non-living systems, now are rapidly altering the genetic composition of living organisms;

3. The electrobiochemical composition of the planet has changed sufficiently to trigger an evolutionary crisis affecting all life from the smallest microbes to the largest complex organisms, including humans.

Goal

To develop a simple explanation for the ATS Research Forum that describes how:

1. Electrochemical pollution and industrial activity alter organic molecules;

2. Altered organic molecules in turn alter living cells, organisms and their genes.

Questions: Can You Help?

Do you have any information, good quotes, or links to basic science sites that can help?

Feedback? Comments? Criticism? Questions?

Special Request: My research focuses on proteins. I can show how electrochemical processes and contamination cause proteins to misfold and become prions, then cause cellular and genetic mutations. As far as I can tell - prions are by far the most important agent causing mutations and evolutionary change. In turn, the most important prion seems to be a misfolded isoform of a-smooth muscle actin (ASMA), simply because it is an actin protein, and therefor can access virtually every living cell in every species and kingdom.

BUT - huge amounts of DNA, fat (lipids), sugar (polysaccharrides), and carbohydrate molecules also circulate in the environment, likely are being altered - and also may be impacting cells and genes in living organisms, either directly or indirectly. ...Anyone know?


General Background

Organic molecules called biomacromolecules are present in all life and non-living systems that make up our earth’s global ecosystem (the ecosphere or biosphere ).

These biomacromolecules cycle constantly through the earth’s air, soil and water; they are present in inorganic matter, and also are the "building blocks of life" that make up living organisms. Acting as both messenger and message, these molecules carry and exchange biochemical information between organisms, between organisms and the planet’s non-living systems, and around and back again. In effect, biomacromolecules continually adjust and balance the molecular composition of life and non-living systems, and act to keep the earth in harmony with itself at the most fundamental level: by standardizing the molecules that make up the planet and all its parts.

Today, pollution also is a defining part of this planet’s ecosphere. Contaminants interract with biomacromolecules, modify their structures, and change their biochemical properties. As a result, altered biomacromolecules change non-living systems like the planet's carbon, nitrogen, and water cycles. In addition, altered biomacromolecules trigger mutations in living organisms.

Glossary

Biogeochemistry: A science that deals with the relation of earth chemicals to plant and animal life in an area; of or relating to the partitioning and cycling of chemical elements and compounds between the living and nonliving parts of an ecosystem; study of microbially-mediated chemical transformations of geochemical interest, for example nitrogen or sulphur cycling.

Biogeochemical Cycles: Geological and biological processes that recycle chemicals vital to life; the circulation of chemical elements (e.g., oxygen, carbon, etc.) from the environment into plants and animals and back again into the environment. In ecology, a biogeochemical cycle is a circuit or pathway by which a chemical element or molecule moves through both biotic ("bio-") and abiotic ("geo-") compartments of an ecosystem. ...The most well-known and important biogeochemical cycles, for example, include the carbon cycle, the nitrogen cycle, the oxygen cycle, the phosphorus cycle, and the water cycle. ...Biogeochemical cycles always involve equilibrium states: a balance in the cycling of the element between compartments. However, overall balance may involve compartments distributed on a global scale.

Microbiology: The branch of biology that deals with microorganisms and their effects on other living organisms.

Molecular Biology: the study of the biochemistry of cells, it is closely linked to cell biology, in particular the biochemistry of DNA and cogeners.

More on Molecular Biology

Central Dogma of Molecular Biology: The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. ...Prions provide the only exception to the dogma so far known.

WHAT DO YOU THINK? ...And can you help out here?

Thanks, sofi

This doesn't make much sense to me. I read the link as to what these biomacromolecules are, and it tells me that they're large, complex biologically forming molecules - such as DNA.

So, I'm trying to figure out what you mean. That there's DNA floating around in the air? Because there is, in the form of microbes. Microbes are everywhere. But how are they causing a mutation in our DNA?

Any DNA that enters our body that is not our own is destroyed, digested so to speak, and fed to us. People are worried about genetically modified foods, and what it does to our DNA. The answer is nothing, we break it down, and use the leftovers to help make more of our own DNA. If you eat a leaf, will you turn into a tree? So why would a genetically modified bigger leaf turn you into canned tuna?

I'm sorry, I just don't see where this research attempt is going. There's no basis, or if there is, there's no explanation of it. It doesn't even seem to qualify as a theory for me. Perhaps you can enlighten me.

Or, if you can't, then step back and review what you know so far, and determine for yourself if it makes any sense. If it does, you should be able to come back and explain it better. If it doesn't, then don't fret and find a new theory.

Had some thoughts about this, myself

Originally posted by soficrow
The goal is to explain exactly and simply how our electrobiochemically altered world is triggering mutation, and causing an evolutionary crisis.

Erm... define "evolutionary crisis"?

For instance, as homo erectus evolved to homo sapiens, our bones became thinner and brain cases larger while our jaws became weaker and the anchoring bony ridge on the top of our skull vanished. We also grew larger.

Are these all crises? Was just one a crisis? And why was it a crisis?

There's other examples of fairly swift evolutionary change that I can list... are they also crises (these are ancient changes; not modern ones)? How does your thesis address this?

Premises

1. Altered organic molecules circulating in the ecosphere cause mutations in living organisms;

Are you treating this as the sole cause of mutations in spite of overwhelming evidence to the contrary? If you're not, how much of an impact does it have in conjunction with and in contrast to, say, radiation (a known and identified mutagen.)?

3. The electrobiochemical composition of the planet has changed sufficiently to trigger an evolutionary crisis affecting all life from the smallest microbes to the largest complex organisms, including humans.

I was reasonably sure I knew that electrochemistry was the study of the chemical reactions that take place at the terminus of a metallic probe when it is inserted in an ionic solution. That it deals with charge transfers and reduction reactions.
en.wikipedia.org...

The use of "electrochemical" to be changed from the science. If this is so, then you will end up with confusing and inefficient research and research that goes nowhere, and your participants are going to either leave in disgust or come up with something that can be hammered apart by anyone with half a semester in biochemistry.

I had some other questions, but I think I should wait until my brain gets untangled.

**fixed quote bracket

[edit on 7-1-2006 by DontTreadOnMe]

Originally posted by Yarium
This doesn't make much sense to me. I read the link as to what these biomacromolecules are, and it tells me that they're large, complex biologically forming molecules - such as DNA.

Biomacromolecules include proteins, fats, sugars, and carbohydrates, as well as DNA. As I stated, altered proteins called prions appear to be most significant (to me at this point) - specifically, the misfolded isoform of "a-smooth muscle actin." Proteins can be altered in the environment or inside cells on exposure to electropollution, and chemical and other contamination - which results in their misfolding. Misfolded proteins have the ability to cause similarly shaped proteins to misfold on contact (re: lock and key theory) - and thereby, to cause mutation and disease.

About protein formation, folding, unfolding and misfolding:

Energy landscapes in protein science

...Finney is examining structures in liquids, and how they change with changes in external conditions such as temperature, pressure, concentration, and added co-solutes.

As Finney explained, solvents are, perhaps obviously, the key to the structures and interactions of molecules in solution. Solvents modulate the interactions between solute molecules; if these are large, flexible molecules such as proteins or nucleic acids, then this includes their conformation in solution. If the solvent conditions change, then structural changes and transitions in molecules can occur. For instance, soap-like molecules undergo assembly processes to form microscopic bubbles known as micelles. On the other hand a natural chain of amino acids will fold into an active protein in the right solvent conditions.

***

Amino Acids React to Form Proteins

Amino acids form polymers through a nucleophilic attack by the amino group of an amino acid at the electrophilic carbonyl carbon of the carboxyl group of another amino acid. The carboxyl group of the amino acid must first be activated to provide a better leaving group than OH-. (We will discuss this activation by ATP latter in the course.) The resulting link between the amino acids is an amide link which biochemists call a peptide bond. In this reaction, water is released. In a reverse reaction, the peptide bond can be cleaved by water (hydrolysis).

When two amino acids link together to form an amide link, the resulting structure is called a dipeptide. LIkewise, we can have tripeptides, tetrapeptides, and other polypeptides. At some point, when the structure is long enough, it is called a protein. There are many different ways to represent the structure of a polypeptide or protein. each showing differing amounts of information.

Proteins are polymers of the bifunctional monomer, amino acids. The twenty common naturally-occurring amino acids each contain an a-carbon, an a-amino group, an a-carboxylic acid group, and an a-side chain or side group. These side chains (or R groups) may be either nonpolar, polar and uncharged, or charged, depending on the pH and pKa of the ionizable group. Two other amino acids occasionally appear in proteins. One is selenocysteine, which is found in Arachea, eubacteria, and animals. Another just recently found is pyrrolysine, found in Arachea. Shultz et al. have gone one step farther. They have engineered bacterial to incorporate two new amino acids, O-methyl-tyrosine and p-aminophenylalanine. More recently, they (Chin et al.) have engineered the yeast strain Saccharomyces cerevisiae to incorporate five new unnatural amino acid (using the TAG nonsense codon and new, modified tRNA and tRNA synthetases) with keto groups that allow chemical modifications to the protein. We will concentrate only the 20 abundant, naturally-occurring amino acids.

Also of interest:

Does an infrasonic acoustic shock wave resonance of the manganese 3+ loaded/copper depleted prion protein initiate the pathogenesis of TSE? Med Hypotheses. 2003 Jun;60(6):797-820. Purdey M. Elworthy, Taunton, Somerset, UK.

So, I'm trying to figure out what you mean. That there's DNA floating around in the air? Because there is, in the form of microbes. Microbes are everywhere. But how are they causing a mutation in our DNA?

Well, just heard about this one: Sperm Can Pick Up Genes from Microbes.

I have focused on proteins, not DNA - proteins are biomacromolecules; contaminations can cause proteins to misfold in the body or in the environment, or cause amino acids to create new protein structures; misfolded proteins circulating in the environment can enter the body, and may have the ability to cause disease, and cellular and genetic change.

For example, ...proteins have been found to account for a large fraction of organic air particulate matter (pdf); Protein-water interactions in a dynamic world; ...protein can readily be detected as a component of dissolved organic matter (DOM) (pdf).

Also see: Unraveling the Mystery of Protein Folding

Any DNA that enters our body that is not our own is destroyed, digested so to speak, and fed to us. People are worried about genetically modified foods, and what it does to our DNA. ... So why would a genetically modified bigger leaf turn you into canned tuna?

The key biomacromolules I've identified are misfolded proeins called prions - please check the relevant links, I think you'll find what you need.

You missed the important statements re proteins and this: "Contaminants interract with biomacromolecules, modify their structures, and change their biochemical properties. As a result, altered biomacromolecules change non-living systems like the planet's carbon, nitrogen, and water cycles. In addition, altered biomacromolecules trigger mutations in living organisms."

...People tend to focus on single contaminants as mutagens or teratogens - the point here is that various contaminants work to alter biomacromolecules, and in the case of prions at least, these altered biomacromolecules access living cells, cause disease, and also can alter genes.

I'm sorry, I just don't see where this research attempt is going. There's no basis, or if there is, there's no explanation of it. It doesn't even seem to qualify as a theory for me. Perhaps you can enlighten me.

Or, if you can't, then step back and review what you know so far, and determine for yourself if it makes any sense. If it does, you should be able to come back and explain it better. If it doesn't, then don't fret and find a new theory.

Maybe I presume too much background knowledge. Could go back and read it again, please? Then let me know. I think the basic info is there - logical and sensible, if a bit sparse.

*******

Originally posted by Byrd

Originally posted by soficrow
The goal is to explain exactly and simply how our electrobiochemically altered world is triggering mutation, and causing an evolutionary crisis.

Erm... define "evolutionary crisis"?

Rapidly accelerating mutation rates and evolutionary change - quite apparent in microbes, fairly apparent in the plant and animal kingdoms, somewhat obscured in humans, but there nonetheless, ie., evidenced by epidemics in chronic disease, other "genetic" diseases.

There's other examples of fairly swift evolutionary change that I can list... are they also crises (these are ancient changes; not modern ones)? How does your thesis address this?

Doesn't at the moment - but good points. Do you know the precipitating conditions for past evolutionary crises?

Premises

1. Altered organic molecules circulating in the ecosphere cause mutations in living organisms;

Are you treating this as the sole cause of mutations in spite of overwhelming evidence to the contrary? If you're not, how much of an impact does it have in conjunction with and in contrast to, say, radiation (a known and identified mutagen.)?

No - I'm suggesting that electropollution in conjunction with chemical and other pollution can cause mutations by first altering biomacromolecules. Pollution does alter biomacromolecules, and in the case of prions at least, these altered biomacromolecules then cause mutation, disease and genetic change.

Over the past century, man has produced electricity, electromagnetic radiation, and ionizing radiation and concentrated them in ways that life as it is is not equipped to tolerate. He has isolated elements and heavy metals, and released these things into the environment in concentrations that life as it is is not equipped to tolerate. He has created over 80,000 synthetic chemicals that life as it is is not equipped to tolerate. These synthetic chemicals come together in the environment, and our bodies, to create a potentially infinite number of new, never-before-seen compounds that life as it is is not equipped to tolerate. And the list goes on. ...I'm saying these contaminants work together to alter the structure and composition of biomacromolecules - which then cause mutation, disease and genetic change.

3. The electrobiochemical composition of the planet has changed sufficiently to trigger an evolutionary crisis affecting all life from the smallest microbes to the largest complex organisms, including humans.

I was reasonably sure I knew that electrochemistry was the study of the chemical reactions that take place at the terminus of a metallic probe when it is inserted in an ionic solution. That it deals with charge transfers and reduction reactions.

These transfers and reduction reactions (also) occur at the molecular and cellular levels. For example:

Zeeman-Stark modeling of the RF EMF interaction with ligand binding A. Chiabrera, B. Bianco, E. Moggia, J.J. Kaufman
Bioelectromagnetics, Volume 21, Issue 4 , Pages 312 - 324, © 2000 Wiley-Liss, Inc. PMID: 10797459

Abstract
The influence of radiofrequency electromagnetic exposure on ligand binding to hydrophobic receptor proteins is a plausible early event of the interaction mechanism. A comprehensive quantum Zeeman-Stark model has been developed which takes into account the energy losses of the ligand ion due to its collisions inside the receptor crevice, the attracting nonlinear endogenous force due to the potential energy of the ion in the binding site, the out of equilibrium state of the ligand-receptor system due to the basal cell metabolism, and the thermal noise. The biophysical output is the change of the ligand binding probability that, in some instances, may be affected by a suitable low intensity exogenous electromagnetic input exposure, e.g., if the depth of the potential energy well of a putative receptor protein matches the energy of the radiofrequency photon. These results point toward both the possibility of the electromagnetic control of biochemical processes and the need for a new database of safety standards.

The use of "electrochemical" to be changed from the science. If this is so, then you will end up with confusing and inefficient research and research that goes nowhere, and your participants are going to either leave in disgust or come up with something that can be hammered apart by anyone with half a semester in biochemistry.

Duh. Sorry. Bioelectrochemical and bioelectrochemistry. Same dynamic, but specifically concerns biological (living) systems and biological compounds. Sometimes called electrobiochemical. ...The language isn't standardized in the literature - and you're right, it results in confusion. A strategy I've seen fairly often.



[Unedited - need movie. Missing some great refs and links - too hard to find right now, but will post soon.]

Originally posted by soficrow
Electropollution and chemical contaminations have altered the structure and composition of the organic molecules that circulate in this planet's ecosphere. Much research describes these altered molecules' impact on non-living systems like the earth's carbon, nitrogen and hydrogen cycles

Sofi, as usual your opinion is respected, but let's see if I can't get some questions answered for my own clarification.

Firstly, what evidence is there that altered organic molecules impact non-living systems, with respect to your hypothesis specifically. What evidence is there to suggest that the structure of organic biomacromolecules can effect the global cycling of nutrients?

Certainly, human based activities can alter the balance of these chemicals, but what you're proposing is completely different. I understood what you were going for with the prions thing we discussed some time ago, but this is a little less clear to me. How can the structure of macromolecules ultimately effect the nutrient cycles. CO2 is CO2, no matter where it came from. Can you elaborate on this idea somewhat?

Similarly, the research investigating the effects of altered organic molecules on living cells and organisms is overshadowed and obscured by the so-called evolution/intelligent design "debates" that pit science against religion - another obviously orchestrated polarization designed to camouflage a real crisis.

Sorry, but I have to disagree completely here. Irrespective of my personal opinion about ID, I don't think it's a deliberate attempt to hide this type of info. This type of info is what can make a scientists career. If a scientist were to postulate this and prove it, it'd be cover of Science, Nature, whichever journal they chose.

Your choice is wording is somewhat difficult to pin down as well. What specifically do you mean by 'altered organic molecules?' That could be anything from a point mutation in DNA, to a prion, to a reduction of a disulfide linkage in protein. Such general wording not only makes the ultimate point difficult for me to elucidate. In fact, it makes the whole point so general, as to pretty much make it inarguable. Of course 'altered organic molecules' have an effect on living cells and organisms. I don't think anyone would debate this, but I think the hypothesis needs to be more specific.

This thread is not a forum for debate on whether or not humans mutate and evolve - the premise is that a) humans do mutate and evolve, and b) the mutation/evolutionary process is escalating. The goal is to explain exactly and simply how our electrobiochemically altered world is triggering mutation, and causing an evolutionary crisis.

Not trying to ignore your explicit instructions, but I DO think it's fair for me to ask what is the basis for your assumption that the evolutionary process is escalating. An increase in the rate of mutation alone is not sufficient evidence for an increase in the evolutionary process specifically. How can you demonstrate this? This is a critical portion of your hypothesis from what I can see.


Premises

1. Altered organic molecules circulating in the ecosphere cause mutations in living organisms;

Fair enough, but no one really disputes this per se. People know that the 'altered organic molecule' Ethidium Bromide can cause mutations, this plus about a billion other chemicals. This in and of itself is not news. Your previous hypothesis, ie: prions initiate genetic change was innovative... at least to my knowledge... though it seems this incarnation of the idea is less specific. Why did that happen?

2. The numbers of altered organic molecules present in the ecosphere have grown exponentially, reached the point of self-organizing criticality and besides affecting the functioning of non-living systems, now are rapidly altering the genetic composition of living organisms;

I think most will agree that the number of newly designed organic molecules has increased exponentially in say the past 200 years or so, but where does this assumption of self-organizing criticality come from. Critical with respect to what specifically? What do you mean by 'self-organized?' And finally what evidence is there to support the idea that this critical point of self-organization has been reached.

I am reasonably familiar with the concept of self-organization and biological systems, especially as per the work of Kaufmann et al. at the Santa Fe institute, so a general description is unnecessary. Perhaps you can provide a more specific definition of self organized criticality, and discuss the evidence for it.

3. The electrobiochemical composition of the planet has changed sufficiently to trigger an evolutionary crisis affecting all life from the smallest microbes to the largest complex organisms, including humans.

I'm having a tough time with this one, Sofi. My biochemistry and molecular biology degrees have not prepard me for a term such as 'electrobiochemical composition of the planet.' I think I understand each word alone, but putting them together leaves me scratching my head. I can think of altered nutrient cycles and things like this... is this what you're going for. Finally what is the evidence to suggest that the electrobiochemical composition of the planet has triggered an evolutionary crisis?

Special Request: My research focuses on proteins. I can show how electrochemical processes and contamination cause proteins to misfold and become prions, then cause cellular and genetic mutations. As far as I can tell - prions are by far the most important agent causing mutations and evolutionary change. In turn, the most important prion seems to be a misfolded isoform of a-smooth muscle actin (ASMA), simply because it is an actin protein, and therefor can access virtually every living cell in every species and kingdom.

We've obviously discussed this before. I got sidetracked (ironically by ID discussions), but to be honest with you. I was never convinced that you made an effective case for this. No offense intended. As I remember, the last thing we talked about was the presence of these specific isoforms of actin in the intestine and whether or not they should have been there. Does that sound about right?

BUT - huge amounts of DNA, fat (lipids), sugar (polysaccharrides), and carbohydrate molecules also circulate in the environment, likely are being altered - and also may be impacting cells and genes in living organisms, either directly or indirectly. ...Anyone know?

These molecules have always been circulating in the environment though. This is nothing new. The concentrations may have changed, but the molecules themselves are nothing new, at least those of biological origin. What evidence is there to suggest that molecules that have pretty much always been a part of the biosphere have suddenly become altered and are now causing genetic damage.

Central Dogma of Molecular Biology: The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. ...Prions provide the only exception to the dogma so far known.

Hmmm... I still don't think I agree that we've demonstrated this. Prions CAN transmit structural information, but don't put information back into the genome. Any changes caused to DNA by prions are not likely to be directed, and can't be really considered information transfer. Protein can't transmit information about it's sequence back to DNA. It MAY be able to alter DNA, but again this isn't 'information transfer' in the sense that the central dogma refers to it.

Thanks in advance for your clarifications.

Oww! My poor little brain! Way too much medical... or at least biological knowledge is needed for me to discuss this subject. I guess I'll stick with cosmology, physics, and philosophy

On that note, why not have Byrd or a moderator move this thread to the Medical Theories section? I'm sure a lot more people there would be able to debate this. In fact I'm pulling my sister, who is studying to become a doctor, into these forums - and she knows a ton! Hopefully she'll start coming online soon and she can debate this with you

Mattison - Gaaaahhh. It will take me hours to write a response. I will of course, but you will need to wait. Thanks for being here.

I wrote this post this am before I logged on:

More on Electromagnetism and Life

Byrd - Inconsistencies and apparent contradictions in the language used to describe "electromagnetism in biological systems" does not result from a lack of scientific rigor. There are several reasons why the language is inconsistent: the study spans several disciplines, and each discipline has its own vocabulary; also, studying and describing the biological effects of electromagnetism - or anything related to electropollution - is "discouraged" in our economy. This blurb explains it best:

The scientific language used to describe "electromagnetism in biological systems" is not consistent. In part, the inconsistencies and apparent contradictions result because the study spans several disciplines, each with its own vocabulary. More to the point, research on electromagnetism in biological systems is fraught with career-killing landmines, and governed by unwritten economic-political policies.

...Newly created sources of electromagnetic fields and radiation are a significant part of our developed world, and industry - and create what is called "electropollution" or "electrosmog." So describing exactly what the effects of electromagnetic pollution are on biological systems is threatening to the economy.

...This state of affairs has created numerous conflicts of interest in the scientific-military-industrial complex. In consequence, scientists have difficulty finding the funds to research electromagnetism in biological systems. Publishing negative results publicly is verboten, and guaranteed to extinguish even the most established star. Researchers who do manage to get funding would rather publish than perish, so they camouflage negative research results with dense, inaccessible, inconsistent and difficult to interpret language.

Source: "Electromagnetism and Life." (c) 2005, Lanie Patrick, Open Access terms. Feel free to copy and distribute with credit to the author.

Every facet of life involves electromagnetic reactions and dynamics - from the atomic level to the molecular, cellular, and then in larger living systems like organs and organisms. Besides impacting living organisms, electromagnetism also affects non-living component parts -biomacromolecules- existing in the environment in non-living systems.

Interestingly, many chemical reactions seen in biology are "forbidden" according to the laws of quantum mechanics. The key to understanding these 'forbidden chemical reactions' - and protein folding, molecular formation, and the like in non-living systems - lies in unravelling the "mystery" of how electromagnetism works in biological systems at the atomic level.

Now, biochemists, molecular biologists, microbiologists, and other life scientists are turning to quantum physicists for help unravelling the mysteries. For example:

Biochemists Turn To Quantum Physics

Charge is a property of electrons most people are familiar with while another property, spin, is lesser known and typically the preserve of physicists. Electron spin occurs in one of two opposing directions - up or down - and biochemists want to start factoring electron spin into their computer simulations of biochemical reactions to make them more accurate.

"Physicists have long known that, according to the laws of quantum mechanics, there are some chemical reactions in our bodies that are 'forbidden' - such as hemoglobin's binding oxygen in our lungs when we breathe. But they do happen nonetheless. So, because these reactions involve electron spin, we decided to take a closer look at them," explained Rodriguez. "Nature loves balance, and you see evidence of it in both charge and spin," Rodriguez continued. "For example, electrons of opposite spin like to pair up with each other as they fly around the nucleus. This allows their spins to balance one another, just as positive and negative charges do between protons and electrons. Even when you have hundreds of electrons forming an immense cloud around a complex molecule, you still see balance in both charge and spin. But sometimes the electrons in metalloproteins seem to be playing a trick on us. As we see with hemoglobin, nature appears to be conserving electronic charge while sacrificing this conservation in spin."

As many of these supposedly forbidden reactions involve biomolecules and transition metals, which can flip back and forth between different spin states under certain conditions, Rodriguez theorized that it was this variability in spin state that was influencing the rate of these reactions. ..."We are creating a new field that attempts to understand biochemical processes at the most fundamental level - that of quantum mechanics. It could be the most important step toward making biochemistry a predictive science rather than a descriptive one," he concluded.

NOTE: I am not saying that all mutation results directly from electropollution. I am saying that electropollution has become a critical component in the complex system that is our ecosphere, and has indirect effects on biological systems.

I am suggesting that we may best understand mutation and evolution by tracking how biomacromolecules become altered, from the atomic level - and then following how they muck up various systems once they are altered. For example, EMF's can catalyze chemical reactions in biomacromolecules. Sometimes these catalyzed reactions occur in proteins, and result in prions that become infectious and then go on to cause disease, mutation and genetic change.

...I want to investigate what more there may be to the story.




ed for clarity


[edit on 4-1-2006 by soficrow]

Originally posted by soficrow
Mattison - Gaaaahhh. It will take me hours to write a response. I will of course, but you will need to wait. Thanks for being here.

I think I have a habit of doing that... I have faith that you'll get back to me, and I can wait. Thanks.

alright here are the facts mutation and evalution takes time. no chemical or radiation causes it, you watch to much tv go read a book LOL j/k

engenerQ, tell that to the Chernobyl kids .

Originally posted by engenerQ
you watch to much tv go read a book LOL j/k

FYI - I never watch any TV - which might explain why I still have control over my own thought processes.

Here's a short bibliography:

Mirage of Health: Utopia's Progress and Biological Change. Rene Dubos, Harper Colophon Books; (c) 1959.

The Body Electric: Electromagnetism and the Foundation of Life. Robert O. Becker and Gary Selden. Quill; (c) 1985.

Plague Time: The New Germ Theory of Disease. Paul W. Ewald, Anchor Books; (c) 2000. Also see Evolution of Infectious Disease.


Enjoy.



sp



[edit on 5-1-2006 by soficrow]

Yarium - Re; your comment that DNA only circulates in the environment via microbes, and my info (thanks to Umbrax' post) that DNA from microbes can enter human sperm. ...I forgot to pull up this bit:

The world is proving to be interconnected in more ways than anyone imagined, some exceedingly subtle but apparently, pivotal. For example, extracellular DNA is found circulating throughout the planet's ecosphere; evidence now shows that circulating DNA is a "multifunctional molecule" with numerous unrecognized roles.

Extracellular DNA plays a pivotal role in deep-sea ecosystems

"Our study shows that the concentration of DNA in deep-sea sediments worldwide is extremely high," study co-author Roberto Danovaro of the Marine Science Institute of the University of Ancona in Italy told The Scientist. "This makes DNA a key molecule once it is dead, as well." Danovaro suggested that researchers consider DNA as a "multifunctional molecule," acting as a reservoir of prokaryotic carbon, nitrogen and phosphorus, all vital to other organisms.

...For decades, scientists measured living biomass, and detected more DNA than expected in all ecosystems.

mattison - Please consider the above Re: your question What evidence is there that altered organic molecules impact non-living systems?

...Not my full response at all, but it brings home the main argument: Given that: Biomacromolecules sequester carbon for example, and carry/circulate other essential elements/nutrients through the ecosphere; It follows that: If the structure and composition of said biomacromolecules changes, then their capacities to fulfill their established roles also will change.


.

Originally posted by soficrow
mattison - Please consider the [below] Re: your question What evidence is there that altered organic molecules impact non-living systems?

...Not my full response at all, but it brings home the main argument: Given that: Biomacromolecules sequester carbon for example, and carry/circulate other essential elements/nutrients through the ecosphere; It follows that: If the structure and composition of said biomacromolecules changes, then their capacities to fulfill their established roles also will change.

Extracellular DNA plays a pivotal role in deep-sea ecosystems

"Our study shows that the concentration of DNA in deep-sea sediments worldwide is extremely high," study co-author Roberto Danovaro of the Marine Science Institute of the University of Ancona in Italy told The Scientist. "This makes DNA a key molecule once it is dead, as well." Danovaro suggested that researchers consider DNA as a "multifunctional molecule," acting as a reservoir of prokaryotic carbon, nitrogen and phosphorus, all vital to other organisms.

...For decades, scientists measured living biomass, and detected more DNA than expected in all ecosystems.

Sofi, I appreciate your efforts at making a rapid reply. A couple of things re: this specific source.

1. How does the "altered organic molecules" fit in here? What I mean is, DNA is pretty much DNA. What specific 'alteration in the DNA molecule are you proposing is the culprit?
   
   
   
   1. Is it sequence based?
      
   2. Is it based on epigenetic changes such as DNA methylation?
      
   3. Is it based on the actual secondary or tertiary structure of the molecule?
      
   
   
2. The other thing that the article specifically points out is that organisms use these molecules as a source of raw materials ie: carbon, reduced nitrogen, etc... how does this fit into your hypothesis. Given this, doesn't this make my first question somewhat irrelevant? How does 'altering' the molecules fit in given that the molecules that make up raw materials, things like CO2, Various amines, acetates, etc, don't really vary structurally, and in general are not chiral? What I mean is does the secondary or tertiary structure, or hell, even the sequence of a DNA molecule make ANY difference if it's not utilized in that form?

Now... if you're proposing uptake of DNA via microorganisms, etc. then that's a somewhat different story. Admittedly, this occurs and is responsible for many genes that we as humans consider 'bad' moving through the various genera of bacteria and other microorganisms. The increase in the frequency of these alleles is a completely different story as well.

So... I guess in summary, I still need clarification as to what you mean by altered.

I didn't see where this reference mentioned any sort of alterations of the molecule. Once again DNA in a free environment like that is very likely being 'altered' but in this case, altered would mean degraded. This is not imply that DNA in 'solution' in the ocean cannot be uptaken and recombined with the genomes of other microorganisms, but the fact of the matter is that the DNA polymer is in a constant state of degradation. The cell does a reasonable job of upkeep, but once that stuff leaves the cell, all bets are off.

Hell, if I store my purified plasmids at 4°C for like 3 months, they're pretty much worthless. I can't imagine how long DNA can remain viable just floating around in the ocean. Of course.... I don't have any 'data' to back this up per se, other than my own personal experience and other similar anecdotal evidence.

Sorry to bog you down, but your statement

If the structure and composition of said biomacromolecules changes, then their capacities to fulfill their established roles also will change.

.
is true on the surface, but we've still not elucidated what these structural alterations are, and further, whether or not the structural changes are relevant at the systemic level in organisms.

Originally posted by mattison0922

Sorry to bog you down, but your statement

If the structure and composition of said biomacromolecules changes, then their capacities to fulfill their established roles also will change.

.
is true on the surface, but we've still not elucidated what these structural alterations are, and further, whether or not the structural changes are relevant at the systemic level in organisms.

Your right. It's just what I wanted you to ponder while waiting for my well articulated, fully substantiated and impeccably referenced reply.

I will first adress the need for complete reverse transcription of protein -> DNA, then post some info on mycoplasma's stranger features.

Central Dogma of Molecular Biology: The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. ...Prions provide the only exception to the dogma so far known.

Hmmm... I still don't think I agree that we've demonstrated this. Prions CAN transmit structural information, but don't put information back into the genome. Any changes caused to DNA by prions are not likely to be directed, and can't be really considered information transfer. Protein can't transmit information about it's sequence back to DNA. It MAY be able to alter DNA, but again this isn't 'information transfer' in the sense that the central dogma refers to it.

considering

www.abovetopsecret.com...

see link above for complete article
Yet such treatments are looking increasingly plausible. In the latest development, normal rats have been made to behave differently just by injecting them with a specific amino acid. The change to their behaviour was permanent. The amino acid altered the way the rat's genes were expressed, raising the idea that drugs or dietary supplements might permanently halt the genetic effects that predispose people to mental or physical illness.

and keeping in mind that anything produced by the body is essentially based on a genetic program, i think it's safe to say that a biomacromolecule (not just proteins, mind you) is able to influence a complex lifeform's genetic base, in any way as long as a there's an appropriate program available in the 'host' cell. Evolutionary speaking, a human should have lots and lots of 'legacy' code available for such (mis)use, even if most of it may be corrupted (junk dna?). cell to cell transfer is apparently child's play - www.abovetopsecret.com... - if it works with foreign lifeforms, it will certainly work within the same species and within the same individual.

Therefore, deriving complete genetic information from proteins is not necessarily a requirement of foreign induced mutation.

========================

Now, on to a case of weird capabilities, which indicates that full reversal of protein synthesis may indeed occur:

Let me introduce you to Mycoplasmal species:

www.newspiritservices.com...

There are 200 species of Mycoplasma. Most are innocuous and do no harm; only four or five are
pathogenic. Mycoplasma fermentans (incognitus strain) probably comes from the nucleus of the
Brucella bacterium. This disease agent is not a bacterium and not a virus; it is a mutated form of
the Brucella bacterium, combined with a visna virus, from which the mycoplasma is extracted.
The pathogenic Mycoplasma used to be innocuous, but biological warfare research conducted
between 1942 and the present time has resulted in the creation of more deadly and infectious
forms of Mycoplasma. Researchers extracted this mycoplasma from the Brucella bacterium and
actually reduced the disease to a crystalline form. They "weaponised" it and tested it on an
unsuspecting public in North America.
..

This little paragraph pretty much contains all i need to make my point. I do no know wether you're inclined to believe this source or not, if you consider it all BS, you don't need to read on.

there are various sources claiming exactly the same

health.benabraham.com...

...There are some facts that may be relevant. Several US government scientists including Dr. Shuy-Ching Lo, of the American Institute of Pathology, hold a patent on a Pathogenic Mycoplasma (mycoplasma fermentans) which has been converted into a crystalline form. In the patent application the diseases AIDS, chronic fatigue syndrome, Wegener’s Granulomatosis, Sarcoidosis, lupus and Alzheimer’s Disease were mentioned as related to this patented form of mycoplasma fermentens. The crystalline form of mycoplasma fermentens contains the part of the brucella bacteria that causes disease in patients. In its crystalline form this mycoplasma can be transmitted into subjects by intravenous administration or injections, spread as an aerosol, implanted by the bite of an insect, or placed into food or water. There is no laboratory evidence for infection by brucella in subjects who have received the “crystalline pathogenic mycoplasma.”...

there's even a copy of that patent circulating on the web, it's on page 30 of this pdf...

---------------

If you're willing to accept the mere existance of crysalline versions of mycoplasma, there's an inconsitency which should be immediately visible to anybody....

DNA/RNA breaks when dehydrated.

Bacteria inhabitating dry environments need elaborate repair mechanisms to cope with the inevitable damage (requiring more genetic code to implement, while mycoplasma's is supposedly minimalistic..) and a tough cell wall is a hallmark of such species.

Another strange aspect is re-crystallisation from solution depending on pH value, which, if i'm not mistaken, indicates the agent's own ph value...

from www.newspiritservices.com...

or

www.mercola.com...

these are all more or less copies of Donald W. Scott's www.consumerhealth.org...

..
Because the crystalline disease agent goes into solution in the blood, ordinary blood and tissue tests will not reveal its presence. The mycoplasma will only crystallize at 8.1 pH, and the blood has a pH of 7.4 pH. So the doctor thinks your complaint is "all in your head".
..

.. which would be 8.1, if you chose to believe the sources. rather strange for something that's supposedly some kind of nucleotid matter, isn't it?


In other words, mycoplasma is either capable of storing its genetic code in an unknown, very durable and compact manner, enduring even complete dehydration, all the while exhibiting peculiar pH values OR it's utilising a different medium to convey it - the vaunted reverse-transcribable biomacromolecule - OR, there are actually another version of mycoplasma, one which is not only cell wall deficient, but also nucleotid deficient (ie prionic), with all associated consequences.

comments welcome, especially regarding the pH value.

Originally posted by Long Lance
I will first adress the need for complete reverse transcription of protein -> DNA,

[snip]

www.abovetopsecret.com...
and keeping in mind that anything produced by the body is essentially based on a genetic program, i think it's safe to say that a biomacromolecule (not just proteins, mind you) is able to influence a complex lifeform's genetic base, in any way as long as a there's an appropriate program available in the 'host' cell. Evolutionary speaking, a human should have lots and lots of 'legacy' code available for such (mis)use, even if most of it may be corrupted (junk dna?). cell to cell transfer is apparently child's play - www.abovetopsecret.com... - if it works with foreign lifeforms, it will certainly work within the same species and within the same individual.

Hmmm... I must be lost. How does ANY of what you've posted argue for reverse transcription of information from the protein level?

Additionally, Your statement:

anything produced by the body is essentially based on a genetic program, i think it's safe to say that a biomacromolecule (not just proteins, mind you) is able to influence a complex lifeform's genetic base, in any way as long as a there's an appropriate program available in the 'host' cell

isn't saying much. So you're saying because things are produced via a genetic program it's likely they can effect the genetic program provided there is a sufficient apparatus to do so.

Ummm... yeah, of course. That's the question though: is there a mechanism whereby altered biomacromolecules, or whatever sofi is calling them can change an organisms genetic program. I say of course there is, depending on which molecules you're talking about. I am still missing your point.

And again I don't see how the links you've posted argue in favor of RT from the protein level to the DNA information.

Therefore, deriving complete genetic information from proteins is not necessarily a requirement of foreign induced mutation.

Of course it's not a requirement, but that's sofi's hypothesis, at least it's one of her hypotheses... can't say for sure that it's this one, but a hypothesis of soficrow's states that information is transferred from proteins, specifically prions back into the genome.

Now, on to a case of weird capabilities, which indicates that full reversal of protein synthesis may indeed occur:

[snip]
This little paragraph pretty much contains all i need to make my point. I do no know wether you're inclined to believe this source or not, if you consider it all BS, you don't need to read on.

Ummm.... I read the whole thing, and again perhaps it escaped me, but very specifically how does ANY of what you've posted imply that

that full reversal of protein synthesis may indeed occur

?

If you're willing to accept the mere existance of crysalline versions of mycoplasma, there's an inconsitency which should be immediately visible to anybody....

What? Gosh, I'm sorry I still don't see your point. Explain this to me like I don't have a BS in Biochemistry, a PhD in Molecular Biology, and haven't worked in a lab for... well pretty much forever.

DNA/RNA breaks when dehydrated.

Hmmm... this is news to me. I dehydrate DNA all the time. It's a great way to store it. Most of the major synthesizers of Nucleic Acid polymers ship their products in dehydrated form. I've got some DNA sitting on my desk right now that's been here for a couple of months, totally dehydrated. Once I rehydrate it, it'll be as good as new. I'm not sure where you're getting your information from but here's some basic nucleic acid polymer chemistry for you.

Polymerization of nucleic acids is referred to in general as a dehydration reaction, a hydrogen and and OH are combined removed from the reactants, and water is formed. Guess what the depolymerization reaction is called: Hydrolysis. In case it isn't incredibly obvious, this means 'cleaved with water' roughly; in fact in this reaction water is added back to the system, breaking the phosphodiester linkage that joins adjacent nucleotides.

So in conclusion, dehydrated is an inherently more stable way to store DNA.

You weren't seriously going to postulate that the information for the 100+ genes in a mycoplasma were encoded in the crystalline protein storage structure were you? Crystals are inherently information poor. They are simply repeats. I would imagine that the coat protein in the mycoplasma is composed at most, 3 or 4 proteins... not much info there.

Another strange aspect is re-crystallisation from solution depending on pH value, which, if i'm not mistaken, indicates the agent's own ph value...

Hmmm you could mean pH dependence is related to the proteins pI value. Proteins don't have an inherent pH, could be pKa values too. Things that are dehydrated also don't have a pH. By definition they can't.

.. which would be 8.1, if you chose to believe the sources. rather strange for something that's supposedly some kind of nucleotid matter, isn't it?

Now I am really lost. Are you saying that because this thing crystallizes at pH 8.1 that it can't be DNA or RNA, because those molecules are acids?

First of all, the nucleic acids are INSIDE the coat. They are not going to be affecting external pH. Secondly, the coat proteins respond because of their inherent protein sequence. A different protein sequence would crystallize at a different pH. These values are dependent of the collective pI value of the coat proteins, not the presence or absence of nucleic acid.

In other words, mycoplasma is either capable of storing its genetic code in an unknown, very durable and compact manner, enduring even complete dehydration, all the while exhibiting peculiar pH values OR it's utilising a different medium to convey it - the vaunted reverse-transcribable biomacromolecule - OR, there are actually another version of mycoplasma, one which is not only cell wall deficient, but also nucleotid deficient (ie prionic), with all associated consequences.

comments welcome, especially regarding the pH value.

Yes, as I mentioned, dehydration is a very stable way to store nucleic acid. However what do you mean exhibiting peculiar pH values. For the most part, I don't think we've developed the technology to measure the pH inside mycoplasma, and again, dehydrated items aren't said to have a pH.

I have a big issue with your 'nucleotide deficient' mycoplasma. You're saying there exists a mycoplasma that contains NO nucleic acid.

I don't say this much, but I don't believe it. I definitely NEED to see a reference re: this. If this were true, evolution wouldn't have been Science magazines top story of the year, this mycoplasma would. Please provide some sort of documentation.

Originally posted by mattison0922
..
[Hmmm... I must be lost. How does ANY of what you've posted argue for reverse transcription of information from the protein level?

i argued that you don't need to do that just to do something, ie. cause a mutation, flow of information would be limited, though, but considering that complex species' genomes contain lots of options, all you'd need is the appropriate key to activate your desired program.

under this circumstance, you wouldn't need reverse-transcription, would you?

Therefore, deriving complete genetic information from proteins is not necessarily a requirement of foreign induced mutation.

Of course it's not a requirement, but that's sofi's hypothesis, at least it's one of her hypotheses... can't say for sure that it's this one, but a hypothesis of soficrow's states that information is transferred from proteins, specifically prions back into the genome.

goal #2
2. Altered organic molecules in turn alter living cells, organisms and their genes.

one of the llinks describes how an amino acid alters gene expression, if you expressed the right genes, you could run any 'code' you wish as long as it's available in the genome, right?

DNA/RNA breaks when dehydrated.

Hmmm... this is news to me. I dehydrate DNA all the time. It's a great way to store it. Most of the major synthesizers of Nucleic Acid polymers ship their products in dehydrated form. I've got some DNA sitting on my desk right now that's been here for a couple of months, totally dehydrated. Once I rehydrate it, it'll be as good as new. I'm not sure where you're getting your information from but here's some basic nucleic acid polymer chemistry for you.

ok, i'm not doubting you, but please would you explain why deinococcus radiodurans supposedly gained its radiation tolerance by developing protective mechanisms against dehydration? such a measure would be useless if DNA easily survived running dry.

You weren't seriously going to postulate that the information for the 100+ genes in a mycoplasma were encoded in the crystalline protein storage structure were you? Crystals are inherently information poor.

it's called crystalline, probably because of the looks of it, doesn't need to be a real crystal.

Hmmm you could mean pH dependence is related to the proteins pI value. Proteins don't have an inherent pH, could be pKa values too. Things that are dehydrated also don't have a pH. By definition they can't.

It supposedly drops out of solution at pH 8.1, what does that tell us about it?

Now I am really lost. Are you saying that because this thing crystallizes at pH 8.1 that it can't be DNA or RNA, because those molecules are acids?
...

First of all, the nucleic acids are INSIDE the coat. They are not going to be affecting external pH. Secondly, the coat proteins respond because of their inherent protein sequence. A different protein sequence would crystallize at a different pH. These values are dependent of the collective pI value of the coat proteins, not the presence or absence of nucleic acid.

so, it is normal for these particles to fall out of solution at a certain pH value.. that would explain how it was created in the first place, wouldn't it


as for the rest, forget it, according to you, it was based on false premises, so. once you explain why bacteria need to protect their genome against dehydration when DNA can be stored dry, i'll consider my entire post refuted.


thnx for your patience, LL

Originally posted by Long Lance
i argued that you don't need to do that just to do something, ie. cause a mutation,

In essence this is true, mutations just happen, one needn't do something to induce mutation. Lots of things cause mutations, yes, but how does acknowledgment that things cause mutations relate to the altered organic molecules sofi mentioned, or the protein to DNA RT you mention?

flow of information would be limited, though, but considering that complex species' genomes contain lots of options, all you'd need is the appropriate key to activate your desired program.

Random mutation in a genome is not 'information flow.' But yes, genomes have lots of options, and you need specific triggers to turn genes on, but again, I'm sorry, but I just don't see how it relates. Usually I'm not this obtuse, sorry.

under this circumstance, you wouldn't need reverse-transcription, would you?

I only mention RT because sofi has brought it up with respect to prions. I am not of the opinion that proteins RT info back into the genome. Sofi seems to feel she has evidence of this though. It's not like I'm saying it's a requirement, I am just trying to address portions of her hypothesis that don't coincide too well with my own understanding of science.

one of the llinks describes how an amino acid alters gene expression, if you expressed the right genes, you could run any 'code' you wish as long as it's available in the genome, right?

Ummmm.... yes. I don't see how this amino acid thing fits in though.

ok, i'm not doubting you, but please would you explain why deinococcus radiodurans supposedly gained its radiation tolerance by developing protective mechanisms against dehydration? such a measure would be useless if DNA easily survived running dry.

D. radiodurans great bug! Hmmm... I am not familiar with this line of thinking. I would say the operative word here is 'supposedly.' Because some scientist speculates that this is the case, doesn't make it so. There may be other factors involved with dehydration, ie: nucleases, etc., like I said, this is news to me. Got any links re: this issue?

Don't take my word for it though. You can order DNA on line, it's usually, like $0.50/base or something. When you recieve it, you'll note that it arrives dehydrated.

it's called crystalline, probably because of the looks of it, doesn't need to be a real crystal.

Everything else you've posted suggests that it's a real crystal, likely composed of just a couple of proteins. However, the point is the same no matter what. You can't extract more information from something than it's capable of carrying. What I mean is 3 or 4 proteins on the outside are inadequate to code more information than the 3 or 4 proteins themselves. Currently information theory doesn't permit removal or more information than a system offers.

It supposedly drops out of solution at pH 8.1, what does that tell us about it?

It tells us that it drops out of solution at pH 8.1, which basically means that at this pH, the proteins, or whatever become 'uncomfortable' (actually, energetically stressed) such that they clump together. This likely caused by one of two things, hydrophobic interactions, or charge-charge interactions. My suspicion is hydrophobic, but there isn't enough information provided for me to know this for certain.

so, it is normal for these particles to fall out of solution at a certain pH value.. that would explain how it was created in the first place, wouldn't it

Apparently it's 'normal' for this to happen, as it does. But I don't see how this offers any explanation as to the origins of mycoplasma or their coat proteins.

as for the rest, forget it, according to you, it was based on false premises, so. once you explain why bacteria need to protect their genome against dehydration when DNA can be stored dry, i'll consider my entire post refuted.

According to me? I just said that's news to me, and offered some examples of why dehydrating Nucleic acids is not necessarily bad. If you've got some refs. or whatever, stating that genomes break when they're dehydrated, I check them out. I never said DNA is impervious to dehydration, I merely offered my own personal experience with dehydrated DNA, mentioned the industry standard for shipping DNA, and mentioned some very basic chemistry that describes biological polymerization reactions. It doesn't mean the case is closed. If you've got something to offer up, by all means, do it. I like to learn new stuff too.

i argued that you don't need to do that just to do something, ie. cause a mutation,

In essence this is true, mutations just happen, one needn't do something to induce mutation. Lots of things cause mutations, yes, but how does acknowledgment that things cause mutations relate to the altered organic molecules sofi mentioned, or the protein to DNA RT you mention?

...

flow of information would be limited, though, but considering that complex species' genomes contain lots of options, all you'd need is the appropriate key to activate your desired program.

Random mutation in a genome is not 'information flow.' But yes, genomes have lots of options, and you need specific triggers to turn genes on, but again, I'm sorry, but I just don't see how it relates. Usually I'm not this obtuse, sorry.

...
I don't see how this amino acid thing fits in though.

It doesn't relate to reverse transcription, it's an alternative, which i posted for the sake of completeness (bad move, i guess), if the mutations caused by these postulated molecules were predictable (ie. NOT random), they would allow to transmit minimalistic signals, namely which dormant string of genome to activate (or which active genes to deactivate), that's why i posted the amino acid case, to show that there are ways to predictably alter genetic processes.

All that needs to be shown at this point (and i don't have any data, so i'll have to stop here) is that the genome can actually re-write itself (as opposed to reconfigure its activities), and i don't see why it couldn't (anything in the body is replicated according to the genome's blueprint) , but then what do i know?

D. radiodurans

great bug! Hmmm... I am not familiar with this line of thinking. I would say the operative word here is 'supposedly.' Because some scientist speculates that this is the case, doesn't make it so. There may be other factors involved with dehydration, ie: nucleases, etc., like I said, this is news to me. Got any links re: this issue?

from www.ornl.gov...

from article
Scientists are unsure how this resistance evolved, although they suspect it may be a side effect of the microbe's ability to survive periods of severe dehydration, which also fragments DNA.

Good enough? i have a question for you: do you use this dried DNA as raw material for replication? if so, that would explain why breakage is irrelevant, wouldn't it?

..
Everything else you've posted suggests that it's a real crystal, likely composed of just a couple of proteins. However, the point is the same no matter what. You can't extract more information from something than it's capable of carrying. What I mean is 3 or 4 proteins on the outside are inadequate to code more information than the 3 or 4 proteins themselves. Currently information theory doesn't permit removal or more information than a system offers.

Yes, but then i'll have to consider my sources bunk (admittedly they are not really satisfctory), because if it's capable of replicating in its 'crystalline' form it needs the information, and that's not the whole story, the pathogen would also need some form of cellular machinery to 'mine' host cell components to reproduce, and i don't know of any lifeform which is capable of surviving complete dryness, which on top of things, litteraly turns to dust (watery dust, of course - sludge?) at a relatively modest pH value of 8.1, while there are (much more complex) species which easily survive 9 and more. that's my problem, something doesn't compute. tbh, next to nothing does, but that's why i brought the subject up in the first place.

peculiar source, but i think it will do
Surprisingly, though, Mono Lake supports a wide array of life from microbes, to plankton, to small shrimp. T. californiensis is right at home there. It thrives in highly alkaline conditions (pH 8-10.5) and at salt concentrations near 20%.

Apparently it's 'normal' for this to happen, as it does. But I don't see how this offers any explanation as to the origins of mycoplasma or their coat proteins.

Rumor has it that some variants were synthesized from a Brucellosis bacterium, if this solidification occured naturally in most organisms, it would explain how it was produced.

Originally posted by Long Lance
It doesn't relate to reverse transcription, it's an alternative, which i posted for the sake of completeness (bad move, i guess), if the mutations caused by these postulated molecules were predictable (ie. NOT random), they would allow to transmit minimalistic signals, namely which dormant string of genome to activate (or which active genes to deactivate), that's why i posted the amino acid case, to show that there are ways to predictably alter genetic processes.

All that needs to be shown at this point (and i don't have any data, so i'll have to stop here) is that the genome can actually re-write itself (as opposed to reconfigure its activities), and i don't see why it couldn't (anything in the body is replicated according to the genome's blueprint) , but then what do i know?

Okay... I think I understand what you're saying (finally! ), yes you are correct, there are predictable ways to alter the genome. We don't necessarily no what the phenotypic outcome of the altered genome will be, but we can alter it predictably.

With respect to the genome rewriting itself: This will probably not happen in large multicellular organisms. I think the logistics could be too difficult. Of course I am assuming that the organism would 'want' to maintain it's genetic integrity, ie: would 'want' all, or at least most cells to carry the same genome. Rewriting a 3 billion base code in each cell of an organism containing 3 trillion cells would be a daunting task indeed.

This is not without precedent though. The immune system maintains a particular type of cell that when presented foreign 'bodies' begins a hypermutation of certain regions of its genome. The hypermutation is an effort to produce a large number of antibodies, one of which will hopefully be effective against the foreign body. This is a great example of non-random mutation brought on by environmental stress, in essence re-writing the genome.

It has also been demonstrated that when bacteria are subjected to stressful conditions, including nutrient deficiency, sub-optimal temperatures, and pH related stress, they will often engage in hypermutation of particular regions of the genome in an effort to adapt.

One such bug, P. aeruginosa (sp?) has been shown to develop the ability to digest nylon oligomers from complete naivety in just 9 days. It does this via hypermutation of extrachromosomal DNA. It has demonstrated a unique ability to develop the ability to digest lots of xenobiotic compounds.

So... in conclusion, there is plenty of evidence to suggest that mutation, or changing the genome is not necessarily a random process.

Good enough? i have a question for you: do you use this dried DNA as raw material for replication? if so, that would explain why breakage is irrelevant, wouldn't it?

Thanks for the link. Did you happen to notice this statement a couple of paragraphs down from the one you posted:

Plausible explanations for the extraordinary DNA-repair capability of D. radiodurans remain elusive in the early analyses of DNA repair genes.

Sounds kind of like these scientists are scratching their heads with this one.

The DNA I am referring to is used for predominantly two things: Firstly, Primers for PCR and DNA sequencing. These are very short molecules, usually not much more than 30bp, which explains why I don't have to worry about them too much.

Secondly, I use dehydrated plasmids all the time. These molecules are significantly bigger, often times upwards of 15kb, which is still nowhere near as big as genome. These molecules are used in 'transforming' bacteria - ie: inserting genes you want them to express. Now it could be that most of these plasmids are degraded and broken up, and I only see the effects of those that are in tact. All that needs to happen is a single bacteria has to 'ingest' a single in tact plasmid, and I'll think it's 'good DNA,' even if 99% of the plasmids are broken up.

However, I DO also know that the spores of many species, including the species I am currently studying, Phytophthora infestans, are stored and remain viable in a state of dessication. However, again, I am talking about spores, not bacterial resting structures, and while there are likely to be similarities, there are also likely to be differences.

Yes, but then i'll have to consider my sources bunk (admittedly they are not really satisfctory), because if it's capable of replicating in its 'crystalline' form it needs the information, and that's not the whole story, the pathogen would also need some form of cellular machinery to 'mine' host cell components to reproduce,

These are all valid points. Perhaps you should consider getting info from... a more primary source.

and i don't know of any lifeform which is capable of surviving complete dryness, which on top of things, litteraly turns to dust (watery dust, of course - sludge?) at a relatively modest pH value of 8.1, while there are (much more complex) species which easily survive 9 and more. that's my problem, something doesn't compute. tbh, next to nothing does, but that's why i brought the subject up in the first place.

That's the great thing about ATS... there's always someone here that knows more about something than you, not you personally, but the collective 'you.'

peculiar source, but i think it will do
Surprisingly, though, Mono Lake supports a wide array of life from microbes, to plankton, to small shrimp. T. californiensis is right at home there. It thrives in highly alkaline conditions (pH 8-10.5) and at salt concentrations near 20%.

Where life can exist, it will. A buddy of mine at Arizona State actually studys bacteria that live under the permafrost in the arctic circle. These bugs have some insanely long doubling time of like 4 months. That they can survive and replicate in those conditions at all is... astonishing.

Rumor has it that some variants were synthesized from a Brucellosis bacterium, if this solidification occured naturally in most organisms, it would explain how it was produced.

I read that in your first post... I was kind of intrigued by it, and thought I'd look into it a little more. I've not had an opportunity to do so yet, but it's on my list.