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Author Topic: Is gene-centered biology due to an experimental mistake?  (Read 4004 times)

Offline Martin J Sallberg

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The experiment that the central dogma of molecular biology is based on is comparisons of transplanted DNA to transplanted proteins. The experiment appeared to show that transplanted DNA caused heritable change in cells, which transplanted proteins did not. Then it was concluded that DNA is a genetic material and proteins are not. But did that experiment destroy the information carried by proteins when they were isolated and transplanted? Unlike DNA, which forms very long strains and has relatively low mobility, proteins come in blocks that are highly mobile. This means that while the structure alone of the DNA can carry a lot of information, the information content of proteins are more likely in their motion patterns. This becomes especially interesting when considering that highly mobile enzmes (chemically active proteins) are processing DNA (DNA cannot even replicate itself independently). It may explain cloned cats with a different fur color than the genome-donating cat, although the effect would most likely be much stronger if the proteins on the chromosomes themselves (and not just those located outside the nucleus) could be transplanted to a different genome without scrambling the protein motion patterns.


 

Offline CliffordK

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #1 on: 14/05/2013 19:58:39 »
Look up Calico & Tortoiseshell cats.

Perhaps due to men getting a single dose of the X-Chromosome, and women getting a double dose of it, for the most part one X-Chromosome in females is inactivated.   However, it is not always the same X Chromosome that is inactivated throughout the body.

Since males get only a single X chromosome, there isn't any X-chromosome inactivation necessary, and thus the X chromosome calico genes would be uniform throughout the body.

In the  Calico/Tortoiseshell cats, in the females, they get some different X chromosome genes activated in different parts of the body causing the calico look. 

while two female cat clones share the same genes, they have different X Chromosome inactivation patterns, and thus different coats.

As far as Genes, Genotypes, Phenotypes, and Inheritance Patterns, these were being determined long before DNA was discovered.  Since determining the structure of DNA in 1953, there has been a lot of evidence to support DNA as carrying genetic information. as well as RNA, tRNA, and mRNA.  Protein sequences match the DNA sequences. 

No doubt we will learn more about gene regulation in the future, and perhaps some formally considered "junk DNA" will be demonstrated to have some purpose.
 

Offline Martin J Sallberg

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #2 on: 15/05/2013 06:27:43 »
Look up Calico & Tortoiseshell cats.

Perhaps due to men getting a single dose of the X-Chromosome, and women getting a double dose of it, for the most part one X-Chromosome in females is inactivated.   However, it is not always the same X Chromosome that is inactivated throughout the body.

Since males get only a single X chromosome, there isn't any X-chromosome inactivation necessary, and thus the X chromosome calico genes would be uniform throughout the body.

In the  Calico/Tortoiseshell cats, in the females, they get some different X chromosome genes activated in different parts of the body causing the calico look. 

while two female cat clones share the same genes, they have different X Chromosome inactivation patterns, and thus different coats.

As far as Genes, Genotypes, Phenotypes, and Inheritance Patterns, these were being determined long before DNA was discovered.  Since determining the structure of DNA in 1953, there has been a lot of evidence to support DNA as carrying genetic information. as well as RNA, tRNA, and mRNA.  Protein sequences match the DNA sequences. 

No doubt we will learn more about gene regulation in the future, and perhaps some formally considered "junk DNA" will be demonstrated to have some purpose.

I never denied that DNA can carry information. I just said that the dogma that proteins should be unable to carry information comes from scrambling of their motion patterns, an artefact of their isolation and transplantation, that proteins carry information but it is in their motion patterns. While DNA carries its information in its sequence which is not scrambled when isolated and transplanted. So I did NOT say "DNA does not matter", but rather "proteins matters at least as much as DNA". And considering that enzymes process DNA which cannot even replicate itself independently, it is likely that those enzymes can directly modify the DNA.
 

Offline CliffordK

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #3 on: 15/05/2013 07:23:43 »
Proteins don't self replicate independent of RNA/DNA.  So, if one started with one cell with a certain set of proteins.  Without the DNA, if the cell replicated a million times, there would be little left of the original protein.

While there is a reverse transcriptase to convert from RNA to DNA, I don't believe there is any way to catalyse Protein/Protein copying, or Protein to RNA/DNA reverse transcription.

Prions are unique among proteins in that they take normal proteins and force them into abnormal conformations, and thus cause disease.  They are "inherited" by eating the brains of one's elders.

There are also other proteins that catalyse protein folding, without which, the cells could not make the proteins that they need.

Red blood cells (RBCs) as well as platelets are a unique group of anuclear cells.  They can obviously perform vital functions in the body, but eventually wear out and must be replaced.  After loosing the nucleus, they no longer can divide.

Anyway, if proteins are required to initiate certain protein folding, perhaps there could be some proteins with multiple conformations that could be inherited, but as of now, only a few prions have been discovered.

One should, of course, also mention that mitochondria, and chloroplasts carry their own DNA outside of the nucleus.

In the  case of mitochondria, while the sperm have their own mitochondria, only the mitochondria from the ovum are kept, and thus inherited through the maternal line.
 

Offline Martin J Sallberg

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #4 on: 15/05/2013 13:30:05 »
Proteins don't self replicate independent of RNA/DNA.  So, if one started with one cell with a certain set of proteins.  Without the DNA, if the cell replicated a million times, there would be little left of the original protein.

While there is a reverse transcriptase to convert from RNA to DNA, I don't believe there is any way to catalyse Protein/Protein copying, or Protein to RNA/DNA reverse transcription.

Prions are unique among proteins in that they take normal proteins and force them into abnormal conformations, and thus cause disease.  They are "inherited" by eating the brains of one's elders.

There are also other proteins that catalyse protein folding, without which, the cells could not make the proteins that they need.

Red blood cells (RBCs) as well as platelets are a unique group of anuclear cells.  They can obviously perform vital functions in the body, but eventually wear out and must be replaced.  After loosing the nucleus, they no longer can divide.

Anyway, if proteins are required to initiate certain protein folding, perhaps there could be some proteins with multiple conformations that could be inherited, but as of now, only a few prions have been discovered.

One should, of course, also mention that mitochondria, and chloroplasts carry their own DNA outside of the nucleus.

In the  case of mitochondria, while the sperm have their own mitochondria, only the mitochondria from the ovum are kept, and thus inherited through the maternal line.

Was I writing unclearly? My point was that since DNA cannot independently self-replicate and there are enzymes involved in making and decomposing DNA, enzymes can and do directly affect the DNA sequence. That allows proteins to actively change the genome, but the way they change it depends on the motion patterns of the proteins. That is why the isolation and transplantation may have erased proteinal effects on the genome by scrambling the motion patterns of the proteins.

Digression: Just because paternal mitochondria are not usually inherited does not mean that they can never be. As far as I know, nobody has tested if environmental stress can trigger paternal inheritance of mitochondria.
 

Offline wolfekeeper

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #5 on: 15/05/2013 14:37:38 »
DNA can't but RNA can independently self-replicate.

Note that there is no complete block to proteins carrying information in biology, and some diseases such as scrapie and CJD are carried only by proteins. However, these known examples are rare exceptions, the vast, vast majority of inheritance is known to be via genetic means (also some other DNA-related epigenetic mechanisms such as methylation.)
 

Offline Martin J Sallberg

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #6 on: 15/05/2013 16:41:24 »
DNA can't but RNA can independently self-replicate.

Note that there is no complete block to proteins carrying information in biology, and some diseases such as scrapie and CJD are carried only by proteins. However, these known examples are rare exceptions, the vast, vast majority of inheritance is known to be via genetic means (also some other DNA-related epigenetic mechanisms such as methylation.)

I was not talking (exclusively) about diseases. Nor was I restricting it to proteins affecting protein folding. I was talking about proteins along the right motion patterns modifying the genome. A few protein molecules invading a cell at haphazard motion patterns does not qualify. I was talking primarily about the apparatus of proteins following motion patterns in the cell itself. In fact, I said that the reason why experiments with transplanted molecules does not support proteins as material of heredity is because the isolation and transplantation of proteins scrambles their motion patterns. The unfair advantage DNA had in the experiments was that it contains information in its sequence chain that is not dependant on motion patterns.
 

Offline wolfekeeper

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #7 on: 15/05/2013 18:24:09 »
Proteins affecting inheritance in higher organisms is ridiculous. How would the signal get from your arm or whatever to the reproductive organs?
 

Offline cheryl j

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #8 on: 16/05/2013 19:08:15 »
What's a motion pattern?
 

Offline cheryl j

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #9 on: 16/05/2013 19:15:53 »

Digression: Just because paternal mitochondria are not usually inherited does not mean that they can never be. As far as I know, nobody has tested if environmental stress can trigger paternal inheritance of mitochondria.

I thought mitochondria in sperm were only found in the tail, and that was why mitochondria DNA was inherited from the mother.
 

Offline dlorde

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #10 on: 17/05/2013 19:16:40 »
I suppose protiens can be considered to carry information by reason of having some function, but to equate this with molecules whose function is informational seems like equivocating 'information'. It may also be that proteins can be triggers for epigenetic changes, but that doesn't seem to be quite what is suggested here.

Perhaps it would be clearer if the OP could describe a real-world example of proteins actively changing the genome?
 

Offline Martin J Sallberg

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #11 on: 21/05/2013 09:15:08 »
Proteins affecting inheritance in higher organisms is ridiculous. How would the signal get from your arm or whatever to the reproductive organs?

Well, the direct effect of proteins on the genome is referring to inside the cell. But once the proteins have affected the genome of one cell, that changed genome can spread by micro-RNA, exosomes, and so on, to other organs including reproductive ones.
 

Offline Martin J Sallberg

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #12 on: 21/05/2013 09:17:22 »
What's a motion pattern?

It is the pattern along which something moves. In eukaryotes, the cytoskeleton is a frame of reference for protein motion patterns, but in all organisms, how proteins move on various surfaces is affected both by the surface itself and by the propulsion of the protein.
 

Offline Martin J Sallberg

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #13 on: 21/05/2013 09:20:03 »

Digression: Just because paternal mitochondria are not usually inherited does not mean that they can never be. As far as I know, nobody has tested if environmental stress can trigger paternal inheritance of mitochondria.

I thought mitochondria in sperm were only found in the tail, and that was why mitochondria DNA was inherited from the mother.

How can you be so sure that certain environmental stresses cannot make the egg cell swallow the tail of the sperm or parts of it?
 

Offline Martin J Sallberg

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #14 on: 21/05/2013 09:21:52 »
I suppose protiens can be considered to carry information by reason of having some function, but to equate this with molecules whose function is informational seems like equivocating 'information'. It may also be that proteins can be triggers for epigenetic changes, but that doesn't seem to be quite what is suggested here.

Perhaps it would be clearer if the OP could describe a real-world example of proteins actively changing the genome?

I never claimed that the simple chemical structure of proteins carried hereditary information, only that the way they move does. For instance, there are lots of enzymes involved in processing DNA.
 

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Re: Is gene-centered biology due to an experimental mistake?
« Reply #14 on: 21/05/2013 09:21:52 »

 

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