DNA Sequencing of living structures

Bishadi

Banned
Banned
IN many frames of reference the idea is that DNA is simply based on the 4 base structures between the esters.

To the extent that the sequence of these is what the genome is.

Now in Cuba, there is a group headed by Sanchez and Grau that have identified and describe the energy upon each as being as important as the sequence itself.

IN which the 'state' (e) of the molecule must be included to perform the linear evolution of the DNA structures.

A comment noticed a few years back within one of their publications shared that DNA is unique in that it is like a computer having its hardware rearranged by the software and vise verse.

Take a peak at what is coming into the mix

Abstract A Boolean structure of the genetic code where Boolean deductions have biological and physicochemical meanings was discussed in a previous paper. Now, from these Boolean deductions we propose to define the value of amino acid information in order to consider the genetic information system as a communication system and to introduce the semantic content of information ignored by the conventional information theory. In this proposal, the value of amino acid information is proportional to the molecular weight of amino acids with a proportional constant of about 1.96×1025 bits per kg. In addition to this, for the experimental estimations of the minimum energy dissipation in genetic logic operations, we present two postulates: (1) the energy E i (i = 1, 2, ..., 20) of amino acids in the messages conveyed by proteins is proportional to the value of information, and (2) amino acids are distributed according to their energy E i so the amino acid population in proteins follows a Boltzmann distribution. Specifically, in the genetic message carried by the DNA from the genomes of living organisms, we found that the minimum energy dissipation in genetic logic operations was close to kTLn(2) joules per bit.

or here is another

A New DNA Sequence Vector Space on a
Genetic Code Galois Field

Robersy Sánchez 1,2, Ricardo Grau 2,3 and Eberto R. Morgado3
1 Research Institute of Tropical Roots, Tuber Crops and Banana (INIVIT). Biotechnology group. Santo Domingo. Villa
Clara. Cuba
{robersy@uclv.edu.cu}
2 Center of Studies on Informatics, Central University of Las Villas, Villa Clara, Cuba
{rgrau@uclv.edu.cu}
3 Faculty of Mathematics Physics and Computation, Central University of Las Villas, Villa Clara, Cuba.
(morgado@uclv.edu.cu)


Abstract ⎯
A new N-dimensional vector space of DNA sequences over the Galois field of the 64 codons (GF (64)) was
recently presented. Although in this vector space, gene point mutations were considered linear transformations or
translations of the wild type gene, deletions and insertions (indel) could not be considered. Now, in order to
include indel mutations, we have defined a new Galois field over the set of elements X1X2X3


Point being the energy upon the mass is just as important as the mass.

For example: a person with a greater education is ofter more capable than another without; pretty much all the same mass but a HUGE difference.

This is what to look for in the future of Genetic understanding.


Enjoy
 
Now in Cuba, there is a group headed by Sanchez and Grau that have identified and describe the energy upon each as being as important as the sequence itself.

Point being the energy upon the mass is just as important as the mass.


I highly doubt that this “energy” is as important as the sequence. Unless Sanchez and Grau (or anyone else) can perform functional experiments that actually link this so-called “energy” to gene regulation or transcription factor binding or histone acetylation or chromatin structure or mRNA stability or any physiological trait, then this remains (IMO) simply an exercise in hand-waving by computer scientists who want to play at being biologists.

Are there any functional experiments in this area?


This is what to look for in the future of Genetic understanding.


Unlikely.
 
I'm not following the abstract; they
propose to define the value of amino acid information in order to consider the genetic information system as a communication system and to introduce the semantic content of information ignored by the conventional information theory
What is "information" in this context? Are they talking about the coded-for amino acids?

A new N-dimensional vector space of DNA sequences over the Galois field of the 64 codons (GF (64))...
A Galois field is simply a finite number space when dealing with abstract mathematics. Exactly what are they trying to show here? Why are they applying theoretical math to DNA?

In any case, there is very little in what you quoted that has to do with energy. The only bit that's related to energy is this:
we found that the minimum energy dissipation in genetic logic operations was close to kTLn(2) joules per bit.
And even there I have doubts as to what is being claimed; the phrase "genetic logic operations" seems quite dubious to me, unless they are building artificial DNA computers rather than studying DNA in a living organism.
 
I highly doubt that this “energy” is as important as the sequence.
Is like saying a dead person can perform as well as a living one; they are the same mass, but the energy upon the mass is dead.

Unless Sanchez and Grau (or anyone else) can perform functional experiments
I can.

When you have a fevor, the nuclear envelope 'temperature' is elevated to enable the cell to build the correct antibodies.

Clear enough?

Are there any functional experiments in this area?
this is simply ONE arena that will change when the sciences/biology/chemistry elevates to comprehend the mass alone does not represent the total potential between interacting structures. The energy upon them structures is just as, if not mor important.

Perhaps try a test; teach one kid something and the other nothing; which will have the greatest potential?
 
I'm not following the abstract; they
What is "information" in this context?
Are you not aware, that a hot pan will give your hand more information than a cold one?

Are they talking about the coded-for amino acids?
They are suggesting there is another value to consider, the energy 'state' of the mass (temp/resonance) rather than just the structure itself.

A Galois field is simply a finite number space when dealing with abstract mathematics. Exactly what are they trying to show here? Why are they applying theoretical math to DNA?
the 'field' is observing the environment....... to change the environment the outcomes will change.

kind of basic

In any case, there is very little in what you quoted that has to do with energy.

Life itself has everything to do with energy and to comprehend that mass is not what makes the greatest impact of life 'existing' by itself, is what the 'paradigm shift' will unfold to mankind.

For example; what is the sun's energy to every life on this earth?

What this will show is that mass does not 'reduce' to enable life (entropic path), it is that the energy 'progresses' in the evolution of living structures.


example: sun light, to plant, to critters, to conscious living mass. (a living being, that by choice, can use its energy to create life)
 
Are you not aware, that a hot pan will give your hand more information than a cold one?
If you can point out what this analogy has to do with showing the effect of energy on the translation of DNA into proteins, then I'll answer the question. At the moment, it is off-topic.
They are suggesting there is another value to consider, the energy 'state' of the mass (temp/resonance) rather than just the structure itself.
That much is clear - but suggesting it as a possibility is very different than suggesting that it is in fact true. The latter requires clear logic and evidence which is either missing int he paper, or simply not included here.
the 'field' is observing the environment....... to change the environment the outcomes will change.

kind of basic
No. A "Galois field" is a math construct involving a group of objects in theoretical numberspace. It is a different use of the word field, and has nothing at all to do with an energy field, or real-world observations.


Life itself has everything to do with energy and to comprehend that mass is not what makes the greatest impact of life 'existing' by itself, is what the 'paradigm shift' will unfold to mankind.
The first half of the sentence is obvious to anyone with a basic understanding pf physics, and even if the second half made sense, it wouldn't be on-topic to your own opening post.
For example; what is the sun's energy to every life on this earth?
The sun is the source of nearly all energy used to fuel life on this planet. This has to do with the hypothesis you proposed in the opening post in what way?
What this will show is that mass does not 'reduce' to enable life (entropic path), it is that the energy 'progresses' in the evolution of living structures.

example: sun light, to plant, to critters, to conscious living mass. (a living being, that by choice, can use its energy to create life)
Unless you have a lot of evidence to support the idea that there is a directed progress of energy in the universe to flow up some sort of hill of complexity, and that conscious living mass is effectively a goal of the universe, you have very little scientific foundation to stand on.

And again this is a very different discussion from the OP. You are assuming that your interpretation of the abstracts you quote in the OP is 100%, then appear to be assuming that it is evidence for your further conclusions about the flow of energy in the universe.

Slow down - take it one step at a time. First lets see if your initial claim that DNA is as effected by energy as it is by it's physical structure seems to be true. It's an intriguing idea, and I won't say it's impossible. But you have to provide evidence for your claim; state your case, not just your conclusion.
-----------------------------------------
When you have a fevor, the nuclear envelope 'temperature' is elevated to enable the cell to build the correct antibodies.

Clear enough?
No, it is not clear enough. Since you are using non-standard terminology to make your point, you need to define your terms. What do you mean by "nuclear envelope 'temperature'"?
 
If you can point out what this analogy has to do with showing the effect of energy on the translation of DNA into proteins, then I'll answer the question. At the moment, it is off-topic.
getting sick of people telling me what my thread 'topic' is.

That much is clear - but suggesting it as a possibility is very different than suggesting that it is in fact true. The latter requires clear logic and evidence which is either missing int he paper, or simply not included here.No.
Sanchez and Grau are the contributers, i pointed out .............. 'they are suggesting'.......

It is ME that is STATING, they are at least observing the energy upon the mass, rather than just the mass itself; and that is what needs to be addressed IN FACT!

A "Galois field" is a math construct involving a group of objects in theoretical numberspace. It is a different use of the word field, and has nothing at all to do with an energy field, or real-world observations.

have you reviewed the paper, math and conclusions?

This group is using MATH to describe a linear progression as in current chemistry, the progression does not have the ability to define, in which the envelope of the total system is relevant.

A newspaper shares information; if you like to read current material than perform the exercise of pursuing the material. Not many smash the reporter as being the idiot.

Do some homework before trying to suggest the math or the use of Galois as irrelevant.

The first half of the sentence is obvious to anyone with a basic understanding pf physics,
You mean, the first part is 'obvious' to anyone of common sense but apparently you are NOT aware of how chemistry is 'actually' used in defining.

For example: can you tell me what the wavelength resonance is, of any single lipid in any living form? Did not ask what temperature, as a temperature can have a bunch of varied 'wavelengths' depending on the mass.

and even if the second half made sense, it wouldn't be on-topic to your own opening post.
Because i am well aware that the sciences are in for a paradigm shift in how life is comprehended. That is MY opinion, as i did not ask or mention that MY opinion even matters or needs your comments.

The sun is the source of nearly all energy used to fuel life on this planet. This has to do with the hypothesis you proposed in the opening post in what way?
The example was to allow common sense to stand and be observed.

Such that the mass is basically a vehicle for the energy to be held upon.


Unless you have a lot of evidence to support the idea that there is a directed progress of energy in the universe to flow up some sort of hill of complexity,
Come on, that is a foolish question.

Can you walk up hill?

So can mass go UP hill based on what ENERGY upon that mass caused?

Yes or NO!

and that conscious living mass is effectively a goal of the universe, you have very little scientific foundation to stand on.

Conscious living mass, is the only living structure in existence known, that can comprehend itself and live longer, by choice. But i will leave that alone so that others can focus on the thread of providing material from OTHERS that what has been established to define the 'progression' of DNA evolution, has more to observe.

That is what this thread is about; that OTHERS have provided a model to share how the progression is possible. (they are just more focused on a single subject whereas MY opinion rolls through all of the sciences)

You are assuming that your interpretation of the abstracts you quote in the OP is 100%,
No i didn't.

then appear to be assuming that it is evidence for your further conclusions about the flow of energy in the universe.
Now that is a fact...... life abuses entropy!

Meaning; when cold, i can CHOOSE to put on a jacket or seek another environment. Then when I want to live longer, i simply can give a single cell, to combine with another single cell, and (know) how a child is, IN FACT of my life and by MY choice, to continue! Ever here of the idea of how LIFE evolves?

Which shows us all that, life has been abusing entropy since the beginning of time and if that 'life' EVER has its chain stopped, that line becomes extinct.

Notice how the change literally applies? The life of mass is not so much the mass, but the energy upon that mass.

Slow down - take it one step at a time. First lets see if your initial claim that DNA is as effected by energy as it is by it's physical structure seems to be true. It's an intriguing idea, and I won't say it's impossible. But you have to provide evidence for your claim; state your case, not just your conclusion.

that is fair and why, to open up a thread like this shares i am not just being esoteric, that others, with as much, or perhaps more material knowledge than I also see that the energy upon the mass must be observed to properly or even try, to define how life evolves and progresses in a linear path.

And the example is shared with a mathematical frame in which the greatest difference between the old and the S/G idea is simply to include the 'envelope' of the systems environment.

Note the difference of an oceanic species and land based; the environment MUST be observed to comprehend the variations of out put.


No, it is not clear enough. Since you are using non-standard terminology to make your point, you need to define your terms. What do you mean by "nuclear envelope 'temperature'"?

The systems environment.

The nuclear envelope (NE) (also known as the perinuclear envelope, nuclear membrane, nucleolemma or karyotheca) is a double lipid bilayer that encloses the genetic material in eukaryotic cells. The NE serves as the physical barrier, separating the contents of the nucleus (DNA in particular) from the cytosol (cytoplasm).




In physics and thermodynamics, temperature is a physical property of a system that underlies the common notions of hot and cold; something that feels hotter generally has the greater temperature. Specifically, temperature is a property of matter.



So at 98.6 the envelop can perform 'x' functions

at 100+ there is a whole different set of functions/processes

all the same mass, but the change is based on the 'energy' state of the mass and what occurs within the 'environment.'

Sorry about being so strange as nothing is about me, it is about simply sharing what is observed and stating what is observed.

The rest is up to the people who want to move forward within the 'evolution of knowledge.'
 
Argghh! You once again do not have the foggiest idea what you are talking about, Bishadi. A mathematical field is any algebraic structure endowed with the operations of addition, subtraction, multiplication, and division. A Galois field is a field in which the number of elements is finite. A Galois field has absolutely nothing to do with energy.


From Robersy Sanchez' entry on scievee.tv: http://www.scivee.tv/user/4481
At present, I am developing a formal algebraic theory of genes and genomes. My research goal is to reach a better comprehension of genome architectures and molecular evolution processes.​

His papers at arXiv: http://arxiv.org/find/q-bio/1/au:+Sanchez_R/0/1/0/all/0/1
 
getting sick of people telling me what my thread 'topic' is.
If you wish to have a discussion with someone you should really try and limit yourself to one topic at a time; in my experience, covering too many areas at once confuses everybody and hinders the progress of conversation. If your topic is something other than what I suggested, then you may need to word your OPs more clearly.
It is ME that is STATING, they are at least observing the energy upon the mass, rather than just the mass itself; and that is what needs to be addressed IN FACT!
I agree; studying the nature of the energy transfer within chemical processes is a complex and necessary area of study. It is and has been ongoing in the fields of chemistry and biology for quite a while now.

The abstracts you quote, however, appear to be discussing anything but the effect of energy on DNA. They appear to be discussing the development of a mathematical model based on the observed behavior of DNA.
have you reviewed the paper, math and conclusions?
I would like to, could you provide a link to the source, please?
A newspaper shares information; if you like to read current material than perform the exercise of pursuing the material. Not many smash the reporter as being the idiot.
I have not smashed you as an idiot. I'm asking that you be more systematic while educating me on the topic you have raised. A reporter should provide both the logic behind their conclusions and provide a reasonable effort in making available the sources of the claims published (barring direct threat to that source).

You are the one making a claim about energy and its effect on DNA, not me. It is not my job to teach myself your theories, it is your job to educate the rest of us.
For example: can you tell me what the wavelength resonance is, of any single lipid in any living form? Did not ask what temperature, as a temperature can have a bunch of varied 'wavelengths' depending on the mass.
Which resonance frequency are you looking for? Are we talking vibrational frequency, or radiation frequency? Are you asking for the specific wavelength of EM radiation that hits a resonance frequency when passing through a lipid mass? If so, what volume are we talking about?
...focus on the thread of providing material from OTHERS that what has been established to define the 'progression' of DNA evolution, has more to observe....That is what this thread is about;...
I'm a little confused on how the authors are attempting to measure "progression of DNA evolution", given that the concept would appear to be at odds with the basic concepts of evolution, at least on its face. Could you address this apparent conflict?
Now that is a fact...... life abuses entropy!

Meaning; when cold, i can CHOOSE to put on a jacket or seek another environment. Then when I want to live longer, ...(know) how a child is, IN FACT of my life and by MY choice, to continue!
I fail to see how your examples of consciousness allowing choice show that "life abuses entropy", or that conscious life is the only thing that can create life, as you asserted earlier, or how any of this has anything to do with your OP. Non-conscious life can reproduce sexually - the only thing different with conscious life reproducing sexually is that it is conscious at the time (unless of course it is drunk at the time).
The life of mass is not so much the mass, but the energy upon that mass....others, with as much, or perhaps more material knowledge than I also see that the energy upon the mass must be observed to properly or even try, to define how life evolves and progresses in a linear path.
Given that we have both living matter and dead matter, this would seem the obvious conclusion; I can't think of any scientist of the past two thousand years who would disagree with your main point here. But evolution does not progress in a linear path, so the entire statement is dubious.
The nuclear envelope (NE) (also known as the perinuclear envelope, nuclear membrane, nucleolemma or karyotheca) is a double lipid bilayer that encloses the genetic material in eukaryotic cells. The NE serves as the physical barrier, separating the contents of the nucleus (DNA in particular) from the cytosol (cytoplasm).
In physics and thermodynamics, temperature is a physical property of a system that underlies the common notions of hot and cold; something that feels hotter generally has the greater temperature. Specifically, temperature is a property of matter.

So at 98.6 the envelop can perform 'x' functions

at 100+ there is a whole different set of functions/processes

all the same mass, but the change is based on the 'energy' state of the mass and what occurs within the 'environment.'
OOOooh. ok. I'm with you now. Yep; chemical reactions and even more subtle behaviors, such as protein folding, are very sensitive to temperature. It is generally accepted that fever in the human body limits the successful metabolism of invading microbes; it would be interesting, too, if certain immune responses were only possible above a certain temperature; or if they were specifically triggered by temperature alone. these should be easy to identify by placing healthy individuals into hotter or colder environments and observe the effects on their immune response.


please finish the following sentence fragments, they are unintelligible:
This group is using MATH to describe a linear progression as in current chemistry, the progression does not have the ability to define, in which the envelope of the total system is relevant.

Notice how the change literally applies?

And the example is shared with a mathematical frame in which the greatest difference between the old and the S/G idea is simply to include the 'envelope' of the systems environment.
 
Argghh! You once again do not have the foggiest idea what you are talking about, Bishadi. A mathematical field is any algebraic structure endowed with the operations of addition, subtraction, multiplication, and division. A Galois field is a field in which the number of elements is finite. A Galois field has absolutely nothing to do with energy.
An what was calculus? I suppose to you Newton was the messiah and His math is the word of God.


From Robersy Sanchez' entry on scievee.tv: http://www.scivee.tv/user/4481
At present, I am developing a formal algebraic theory of genes and genomes. My research goal is to reach a better comprehension of genome architectures and molecular evolution processes.​

His papers at arXiv: http://arxiv.org/find/q-bio/1/au:+Sanchez_R/0/1/0/all/0/1

at least the man is pursuing what you care little of

at least the man is aware NO WHERE on the globe is the evolution of life performed, in math, at the molecular level and capable of addressing the billion or so lipids of the genome/DNA.

at least them folks are working on it and

at least i am capable of reading the facts of how HE is different than your chemistry books

at least HE IS WORKING and EVOLVING in knowledge, comprehension and pursuits.

NO ONE said, the man's work is perfect.

As it would be as STUPID as suggesting NEWTON's mechanics were absolute.

Or Einstein, or or or or .......... 'we the people' are within the evolution of knowledge right now.

Either get with the program of 'developing' or perhaps go lay by your dish and stick with assisting the kids with blowing up ballons.
 
If you wish to have a discussion with someone you should really try and limit yourself to one topic at a time;
Perhaps like sticking with what the thread is about?

I agree... the thread shares how a group has changed 'their' way to observe evolutionin and using a NEW form of representation.

and all i get from this peanut gallery is EVERYTHING IS WRONG that does not meet with the currently established models
The abstracts you quote, however, appear to be discussing anything but the effect of energy on DNA. They appear to be discussing the development of a mathematical model based on the observed behavior of DNA.
behavior of DNA? I thought they were working on the evolution or progressions and how the 'environment' can affect the changes to the DNA chain.


I would like to, could you provide a link to the source, please?
sure

http://www.scivee.tv/user/4481

They be from Cuba. See the list of publications and even the man's picture.

I have not smashed you as an idiot. I'm asking that you be more systematic while educating me on the topic you have raised. A reporter should provide both the logic behind their conclusions and provide a reasonable effort in making available the sources of the claims published (barring direct threat to that source).
Wow.... I would love to walk you through. Please be patient with me as i try to offer data that can help.

You are the one making a claim about energy and its effect on DNA, not me. It is not my job to teach myself your theories, it is your job to educate the rest of us.
Wow. Now you are bringing me to my knees........... you have my attention and i will try

Which resonance frequency are you looking for? Are we talking vibrational frequency, or radiation frequency?
I was asking if the existing 'chemistry' or 'science' of DNA, lipids, living structures has any reference to these properties and then if you know or have data on what the 'f' is of any base lipids.

can we observe this on another thread?

I'm a little confused on how the authors are attempting to measure "progression of DNA evolution", given that the concept would appear to be at odds with the basic concepts of evolution, at least on its face. Could you address this apparent conflict?
Awesome question!

IN chemistry the progression is oosually considered a reduction of chemical potential. When it can be noted that energy upon mass can combine based on the resonance of the structure. For example the phospholipid bilayers of the cell walls. Them lipids associate and combine with no peptide bonds between the lipids. The resonance is what maintains the structures integrity.

Same with the plug of the nucleus's nuclear pore. It appears the energy upon the mass is maintaining the mass to a location with no structure holding it.

Now in an evolutionary point of view, we can find a wave can combine with other waves and increase their total potential upon that mass (think of rogue waves). The point being shared is by including the energy upon the structures rather than the structures themselves, there is an increases capablility and total potential upon the system.

And like a plant; they can and do combine mass and energy (light) to build structures, then the process to evolving mass can be identified by including the importance of the three, mass, energy and time, for life to evolve.

To me, if the rules do not apply at the ONE atom at a time system, then a revamp has been neccessary.

I fail to see how your examples of consciousness allowing choice show that "life abuses entropy",
if i was a rock, i would have no choice to 'create' .....to move, to consume mass ....to overcome equilibrium.

Point being, i am just mass... so the rules must be applicable to me and that rock. This allows the basics; that life is of the energy upon the rocks (mass), not the rocks themselves.

or that conscious life is the only thing that can create life,
Go out back today and plant a tree. IN a few years, you could have 'created' a whole system of a living environment based on that one idea. You by choice, could plant what type is 'good' for your area, add water and 'good' soil based on what you know, find and comprehend.

You by choice, could make a child and live within that choice, even when you return to the soil.

Non-conscious life can reproduce sexually -
Awe so now you see life has intent/instinct. (it is 'intending' to continue/ an entropy buster)

As what 'is' the life of mass?

Such that to tap the surface of a flat pond, we see the wave is concentrated at the initial point of impact by a cause. The wave rolls away from the point of impact and it appears as time continues the wave goes further away and is getting smaller as we see the pond return to equilibriate.

All that is normal in today's observance but then remember, the impact was purposed or of a cause, as well the wave, perhaps is not simply getting smaller but entangling more mass from its point of impact. And no matter how you try, the impact DID occur and did entangle more mass and not only is 'still there' but continuing in time. These are facts and all i did was open up new points to view that are relevant.


the only thing different with conscious life reproducing sexually is that it is conscious at the time (unless of course it is drunk at the time).Given that we have both living matter and dead matter, this would seem the obvious conclusion; I can't think of any scientist of the past two thousand years who would disagree with your main point here. But evolution does not progress in a linear path, so the entire statement is dubious.
I disagree but thanks for making your point in an articulate way.

WE all know, the idea of trial and error makes the evolution of species appear random but when we go into the atom to atom relations, then predictability is easy when observing the environment and energy upon the mass, rather than just the mass getting lucky. And this can be identified as possible by observing life itself (energy upon the mass) having 'intent.' (purposed to continue)

OOOooh. ok. I'm with you now. Yep; chemical reactions and even more subtle behaviors, such as protein folding, are very sensitive to temperature. It is generally accepted that fever in the human body limits the successful metabolism of invading microbes; it would be interesting, too, if certain immune responses were only possible above a certain temperature; or if they were specifically triggered by temperature alone. these should be easy to identify by placing healthy individuals into hotter or colder environments and observe the effects on their immune response.
Now you are thinking like a scientist..... using your ideas to combine what you experience with what you can understand.

That is what i do! I try and comprehend how things works, as well how math defines, as well to what i can experience and perform.

WE THE PEOPLE are who is capable of these duties and the only thing that really makes ONE person develop and learn beyond the next is to be honest with the these forms of comprehension.


please finish the following sentence fragments, they are unintelligible:
i am trying......



and thank you for being patient (thanks for the post)
 
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<completely incoherent post elided>

Bishadi, read what I said. I didn't mention Newton or Einstein, period. I was merely addressing your misconception encapsulated in this mismash statement from the OP: "Point being the energy upon the mass is just as important as the mass."

Sanchez' second paper talked about looking at DNA from the perspective of Galois fields. Galois fields of course have nothing to do with energy.
 
Bishadi, read what I said. I didn't mention Newton or Einstein, period. I was merely addressing your misconception encapsulated in this mismash statement from the OP:
how is stating the energy upon mass is as important as the mass itself, is not comprehendible?

especially when addressing life and the evolution of life? That is like saying that 'car' is awesome but not undertanding it is useless without gasoline.

please tell me this? :shrug:

"Point being the energy upon the mass is just as important as the mass."

Sanchez' second paper talked about looking at DNA from the perspective of Galois fields. Galois fields of course have nothing to do with energy.

so let me get this straight, :bugeye: you are foolish enough to state that using a mathematical frame to apply values to a system of DNA's evolution has nothing to do with the energy of the mass because the namesake Galois did not use it to define energy?

That is like saying, you cannot use a calulator to add up a census.

Wow!

perhaps read what these guys have shared

we propose to define the value of amino acid information in order to consider the genetic information system as a communication system and to introduce the semantic content of information ignored by the conventional information theory.
This shares that they are including the energy upon the mass such as the standard (current) model ignors it.

In this proposal, the value of amino acid information is proportional to the molecular weight of amino acids with a proportional constant of about 1.96×1025 bits per kg.
this shares that the energy of the structure is related to the structures 'molecular weight'.

In addition to this, for the experimental estimations of the minimum energy dissipation in genetic logic operations, we present two postulates: (1) the energy E i (i = 1, 2, ..., 20) of amino acids in the messages conveyed by proteins is proportional to the value of information, and (2) amino acids are distributed according to their energy E i so the amino acid population in proteins follows a Boltzmann distribution. Specifically, in the genetic message carried by the DNA from the genomes of living organisms, we found that the minimum energy dissipation in genetic logic operations was close to kTLn(2) joules per bit.

With experimental evidence and the math to define it, they share their proposal and have postulated that the protiens potential is proportional to the value of the energy upon the mass.

Not enjoying you nor your comprehension.....

if you cannot comprehend what Sanchez and Grau have performed, and published, then go play else where.....
 
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how is stating the energy upon mass is as important as the mass itself, is not comprehendible?
Because (a) it is meaningless gibberish, (b) you are jumping to unwarranted conclusions, and (c) Galois fields have nothing to do with energy. Google the phrase "Galois field".

All I did in my first post in this thread was to try to lead you from your unwarranted conclusions and to post links to Sanchez' work (something you did not do). When you quote something available on the web, give the URL from which you extracted the quote.

In particular, I made no comment on the validity of Sanchez' work. I am not qualified to do so. And neither are you.
 
and all i get from this peanut gallery is EVERYTHING IS WRONG that does not meet with the currently established models
Just to be clear - I was not attacking the quoted areas of study because they apparently disagreed with accepted theory; I pointed out that they appeared to disagree with accepted theory, but your post did not include the needed volume of evidence to support such a break.

Having read four of the associated papers, thanks to D H's link, it seems that we both were mis-understanding the purpose of them; The Genetic Boolean Code Lattice discusses the potential for creating a better logical coding language from which one could determine a relationship between a genetic codon and the hydrophobic qualities of its associated amino acid (given that we currently still use a brute-force mapping to link codons to their protein output, this sort of coding language could indeed be useful in understanding *why* UUU codes for Lucine); The Energy Cost of Protein Messages Leads to a New Protein Information Law attempts to show the relationship between the redundant coding of codons to amino acids and the energy requirements for each of those codings - resulting in an efficiency ratio of (unique information)/(energy needed/wasted); Algebraic Hypotheses on a Primeval Genetic Code (the one utilizing the Galois fields) suggests a mathematical framework for showing the possible levels of complexity in a DNA structure with additional base pairs beyond those found today; and lastly A New DNA Sequence Vector Space on a Genetic Code Galios Field, which addresses the same concept, but in a more rigorously mathematical manner.

I will need to spend more time on each of the papers to grasp all the concepts involved; admittedly, a number of the mathematical mechanisms used are outside of my familiarity. However, I still do not see research of the action of energy on matter as you initially claimed; I see a study of the efficiency of the current DNA coding method, and a question as to the possible areas of improvement or mechanisms for origination of the method of encoding, without reducing the range of the final result set.
behavior of DNA? I thought they were working on the evolution or progressions and how the 'environment' can affect the changes to the DNA chain.
From reading the papers, it seems that the current state of DNA and how it functions across multiple forms of life are used as the base model for what then becomes a theoretical model assuming additional undefined base pairs or algebraic coding models for hydrophobic patterns.
I was asking if the existing 'chemistry' or 'science' of DNA, lipids, living structures has any reference to these properties and then if you know or have data on what the 'f' is of any base lipids.

can we observe this on another thread?
Certainly, though to be honest, I'm still not sure what you are looking for. A physical property of the chemical structures you refer to? What resonance exactly are we looking for? Some sort of bonding frequency range, most likely defined by the electron shells of the lipid atoms? Or a molecular vibrational resonance/oscillation pattern?
IN chemistry the progression is oosually considered a reduction of chemical potential. When it can be noted that energy upon mass can combine based on the resonance of the structure. For example the phospholipid bilayers of the cell walls. Them lipids associate and combine with no peptide bonds between the lipids. The resonance is what maintains the structures integrity.
This is new use of otherwise standard terminology for me; lets try and agree on terminology and our understanding of how lipid layer form in water solutions. My understanding is that the molecular structure of lipids (http://www.agen.ufl.edu/~chyn/age2062/lect/lect_06/4_18.GIF) cause the hydrophobic ends of the molecule to align in reaction to the external environment, while the hydrophilic end create weak hydrogen bonds with the surrounding aqueous environment - not due to a form of resonance bonding between the lipids themselves. Do you disagree with this mechanism, proposed by Gorter and Grendel in 1925, or am I misunderstanding your point?

Same with the plug of the nucleus's nuclear pore. It appears the energy upon the mass is maintaining the mass to a location with no structure holding it.
Given that the atoms within a molecule will rarely if ever actually make physical contact, all chemical interaction is made via energetic fields. I do not see the correlation of this to how lipids arrange themselves, however.
Now in an evolutionary point of view, we can find a wave can combine with other waves and increase their total potential upon that mass (think of rogue waves).
What would a "wave" be, within an evolutionary theory?
And like a plant; they can and do combine mass and energy (light) to build structures, then the process to evolving mass can be identified by including the importance of the three, mass, energy and time, for life to evolve.

To me, if the rules do not apply at the ONE atom at a time system, then a revamp has been neccessary.
I don't think I'm familiar with this one-atom at a time system you seem to be trying to discredit. I don't think it exists in the manner you seem to think it does.
if i was a rock, i would have no choice to 'create' .....to move, to consume mass ....to overcome equilibrium.
Does a nematode have a choice to create? It is alive, but most of us do not consider them to be conscious life.
Point being, i am just mass... so the rules must be applicable to me and that rock. This allows the basics; that life is of the energy upon the rocks (mass), not the rocks themselves.
This is elementary. The human body is made up of numerous chemical compounds. But piling those same compounds together on the ground does not make a human being - how they are put together and how they interact is what makes a human from dirt.
Go out back today and plant a tree. IN a few years, you could have 'created' a whole system of a living environment based on that one idea. You by choice, could plant what type is 'good' for your area, add water and 'good' soil based on what you know, find and comprehend.

You by choice, could make a child and live within that choice, even when you return to the soil.
I completely disagree. I may have actively chosen which environment has thrive in that area, but I sure as hell did not create life. The tree's parents created the acorn - all I did was plant it.
Awe so now you see life has intent/instinct. (it is 'intending' to continue/ an entropy buster)
No, I do not. Life that has not drive to life will not live. IMO, the simplest reason why all life has an innate drive for survival is that all life that *didn't* never lived long enough to have offspring.

You want desperately to live because your ancestors did too, and fought tooth and nail to do so.
As what 'is' the life of mass?

Such that to tap the surface of a flat pond, we see the wave is concentrated at the initial point of impact by a cause. The wave rolls away from the point of impact and it appears as time continues the wave goes further away and is getting smaller as we see the pond return to equilibriate.
Given that I cannot succinctly answer the question "what is life", I can't address your point here. What appears to differentiate living matter from non-living matter? That it exhibits certain behavior, most notably homeostasis, consumption, reproduction, etc: or, as was recently suggested in another thread - that is actively reduces its internal entropy.

Are you trying to suggest that the lake, having been given energy through an outside force, is not alive simply because that energy dissipated?
I disagree but thanks for making your point in an articulate way.

WE all know, the idea of trial and error makes the evolution of species appear random but when we go into the atom to atom relations, then predictability is easy when observing the environment and energy upon the mass, rather than just the mass getting lucky. And this can be identified as possible by observing life itself (energy upon the mass) having 'intent.' (purposed to continue)
I do not agree with you at all either. Life does not appear to have intent to change, and this idea has been suggested and falsified dozens of times over. Individual living things have a drive to survive, but as I mention above, this can be easily explained by ancestrial survival drive, rather than a brand new concept of energy acting apon matter in a near-intelligent fashion as you seem to be suggesting.

Mass does not get "lucky" during evolution. Random mutations in DNA due to transcription errors and random alterations in the physical structure of existing DNA to bombardment by external radiation (energy!) leads to physical changes in the individual organism, which can then be acted apon by natural pressures from organism environment.
Now you are thinking like a scientist..... using your ideas to combine what you experience with what you can understand.
But if you take my suggested method of testing, and place healthy people into cold and hot environments, they do not exhibit symptoms of immune response. So it does not appear that temperature (or available energy at the atomic level) is what controls the activity of protein translation, at least for immune response.
-------------------------

At this point, I feel like two things are going on in this discussion, you are pointing at the sky and saying "Look, don't you see?? it's blue!", and then handing me a pigeon with which to prove your point.

I'm in no way disagreeing that the sky is blue - I'm asking in what way the pigeon you have given me has anything to do with the topic being discussed.
 
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so let me get this straight, :bugeye: you are foolish enough...
calling others foolish is not appropriate.
we propose to define the value of amino acid information in order to consider the genetic information system as a communication system and to introduce the semantic content of information ignored by the conventional information theory.
This shares that they are including the energy upon the mass such as the standard (current) model ignors it.
I do not see your interpretation at all. The authors are stating that the current understanding of the information contained within DNA codons is inadequate because the current theory does not taking to account the semantic ruleset that seems to govern that code - nothing to do with energetic influence.

In this proposal, the value of amino acid information is proportional to the molecular weight of amino acids with a proportional constant of about 1.96×1025 bits per kg.
this shares that the energy of the structure is related to the structures 'molecular weight'.
Information in this paper is not energy - it is the concept of what final product the condon is coding for.

As expressed by the authors: "This information has no value to the organism, but only to the protein itself". This information isn't conscious thought - it is unconscious data.
 
Having read four of the associated papers, thanks to D H's link, it seems that we both were mis-understanding the purpose of them; The Genetic Boolean Code Lattice discusses the potential for creating a better logical coding language from which one could determine a relationship between a genetic codon and the hydrophobic qualities of its associated amino acid (given that we currently still use a brute-force mapping to link codons to their protein output, this sort of coding language could indeed be useful in understanding *why* UUU codes for Lucine); The Energy Cost of Protein Messages Leads to a New Protein Information Law attempts to show the relationship between the redundant coding of codons to amino acids and the energy requirements for each of those codings - resulting in an efficiency ratio of (unique information)/(energy needed/wasted); Algebraic Hypotheses on a Primeval Genetic Code (the one utilizing the Galois fields) suggests a mathematical framework for showing the possible levels of complexity in a DNA structure with additional base pairs beyond those found today; and lastly A New DNA Sequence Vector Space on a Genetic Code Galios Field, which addresses the same concept, but in a more rigorously mathematical manner.
Wow.....

you do comprehend and beginning to open your eyes.....

Certainly, though to be honest, I'm still not sure what you are looking for. A physical property of the chemical structures you refer to? What resonance exactly are we looking for? Some sort of bonding frequency range, most likely defined by the electron shells of the lipid atoms? Or a molecular vibrational resonance/oscillation pattern?
there are no peptide (shell bonds) and it appears that an old Nobel winner had the same idea many years ago (me not the first, nor want to be)

http://nobelprize.org/nobel_prizes/chemistry/laureates/2006/kornberg-autobio.html

My adult scientific career began with graduate study in chemical physics with Harden McConnell at Stanford. I had the idea of elucidating the mechanism of ion transport across biological membranes by nuclear resonance. I thought ion transport must involve rotation of the transport protein in the membrane. Struggling to prove this wrong idea, it occurred to me to study the rotation in the membrane of a lipid molecule, about 1,000 molecular weight, rather than a protein fifty times larger. This led to my discoveries, by nuclear and paramagnetic resonance methods, of phospholipid flip-flop, an exceedingly slow process, and lateral diffusion, exceedingly fast (Kornberg and McConnell, 1971a ; Kornberg and McConnell, 1971b).
the point made was, the idea is not even clearly understood nor is it even conveyed in the sciences

This is new use of otherwise standard terminology for me;
i understand

lets try and agree on terminology and our understanding of how lipid layer form in water solutions. My understanding is that the molecular structure of lipids (http://www.agen.ufl.edu/~chyn/age2062/lect/lect_06/4_18.GIF) cause the hydrophobic ends of the molecule to align in reaction to the external environment, while the hydrophilic end create weak hydrogen bonds with the surrounding aqueous environment - not due to a form of resonance bonding between the lipids themselves. Do you disagree with this mechanism, proposed by Gorter and Grendel in 1925, or am I misunderstanding your point?
Me not a hydrophillic/hydrophobic kind of guy as the mechanics falls onto a water and oil or clearly the bohr atom in which it is because of electon shells, when i pose that the energy is what causes the lipids, to associate.

For example; take a cup of cold coffee and add a dry creamer. Offers all the water and oil examples you want. Now heat up that cup and add creamer. It was not that the additional HEAT offered the extra electrons, to allow the hydrophillic/hydrophobic properties to combine, it was the energy (em) that changed the state of the mass to allow the creamer to combine with the hot coffee.

Given that the atoms within a molecule will rarely if ever actually make physical contact, all chemical interaction is made via energetic fields.
Now you thinking....... so what is that 'field' in chemistry?

I do not see the correlation of this to how lipids arrange themselves, however.
What would a "wave" be, within an evolutionary theory?
EM/ electromagnetism/light in any of her spectrum. For example; a radio wave can have a 25000 mile wavelength or a gamma could be in the pico range.

In either case, the energy is electric and magnetic fields at perpendicular planes, upon the mass it is upon and be oriented to its source and/or environment. Think of em upon mass as an atom with a cross of energy upon the structure resonating. If a bunch of lipids are with this resonant state then see the tails vibrating (resonating) with each other like a set of guitar strings harmonizing. Nothing is touching but the energy upon the structures is associating.

I don't think I'm familiar with this one-atom at a time system you seem to be trying to discredit.
I suggest the new 'creation' will unfold existence from atoms and energy forward versus adam and eve backwards.

. I may have actively chosen which environment has thrive in that area, but I sure as hell did not create life. The tree's parents created the acorn - all I did was plant it.
Fair but then you must also do the same scientifically, such that to observe and atom and energy combination then to be causal, the mass must begin evolving from absolute cold (no energy/BEC) and be defined forward. Or better still, if an electron is being taken from another atom to ionize the second, then the system to remove that electron is relevant to the order of events. And we all know in electronics no electron can move without a circuit/system and in all case, electro-magnetism in the base cause in all cases; whether of impacts, photoelectric or simple electrical generation; it will come down to em in one form or another.


Life that has not drive to life will not live. IMO, the simplest reason why all life has an innate drive for survival is that all life that *didn't* never lived long enough to have offspring.
then that chain will perish/extinct.

Given that I cannot succinctly answer the question "what is life", I can't address your point here.
fair and why that comprehension is what has been MY drive for almost 30 years. I could give a hoot about any prize, i want UNDERSTANDING to exist. (mass to comprehend how it is alive)

i want my children to understand what LIFE IS, that is equal to all mankind!

And when you figure out what this all means, then you will know who I am.

What appears to differentiate living matter from non-living matter? That it exhibits certain behavior, most notably homeostasis, consumption, reproduction, etc: or, as was recently suggested in another thread - that is actively reduces its internal entropy.
Gotta love that entropy buster; life.

Are you trying to suggest that the lake, having been given energy through an outside force, is not alive simply because that energy dissipated?
No.... i am suggesting, the closed system of equilibrium does not exists. Such that NEVER does energy simply equilibriate but that every action does continue, whether observable or not.

Just as them guys Penzias and Wilson shares with CMB. Cosmic backgraound radiation; that radiation is supposed to be the existing remnant of the BB. SO where is the entropy to that; it still exists and affecting mass over time.

I do not agree with you at all either. Life does not appear to have intent to change,
to survive and will change based on the environment (darwin) (or simply knowledge evolves)

and this idea has been suggested and falsified dozens of times over. Individual living things have a drive to survive, but as I mention above, this can be easily explained by ancestrial survival drive, rather than a brand new concept of energy acting apon matter in a near-intelligent fashion as you seem to be suggesting.
same energy, new paradigm of how to observe, that's all.

Mass does not get "lucky" during evolution. Random mutations in DNA due to transcription errors and random alterations in the physical structure of existing DNA to bombardment by external radiation (energy!)
ME not a random kind of guy, otherwise science is moot.

leads to physical changes in the individual organism, which can then be acted apon by natural pressures from organism environment.
But if you take my suggestion method of testing, and place healthy people into cold and hot environments, they do not exhibit symptoms of immune response.
then why put on a jacket, you state you will not catch a cold

The topic is on how a group is defining the evolution of DNA within a mathematical frame that brings the energy state of the mass to the system.

Not my fault it is unique to most.
 
calling others foolish is not appropriate.
and i ooosually do not state such unless a foolish assumption is made that contradicts what is true.

meaning, if i am wrong, i would love to know why and then have the data to observe. And since, the study of mass and energy is about all i do, i suggest any who claim foul best have new evidence because most of the old stuff, found all over the globe has been observed before opening up my keyboard.


I do not see your interpretation at all.
and that error of communicating into words is what i can be held accountable to

the words to describe what has already been understood mathematically, scientifically and with evidence from every corner of this globe, is what i am learning how to do.

But be certain, that single frame such as einstein's E=mc2 is not a line item i will put into print. If someone figures it out, then i suggest keep it within as the globe is not ready until the responsibility is understood.

and that means, life must be understood and that what we as people, equal upon this existence, must be responsible to every action we impose to existence because nothing will undo what we cause to existence. No toys will be built by anything i do but if you want to know life and how to live forever, then take a seat.
 
Me not a hydrophillic/hydrophobic kind of guy as the mechanics falls onto a water and oil or clearly the bohr atom in which it is because of electon shells, when i pose that the energy is what causes the lipids, to associate.
It doesn't matter much what kind of a guy you are, Hydrogen bonding occurs between strongly polarized molecules.
I suggest the new 'creation' will unfold existence from atoms and energy forward versus adam and eve backwards.
This is theology, wrong subforum.
Fair but then you must also do the same scientifically, such that to observe and atom and energy combination then to be causal, the mass must begin evolving from absolute cold (no energy/BEC)
Matter does not "evolve" from cold to hot. energy is applied to it, and it warms up. You are mixing terms.
Gotta love that entropy buster; life.
Life doesn't bust entropy, it reduces entropy internally, but creates more entropy overall in the process - it just vents that entropy to the outside environment, mainly as heat. Overall entropy of the system still increases.
to survive and will change based on the environment (darwin) (or simply knowledge evolves)
The unconscious action of physical pressure on an individual organism, such as a cold winter day killing an animal out in the open, is drastically different than the idea that a conscious awareness has knowledge of where life wants to evolve to.
same energy, new paradigm of how to observe, that's all.
Not if you are suggesting that evolution has a goal, or an awareness.
ME not a random kind of guy, otherwise science is moot.
Your feelings on the matter don't change the reality of the spooky world of the very small. Show that randomness at the subatomic level is invalid, or learn to deal with its consequences.

And a universe that is not fully deterministic is not one without viable science. Look at atomic power. That came out of theories based on a random sub-atomic world.
then why put on a jacket, you state you will not catch a cold
Place healthy people barefoot into cold, wet rooms; they do not suffer from 'colds' any more than the regular, warm, population.

Getting physically cold does not make one sick - that is the result of a biological invasion by a microbe. In the case of "catching a cold" that microbe is the rhinovirus of the Picornaviridae family.
The topic is on how a group is defining the evolution of DNA within a mathematical frame that brings the energy state of the mass to the system.
I have already pointed out that while two of the studies do indeed attempt to define a mathematical model for how DNA might have formed millions of years ago, it says nothing at all about the bringing the energy state of the mass to the system.

Consideration for the energy state of the mass was part of the existing model, and has been for centuries. EM radiation, atomic bonding, and chemical reactions all fundamentally rely on energetic interactivity with matter; are you unaware that what you are suggesting is in no way new?

In the mid 1980's my step-father co-authored a series of papers which helped define the layout of electron orbitals. The entire aspect of those papers centered on how energy and matter work together; unsurprising considering energy and matter are different forms of the same thing. If your entire point is that scientists need to consider not just the physical structure of matter when studying the atomic and molecular world, you're about 150 years late.
 
river-wind,

Best not to argue with a troll, according to his logic not only does life bust thermodynamics but so do air-conditioners and refrigerators.
 
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