Is Information Only Present in the Genome?

[Michael_Okoko]

@Geremy

I will allow the physicist Paul Davies explain it, in his paper “The Algorithmic Origins of Life he wrote:

The algorithm for building an organism is therefore not only stored in a linear digital sequence (tape), but also in the current state of the entire system (e.g. epigenetic factors such as the level of gene expression, post-translational modifications of proteins, methylation patterns, chromatin architecture, nucleosome distribution, cellular phenotype and environmental context). The algorithm itself is therefore highly delocalized, distributed inextricably throughout the very physical system whose dynamics it encodes. Moreover, although the ribosome provides a rough approximation for an UC (see endnote 5), universal construction in living cells requires a host of distributed mechanisms for reproducing an entire cell.

Paul Davies is wrong. The algorithm or instructions for building an organism is only present in its genome. This is basic biology and its learned from biologists not physicists. I don’t think you would want @John_Harshman teaching you about rocket building science. Tweaking the genome sequence can change gene expression patterns, alter post-translational processes, chromatin structure and every other thing Paul mentioned. Epigenetic mechanisms don’t require modifying the genome sequence, but they need the genome to work as well. Its all about the genome.

The rest of your post just seemed to be moving in no specific direction. No one here doubts physico-chemical forces can influence biological activity, and it appears you seem to think we do have such doubts. For example, high cell density (a mechanical pressure) impedes the proliferation or locomotion of cells, but this property depends on the genome: metastatic tumor cells pick up genome changes which allow them to overcome this mechanical pressure, spread to other parts of the body, and found new tumor cell lineages in those places; during embryonic development or wound healing, contact inhibition of proliferation can also be reversed. The point is, its all about the genome.

[Rumraket (Mikkel R.)]

@Michael_Okoko

Paul Davies is wrong.

I don’t agree. Nothing he says there is wrong as far as I can see. There is no use rebutting one false dichotomy with another. It is wrong to say genes are the exclusive causes of everything, just as it is wrong to say environment is. It is the interaction between the two that explains gene expression and development, and evolution can thus influence gene expression and development.

No cell ever divided in two that didn’t also pass on roughly half of it’s cytoplasmic contents. While this is continously replaced, it’s presence is a necessary component of any explanation for the gene expression profile of that cell at any given moment. And as far as we can tell, this must have been true all the way back to the origin of cellular life.

[Michael_Okoko]

From Geremy’s quote, Paul Davies says:

The algorithm for building an organism is therefore not only stored in a linear digital sequence (tape),

This is wrong. The linear sequence of nucleotides in DNA completely determines what features an organism inherits or acquires. DNA and only DNA stores that information. The precise, differential expression of hemoglobin genes, for example, is dependent on the regulatory regions in DNA. Altering those regulatory sequences indiscriminately will disrupt the pattern of globin gene expression observed from infancy through adulthood.

@Rumraket

It is wrong to say genes are the exclusive causes of everything, just as it is wrong to say environment is

That’s not what I am saying. I agreed elsewhere that the environment influences gene expression patterns, which in turn influences the growth and development of organisms. I am just saying that the information needed to build an organism lies solely in the genome, not the environment (which Geremy seems to be arguing for).

@Rumraket

No cell ever divided in two that didn’t also pass on roughly half of it’s cytoplasmic contents. While this is continously replaced, it’s presence is a necessary component of any explanation for the gene expression profile of that cell at any given moment. And as far as we can tell, this must have been true all the way back to the origin of cellular life.

I don’t disagree with anything here, but the fact remains that the genome is the sole unit of inheritance.

[Mercer (John Mercer)]

@Michael_Okoko

This is wrong. The linear sequence of nucleotides in DNA completely determines what features an organism inherits or acquires. DNA and only DNA stores that information.

I think that Rum’s point is that genomes don’t work in the absence of the cellular environment. There is some information in that environment, just not very much relative to the genome.

[Michael_Okoko]

@Mercer

I think that Rum’s point is that genomes don’t work in the absence of the cellular environment

I did not deny this. It is a fact. What I am saying is that only genomes store information needed to build organisms, while specific environments influence what and when information in genomes should be used. In contrast, Paul Davies says that that information is not stored in only genomes which is empirically false.

@Mercer

There is some information in that environment, just not very much relative to the genome.

Heritable information from the environment without a genome, evidence?

[Mercer (John Mercer)]

Not THE environment, the environment provided by the egg or other cell.

[Michael_Okoko]

I know, but it didn’t meet my request. Provide evidence that there is heritable information in an environment like an egg cell that is passed on to offspring without DNA (nuclear and mitochondrial)?

Get it that I agree with you and Mikkel that environments determine how segments of DNA are expressed. Liver and brain cells get the same DNA, but express them differently, accounting for their differences. Similarly, at infancy and during early childhood, the hemoglobin genes expression pattern is different from what is observed during adulthood. The point is clear, genes and environment influence the behaviors of organisms, however, DNA alone carries the information.

[Witchdoc]

@Michael_Okoko

The point is clear, genes and environment influence the behaviors of organisms, however, DNA alone carries the information .

I understand what you’re getting at, but books, plays, TV, other people, and of course, histone modification is kinda a direct refutation of the literal meaning of what you wrote.

[Rumraket (Mikkel R.)]

@Michael_Okoko

In contrast, Paul Davies says that that information is not stored in only genomes which is empirically false.

I’m sorry but what you’re saying just isn’t true. There is such a thing as compositional information, that is information that is stored in the form of the composition of cellular(or other types of compartmental) constituents, and it can be heritable. Mercer is right here, and so is Paul Davies.

The concept of compositional information is even employed to analyze the question of the origin of life, to explain how a form of information inheritance could have worked (and evolved) even prior to the emergence of digital polymers like RNA or DNA.

See:
https://www.pnas.org/content/97/8/4112.short

https://www.sciencedirect.com/science/article/abs/pii/S0022519301924403

It is pretty clear that compositional inheritance still occurs to this day(the contents of the cytoplasm is passed on, and these contents affect the expression of genes in daughter cells, thus information must have been passed on with the cytoplasmic contents too), though it is now (and has been for a long time) of course tightly interlinked with genetic inheritance.

[Michael_Okoko]

@Witchdoc

I understand what you’re getting at, but books, plays, TV, other people, and of course, histone modification is kinda a direct refutation of the literal meaning of what you wrote.

No it is not. I don’t see why you guys should disagree with me here. Only DNA carries information needed to build organisms, however, components (like covalently modified histones and transcription factors) of the specific environment DNA finds itself in determines how the information it carries is used.

Epigenetic traits don’t refute my claim because they still require DNA, directly and indirectly, for their transmission.

[Mercer (John Mercer)]

Gurdon, J. B.; Elsdale, T. R.; Fischberg, M. (1958). “Sexually Mature Individuals of Xenopus laevis from the Transplantation of Single Somatic Nuclei”.

Nature. 182 (4627): 64–65. Bibcode:1958Natur.182…64G. doi:10.1038/182064a0. PMID 13566187.

[John_Harshman]

Put even more simply, the differences between species result from differences in their genomes. That’s the only thing inherited stably across many generations. Everything @Geremy is on about is downstream from the genome, and must be, because zygotes at the one-celled stage don’t have any of the properties he mentions.

Incidentally, what he’s talking about used to be called epigenetics, before that term was appropriated for something else.

[Michael_Okoko]

@Mercer

Gurdon, J. B.; Elsdale, T. R.; Fischberg, M. (1958). “Sexually Mature Individuals of Xenopus laevis from the Transplantation of Single Somatic Nuclei”.

Nature. 182 (4627): 64–65. Bibcode:1958Natur.182…64G. doi:10.1038/182064a0. PMID 13566187.

Nothing in this article even hints at supporting the proposition that biological environments store heritable information which can be passed on without the agency of DNA. They transferred nuclei which contained DNA to enucleated egg cells, enabling their development into mature frogs. This supports my contention that DNA is the only holder of heritable information.

@Rumraket

I’m sorry but what you’re saying just isn’t true. There is such a thing as compositional information, that is information that is stored in the form of the composition of cellular(or other types of compartmental) constituents, and it can be heritable. Mercer is right here, and so is Paul Davies.

I am willing to change my mind, but you have to provide evidence that heritable information is stored somewhere other than DNA and that the information is transmissible without the agency of DNA?

@Rumraket

The concept of compositional information is even employed to analyze the question of the origin of life, to explain how a form of information inheritance could have worked (and evolved) even prior to the emergence of digital polymers like RNA or DNA.

We are discussing what obtains in present life forms and not prebiotic times. In modern organisms, DNA and RNA are the only stores of heritable information. That information is not stored in organelles or other biomolecules.

[Rumraket (Mikkel R.)]

@Michael_Okoko

I am willing to change my mind, but you have to provide evidence that heritable information is stored somewhere other than DNA

Okay. Imagine I give you an organisms DNA. You don’t know what organism it is, under what conditions it lives, or anything. I just give you it’s DNA sequence and nothing else. Now, you can’t cheat and go compare it’s genome to other organisms in some database to get some sort of idea of how it lives and behaves and what it’s phenotypes are likely to be (if you do, you’re getting your information from something other than DNA).

Can you predict from that alone the physiology and behavior of the organism? If I were to provide you a hypothetical environment (say it lives at 90 degrees C water in some geothermal hotspring), can you predict it’s expression profile from that at any given moment?

No, you can’t do that because you have no idea what genes will be expressed at that moment. Not even with a supercomputer to sort of simulate it, because all the simulation has to work with is a piece of DNA. That does not an organism make.

The reason you don’t know what genes will be expressed is that I haven’t told you the information you need to predict that. That is information about the cytoplasmic contents. What does the cytoplasm (including the nucleus and other organelles if it’s a eukaryote) contain? What sits in the membrane? Is it a double membrane? What is the composition of that membrane? Is there a cell wall? Is it actively being constructed or degraded?

Regulatory elements, metabolites, signaling factors, transport proteins, membrane channels, receptors etc.

It’s expression profile, and subsequent behavior going forward, significantly depends on what proteins, metabolites, signaling factors, and other regulatory molecules were previously expressed. If there is dextrose in the environment, will the organism take that in? Is there a receptor or transport protein for that? Is it active?

Since you don’t have this information you can’t predict it’s behavior. If you can’t predict it’s behavior you’re missing information. So the cytoplasm and membrane and all that other stuff must contain information too.

If I were to give you the full set of information about the state of the organism at some instant (what it contains, where these contents are located in relation to each other, what it’s membrane is like and so on), then you can predict it’s behavior (at least with a sufficiently powerful computer) going forward. You couldn’t possibly do this with the DNA alone.

That’s really all there is to it.

@Michael_Okoko

and that the information is transmissible without the agency of DNA?

DNA alone has no “agency”. DNA is replicated by the interaction of many constituents of the cell, most of which themselves are the products of the transcription and translation of DNA, and this mutual dependence and cycle of replication, transcription, translation, and so on must go back to the origin of cells, and if genes came before cells, back to even that.

[Michael_Okoko]

@Rumraket

Can you predict from that alone the physiology and behavior of the organism?

I wouldn’t, but this is irrelevant to the point I am making, because whether or not I know the organismal or cellular source of that DNA, that DNA serves as the only means of storing heritable information needed to build that source.

@Rumraket

The reason you don’t know what genes will be expressed is that I haven’t told you the information you need to predict that.

This is a strawman Rum. I am not interested in knowing where that DNA came from or predicting its expression profile. All I am saying is that the DNA moiety is the only store of heritable information needed to make whatever organism it came from. I am beginning to sound repetitive.

@Rumraket

It’s expression profile, and subsequent behavior going forward, significantly depends on what proteins, metabolites, signaling factors, and other regulatory molecules were previously expressed

I agree entirely with this. Only DNA holds the information, while components of the environment influence when and how much of that information is utilized.

@Rumraket

DNA alone has no “agency”

Strawman. I never claimed DNA alone has agency, rather I said heritable information is transmissible via the DNA which is molecular means of biological inheritance.

@Rumraket

DNA is replicated by the interaction of many constituents of the cell, most of which themselves are the products of the transcription and translation of DNA, and this mutual dependence and cycle of replication, transcription, translation, and so on must go back to the origin of cells, and if genes came before cells, back to even that.

Everything here is correct, but it doesn’t disturb my evidence-based stance that DNA or RNA is the only means of storing and transmitting heritage biological information in extant organisms. I am yet to see evidence supporting the ability of other biomolecules or organelles to keep and transfer biological information from parents to progeny.

[RonSewell (RonS)]

Paul Davies quote, Bold mine:

@Geremy

The algorithm for building an organism is therefore not only stored in a linear digital sequence (tape), but also in the current state of the entire system (e.g. epigenetic factors such as the level of gene expression, post-translational modifications of proteins, methylation patterns, chromatin architecture, nucleosome distribution, cellular phenotype and environmental context). The algorithm itself is therefore highly delocalized, distributed inextricably throughout the very physical system whose dynamics it encodes.

DNA is part of a system, and at any instant the definition of the system as an entirety requires the complete accounting of epigenetics, cytoplasm, extra-cellular environmental factors, and so forth. Somewhat akin to a Newtonian system, one instantaneous state leads to the next and so forth indefinitely, so in that sense can be considered information which is passed on. On that level, I concur with the gist of Davies, @Rumraket and @Mercer.

OTOH, It is true that DNA comes closest to being a repository of the digital component of the system, and variation there is the definition of evolution.

I’m a layperson, and susceptible to misapprehension, but the more I learn the more my take away is that DNA is always interacting with an analog world, and the traffic does not run in just one direction. Proteins boil down to molecular electrostatic shapes, and mutations in DNA constantly toy with these. Some proteins are exact or die, but most are not near so fragile as I used to think. So changes in DNA are in a feedback loop involving variation in protein affinity, spacing, fit, amplitude, and expression, and of course protein variation is itself tested in the analog environment. So the feedback is not just developmental, but also evolutionary.

One reason this is significant to me is that creationists tend to view DNA as static information which was optimized to produce some platonic ideal, stands on its own, and can only be degraded by typos. But the genetic code is not like a volume of Shakespeare, definitely not at all like a computer program, the key difference being that DNA is part of a system where analog feedback plays an essential role. If there is room for improvement, more often than not life will seek it out.

[T_aquaticus]

@RonSewell

DNA is part of a system, and at any instant the definition of the system as an entirety requires the complete accounting of epigenetics, cytoplasm, extra-cellular environmental factors, and so forth. Somewhat akin to a Newtonian system, one instantaneous state leads to the next and so forth indefinitely, so in that sense can be considered information which is passed on. On that level, I concur with the gist of Davies, @Rumraket and @Mercer.

Using the computer analogy, DNA is the hardware and software. The environment is pushing keys and moving the mouse. If we want to describe the output at any one time then we have to consider the hardware, software, and inputs.

[Michael_Okoko]

@Geremy

The algorithm for building an organism is therefore not only stored in a linear digital sequence (tape), but also in the current state of the entire system

The above is empirically false. The complete set of instructions or algorithm needed to build organisms only resides in DNA.

@RonSewell

DNA is part of a system, and at any instant the definition of the system as an entirety requires the complete accounting of epigenetics, cytoplasm, extra-cellular environmental factors, and so forth

Yes DNA is part of every biological system, but only DNA holds information needed to build those systems. It is vital to clarify that I am not saying DNA alone builds organisms, as that is false, but that it is the only keeper of that information needed to do so.

[Rumraket (Mikkel R.)]

@Michael_Okoko

@Rumraket

The reason you don’t know what genes will be expressed is that I haven’t told you the information you need to predict that.

This is a strawman Rum.

I just don’t agree with this. If, given only the DNA sequence, you don’t know what genes will be expressed under some given conditions without information about the structure and cytoplasmic contents of the cell in addition to knowing it’s genome sequence, then you are missing information, information which must then be present in the structure and contents of the cell. It is only through the totality of this information that you can construct a new cell, and understand how the present cell functions. This information is also copied and passed on (though less accurately than DNA), in addition to the DNA.

@Michael_Okoko

I am not interested in knowing where that DNA came from or predicting its expression profile.

No, we are answering the question whether information is only stored in the DNA. That’s it. Is there information in other parts of cellular life forms than their genomes? Yes. Is it passed on? Yes. Is it crucial to understanding the function and behavior of the organism? Yes.

[swamidass (S. Joshua Swamidass)]

@Michael_Okoko

Nothing in this article even hints at supporting the proposition that biological environments store heritable information which can be passed on without the agency of DNA.

Well it’s trivally obvious that the environment does store heritable information which is passed on without the agency of DNA.

On a different note, I didn’t know that DNA could conceivably have agency in the first place! Next thing, you will be telling us it’s selfish too!