Is Information Only Present in the Genome?

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#13

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.

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?

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.

#14

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.

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.

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#15

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.

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.

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.

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.

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.

#16

Paul Davies quote, Bold mine:

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.

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#17

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.

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#18

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

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.

#19

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.

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.

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#20

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!

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#21

They did. What were the controls?

Or in the form of a question to ponder, if we put a sister intestinal cell of the nuclear donor in the dish with the recipient oocyte, will it develop into a frog?

If not, why not?

#22

It would seem to me that “the structure and cytoplasmic contents” would be part of “some given conditions”. Now it’s true that a one-celled zygote has some cytoplasmic contents, but the important ones for development are the various maternal transcripts and proteins deposited in the egg, and those trace back directly to maternal DNA. Any maternal cytoplasm is so diluted after a few cell generations that it would seem unable to be important in later development.

But more importantly, we’re talking about evolution here, and none of this cytoplasmic inheritance is stable or dependable enough to be relevant to the differences between species. Evolution is all about genomes, and phenotypes, etc., affect evolution only to the extent that they have genetic bases.

Sort of. Individuals of most species inherit their locations from their parent. But is this significant information? Is it evolutionarily important?

#23

I don’t know what all “creationists” say, but Jonathan Wells has often made the point that DNA alone does not determine developmental outcomes; the organismal environment in which the zygote develops also plays a role. He certainly doesn’t believe that things are as simple as reading off the DNA sequence, and presto!, the new organism appears. For him, there is much environmental information that interacts with the DNA information to produce the overall result. I heard him say this at a talk at a conference, and I’ve seen him say it in print as well, though I can’t summon any articles to mind at the moment. If Paul Nelson @pnelson is listening in on this discussion, he probably could tell us where Jonathan (and others) have said similar things.

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#24

If Jonathan Wells’ ideas on this were correct, no one could ever have regenerated normal, fertile plants from isolated protoplasts. This example and other cell fusion experiments in plants pretty clearly refute Wells’ notions.

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#25

I think that there are too many direct evidences of plants and animals inheriting non genetic information, for anyone to sustain the claim that only genetic information is inherited. For example some lizards have a plastic physiological response to their diet, which can alter the shape of their head, teeth, and digestive tract simply by changing their diet.
https://www.jstor.org/stable/10.1086/651704?casa_token=fxtwgHkpAZUAAAAA%3AFY0E0FH9NTWT39KrAPQRuqTUEf54gPVpAn2JLpVGZUmrx_NESpl0psBKkDDyj6Grh3ivi_8HSSGqCvxwaKuW2I8cBfiBAhnhWh5WyZlLCEitqEfXSI0&seq=1

It is also true that some species of reptiles, amphibians and fish have their sex determined by the ambient temperature. In the case of lizards this happens both with species that have established genetic sex differentiation and those that don’t.

So while genetic inheritance is extremely important, I think that the natural world is full of examples that other factors are important as well.

#26

I agree with this, but it is still irrelevant to my point. More so, I am only talking about heritable information which can be passed down through generations of progeny, not the entire information present in cells. DNA is the only molecule that serves that function.

Is there heritable information which is passed down through generations of offspring? No.

I disagree. Again show me data that demonstrates your claim which is that something other than DNA can store and transmit biological information needed to build organisms?

Humans can make globins. Is the information needed to make those globins stored anywhere else other than DNA? Can the information needed to make globins be passed on to progeny without the agency of DNA?

If you still feel confident in the claim that biological systems asides DNA store and transmit heritable information, by all means show me the data.

#27

It doesn’t matter what controls they used, because they had DNA as well. The study is of no relevance to our discourse.

Therein lies the misunderstanding. The actual development of organisms depends on DNA and the environment that DNA molecule is kept within. The information itself is solely kept in DNA, and transmitted only through it during cell division or any other process. This is basic biology.

When a cell divides, its daughter cells gets a fraction of its cytoplasm and membrane constituents. This fraction holds information needed to utilize the organism-building information contained in DNA. That’s it.

None of you have been able to provide any sort of data that shows heritable information needed to build organisms can persevere and transmit through anything other than DNA.

#28

You’re contradicting yourself now, and you seem to have conceded the point.

This question of whether the the information perseveres indefinitely unaltered from generation to generation is irrelevant. It is information and is necessary to construct the daughter cells, and for the functions of the cells. The information in DNA also changes over time, just much more slowly. No replicative process known is perfect(which is why evolution is not only possible, but inevitable).

The compositional information is of course relatively stably inherited simply by division. If you divide the contents of a cell in two, both halves retain the same relative proportions of contents. Compositional information is retained, even if you divide them unequally (30:70 by volume, for example). They still do if you do it again. While you end up with a smaller total volume, the compositional information of that fraction is still retained. And you can keep doing this until you are down to individual molecules, at which point the information is then lost if you keep going.
Now what actually happens is that cells go back to growing after cell division, synthesizing new constituents to fill the volume of the cell. When this occurs, the previous generation’s contents are diluted in the newly synthesized contents, and so the compositional information is gradually lost more quickly with each passing generation until eventually after a few generations it’s completely gone. That doesn’t mean it wasn’t information, nor does it mean it didn’t contribute causally to the construction and functions of the cell when it was present.

In terms of the relative contributions I would definitely agree that DNA holds vastly more information than the remaining parts of the cells, which we can see if we imagine losing a large fraction of the cytoplasmic contents, the cell, as long as there are still a few remaining of the necessary regulatory proteins, transcription factors(RNA polymerase) and transcripts, and still-active ribosomes (and the cell-membrane remains intact to prevent loss of homeostasis), can then effectively be regenerated. The DNA is necessary to accomplish this, and basically everything can be re-created with a small remainder of the cellular contents plus the DNA.

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#29

No and no.

I am really surprised you can’t get my simple point. The information needed to make every RNA and protein molecule (which in turn direct the synthesis of other constituents) within a cell or organism is found only in DNA. This is true whether or not that DNA molecule is right there in the organism or in a test tube in Lenski’s lab.

The cytoplasmic contents gotten by daughter cells only have information (like particular ligands they bind to initiate or repress a signalling cascade) needed to utilize information contained in DNA. That’s why we can comfortably express certain human genes in yeast or E .coli using the native biosynthetic machinery in those organisms.

That’s why I kept on saying you were strawmanning me. It is this information that I have been harping on since, the type only DNA stores and transmits across generations. The type of information DNA stores is specific and will only produce the organism it came from, unless altered significantly. Non-DNA components don’t carry such information.

It is information needed to construct anything, by reading DNA. The information in DNA can only be used to construct particular things (and that’s what I mean by heritable information). The information in DNA is akin to the blueprint of a house, while the information held by the mason (proteins and RNA) can be used to actualize any blueprint.

Yes, there is compositional information, but the one DNA holds is a template or guide for the construction of entire organisms, while the information held by non-DNA components allows them to control when, where and how much DNA information is utilized.

All excerpts are from Molecular Biology of the Cell, sixth edition, page 369 (emphases mine) and they aptly state what I have been saying in this thread since it began.

If hereditary information was present in something other than DNA, then these excerpts don’t make sense.

#30

They had the same DNA, thus it is very relevant.

And that environment provides information. Not all information is digital.

And some of that essential information is inherited but not encoded in DNA.

It does. It does not, however, encode all of the information required to construct a new organism. You’re conflating nucleic acids with information.

#31

I think we would all agree that phenotypic plasticity has its role, but it isn’t powerful enough to explain the differences between species. It isn’t as if you can put humans in the same jungle as chimps and have humans suddenly giving birth to chimps.

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#32

Well, for example, culture is heritable. And it is encoded in biological societies and cultural artifacts, not DNA.

Globin genes are stored in GenBank, and humanity bequeaths this information, the information to make globin genes of far more sorts than we see in human genomes, to the progeny of all humankind. This information is stored in silicon, not DNA.

So yes, I am very confident that there is heritable information of many sorts stored outside of DNA.

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