Is Information Only Present in the Genome?

[Eddie (Edward Robinson)]

@Michael_Okoko

To be regarded as a molecular means of inheritance,

Whoa! Slow down. This discussion started when you quoted a passage from Paul Davies, and declared that the claim in that passage was “wrong.” I have just looked at the passage again. It seems to be about:

@Geremy

The algorithm for building an organism

I don’t see any discussion of “inheritance” in the passage. (Or, for that matter, of evolution.) It looks to me as if Davies is saying that when individual organisms are built up, information determining the final form of the organism comes not only from the DNA but also from other sources. As far as I can tell, he is talking about ontogenesis, not phylogenesis. You seem to be criticizing him as if he is making a claim about phylogenesis. I think that is why you don’t understand the objections of the others. They are saying that as an account of ontogenesis, Davies’s remarks are unobjectionable. And you are not seeing this.

[John_Harshman]

@Eddie

This discussion started when you quoted a passage from Paul Davies, and declared that the claim in that passage was “wrong.”

This particular thread might have, but the original discussion was embedded in Geremy’s ideas about evolution. Some people have departed from that original topic, but Michael is trying to maintain it, properly in my opinion.

[Eddie (Edward Robinson)]

@John_Harshman

This particular thread might have, but the original discussion was embedded in Geremy’s ideas about evolution. Some people have departed from that original topic, but Michael is trying to maintain it, properly in my opinion.

Well, if that is the case, maybe the title of this discussion should be changed from “Is Information Only Present in the Genome?” to something like, “Is All Biological Information, Whether in Ontogeny Resident in the Genome or outside of It, Ultimately Derived by Inheritance from DNA?” I think the latter is the question Michael Okoko wants to talk about. But with the title as it stands, I think that most of the biologists here have said that the answer is “No.” Would you agree that with the title as it stands, the answer is “No”?

[deuteroKJ (Kenneth Turner)]

As a complete novice to the subject at hand and with no dog in the fight, let me just say how fascinating and invigorating it is to observe the interaction here. We have those who usually agree on topics but now disagree. And vice versa. On behalf of “the rest of us,” I really commend you all. This is not the type of discussion that is normally open for public perusal. But it’s really helpful for those of us (lurkers) trying to get into the weeds a bit. A real tribute to the aim Peaceful Science, methinks.

[Rumraket (Mikkel R.)]

@Eddie

Well, if that is the case, maybe the title of this discussion should be changed from “Is Information Only Present in the Genome?” to something like, “Is All Biological Information, Whether in Ontogeny Resident in the Genome or outside of It, Ultimately Derived by Inheritance from DNA?” I think the latter is the question Michael Okoko wants to talk about. But with the title as it stands , I think that most of the biologists here have said that the answer is “No.” Would you agree that with the title as it stands , the answer is “No”?

I agree with this.

There are two different questions being addressed.

[Rumraket (Mikkel R.)]

@John_Harshman

This particular thread might have, but the original discussion was embedded in Geremy’s ideas about evolution.

True, but I don’t think we are required to rebut a factually correct statement by Paul Davies to be able to also rebut Geremy’s highly idiosyncratic ideas about the causal relationship between evolution and phenotype.

The fact that at some given moment the information required to fully understand how a multicellular organism is constructed from a single cell, is distributed among it’s contents and doesn’t reside exclusively in the DNA, doesn’t mean Geremy is right to say changes in DNA holds little to no power of influence on those other bits.

It simply doesn’t follow, and we can explain why, and show with examples how it does hold such evolutionarily relevant powers of influence on the development and phenotypes of multicellular organisms.

[Eddie (Edward Robinson)]

@deuteroKJ

We have those who usually agree on topics but now disagree. And vice versa.

I agree with this. And I agree with your implied sentiment, i.e., that it would be wonderful if the agreements and disagreements on this site more often crossed “party lines” than they do. I weary of the “We must oppose this because X said it, lest we seem to give any credibility to X” reflex that too often operates here.

I first learned that in ontogeny, DNA does not contain all the requisite information for organism-building, from ID writers. Doubtless the others here did not learn it from ID writers, but knew it independently, as a result of their biological studies. Still, that I could learn it from ID writers shows that ID writers are not completely out to lunch on biological matters.

Any time that I, with my limited knowledge of biology, can chip in and support atheist colleagues here, when they happen to be right, I’m happy to do that.

[Michael_Okoko]

@Mercer

Wrong. The organization, which is information, is never lost

I am not wrong because the information required to maintain cellular organization resides in the nucleotide sequences of an organism’s genome. If DNA changes significantly, cellular organization changes as well and that change is passed on to all future progeny.

@Mercer

No, the fundamental organization of the cell is not stored in DNA.

AFAIK, proteins and RNA are responsible for the fundamental organization of cells. The information needed to make all of these proteins and RNA reside in DNA. Thus, information needed to sustain the fundamental organization of the cell is stored in DNA.

[Mercer (John Mercer)]

@Michael_Okoko

I am not wrong because the information required to maintain cellular organization resides in the nucleotide sequences of an organism’s genome.

You are wrong because the information required to establish cellular organization does not reside in the genome, nor should it. That information must be inherited. This flows from common descent, Michael.

@Michael_Okoko

Thus, information needed to sustain the fundamental organization of the cell is stored in DNA.

Information needed to establish the fundamental organization of the cell is not stored anywhere, except in the fundamental organization itself.

No amount of goalpost-moving will change that.

You are, however, free to spend your entire career trying to establish cellular organization using only DNA, RNA, and proteins, although I’d suggest trying to establish the organization of mitochondria as a warmup.

[Art (Arthur Hunt)]

@Mercer

@Michael_Okoko

Thus, information needed to sustain the fundamental organization of the cell is stored in DNA.

Information needed to establish the fundamental organization of the cell is not stored anywhere, except in the fundamental organization itself.

With many apologies for joining this thread very belatedly -

I am inclined to agree with @Michael_Okoko on this, although I must admit that the discussion in this thread is somewhat confusing. I think it is safe to say that the fundamental organization of the cell is some sum of the properties of the proteins and enzymes that establish and maintain this organization. (Along with other regulatory features including RNAs.) In this sense, the connection with proteins and enzymes is a connection with the genome. Put another way, heritable changes in the genes that encode the myriad network of factors that contribute to this organization can and do change the nature of this organization, in ways often manifest as phenotypic alterations. I don’t think any of these statements are all that remarkable, and I am bit a bit confused as to the points of contention here.

(As an aside, I seem to recall taking Meyer to task for claiming that there are no known mutations in genes encoding cytoskeletal components that could change cellular organization - this happened at my visit to Biola, and I believe (although I cannot find the thread at the moment) that @Mercer agreed with my disagreement with Meyer on this point. My recollection, if accurate, makes this current thread all the more confusing. This is something I pressed Meyer on because Meyer, taking cues from Wells, sees this as a way to disconnect form and function from “the DNA”, and thus strike a big blow against “Darwinian evolution”.)

I will reiterate some common observations that, in my opinion, are very telling. First, is is possible (in fact, routine) to separate a cell in a plant from all neighboring cells (this is true for somatic and germline cells, which in plants is a blurry distinction), erase all organizational/positional information such as might be conferred by gametes, neighbors in the tissue, etc., so as to yield a spherical cell, and subsequently regenerate a normal, fertile plant. In so doing, it is demonstrated that the newly-regenerated plant did not require positional or physical information from prior generations in order to form. It would thus seem that “the DNA” suffices for the determination of form and function of a new multicellular individual. (I am not saying that the internal organization of the protoplast is erased, but rather that any organization that exists is entirely separated from prior generations.)

In addition to this, it is also possible to mix-and-match, as it were, nuclei (genomes) from one plant with the cytoplasm (structural components as well as organellar genomes) of another. What is found when this is done that the plants regenerated from such hybrid cells take on the appearance of the donor of the nucleus. In other words, form and function are dictated by the nucleus (genome, “DNA”, or whatever). (Google the term “cybrid” to dive into this fascinating world.)

These examples, I believe, support the statements that @Michael_Okoko is making in this thread. As I state above, I am not sure what the points of contention are.

@Eddie

I first learned that in ontogeny, DNA does not contain all the requisite information for organism-building, from ID writers.

The examples I describe in this post refute the suggestions of these “ID writers” in no uncertain terms.

[Michael_Okoko]

@Mercer

You are wrong because the information required to establish cellular organization does not reside in the genome, nor should it. That information must be inherited. This

Finally, you get me. This is what I have been trying to hit at since this thread began. I explained earlier that DNA has all the information needed to build cells in a passive sense: you require hemoglobin, catalase, microRNAs, it has information to make all of that. However, to use that information to build (in an active sense) you require other parts of the cells as well. I was not wrong.

@Mercer

That information must be inherited

Yes it has to. DNA on its own is useless, we need other cellular parts to interpret its encoded information. Those parts are directly inherited following cell division. However, this directly inherited information outside DNA is temporal as the biomolecules like proteins which carry them are eventually degraded. Only DNA persists and the information it holds. Thus, cellular organization persists due to DNA.

@Mercer

You are, however, free to spend your entire career trying to establish trueular organization using only DNA, RNA, and proteins, although I’d suggest trying to establish the organization of mitochondria as a warmup.

LOL, no thank you. I can’t spend my time onmisdirected quest.

[Michael_Okoko]

@Art

I think it is safe to say that the fundamental organization of the cell is some sum of the properties of the proteins and enzymes that establish and maintain this organization. (Along with other regulatory features including RNAs.) In this sense, the connection with proteins and enzymes is a connection with the genome. Put another way, heritable changes in the genes that encode the myriad network of factors that contribute to this organization can and do change the nature of this organization, in ways often manifest as phenotypic alterations

Thank you.

@Art

These examples, I believe, support the statements that @Michael_Okoko is making in this thread. As I state above, I am not sure what the points of contention are.

Thanks again.

[Mercer (John Mercer)]

@Art

I think it is safe to say that the fundamental organization of the cell is some sum of the properties of the proteins and enzymes that establish and maintain this organization.

I would not, because cells do not self-assemble from those components.

@Art

Put another way, heritable changes in the genes that encode the myriad network of factors that contribute to this organization can and do change the nature of this organization, in ways often manifest as phenotypic alterations.

They do manifest as alterations, but the fundamental structure of the cell remains.

@Art

I will reiterate some common observations that, in my opinion, are very telling. First, is is possible (in fact, routine) to separate a cell in a plant from all neighboring cells (this is true for somatic and germline cells, which in plants is a blurry distinction), erase all organizational/positional information such as might be conferred by gametes, neighbors in the tissue, etc., so as to yield a spherical cell, and subsequently regenerate a normal, fertile plant. In so doing, it is demonstrated that the newly-regenerated plant did not require positional or physical information from prior generations in order to form.

But you still started with a cell that inherited its organization. That’s information.

@Art

In addition to this, it is also possible to mix-and-match, as it were, nuclei (genomes) from one plant with the cytoplasm (structural components as well as organellar genomes) of another. What is found when this is done that the plants regenerated from such hybrid cells take on the appearance of the donor of the nucleus. In other words, form and function are dictated by the nucleus (genome, “DNA”, or whatever). (Google the term “cybrid” to dive into this fascinating world.)

The form of the cell itself is not. It must be inherited. It seems obvious, at least to me, from common descent. There’s simply no reason to hypothesize that it would be stored in DNA.

@Michael_Okoko

Finally, you get me. This is what I have been trying to hit at since this thread began. I explained earlier that DNA has all the information needed to build cells in a passive sense :

The active sense is information inherited outside of DNA.

@Michael_Okoko

However, to use that information to build (in an active sense) you require other parts of the cells as well.

Therefore all of the necessary information is not stored in DNA. It’s not just the parts, it’s their organization.

[Eddie (Edward Robinson)]

@Art

The examples I describe in this post refute the suggestions of these “ID writers” in no uncertain terms.

Actually, you have only refuted it in the case of plants. And by the way, I was not endorsing everything ever said by Meyer, Wells, etc. on this topic. I was merely agreeing with Mercer and Rumraket that in ontogeny DNA is not the only source of information. Even if you completely disagree with the ID folks on many other points, surely you don’t disagree about that?

[Art (Arthur Hunt)]

@Eddie

Actually, you have only refuted it in the case of plants.

LOL. The typical refuge of the ID anti-evolutionist. “I didn’t mean that!”

Wells et al. are wrong. Period.

[Eddie (Edward Robinson)]

Never mind Wells. Never mind ID. Pretend ID never existed, and creationism, too. Just think straight biology.

Read the question at the top of the page. The question is: “Is Information Only Present in the Genome?”

In your view, is the correct answer to that question “Yes” or “No”?

Mercer and Rumraket say that the answer is “No”. What do you say?

[Michael_Okoko]

@Mercer

The active sense is information inherited outside of DNA.

Ultimately, the information is inherited from DNA, let me explain what I mean.

To make the beta globin chain of hemoglobin, we need the information encoded in the beta globin gene and its regulatory sequences. To use that information, transcription factors need to bind regulatory sequences (regseqs) upstream of the gene to initiate it’s expression. To successfully bind those regseqs, a transcription factor must possess the right combination and arrangement of amino acids and/or cofactors in its DNA-binding site. As you know, the precise three-dimensional structure of a protein is mostly a consequence of its primary sequence and that primary sequence is pieced together by reading information from DNA. If the target DNA segment is altered significantly or the binding site amino acids are changed following an alteration in DNA, that could alter the transcription patterns in that organism, changing its cellular organization in some way. If that change persists, it is passed down to progeny.

In this sense, DNA encodes all the information needed to maintain cellular organization and progeny inherit it from parents. To use that information, progeny must inherit other cellular constituents (like transcription factors or maternal RNAs) as well. The information (its composition and order) in the primary sequence of an inherited transcription factor allows it to bind certain DNA segments and actively contribute to maintaining cellular organization.

@Mercer

Therefore all of the necessary information is not stored in DNA.

All of the necessary information needed to sustain is stored in DNA. All of the necessary information to do the actual sustaining and/or establishing lies in DNA and other cell parts. The former is passive, the latter is active.

[Art (Arthur Hunt)]

@Mercer

@Art

I think it is safe to say that the fundamental organization of the cell is some sum of the properties of the proteins and enzymes that establish and maintain this organization.

I would not, because cells do not self-assemble from those components.

@Mercer, surely you agree that “the fundamental organization of the cell is some sum of the properties of the proteins and enzymes that establish and maintain this organization”. I don’t mean, and I rather suspect that @Michael_Okoko also does not, that dissasembled cells will spontaneously assemble. The “sum of the properties…” would include those aspects of organization, interactions, organization,and the like that are passed on frm generation to generation.

@Mercer

@Art

Put another way, heritable changes in the genes that encode the myriad network of factors that contribute to this organization can and do change the nature of this organization, in ways often manifest as phenotypic alterations.

They do manifest as alterations, but the fundamental structure of the cell remains.

I believe this is quite in line with what @Michael_Okoko is saying.

@Mercer

@Art

I will reiterate some common observations that, in my opinion, are very telling. First, is is possible (in fact, routine) to separate a cell in a plant from all neighboring cells (this is true for somatic and germline cells, which in plants is a blurry distinction), erase all organizational/positional information such as might be conferred by gametes, neighbors in the tissue, etc., so as to yield a spherical cell, and subsequently regenerate a normal, fertile plant. In so doing, it is demonstrated that the newly-regenerated plant did not require positional or physical information from prior generations in order to form.

But you still started with a cell that inherited its organization. That’s information.

Let’s recall the additional parenthetical statement:

@Art

(I am not saying that the internal organization of the protoplast is erased, but rather that any organization that exists is entirely separated from prior generations.)

There are obvious aspects of cellular organization that protoplasts retain (some complement of ribosomes and organelles, the plasma membrane, etc.), but I think it a stretch to suggest that much of the internal organization of the protoplast (extent, structure, and organization of the cytoskeleton, structure and organization of the nucleus and organelles, the endomembrane system, etc.) is retained in the course of isolating and culturing protoplasts. But I can agree that there is a minimal amount of information, as it were, that even protoplasts retain. I don’t see what is controversial about acknowledging the link between this information and the genome.

[Michael_Okoko]

@Art

As I state above, I am not sure what the points of contention are.

Geremy posted a quoted from Paul Davies, which said the algorithm for building living forms were stored in genomes and other parts of a cell. I disagreed, saying only DNA holds such information.

[Art (Arthur Hunt)]

@Eddie

Never mind Wells. Never mind ID. Pretend ID never existed, and creationism, too. Just think straight biology.

Read the question at the top of the page. The question is: “Is Information Only Present in the Genome?”

In your view, is the correct answer to that question “Yes” or “No”?

Mercer and Rumraket say that the answer is “No”. What do you say?

As the subsequent reply by @Michael_Okoko shows, I don’t believe anyone in this thread has answered in the affirmative.

Which is why the entire thread is a bit surreal.