Is Information Only Present in the Genome?

[Michael_Okoko]

@CrisprCAS9

This thread is weird.

I agree. Let me lay out what I really mean by DNA having all the information needed to build organisms.

Humans need hemoglobin, viruses don’t. The human genome has information needed to make this protein, but viruses don’t. Similarly, there are thousands of proteins and RNA molecules which serve one or more functions within and/or outside our cells. DNA encodes information encodes needed to make all these proteins and RNA. Proteins and RNA molecules don’t encode information to make themselves. Since these proteins and RNA control the production and development of organisms, it means DNA essentially has all the information needed to make and develop new organisms.

@CrisprCAS9

If we are talking about the context of a few thousand generations, the only relevant factor of heredity is the genome.

True.

@CrisprCAS9

At the same time, it is obviously wrong to same that only the information of the genome is needed for organisms to develop.

True and its a wonder they can’t see I agree with this. DNA has all the information needed to build organisms in a passive sense (just like the blueprint of a house), while non-DNA components have the information to facilitate the actual building process. The building process requires preexisting cellular components derived from parent organisms to interact with segregated DNA in daughter cells.

Is anything wrong with this?

[swamidass (S. Joshua Swamidass)]

@John_Harshman

@swamidass

Some of those inherited differences (certainly not all) can be caused in part or even completely by cultural or environmental inheritance, independent of DNA.

Could you name a couple?

E.g. primary language. You most likely speak the same language as your parents, and you did not get that from DNA.

[John_Harshman]

@swamidass

E.g. primary language. You most likely speak the same language as your parents, and you did not get that from DNA.

The topic to which you were responding was differences between species. That wasn’t an example of such a difference.

[Michael_Okoko]

Those who think DNA doesn’t possess all hereditary information should interpret this excerpt from the Molecular Biology of the Cell

It is scarcely to be expected that they would all store their information in the same form, or that the archives of one type of cell should be readable by the information-handling machinery of another. And yet it is so. All living cells on Earth store their hereditary information in the form of double-stranded molecules of DNA—long, unbranched, paired polymer chains, formed always of the same four types of monomers .

The above represents my position. Are they wrong about this or defining hereditary information in a way different from yours? You guys are way experienced than me, so I might not be seeing what’s in your mindscape.

[Mercer (John Mercer)]

@Michael_Okoko

…the peculiar egg cell environments had the necessary cues to spur this development. This has been my position all along.

Cues are information. Your position has been to deny that.

@Michael_Okoko

The environment in question basically consists of RNA and proteins, all of whose biosynthetic information is stored in DNA.

It also consists of lipids organized into complex organelles. That information is not in DNA.

There are ions and spatial information too.

[Michael_Okoko]

@Mercer

Cues are information. Your position has been to deny that.

Strawman. In previous posts, I had clearly recognized there is information in non-DNA components of cells, but I denied it is heritable like the information in DNA.

@Mercer

It also consists of lipids organized into complex organelles. That information is not in DNA.

Proteins direct the synthesis of structural lipids and carbohydrates. Protein biosynthetic data is encoded in DNA. Thus, DNA indirectly contains information needed to make the constituents of organelles.

@Mercer

There are ions and spatial information too.

This too is largely controlled by DNA indirectly. For example, you know the concentration gradient across cellular membranes for certain ions are maintained by the action of protein pumps and channels, whose biosynthetic information is still stored in DNA.

Can you address the excerpt I cited from the Molecular Biology of the Cell, because it echoes what I have been saying all along. Are the authors right or wrong in saying that all hereditary information is stored in DNA?

[Rumraket (Mikkel R.)]

@Michael_Okoko

Strawman. In previous posts, I had clearly recognized there is information in non-DNA components of cells, but I denied it is heritable like the information in DNA.

It doesn’t have to be heritable like the information in DNA. Whatever you might mean exactly by “like”.

Is it as stably heritable? No. Does that make it not heritable at all? No.

@Michael_Okoko

Are the authors right or wrong in saying that all hereditary information is stored in DNA?

They’re wrong. Edit: Actually re-reading their statement it’s somewhat more ambigous than your characterization here. You’re using the word “all” about the information, where they do not. They might have intended that, I dont know, but if they did then I think they’re wrong.

[Michael_Okoko]

@Rumraket

They’re wrong. Edit: Actually re-reading their statement it’s somewhat more ambigous than your characterization here. You’re using the word “all” about the information, where they do not. They might have intended that, I dont know, but if they did then I think they’re wrong.

Their view on this fully aligns with mine. See this other quote from page 3

Using chemical methods, scientists have learned how to read out the complete sequence of monomers in any DNA molecule—extending for many millions of nucleotides—and thereby decipher all of the hereditary information that each organism contains.

Saying they are wrong doesn’t cut it for me. I think our point of disagreement lies in what we define hereditary information as. What is it?

@Rumraket

Is it as stably heritable? No. Does that make it not heritable at all? No.

I guess this is also where we differ. The cytoplasmic contents gotten from parents do not really count as hereditary molecules, in my opinion, since they don’t persist like DNA. When those directly inherited constituents like receptors are degraded, the information in DNA is read to make new ones. If the DNA is altered in some way that affects the nature of those receptors (like reduced sensitivity to some signal), this modified information is continuously passed on to progeny during mitosis and eventual cell division. The ability of DNA to store and transmit information over long periods counts as real inheritance, and it carries all the information needed to build organisms.

[Eddie (Edward Robinson)]

@John_Harshman

I believe you have lost sight of the topic, which is, or at least used to be, evolution.

Based on the title of this page, I would say the topic is, “Is Information Only Present in the Genome?” I don’t see the word “evolution” in there. Also, the quoted passage from Paul Davies which Michael Okoko used as his lead-off – intending to show Davies was wrong – does not seem to mention evolution, and doesn’t seem to be primarily (if at all) about evolution. I took the subject to be whether or not there was information, responsible for the development of an organism, that resided elsewhere than in its DNA. It seems to me that Mercer and Rumraket are saying, “Yes, there is,” and based on my reading (though I claim no biological expertise, only a lay reader’s understanding), I think they are right.

@T_aquaticus

I think we would all agree that phenotypic plasticity has its role, but it isn’t powerful enough to explain the differences between species.

I don’t say that it is. And I don’t know what Wells says about the differences between species. I mentioned him only because he seems to think that the development of an organism isn’t 100% caused by its DNA alone, but by its DNA in interplay with the whole organismal environment. If I can find the article(s) where he discusses this, I will cite it(them).

[Mercer (John Mercer)]

@Michael_Okoko

Strawman. In previous posts, I had clearly recognized there is information in non-DNA components of cells, but I denied it is heritable like the information in DNA.

In what way is the information in the oocyte not inherited?

@Michael_Okoko

Proteins direct the synthesis of structural lipids and carbohydrates.

They do, but I’m not talking about their synthesis.

@Michael_Okoko

Thus, DNA indirectly contains information needed to make the constituents of organelles.

We’re not talking about making them.

@Michael_Okoko

This too is largely controlled by DNA indirectly. For example, you know the concentration gradient across cellular membranes for certain ions are maintained by the action of protein pumps and channels, whose biosynthetic information is still stored in DNA.

But we aren’t talking about their synthesis. That’s not the information that is inherited through the oocyte.

@Michael_Okoko

@Mercer

It does not, however, encode all of the information required to construct a new organism.

Yes it does and Molecular Biology of the Cell agrees with me.

It does not:

@Michael_Okoko

An organism’s DNA encodes all of the RNA and protein molecules required to construct its cells. Yet a complete description of the DNA sequence of an organism—be it the few million nucleotides of a bacterium or the few billion nucleotides of a human—no more enables us to reconstruct the organism than a list of English words enables us to reconstruct a play by Shakespeare.

[John_Harshman]

@Mercer

In what way is the information in the oocyte not inherited?

Because it has to be generated anew in every oocyte. The zygote inherits cytoplasm from the oocyte, but the next generation of oocytes does not.

[AlanFox]

I’m with Michael on this. For traits to be heritable they must be visible to selection. The burden is on those who claim epigenetic inheritance is a significant process to support it.

But there’s a harder question in how behavioural traits are inherited.

[Michael_Okoko]

@Mercer

In what way is the information in the oocyte not inherited?

It is not persistent like that in DNA.

@Mercer

They do, but I’m not talking about their synthesis.

DNA >>> mRNA >>> Proteins >>> membrane lipids. Its pretty clear the information needed to make the enzymes and proteins for membrane lipid biosynthesis and maintenance lies in DNA.

@Mercer

It does not:

@Michael_Okoko

An organism’s DNA encodes all of the RNA and protein molecules required to construct its cells. Yet a complete description of the DNA sequence of an organism—be it the few million nucleotides of a bacterium or the few billion nucleotides of a human—no more enables us to reconstruct the organism than a list of English words enables us to reconstruct a play by Shakespeare.

That completely agrees with everything I have said. I have said, over and over, that only DNA encodes all the information needed to build organisms, but that we need the information in non-DNA parts to use the stored information, as well as aid in its transmission to progeny.

Its true that daughter cells get a fraction of their parents following cell division, but that is due to the nature of cytokinesis. These directly inherited components all get eliminated eventually, but only DNA remains with the information it carries. It is in this sense that DNA serves as the only store of heritable information.

[Rumraket (Mikkel R.)]

@Michael_Okoko

I have said, over and over, that only DNA encodes all the information needed to build organisms, but that we need the information in non-DNA parts to use the stored information, as well as aid in its transmission to progeny.

I really think you’re contradicting yourself, but I’m running out of desire to keep arguing about it.

[John_Harshman]

@AlanFox

For traits to be heritable they must be visible to selection.

Say what?? I think you have that backwards: for traits to be visible to selection they must be heritable.

@AlanFox

But there’s a harder question in how behavioural traits are inherited.

Some behavioral traits aren’t inherited except by imitation. What’s inherited is the ability to learn, and that ability is sometimes biased toward particular sorts of behavior. And sometimes the imitation isn’t of conspecifics, incidentally. Consider widowbirds, brood parasites that learn their songs from their “fathers”.

[T_aquaticus]

@Eddie

I don’t say that it is. And I don’t know what Wells says about the differences between species. I mentioned him only because he seems to think that the development of an organism isn’t 100% caused by its DNA alone, but by its DNA in interplay with the whole organismal environment.

That would seem to be the consensus view in biology. Where paths diverge is when someone tries to deny the role of DNA in the process. To use an analogy, it would be accurate to say that your car is moved around by the wind as you drive. It wouldn’t be accurate to say that the wind is the best explanation for your car going 65 mph down the highway.

[Mercer (John Mercer)]

@Michael_Okoko

It is not persistent like that in DNA.

That cellular organization persists through generations and must be inherited. It is not “encoded” in DNA anywhere.

@Michael_Okoko

@Mercer

They do, but I’m not talking about their synthesis.

DNA >>> mRNA >>> Proteins >>> membrane lipids. Its pretty clear the information needed to make the enzymes and proteins for membrane lipid biosynthesis and maintenance lies in DNA.

Wow, Michael. I pointed out that I’m not talking about synthesis, and you come back with the information needed for biosynthesis?

You’re not paying any attention.

@Michael_Okoko

That completely agrees with everything I have said.

No, because DNA is not sufficient.

@Michael_Okoko

I have said, over and over, that only DNA encodes all the information needed to build organisms, but that we need the information in non-DNA parts to use the stored information, as well as aid in its transmission to progeny.

You’re contradicting yourself. If we need the organizational information that is not stored in DNA, then DNA cannot contain all of the stored information.

@Michael_Okoko

Its true that daughter cells get a fraction of their parents following cell division…

It’s true but irrelevant to my point. The daughter cells inherit ALL of their organizational information from the parental cell.

Mitochondria are a miniature version of this. If we put mitochondrial DNA in a cell lacking mitochondria, will that produce mitochondria?

Why is the germline set aside so early in development?

@Michael_Okoko

The cytoplasmic contents gotten from parents do not really count as hereditary molecules, in my opinion, since they don’t persist like DNA.

Neither the contents nor their synthesis are the point.

The cellular organization from parents persists, is not and has never been stored in DNA, yet is inherited.

Theologically, if one were so inclined (I am not), one could even stuff the teeny-tiny ID version of the Christian God into that process for safekeeping.

[Mercer (John Mercer)]

@John_Harshman

Because it has to be generated anew in every oocyte.

No, that cellular organization is persistent and never generated anew. It’s consistent with the setting aside of the germline during very early development. If it were generated anew, there’d be no evolutionary need for all that sequestration and it would be generated anew at reproductive maturity.

[Eddie (Edward Robinson)]

@T_aquaticus

Where paths diverge is when someone tries to deny the role of DNA in the process.

I don’t do that, and I don’t know anyone who does.

@Mercer

Theologically, if one were so inclined (I am not), one could even stuff the teeny-tiny ID version of the Christian God into that process for safekeeping.

Except for this last little unjust jab, I agree with all of Mercer’s corrections to Okoko. Again, I claim no expertise, but everything Mercer says is consistent with my own reading. I would add that, while Mercer doubtless learned all of this from non-ID authors, it is also very commonly found in ID authors. It’s a commonplace among ID writers that DNA, though obviously important, is not the whole story regarding information necessary to the organism. Interesting that they and Mercer are on the same page, at least regarding this one important point.

[AlanFox]

@John_Harshman

I think you have that backwards: for traits to be visible to selection they must be heritable.

Well, I meant adaptive evolution will only happen with feedback between phenotype and genotype. I’m not a fan of neutral theory. Can it not therefore be both.

@John_Harshman

Some behavioral traits aren’t inherited except by imitation.

Sure but I was thinking of simpler examples of innate behaviour such as web construction in arachnids.