Is Information Only Present in the Genome?

[Michael_Okoko]

@Art

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.

I agreed to this a long time ago. The nature of cell division ensures that daughter cells inherit some of the cellular constituents of their parents, but these constituents will eventually disappear. To replace degraded components, we need information (like a blueprint) to synthesize new ones. Only genomes carry such information. Every single protein in our cells is synthesized using information from DNA and proteins are the mainstay of any cell or organisms. Thus, its obvious that what cellular organization should be is kept in DNA, however, to go from DNA to that cellular organization we need other cell parts.

For example, in a typical mammalian cell the cytoplasmic levels of sodium ions is far below extracellular levels. This chemical gradient is integral to the existence and functions of the cell. To maintain this gradient, we need sodium pumps which push sodium ions against their concentration gradient into the extracellular space. Sodium pumps are proteins capable of utilizing ATP as a source of free energy to expel sodium ions from the cell. During cell division, parental sodium pumps are passed down to progeny, but these pumps don’t last forever and eventually degraded. The information needed to make them persists in DNA, so it means that as long as the cell can tap into that information, it will keep on maintaining its organization by always making new pumps to replace degraded ones. It is this sense that DNA hold all the information needed to maintain or establish cellular organization.

Why Mercer and Rum disagree within this beats me.

[RonSewell (RonS)]

I believe all the scientists here agree on all the biology, and Paul Davies himself did not say anything otherwise. The contention is with regards to the meaning of information. This thread is titled, “Is Information Only Present in the Genome”, and the answer is no, unless you a priori define information as genetic information.

If the extranuclear environment has any degree of organization, that is information by definition. It is not complete entropy, so it is information. It’s current state must and will relate to future states, however weakly and ephemerally. The way I read Davie’s statement is that the genetic code has always been a unbroken part of a larger biological system, and reaching back into time and physics there has never been a moment of discontinuity in that regard. His point is not to diminish genetics but to emphasize its integrated nature.

This is no support to the idea that, because there is a mechanical aspect to such information, that design is implied. That misconceived notion is what kicked off this discussion.

EDIT: grammar, diction

[Mercer (John Mercer)]

@Art

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.

Good, but I don’t know what you mean by “the link.”

@Michael_Okoko

The nature of cell division ensures that daughter cells inherit some of the cellular constituents of their parents, but these constituents will eventually disappear. To replace degraded components, we need information (like a blueprint) to synthesize new ones.

My point is that the blueprint is inherited. You’re conflating the recipes in DNA with the blueprint that is not stored in DNA.

@Michael_Okoko

Thus, its obvious that what cellular organization should be is kept in DNA, however, to go from DNA to that cellular organization we need other cell parts.

No, that’s not obvious at all. Common descent offers zero reason for that organization to be stored in DNA, because it’s always been present.

@RonSewell

I believe all the scientists here agree on all the biology, and Paul Davies himself did not say anything otherwise. The contention is with regards to the meaning of information .

Beautifully put.

[Michael_Okoko]

@RonSewell

This thread is titled, “Is Information Only Present in the Genome”, and the answer is no, unless you a priori define information as genetic information.

The thread title asked the wrong question, because everyone here agrees there is information outside genomes.

What I disagreed with in the Imari Walker and Paul Davies paper is in the boldened part of the quote:

In spite of the striking similarities between an UC and modern life, there are some important differences. DNA does not contain a blueprint for building the entire cell, but instead contains only small parts of a much larger biological algorithm, which may be roughly described as the distributed ‘top-down’ control of an organism. 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.

https://royalsocietypublishing.org/doi/10.1098/rsif.2012.0869

This seems wrong. AFAIK proteins, enzymes and RNA molecules maintain or establish cellular organization. Your cells can take in or remove certain ions, sense certain signals, and do a lot of other stuff thanks to the aforementioned biomolecules, especially proteins. Proteins are the workhorse of cells. Since DNA holds information (exact linear sequence of nucleotides in genes and their regulatory sequences) needed to make those proteins (which will then go on to shape cellular organization), its obvious DNA contains the blueprint for constructing cells. These are excerpts from Molecular Biology of the Cell, sixth edition, pages 369 and 7 respectively and they disagree with the Davies paper.

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. In both cases, the problem is to know how the elements in the DNA sequence or the words on the list are used. Under what conditions is each gene product made, and, once made, what does it do?

In all cells, the expression of individual genes is regulated: instead of manufacturing its full repertoire of possible proteins at full tilt all the time, the cell adjusts the rate of transcription and translation of different genes independently, according to need. Stretches of regulatory DNA are interspersed among the segments that code for protein, and these noncoding regions bind to special protein molecules that control the local rate of transcription. The quantity and organization of the regulatory DNA vary widely from one class of organisms to another, but the basic strategy is universal. In this way, the genome of the cell—that is, the totality of its genetic information as embodied in its complete DNA sequence— dictates not only the nature of the cell’s proteins, but also when and where they are to be made.

[Michael_Okoko]

@Mercer

Common descent offers zero reason for that organization to be stored in DNA,

Proteins control that organization and how those proteins should act is a function of their amino acid order and composition, which in turn is a function of the DNA sequence which encodes them. What that organization should be is conserved in DNA.

@Mercer

You’re conflating the recipes in DNA with the blueprint that is not stored in DNA.

The blueprint is ultimately stored in DNA.

[Geremy (Geremy D. Lawrence)]

I hope everyone is doing well. Here’s an article that talks about the so called “xenobots” developed by Michael Levin which and his team,
and its implications for the role of genetics in development.

How xenobots reshape our understanding of genetics | Aeon Essays

I would like to hear your thoughts on this article.

[nwrickert (Neil Rickert)]

The Aeon article seems reasonable to me. But note that I am not a biologist.

It has long seemed to me that the idea of DNA as a blueprint is just wrong. Rather, the DNA defines a development program, and what actually develops depends also on the environment. For humans, development continues through childhood.

[Mercer (John Mercer)]

@nwrickert

The Aeon article seems reasonable to me. But note that I am not a biologist.

It has long seemed to me that the idea of DNA as a blueprint is just wrong.

You are right that it is wrong. There clearly is a massive amount of currently indecipherable analog information (the most obvious being spatial cues) required.

[Michael_Okoko]

I think this thread should be closed since I gave up my position that DNA is a blueprint for the growth and development of organisms.